MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Systematic and Applied Microbiology' source. Thu, 09 Feb 2012 21:35:10 +0100 http://www.medworm.com/index.php?rid=5637907&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22280898%26dopt%3DAbstract Authors: Rashid MH, Schäfer H, Gonzalez J, Wink M Abstract In order to determine the bacterial diversity and the identity of rhizobia nodulating lentil in Bangladesh, we performed a phylogenetic analysis of housekeeping genes (16S rRNA, recA, atpD and glnII) and nodulation genes (nodC, nodD and nodA) of 36 bacterial isolates from 25 localities across the country. Maximum likelihood (ML) and Bayesian analyses based on 16S rRNA sequences showed that most of the isolates (30 out of 36) were related to Rhizobium etli and Rhizobium leguminosarum. Only these thirty isolates were able to re-nodulate lentil under laboratory conditions. The protein-coding housekeeping genes of the lentil nodulating isolates showed 89.1-94.8% genetic similarity to the corresponding genes of R. etli and R. l... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637907 Tue, 24 Jan 2012 05:00:00 +0100 5637907 http://www.medworm.com/index.php?rid=5637906&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22280899%26dopt%3DAbstract Authors: Zhang L, Xi L, Ruan J, Huang Y Abstract Two Gram-positive, rod-shaped bacterial strains, H101(T) and H207, were isolated from deep sea water collected from South-West Indian Ocean. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to one another (100% similarity), and had the closest relationship with Microbacterium hominis NBRC 15708(T) and Microbacterium insulae KCTC 19247(T) (98.2-98.3% similarities). DNA-DNA hybridization value between strains H101(T) and H207 was 87.2±3.7%, and the values between the two strains and the closely related type strains were well below 70%. The two strains also shared a number of physiological and biochemical characteristics that were distinct from the closely related species, and grew at 2-... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637906 Tue, 24 Jan 2012 05:00:00 +0100 5637906 http://www.medworm.com/index.php?rid=5637908&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22277323%26dopt%3DAbstract Authors: Brito A, Ramos V, Seabra R, Santos A, Santos CL, Lopo M, Ferreira S, Martins A, Mota R, Frazão B, Martins R, Vasconcelos V, Tamagnini P Abstract Cyanobacteria are important primary producers, and many are able to fix atmospheric nitrogen playing a key role in the marine environment. However, not much is known about the diversity of cyanobacteria in Portuguese marine waters. This paper describes the diversity of 60 strains isolated from benthic habitats in 9 sites (intertidal zones) on the Portuguese South and West coasts. The strains were characterized by a morphological study (light and electron microscopy) and by a molecular characterization (partial 16S rRNA, nifH, nifK, mcyA, mcyE/ndaF, sxtI genes). The morphological analyses revealed 35 morphotypes (15 genera and 16 ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637908 Mon, 23 Jan 2012 05:00:00 +0100 5637908 http://www.medworm.com/index.php?rid=5637909&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22265597%26dopt%3DAbstract Authors: Aserse AA, Räsänen LA, Assefa F, Hailemariam A, Lindström K Abstract The diversity and phylogeny of 32 rhizobial strains isolated from nodules of common bean plants grown on 30 sites in Ethiopia were examined using AFLP fingerprinting and MLSA. Based on cluster analysis of AFLP fingerprints, test strains were grouped into six genomic clusters and six single positions. In a tree built from concatenated sequences of recA, glnII, rpoB and partial 16S rRNA genes, the strains were distributed into seven monophyletic groups. The strains in the groups B, D, E, G1 and G2 could be classified as Rhizobium phaseoli, R. etli, R. giardinii, Agrobacterium tumefaciens complex and A. radiobacter, respectively, whereas the strains in group C appeared to represent a novel species. R. pha... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637909 Fri, 20 Jan 2012 05:00:00 +0100 5637909 http://www.medworm.com/index.php?rid=5637911&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22264503%26dopt%3DAbstract Authors: Gougoulias C, Shaw LJ Abstract We explicitly tested for the first time the 'environmental specificity' of traditional 16S rRNA-targeted Fluorescence In Situ Hybridization (FISH) through comparison of the bacterial diversity actually targeted in the environment with the diversity that should be exactly targeted (i.e. without mismatches) according to in silico analysis. To do this, we exploited advances in modern Flow Cytometry that enabled improved detection and therefore sorting of sub-micron-sized particles and used probe PSE1284 (designed to target Pseudomonads) applied to Lolium perenne rhizosphere soil as our test system. The 6-carboxyfluorescein (6-FAM)-PSE1284-hybridized population, defined as displaying enhanced green fluorescence in Flow Cytometry, represented 3.51... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637911 Thu, 19 Jan 2012 05:00:00 +0100 5637911 http://www.medworm.com/index.php?rid=5637910&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22264799%26dopt%3DAbstract Authors: Okten HE, Yilmaz LS, Noguera DR Abstract The principle that the small subunit ribosomal RNA (ssu rRNA) is generally accessible to oligonucleotide probes designed to have high thermodynamic affinity was tested with Stenotrophomonas maltophilia, Rhodobacter sphaeroides, Bacillus subtilis, and Saccharomyces cerevisiae. Fluorescein-labeled probes, designed to have ΔG(overall)°=-14±1 and to avoid the potential of nucleobase-specific quenching, were used to target 20 randomly selected sites in each organism. A site was considered accessible if probe brightness was at least 10 times the background signal. With 30-h hybridizations, 71 out of 80 target sites passed the accessibility criterion. Three additional sites were demonstrated to be accessible with either longer hybridiza... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5637910 Wed, 18 Jan 2012 05:00:00 +0100 5637910 http://www.medworm.com/index.php?rid=5577651&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227311%26dopt%3DAbstract Authors: Zamora L, Fernández-Garayzábal JF, Svensson-Stadler LA, Palacios MA, Domínguez L, Moore ER, Vela AI Abstract Eighteen isolates of a Gram-negative, catalase and oxidase-positive, rod-shaped bacterium, recovered from diseased rainbow trout (Oncorhynchus mykiss), were characterized, using a polyphasic taxonomic approach. Studies based on comparative 16S rRNA gene sequence analysis showed that that the eighteen new isolates shared 99.2-100% sequence similarities. Phylogenetic analysis revealed that isolates from trout belonged to the genus Flavobacterium, showing the highest sequence similarities to F. chungangense (98.6%), F. frigidimaris (98.1%), F. hercynium (97.9%) and F. aquidurense (97.8%). DNA-DNA reassociation values between the trout isolates (exemplified by strain... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5577651 Thu, 05 Jan 2012 05:00:00 +0100 5577651 http://www.medworm.com/index.php?rid=5577652&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22225994%26dopt%3DAbstract Authors: Endo A, Futagawa-Endo Y, Schumann P, Pukall R, Dicks LM Abstract Five strains of bifidobacteria were isolated from faeces of a common marmoset (Callithrix jacchus) and a red-handed tamarin (Saguinus midas). The five isolates clustered inside the phylogenetic group of the genus Bifidobacterium but did not show high sequence similarities between the isolates and to known species in the genus by phylogenetic analysis based on 16S rRNA gene sequences. Sequence analyses of dnaJ1 and hsp60 also indicated their independent phylogenetic positions to each other in the Bifidobacterium cluster. DNA G+C contents of the species ranged from 57.3 to 66.3mol%, which is within the values recorded for Bifidobacterium species. All isolates showed fructose-6-phosphate phosphoketolase activity... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5577652 Wed, 04 Jan 2012 05:00:00 +0100 5577652 http://www.medworm.com/index.php?rid=5577654&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22221858%26dopt%3DAbstract Authors: Carro L, Spröer C, Alonso P, Trujillo ME Abstract It was recently reported that Micromonospora inhabits the intracellular tissues of nitrogen fixing nodules of the wild legume Lupinus angustifolius. To determine if Micromonospora populations are also present in nitrogen fixing nodules of cultivated legumes such as Pisum sativum, we carried out the isolation of this actinobacterium from P. sativum plants collected in two man-managed fields in the region of Castilla and León (Spain). In this work, we describe the isolation of 93 Micromonospora strains recovered from nitrogen fixing nodules and the rhizosphere of P. sativum. The genomic diversity of the strains was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). Forty-six isolates and 34 reference strains ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5577654 Tue, 03 Jan 2012 05:00:00 +0100 5577654 http://www.medworm.com/index.php?rid=5577653&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22221859%26dopt%3DAbstract Authors: Maynaud G, Willems A, Soussou S, Vidal C, Mauré L, Moulin L, Cleyet-Marel JC, Brunel B Abstract Bacterial strains from Zn-Pb mine tailings were isolated by trapping with Anthyllis vulneraria, a legume-host suitable for mine substratum phytostabilisation. Sequence analysis of the 16S rRNA gene and three housekeeping genes (atpD, dnaK and recA) showed that they were related to those of the genus Aminobacter. DNA-DNA relatedness of representative isolates supported the placement of novel strains in Aminobacter as a new species. Phenotypic data emphasize their differentiation from the other related species of Aminobacter and Mesorhizobium. Aminobacter isolates exhibited nodA sequences tightly related with M. loti as the closest nodA relative. By contrast, their nodA sequences... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5577653 Tue, 03 Jan 2012 05:00:00 +0100 5577653 http://www.medworm.com/index.php?rid=5531239&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178390%26dopt%3DAbstract Authors: Risal CP, Djedidi S, Dhakal D, Ohkama-Ohtsu N, Sekimoto H, Yokoyama T Abstract Nepal consists wide range of climatic and topographical variations. Here, we explored the phylogeny of native mungbean bradyrhizobia isolated from different agro-ecological regions of Nepal and accessed their nodulation and nitrogen fixation characteristics. Soil samples were collected from three agro-ecological regions with contrasting climate and topography. A local mungbean cultivar, Kalyan, was used as a trap plant. We characterized isolates based on the full nucleotide sequence of the 16S rRNA, ITS region, and nodA genes; and partial sequences of nodD1 and nifD genes. We found 50% of isolates phylogenetically related to B. yuanmingense, 13% to B. japonicum, 8% to B. elkanii, and 29% to nove... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5531239 Thu, 15 Dec 2011 05:00:00 +0100 5531239 http://www.medworm.com/index.php?rid=5531240&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22172557%26dopt%3DAbstract Authors: Rong X, Huang Y Abstract Streptomyces hygroscopicus and related species are the most well known candidate producers of antibiotics and many other industrially and agronomically important secondary metabolites in the genus Streptomyces. Multilocus sequence analysis (MLSA) has shown to be a powerful and pragmatic molecular method for unraveling streptomycete diversities. In this investigation, a multilocus phylogeny of 58 representatives of the S. hygroscopicus 16S rRNA gene clade including S. violaceusniger and related species was examined. The result demonstrated that the MLSA data were helpful in defining members of the S. hygroscopicus clade, providing further evidence that the MLSA scheme of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is a valuable alterna... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5531240 Tue, 13 Dec 2011 05:00:00 +0100 5531240 http://www.medworm.com/index.php?rid=5531241&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22169565%26dopt%3DAbstract Authors: Kämpfer P, Wellner S, Lohse K, Martin K, Lodders N Abstract A bright yellow pigmented bacterium was isolated from the leaf surface of Trifolium repens in Germany. Comparative analysis of 16S rRNA gene sequences showed that this bacterium is most closely related to Duganella zoogloeoides IAM 12670(T), with a similarity of 99.3%, but revealed only a moderate similarity (96.8%) to the second Duganella species, Duganella violaceinigra YIM 31327(T). Strain T54(T) is clearly different from D. zoogloeoides IAM 12670(T) in that DNA-DNA hybridization revealed a similarity value of 46% (reciprocal 42%). Ubiquinone (Q-8) was the respiratory quinone and the predominant polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids and one aminol... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5531241 Thu, 08 Dec 2011 05:00:00 +0100 5531241 http://www.medworm.com/index.php?rid=5531243&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154623%26dopt%3DAbstract Authors: Han JH, Cho MH, Kim SB Abstract The phylogenetic relationship among the three genera of the family Streptomycetaceae was examined using the small and large subunit ribosomal RNA genes, and the gyrB, rpoB, trpB, atpD and recA genes. The total stretches of the analyzed ribosomal genes were 4.2kb, and those of five protein coding genes were 4.5kb. The resultant phylogenetic trees confirmed that each genus formed an independent clade in the majority of cases. The G+C contents of rRNA genes were 56.9-58.9mol%, and those of protein coding genes were 65.4-72.4mol%, the latter being closer to those of the genomic DNAs. The average nucleotide sequence identity between the organisms were 94.1-96.4% for rRNA genes and 85.7-90.6% for protein coding genes, thus indicating that protein ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5531243 Wed, 07 Dec 2011 05:00:00 +0100 5531243 http://www.medworm.com/index.php?rid=5531244&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22154008%26dopt%3DAbstract Authors: Röske K, Sachse R, Scheerer C, Röske I Abstract Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in s... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5531244 Tue, 06 Dec 2011 05:00:00 +0100 5531244 http://www.medworm.com/index.php?rid=5454974&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22115847%26dopt%3DAbstract Authors: Zamora L, Fernández-Garayzábal JF, Palacios MA, Sánchez-Porro C, Svensson-Stadler LA, Domínguez L, Moore ER, Ventosa A, Vela AI Abstract Genotypic and phenotypic analyses were performed on five Gram-negative, catalase and oxidase-positive, rod-shaped bacteria isolated from the gill and liver of four rainbow trout. Studies based on comparative 16S rRNA gene sequence analysis showed that the five new isolates shared 99.8-100% sequence similarity and that they belong to the genus Chryseobacterium. The nearest phylogenetic neighbours of the strain 701B-08(T) were Chryseobacterium ureilyticum F-Fue-04IIIaaaa(T) (99.1% 16S rRNA gene sequence similarity) and Chryseobacterium joosteii LMG 18212(T) (98.6%). DNA-DNA hybridization values between the five isolates were 91-99% and ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5454974 Tue, 22 Nov 2011 05:00:00 +0100 5454974 http://www.medworm.com/index.php?rid=5417898&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22055753%26dopt%3DAbstract This study used multilocus sequence analysis to identify 36 V. harveyi-like isolates obtained from a wide range of sources in Australia and to re-evaluate the identity of important pathogens. Phylogenies inferred from the 16S rRNA gene and five concatenated protein-coding genes (rpoA-pyrH-topA-ftsZ-mreB) revealed four well-supported clusters identified as V. harveyi, V. campbellii, V. rotiferianus and V. owensii. Results revealed that important V. campbellii and V. owensii prawn pathogens were previously misidentified as V. harveyi and also that the recently described V. communis sp. nov. is likely a junior synonym of V. owensii. Although the MLSA topologies corroborated the 16S rRNA gene phylogeny, the latter was less informative than each of the protein-coding genes taken singularly or t... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5417898 Wed, 02 Nov 2011 04:00:00 +0100 5417898 http://www.medworm.com/index.php?rid=5378874&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22036527%26dopt%3DAbstract Authors: Jansson DS, Persson M, Zimmerman U, Johansson KE Abstract Brachyspira spp. are anaerobic intestinal spirochaetes that colonize vertebrates. Some species cause enteric diseases in pigs, chickens and possibly in humans, whereas others display a commensual relationship with their hosts. The aims were to investigate the prevalence among colonized free-living wild mallards (Anas platyrhynchos) of three enteropathogenic Brachyspira spp., and to describe the biodiversity of Brachyspira spp. isolates. Isolates from 150 birds were screened by PCR for 3 pathogenic Brachyspira spp., and 35 isolates from 20 mallards, 4 pigs and 1 chicken were subjected to phenotypic tests, 9 diagnostic PCRs, sequencing of the 16S rRNA and NADH oxidase (nox) genes, phylogenetic analysis and nox gene re... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5378874 Thu, 27 Oct 2011 04:00:00 +0100 5378874 http://www.medworm.com/index.php?rid=5325207&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22000032%26dopt%3DAbstract Authors: Wellner S, Lodders N, Kämpfer P Abstract On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7)CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers th... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5325207 Wed, 12 Oct 2011 04:00:00 +0100 5325207 http://www.medworm.com/index.php?rid=5275733&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21959289%26dopt%3DAbstract Authors: Foesel BU, Drake HL, Schramm A Abstract Three Gram-negative bacterial strains were isolated from the biofilter of a recirculating marine aquaculture. They were non-pigmented rods, mesophiles, moderately halophilic, and showed chemo-organoheterotrophic growth on various sugars, fatty acids, and amino acids, with oxygen as electron acceptor; strains D9-3(T) and D11-58 were in addition able to denitrify. Phototrophic or fermentative growth could not be demonstrated. Phylogenetic analysis of the 16S rRNA gene sequences placed D9-3(T) and D11-58, and D1-19(T) on two distinct branches within the alpha-3 proteobacterial Rhodobacteraceae, affiliated with, but clearly separate from, the genera Rhodobacter, Rhodovulum, and Rhodobaca. Based on morphological, physiological, and 16S rR... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5275733 Tue, 27 Sep 2011 04:00:00 +0100 5275733 http://www.medworm.com/index.php?rid=5275735&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21943677%26dopt%3DAbstract Authors: Monfredini L, Settanni L, Poznanski E, Cavazza A, Franciosi E Abstract The microbial composition and its spatial distribution of Grana Trentino, a hard Parmesan-like cheese, was determined, from vat milk to cheese. After cutting along the vertical axis of the cheese wheels, three layers were sampled diagonally across the cheese: under the cheese rind, an intermediate section and the cheese core. After two different ripening periods (9 and 18 months), the cheese samples were analysed using traditional culture dependent and culture independent methods. Milk samples were dominated by mesophilic and psychrophilic bacterial counts. Thermophilic bacteria (Lactobacillus helveticus) were found in high amounts in cooked whey and natural whey starter cultures. After 9 months of ripe... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5275735 Wed, 21 Sep 2011 04:00:00 +0100 5275735 http://www.medworm.com/index.php?rid=5275734&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21943678%26dopt%3DAbstract Authors: Lindenstrauß AG, Pavlovic M, Bringmann A, Behr J, Ehrmann MA, Vogel RF Abstract Enterococcus faecalis and Enterococcus faecium are human commensals frequently found in fermented foods or used as probiotics, but also recognized as opportunistic pathogens. We investigated 62 Enterococcus strains isolated from clinical, food and environmental origins towards a rationale for safety evaluation of strains in food or probiotic applications. All isolates were characterised with respect to the presence of the virulence determinants fsrB, sprE, gelE, ace, efaAfs/fm, as, esp, cob and the cytolysin operon. In addition RAPD-PCR was used to obtain genomic fingerprints that were clustered and compared to phenotypic profiles generated by MALDI-TOF-MS. The gelatinase phenotype (GelE) and ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5275734 Wed, 21 Sep 2011 04:00:00 +0100 5275734 http://www.medworm.com/index.php?rid=5275737&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21940129%26dopt%3DAbstract In this study, the genomic analysis by Insignia was conducted on Vibrio parahaemolyticus, a halophilic gram-negative bacteria which constitutes a leading cause of seafood-borne disease. Insignia was used to identify 37 V. parahaemolyticus-specific signatures and to design PCR assays to validate the representative signature sequences by TaqMan essays. The 37 assays targeted loci distributed around the genome and detected genes coding for hypothetical proteins and for proteins involved in adhesion, starvation and virulence. A panel of V. parahaemolyticus environmental strains isolated from the North Adriatic Sea (Italy) and from the Black Sea (Georgia) was used to validate the selected signatures. The signature assays revealed both sensitive and specific and the method allowed a more accurat... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5275737 Tue, 20 Sep 2011 04:00:00 +0100 5275737 http://www.medworm.com/index.php?rid=5275736&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21940130%26dopt%3DAbstract Authors: Tomida J, Sakamoto D, Sugita T, Fujiwara N, Naka T, Hamada M, Morita Y, Kawamura Y Abstract Novel actinobacterial strains, PAGU 1247(T), PAGU 1251 and PAGU 1252, were isolated from the skin of atopic dermatitis patients and were characterized using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that these isolates were located within the family Dermacoccaceae. The most closely related species of PAGU 1247(T) in phylogenetic terms was Branchiibius hedensis Mer 29717(T), with 16S rRNA gene sequence similarity of 99.6%, although the DNA-DNA relatedness value was less than 43.9%. Some biochemical traits, such as lipase (C14) and α-galactosidase activity, could distinguish these isolates from B. hedensis. Strain PAGU 1247(T) contained iso-... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5275736 Tue, 20 Sep 2011 04:00:00 +0100 5275736 http://www.medworm.com/index.php?rid=5244923&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21924574%26dopt%3DAbstract Authors: Shivali K, Ramana VV, Ramaprasad EV, Sasikala C, Ramana CV Abstract Three strains (JA349(T), JA553(T), JA439) of phototrophic sulphur bacteria were isolated from marine habitats of India. 16S rRNA gene sequence of the three strains clustered phylogenetically with members of the genus Marichromatium of the family Chromatiaceae belonging to the class Gammaproteobacteria. All the strains shared highest sequence similarity with the type strains of Marichromatium spp. (96-99% sequence similarity) and the new strains were characterized based on polyphasic taxonomy. Strains JA349(T) and JA553(T) can be distinguished from closest relative species of the genus Marichromatium with respect to distinct differences in cellular polar lipids, fatty acids and carbon/nitrogen sources utili... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5244923 Wed, 14 Sep 2011 04:00:00 +0100 5244923 http://www.medworm.com/index.php?rid=5217622&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21899973%26dopt%3DAbstract Authors: Albuquerque L, França L, Rainey FA, Schumann P, Nobre MF, da Costa MS Abstract Two isolates, with an optimum growth temperature of about 35-37°C and an optimum pH for growth between 6.5 and 7.5, were recovered from a deep mineral water aquifer in Portugal. Strains form rod-shaped cells and were non-motile. These strains were non-pigmented, strictly aerobic, catalase and oxidase positive. Strains F2-233(T) and F2-223 assimilated carbohydrates, organic acids and amino acids. Major fatty acids were novel iso internally branched such as 17:0 iso 10-methyl, 17:0 iso and 15:0 iso 8-methyl. The peptidoglycan contained meso-diaminopimelic acid and menaquinone MK-7 was the major respiratory quinone. Analysis of the 16S rRNA gene shows the strains to cluster with species of the ge... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5217622 Mon, 05 Sep 2011 04:00:00 +0100 5217622 http://www.medworm.com/index.php?rid=5217654&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21889861%26dopt%3DAbstract Authors: Cui HL, Mou YZ, Yang X, Zhou YG, Liu HC, Zhou PJ Abstract Two extremely halophilic archaeal strains GX3(T) and GX26(T) were isolated from the Gangxi marine solar saltern near the Weihai city of Shandong Province, China. Cells from the two strains were pleomorphic and stained Gram-negative, colonies were red-pigmented. Strains GX3(T) and GX26(T) were able to grow at 25-50°C (optimum 37°C), at 1.4-5.1M NaCl (optimum 3.1M), at pH 5.5-9.5 (optimum pH 7.0) and neither strain required Mg(2+) for growth. Cells lyse in distilled water and the minimal NaCl concentration to prevent cell-lysis was 8% (w/v). The major polar lipids of the two strains were PA (phosphatidic acid), PG (phosphatidylglycerol), PGP-Me (phosphatidylglycerol phosphate methyl ester) and three major glycolipid... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5217654 Thu, 01 Sep 2011 04:00:00 +0100 5217654 http://www.medworm.com/index.php?rid=5217623&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21889862%26dopt%3DAbstract Authors: Wienemann T, Schmitt-Wagner D, Meuser K, Segelbacher G, Schink B, Brune A, Berthold P Abstract The diet of wild capercaillie differs strongly between seasons. Particularly during winter, when energy demands are high and the birds forage solely on coniferous needles, microbial fermentations in the ceca are considered to contribute significantly to the energy requirement and to the detoxification of the resinous diet. Here, we present the first cultivation-independent analysis of the bacterial community in the cecum of capercaillie, using the 16S rRNA gene as a molecular marker. Cloning and fingerprinting analyses of cecum feces show distinct differences between wild and captive birds. While certain lineages of Clostridiales, Synergistetes, and Actinobacteria are most preval... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5217623 Thu, 01 Sep 2011 04:00:00 +0100 5217623 http://www.medworm.com/index.php?rid=5192383&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21885227%26dopt%3DAbstract In this study, the taxonomic status of anoxygenic photosynthetic bacteria belonging to the genus Allochromatium is revisited. The inter- and intraspecies relationship of seven Allochromatium strains, including a set of well described type strains, were examined by DNA-DNA hybridization (DDH) and multilocus sequence analysis (MLSA) using segments of seven protein-coding genes. The re-sequencing of the 16S rRNA, the internal transcriber spacer (ITS), multi-gene analysis and DDH comparison indicated that both type strains Allochromatium vinosum DSM 180(T) and Allochromatium minutissimum DSM 1376(T) are closely related to each other forming an independent cluster together with the strains A. vinosum DSM 183 and DSM 1686. The internal comparison of members of this A. vinosum phylogroup showed v... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5192383 Mon, 29 Aug 2011 23:00:00 +0100 5192383 http://www.medworm.com/index.php?rid=5096081&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21802235%26dopt%3DAbstract This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5096081 Tue, 26 Jul 2011 23:00:00 +0100 5096081 http://www.medworm.com/index.php?rid=5096100&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21782367%26dopt%3DAbstract Authors: Scotta C, Bennasar A, Moore ER, Lalucat J, Gomila M Three ceftazidime-resistant strains isolated from the sewage water of a municipal hospital in Palma de Mallorca, Spain, were analysed phenotypically and genotypically to clarify their taxonomic positions. Sequence determinations and phylogenetic analyses of the 16S rRNA genes indicated that strains CS20.3(T), CS39 and CS41 were affiliated with the species of the alphaproteobacterial genus Brevundimonas, most closely related to B. bullata, B. diminuta, B. naejangsanensis and B. terrae. Additional sequences analyses of the ITS1 region of the rRNA operon and the genes for the housekeeping enzymes DNA gyrase β-subunit and RNA polymerase β-subunit, genomic DNA-DNA hybridisation similarities, cell fatty acid profiles and physiolo... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5096100 Tue, 19 Jul 2011 23:00:00 +0100 5096100 http://www.medworm.com/index.php?rid=5049807&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21757309%26dopt%3DAbstract Authors: Chahboune R, Barrijal S, Moreno S, Bedmar EJ From a total of 73 bacterial strains isolated from root nodules of Cytisus villosus grown in soils of the central-western region of the Moroccan Rif, 68 strains clustered into 19 repetitive extragenic palindromic (REP)-polymerase chain reaction (PCR) groups. The nearly complete 16S rRNA gene sequence from each strain showed they were closely related to members of the genus Bradyrhizobium of the Alphaproteobacteria, but affiliation at the species level was not clear. Sequencing of the housekeeping genes glnII and recA, and their concatenated phylogenetic analysis showed that 11 out of the 19 strains belong to Bradyrhizobium canariense and that another three strains were Bradyrhizobium japonicum. The remaining five strains represented... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5049807 Mon, 11 Jul 2011 23:00:00 +0100 5049807 http://www.medworm.com/index.php?rid=5000543&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21723060%26dopt%3DAbstract Authors: Figueras MJ, Levican A, Collado L, Inza MI, Yustes C As part of a study carried out for detecting Arcobacter spp. in shellfish, three mussel isolates that were Gram-negative slightly curved rods, non-spore forming, showed a new 16S rDNA-RFLP pattern with a specific identification method for the species of this genus. Sequences of the 16S rRNA gene and those of the housekeeping genes rpoB, gyrB and hsp60 provided evidence that these mussel strains belonged to an unknown genetic lineage within the genus Arcobacter. The similarity between the 16S rRNA gene sequence of the representative strain (F79-6(T)) and type strains of the other Arcobacter species ranged between 94.1% with A. halophilus and 99.1% with the recently proposed species A. defluvii (CECT 7697(T)). DDH results betw... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=5000543 Tue, 28 Jun 2011 23:00:00 +0100 5000543 http://www.medworm.com/index.php?rid=4905447&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21641139%26dopt%3DAbstract In conclusion, a rapid, accurate and cost-effective assay was successfully developed for species identification of the members of the L. plantarum group. PMID: 21641139 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4905447 Wed, 01 Jun 2011 23:00:00 +0100 4905447 http://www.medworm.com/index.php?rid=4905465&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640537%26dopt%3DAbstract Authors: Gogleva AA, Kaparullina EN, Doronina NV, Trotsenko YA Two newly isolated obligate methanol-utilizing bacteria (strains Iva(T) and Lap(T)) with the ribulose monophosphate pathway of C(1) assimilation are described. The isolates are strictly aerobic, Gram negative, asporogenous, motile rods multiplying by binary fission, mesophilic and neutrophilic, synthesize indole-3-acetate. The prevailing cellular fatty acids are straight-chain saturated C(16:0) and unsaturated C(16:1) acids. The major ubiquinone is Q-8. The predominant phospholipids are phosphatidylethanolamine, phosphatidylglycerol and cardiolipin. Ammonia is assimilated by glutamate dehydrogenase. The DNA G+C contents of strains Iva(T) and Lap(T) are 54.0 and 50.5mol% (T(m)), respectively. Based on 16S rRNA gene sequence ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4905465 Tue, 31 May 2011 23:00:00 +0100 4905465 http://www.medworm.com/index.php?rid=4905456&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640538%26dopt%3DAbstract Authors: Márquez MC, Carrasco IJ, de la Haba RR, Jones BE, Grant WD, Ventosa A A polyphasic taxonomic study was performed on seven Bacillus-like bacteria isolated from three hypersaline and alkaline lakes located in China, Kenya and Tanzania. All strains were moderately halophilic and alkaliphilic, Gram positive, motile rods. The DNA G+C content from the seven isolates ranged from 42.2 to 43.4mol% and their major fatty acid was anteiso-C(15:0). Strain CG1(T), selected as representative strain of the isolates, possesses meso-diaminopimelic acid in the cell wall peptidoglycan, MK-7 as the predominant menaquinone and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major polar lipids. Comparative 16S rRNA gene sequence analysis indicated that the isolates ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4905456 Tue, 31 May 2011 23:00:00 +0100 4905456 http://www.medworm.com/index.php?rid=4802608&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21493030%26dopt%3DAbstract This study presents a genetic characterization of 27 potentially toxic cyanobacterial strains isolated from seven reservoirs located in the north and centre of Tunisia. These strains belonged mainly to Microcystis aeruginosa, Cylindrospermopsis raciborskii and Planktothrix agardhii species. Their toxicological potential was evaluated by molecular biology tools, which showed that none of the isolated strains carried segments of the gene cluster responsible for the production of cylindrospermopsin and saxitoxin. The majority of Microcystis isolates were able to synthesize microcystin, since they presented the six characteristic segments of the microcystin synthetase mcy cluster (mcyA, -B, -C, -D, -E and -G). This was further confirmed by MALDI-TOF analysis that showed the presence of eight m... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802608 Tue, 10 May 2011 08:46:20 +0100 4802608 http://www.medworm.com/index.php?rid=4802606&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21497473%26dopt%3DAbstract Authors: Ampomah OY, Huss-Danell K Very little is known about the genetic diversity and phylogeny of rhizobia nodulating Lotus species in northern temperate regions. We have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from Lotus corniculatus and Anthyllis vulneraria from different geographic sites and habitats in Sweden by restriction fragment length polymorphism (RFLP) of the internal transcribed spacer between their 16S rRNA and 23S rRNA (IGS) region. A high diversity consisting of 26 IGS types from 54 L. corniculatus isolates and five IGS types from seven A. vulneraria isolates was found. The 16S rRNA sequences and phylogeny of representatives of the different IGS types showed four interesting exceptions from the majority of the isolates... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802606 Tue, 10 May 2011 08:46:10 +0100 4802606 http://www.medworm.com/index.php?rid=4802605&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498017%26dopt%3DAbstract Authors: Salman V, Amann R, Girnth AC, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properti... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802605 Tue, 10 May 2011 08:46:06 +0100 4802605 http://www.medworm.com/index.php?rid=4802604&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498018%26dopt%3DAbstract Authors: Chang YL, Wang ET, Sui XH, Zhang XX, Chen WX As an introduced plant, Lablab purpureus serves as a vegetable, herbal medicine, forage and green manure in China. In order to investigate the diversity of rhizobia associated with this plant, a total of 49 rhizobial strains isolated from ten provinces of Southern China were analyzed in the present study with restriction fragment length polymorphism and/or sequence analyses of housekeeping genes (16S rRNA, IGS, atpD, glnII and recA) and symbiotic genes (nifH and nodC). The results defined the L. purpureus rhizobia as 24 IGS-types within 15 rrs-IGS clusters or genomic species belonging to Bradyrhizobium, Rhizobium, Ensifer (synonym of Sinorhizobium) and Mesorhizobium. Bradyrhizobium spp. (81.6%) were the most abundant isolates, half ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802604 Tue, 10 May 2011 08:46:03 +0100 4802604 http://www.medworm.com/index.php?rid=4802603&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498019%26dopt%3DAbstract This study revealed a geographical distribution of cowpea bradyrhizobia which seemed to be related to the differences in the environmental characteristics (soil type and soil pH, temperature, climate, moisture) of the different regions in Japan. PMID: 21498019 [PubMed - in process] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802603 Tue, 10 May 2011 08:45:59 +0100 4802603 http://www.medworm.com/index.php?rid=4802602&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21498020%26dopt%3DAbstract Authors: Westerholm M, Roos S, Schnürer A Four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains Re1(T), Re2, T1 and T2, were isolated from two different mesophilic methanogenic systems. The strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. Comparative 16S rRNA gene sequence analysis confirmed that the strains belong to the Firmicutes-Clostridia class. The most closely related species to strains Re1(T), Re2, T1 and T2 was Tepidanaerobacter syntrophicus, with a 16S rRNA gene sequence identity of 96%. The DNA-DNA relatedness of strains Re2, T1 and T2 to strain Re1(T) was 92, 102, 81%, respectively. The gene encoding the acetogen key enzyme formyltetrah... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802602 Tue, 10 May 2011 08:45:55 +0100 4802602 http://www.medworm.com/index.php?rid=4802607&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21497273%26dopt%3DAbstract Authors: Munoz R, Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Oliver Glöckner F, Rosselló-Móra R PMID: 21497273 [PubMed - in process] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802607 Sat, 30 Apr 2011 23:00:00 +0100 4802607 http://www.medworm.com/index.php?rid=4802594&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21536398%26dopt%3DAbstract Authors: Sha Q, Gunathilake A, Forstner MR, Hahn D The diversity and distribution of salmonellae in freshwater biofilms were analyzed at a fine scale (i.e. in 20 locations from a 324cm(2) area) for two sites in San Marcos, TX. A concrete storm water overflow channel (City Park) was sampled 4 times and a concrete surface in the spring-fed headwaters of the San Marcos River (Spring Lake) 5 times between April and September 2009, and each biofilm sample analyzed by a combination of traditional enrichment methods and molecular techniques. PCR detection of the invA gene, that encodes a protein of a type III secretion system present in salmonellae, after semi-selective enrichment of salmonellae was achieved in biofilms from all 20 locations at the City Park site, with locations generally bei... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802594 Fri, 29 Apr 2011 23:00:00 +0100 4802594 http://www.medworm.com/index.php?rid=4802595&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21531520%26dopt%3DAbstract Authors: Perrineau MM, Le Roux C, de Faria SM, de Carvalho Balieiro F, Galiana A, Prin Y, Béna G Acacia mangium is a legume tree native to Australasia. Since the eighties, it has been introduced into many tropical countries, especially in a context of industrial plantations. Many field trials have been set up to test the effects of controlled inoculation with selected symbiotic bacteria versus natural colonization with indigenous strains. In the introduction areas, A. mangium trees spontaneously nodulate with local and often ineffective bacteria. When inoculated, the persistence of inoculants and possible genetic recombination with local strains remain to be explored. The aim of this study was to describe the genetic diversity of bacteria spontaneously nodulating A. mangium in Brazil ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802595 Thu, 28 Apr 2011 23:00:00 +0100 4802595 http://www.medworm.com/index.php?rid=4802596&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21530125%26dopt%3DAbstract Authors: Verbaendert I, Boon N, De Vos P, Heylen K Although several Gram-positive denitrifiers have been characterized in the past, there is still uncertainty about the occurrence of the denitrification trait among these bacteria. In an isolation campaign on luvisol soil, Bacillus spp. were among the most abundant retrieved cultured denitrifiers next to members of Rhizobiaceae family and genus Cupriavidus. Subsequent screening of 180 representatives of the genus Bacillus (encompassing more than half of the current validly described species diversity in Bacillus) was performed and demonstrated the potential for dissimilatory reduction of nitrogen compounds in 45 of the 87 investigated species, with 19 species containing denitrifying members. The influence of several electron donors and ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802596 Tue, 26 Apr 2011 23:00:00 +0100 4802596 http://www.medworm.com/index.php?rid=4802597&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514760%26dopt%3DAbstract Authors: Stępkowski T, Zak M, Moulin L, Króliczak J, Golińska B, Narożna D, Safronova VI, Mądrzak CJ Forty three Bradyrhizobium strains isolated in Poland from root nodules of lupin species (Lupinus albus, L. angustifolius and L. luteus), and pink serradella (Ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpD, glnII and recA) and nodulation (nodA) gene sequences. Additionally, seven strains originating from root-nodules of yellow serradella (O. compressus) from Asinara Island (Italy) were included in this study. Phylogenetic trees revealed that 15 serradella strains, including all yellow serradella isolates, and six lupin strains grouped in Bradyrhizobium canariense (BC) clade, whereas eight strains from pink serradella and 15 lupin strain... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802597 Wed, 20 Apr 2011 23:00:00 +0100 4802597 http://www.medworm.com/index.php?rid=4802599&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514081%26dopt%3DAbstract Authors: Kristiansen A, Pedersen KH, Nielsen PH, Nielsen LP, Nielsen JL, Schramm A Biological air filters represent a promising tool for treating emissions of ammonia and odor from pig facilities. Quantitative fluorescence in situ hybridization (FISH) and 16S rRNA gene sequencing were used to investigate the bacterial community structure and diversity in a full-scale biofilter consisting of two consecutive compartments (front and back filter). The analysis revealed a highly specialized bacterial community of limited diversity, dominated by a few groups of Betaproteobacteria (especially Comamonas) and diverse Bacteroidetes. Actinobacteria, Gammaproteobacteria, and betaproteobacterial ammonia oxidizers (Nitrosomonas eutropha/Nitrosococcus mobilis-lineage) were also quantitatively importa... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802599 Tue, 19 Apr 2011 23:00:00 +0100 4802599 http://www.medworm.com/index.php?rid=4802598&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21514082%26dopt%3DAbstract Authors: Verslyppe B, De Smet W, De Baets B, De Vos P, Dawyndt P Each transfer of a microbial strain between a Biological Resource Center (BRC) and an individual researcher or another BRC imposes a risk of contamination or human error. Such artifacts jeopardize the quality of scientific results. In order to trace back possible scientific discrepancies that can be linked to failure of authenticity of the biological material involved, we launched the 'Make Histri' project that aims at reconstructing the exchange history ('Histri') of all bacterial and archaeal type strains as can be deduced from the information contained in BRC online catalogs. A Histri, visualized as a rooted tree, contains all known strain numbers attributed to the various cultures of a given strain, annotated with add... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802598 Tue, 19 Apr 2011 23:00:00 +0100 4802598 http://www.medworm.com/index.php?rid=4802600&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21507592%26dopt%3DAbstract Authors: Addison S, Slade A, Dennis M The microbial composition in a pulp and paper wastewater aerated lagoon system was analysed using fluorescence in situ hybridisation (FISH) to gain further understanding of the effect of substrate composition on microbial diversity for improved management of wastewater treatment systems. Few experiments have been conducted to tease apart the factors influencing the composition and abundance of certain groups within these wastewaters. Specific probes were used to investigate and enumerate the different bacterial groups present at particular stages through the treatment system over an extended period. Community composition and abundance of specific groups differed through the system however temporal stability was retained despite significant variabil... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802600 Sun, 17 Apr 2011 23:00:00 +0100 4802600 http://www.medworm.com/index.php?rid=4802601&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21501941%26dopt%3DAbstract Authors: Peeters K, Ertz D, Willems A We studied the culturable heterotrophic bacterial diversity present at the site of the new Princess Elisabeth Station at Utsteinen (Dronning Maud Land, East Antarctica) before construction. About 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. They were grouped using rep-PCR fingerprinting and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 93 representatives showed that the isolates belonged to five major phyla: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus. Isolates related to the genus Arthrobacter were the most prevalent whereas the genera Hymenobacter, Deinococcus, Cryoba... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4802601 Sat, 16 Apr 2011 23:00:00 +0100 4802601 http://www.medworm.com/index.php?rid=4637763&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21420266%26dopt%3DAbstract Authors: Sánchez-Cañizares C, Rey L, Durán D, Temprano F, Sánchez-Jiménez P, Navarro A, Polajnar M, Imperial J, Ruiz-Argüeso T Lupinus mariae-josephi is a recently described endemic Lupinus species from a small area in Eastern Spain where it thrives in soils with active lime and high pH. The L. mariae-josephi root symbionts were shown to be very slow-growing bacteria with different phenotypic and symbiotic characteristics from those of Bradyrhizobium strains nodulating other Lupinus. Their phylogenetic status was examined by multilocus sequence analyses of four housekeeping genes (16S rRNA, glnII, recA, and atpD) and showed the existence of a distinct evolutionary lineage for L. mariae-josephi that also included Bradyrhizobium jicamae. Within this lineage, the tested isolates clu... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4637763 Thu, 17 Mar 2011 00:00:00 +0100 4637763 http://www.medworm.com/index.php?rid=4578035&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21392917%26dopt%3DAbstract Authors: Verbeke TJ, Sparling R, Hill JE, Links MG, Levin D, Dumonceaux TJ D.R. Zeigler determined that the sequence identity of bacterial genomes can be predicted accurately using the sequence identities of a corresponding set of genes that meet certain criteria [32]. This three-gene model for comparing bacterial genome pairs requires the determination of the sequence identities for recN, thdF, and rpoA. This involves the generation of approximately 4.2kb of genomic DNA sequence from each organism to be compared, and also normally requires that oligonucleotide primers be designed for amplification and sequencing based on the sequences of closely related organisms. However, we have developed an analogous mathematical model for predicting the sequence identity of whole genomes based on ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4578035 Tue, 08 Mar 2011 00:00:00 +0100 4578035 http://www.medworm.com/index.php?rid=4578034&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21392918%26dopt%3DAbstract In this study, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl(+) Plt(+) strains isolated from tobacco, cotton or wheat on different continents. Phl(+) Plt(+) strains clustered separately from their nearest phylogenetic neighbors (i.e. species from the 'P. syringae', 'P. fluorescens' and 'P. chlororaphis' species complexes) based on rpoB, rpoD or gyrB phylogenies. DNA-DNA hybridization experiments clarified that Phl(+) Plt(+) strains formed a tight genomospecies that was distinct from P. syringae, P. fluorescens, or P. chlororaphis type strains. Within Phl(+) strains, the Phl(+) Plt(+) strains were differentiated from other biocontrol fluorescent Pseudomonas strains that produced Phl but not Plt, based on phenotypic and... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4578034 Tue, 08 Mar 2011 00:00:00 +0100 4578034 http://www.medworm.com/index.php?rid=4578036&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21377821%26dopt%3DAbstract Authors: Hayes D, Izzard L, Seviour R Despite their widespread use, our understanding of the microbial ecology of the autothermal thermophilic aerobic digesters (ATAD) used to dispose of sludge from wastewater treatment plants is poor. Applying both culture-dependent and molecular methods to two ATAD systems in Victoria, Australia treating different wastewaters revealed that their communities were highly specialized. Denaturing gradient gel electrophoresis (DGGE) profiling suggested differences in their population compositions and both changed over time. However, both showed low level biodiversity, and contained several novel bacterial populations. 16S rRNA clone library data and FISH analyses showed that Thermus thermophilus dominated both communities and that of a third ATAD plant in... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4578036 Fri, 04 Mar 2011 00:00:00 +0100 4578036 http://www.medworm.com/index.php?rid=4578037&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21353754%26dopt%3DAbstract Authors: Martinez-Murcia AJ, Monera A, Saavedra MJ, Oncina R, Lopez-Alvarez M, Lara E, Figueras MJ A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4578037 Thu, 24 Feb 2011 00:00:00 +0100 4578037 http://www.medworm.com/index.php?rid=4578038&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21353426%26dopt%3DAbstract Authors: Kubo K, Knittel K, Amann R, Fukui M, Matsuura K At the Nakabusa hot spring, Japan, dense olive-green microbial mats develop in regions where the slightly alkaline, sulfidic effluent has cooled to 65°C. The microbial community of such mats was analyzed by focusing on the diversity, as well as the in situ distribution and function of bacteria involved in sulfur cycling. Analyses of 16S rRNA and functional genes (aprA, pufM) suggested the importance of three thermophilic bacterial groups: aerobic chemolithotrophic sulfide-oxidizing species of the genus Sulfurihydrogenibium (Aquificae), anaerobic sulfate-reducing species of the genera Thermodesulfobacterium/Thermodesulfatator, and filamentous anoxygenic photosynthetic species of the genus Chloroflexus. A new oligonucleotide probe... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4578038 Wed, 23 Feb 2011 00:00:00 +0100 4578038 http://www.medworm.com/index.php?rid=4524809&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21345635%26dopt%3DAbstract Authors: Kriwy P, Uthicke S Microbial communities are potential indicators for water quality as they respond rapidly to environmental changes. In the Whitsunday Islands, Australia, microbial biofilm communities from two offshore islands were compared to those from two inshore islands subjected to poor water quality. Biofilm community composition was characterized using three culture-independent molecular techniques. The clone libraries indicated high genetic diversity, with somewhat higher scores in the offshore sites (57%) compared to the inshore sites (41%). The majority of microbes in the biofilms were related to Alphaproteobacteria (39.8%), Gammaproteobacteria (14.1%), Bacteroidetes (13.2%), diatoms (8.3%) and Cyanobacteria (3.9%). Redundancy analysis (RDA) for the CARD-FISH data s... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4524809 Mon, 21 Feb 2011 00:00:00 +0100 4524809 http://www.medworm.com/index.php?rid=4524810&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21316894%26dopt%3DAbstract Authors: Malinowska-Pańczyk E, Kołodziejska I, Saryczew M The aim of this study was to examine the effect of pressure treatment at 193MPa and -20°C on membrane damage, changes in activity of membrane-bound ATPases and degradation of nucleic acids. The experiments were carried out with three Escherichia coli strains, in the exponential and stationary phases of growth, and differing in sensitivity to pressure. All E. coli strains subjected to pressure in the exponential phase of growth were inactivated by 6 log cycles, independently of the strain, which was accompanied by a total loss of ability to plasmolyse, an increase in irreversible membrane permeability to PI, and a reduction of cellular ATP by more than 80%. After pressure treatment of stationary phase cells, the relationship b... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4524810 Fri, 11 Feb 2011 00:00:00 +0100 4524810 http://www.medworm.com/index.php?rid=4469116&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21310572%26dopt%3DAbstract Authors: Bautista GH, Cruz HA, Nesme X, Valdés M, Mendoza HA, Fernandez MP Amplified fragment length polymorphism (AFLP) was tested as an alternative to the DNA-DNA hybridization technique (DDH) to delineate genomospecies and the phylogenetic structure within the genus Frankia. Forty Frankia strains, including representatives of seven DDH genomospecies, were typed in order to infer current genome mispairing (CGM) and evolutionary genomic distance (EGD). The constructed phylogeny revealed the presence of three main clusters corresponding to the previously identified host-infecting groups. In all instances, strains previously assigned to the same genomospecies were grouped in coherent clusters. A highly significant correlation was found between DDH values and CGM computed from AFLP data... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469116 Tue, 08 Feb 2011 00:00:00 +0100 4469116 http://www.medworm.com/index.php?rid=4469117&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21306854%26dopt%3DAbstract Authors: Rogel MA, Ormeño-Orrillo E, Martinez Romero E Legume specificity is encoded in rhizobial genetic elements that may be transferred among species and genera. Dissemination (by lateral transfer) of gene assemblies dictating host range accounts for the existence of the same biological variant (biovar) in distinct microbiological species. Different alternative biovars may exist in a single species expanding their adaptation to different niches (legume nodules). A review of all reported biovars is presented. Instead of the term biovar, symbiotic variant (symbiovar) is proposed as a parallel term to pathovar in pathogenic bacteria. Symbiovars should be determined based on the symbiotic capabilities in plant hosts, distinguished by the differences in host range and supported by symbi... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469117 Mon, 07 Feb 2011 00:00:00 +0100 4469117 http://www.medworm.com/index.php?rid=4469121&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21300507%26dopt%3DAbstract In this study, bacterial populations associated with spontaneous sorghum fermentations were examined using a culture-independent strategy based on denaturing gradient gel electrophoresis and sequence analysis of V3-16S rRNA gene amplicons, and a culture-dependent strategy using conventional isolation based on culturing followed by 16S rRNA and/or pheS gene sequence analysis. The entire fermentation process was monitored over a 54h period and two phases were observed with respect to pH evolution and microbial succession. The first phase of the process (0-6h) was characterized by relatively high pH conditions and the presence of Enterococcus mundtii, albeit that this species was only detected with the culture-dependent approach. The second phase of the fermentation process (12-54h) was chara... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469121 Sat, 05 Feb 2011 00:00:00 +0100 4469121 http://www.medworm.com/index.php?rid=4469120&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21300508%26dopt%3DAbstract In this study, LAB were isolated from faecal samples of breast feeding mothers living in Syria, from faeces of their infants, from breast milk as well as from fermented food, typically consumed in Syria. A total of 700 isolates were characterized by genetic fingerprinting with random amplified polymorphic DNA (RAPD) and identified by comparative 16S rDNA sequencing and Matrix Assisted Laser Desorption Ionization-Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) analyses. Thirty six different species of Lactobacillus, Enterococcus, Streptococcus, Weissella and Pediococcus were identified. RAPD and MALDI-TOF-MS patterns allowed comparison of the lactic microbiota on species and strain level. Whereas some species were unique for one source, Lactobacillus plantarum, Lactobacillus fermentum, Pedi... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469120 Sat, 05 Feb 2011 00:00:00 +0100 4469120 http://www.medworm.com/index.php?rid=4469119&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21300509%26dopt%3DAbstract This study assessed the suitability of MALDI-TOF MS for their identification. 69 strains of different biological and geographic origins, identified by partial hsp60 gene sequencing as S. intermedius (n=15), S. pseudintermedius (n=32) and S. delphini (n=22), were analyzed by MALDI-TOF MS. The estimated sensitivity, specificity and efficiency were calculated. In addition we computed the agreement between the outcome of MALDI-TOF MS identification and partial hsp60 gene sequencing. The sensitivity of MALDI-TOF MS was higher for S. intermedius [0.95 (95% CI: 0.68-0.99)], than for S. pseudintermedius [0.78 (95% CI: 0.60-0.90)] and S. delphini [0.64 (95% CI: 0.41-0.83)], whereas the specificity was 1 for S. intermedius and S. delphini and 0.97 (95% CI: 0.86-0.99) for S. pseudintermedius. The Coh... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469119 Sat, 05 Feb 2011 00:00:00 +0100 4469119 http://www.medworm.com/index.php?rid=4469118&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21300510%26dopt%3DAbstract Authors: Moore ER, Rosselló-Móra R PMID: 21300510 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469118 Sat, 05 Feb 2011 00:00:00 +0100 4469118 http://www.medworm.com/index.php?rid=4469123&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21295428%26dopt%3DAbstract Authors: De Bruyne K, Slabbinck B, Waegeman W, Vauterin P, De Baets B, Vandamme P At present, there is much variability between MALDI-TOF MS methodology for the characterization of bacteria through differences in e.g., sample preparation methods, matrix solutions, organic solvents, acquisition methods and data analysis methods. After evaluation of the existing methods, a standard protocol was developed to generate MALDI-TOF mass spectra obtained from a collection of reference strains belonging to the genera Leuconostoc, Fructobacillus and Lactococcus. Bacterial cells were harvested after 24h of growth at 28°C on the media MRS or TSA. Mass spectra were generated, using the CHCA matrix combined with a 50:48:2 acetonitrile:water:trifluoroacetic acid matrix solution, and analyzed by the c... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469123 Wed, 02 Feb 2011 00:00:00 +0100 4469123 http://www.medworm.com/index.php?rid=4469124&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21292417%26dopt%3DAbstract Authors: Veloo AC, Erhard M, Welker M, Welling GW, Degener JE Gram-positive anaerobic cocci (GPAC) are part of the commensal microbiota of humans and are a phylogenetically heterogeneous group of organisms. To evaluate the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of GPAC, a database was constructed, using reference strains of commonly encountered GPAC and clinical isolates of which the sequence of the 16S rRNA gene was determined. Subsequently, the database was validated by identifying 107 clinical isolates of GPAC. Results were compared with the identifications obtained by 16S sequencing or fluorescent in situ hybridization (FISH). Strains belonging to the same species grouped together, in most ca... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469124 Tue, 01 Feb 2011 00:00:00 +0100 4469124 http://www.medworm.com/index.php?rid=4469125&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21288677%26dopt%3DAbstract Authors: Welker M, Moore ER In the last few years matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been increasingly studied and applied for the identification and typing of microorganisms. Very recently, MALDI-TOF MS has been introduced in clinical routine microbiological diagnostics with marked success, which is remarkable considering that not long ago the technology was generally seen as being far from practical application. The identification of microbial isolates by whole-cell mass spectrometry (WC-MS) is being recognized as one of the latest tools forging a revolution in microbial diagnostics, with the potential of bringing to an end many of the time-consuming and man-power-intensive identification procedures that have been used for ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469125 Mon, 31 Jan 2011 00:00:00 +0100 4469125 http://www.medworm.com/index.php?rid=4469126&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21282025%26dopt%3DAbstract Authors: Pang H, Qin G, Tan Z, Li Z, Wang Y, Cai Y One hundred and fifty-six strains isolated from corn (Zea mays L.), forage paddy rice (Oryza sativa L.), sorghum (Sorghum bicolor L.) and alfalfa (Medicago sativa L.) silages prepared on dairy farms were screened, of which 110 isolates were considered to be lactic acid bacteria (LAB) according to their Gram-positive and catalase-negative characteristics and, mainly, the lactic acid metabolic products. These isolates were divided into eight groups (A-H) based on the following properties: morphological and biochemical characteristics, γ-aminobutyric acid production capacity, and 16S rRNA gene sequences. They were identified as Weissella cibaria (36.4%), Weissella confusa (9.1%), Leuconostoc citreum (5.3%), Leuconostoc lactis (4.9%), Leu... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4469126 Sat, 29 Jan 2011 00:00:00 +0100 4469126 http://www.medworm.com/index.php?rid=4399978&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21257278%26dopt%3DAbstract Authors: Vandamme P, Dawyndt P The Burkholderia cepacia complex is a group of closely related species with conflicting biological properties. Triggered by the devastating effect of pulmonary infections in cystic fibrosis patients, the scientific community generated an unusually large amount of taxonomic data for these bacteria during the past 15 years. This review presents the polyphasic, multilocus and genomic methodology used for the classification and identification of these bacteria. The current state-of-the-art demonstrates that present day taxonomists can replace traditional DNA-DNA hybridizations for species level demarcation and 16S rRNA sequence analysis for studying phylogeny by superior whole genome sequence-based parameters within the framework of polyphasic taxonomic studi... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399978 Fri, 21 Jan 2011 00:00:00 +0100 4399978 http://www.medworm.com/index.php?rid=4399977&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21257279%26dopt%3DAbstract Authors: Shah HN, Rajakaruna L, Ball G, Misra R, Al-Shahib A, Fang M, Gharbia SE Strains (n=99) of Staphylococcus aureus isolated from a large number of clinical sources and tested for methicillin sensitivity were analysed by MALDI-TOF-MS using the Weak Cation Exchange (CM10) ProteinChip Array (designated SELDI-TOF-MS). The profile data generated was analysed using Artificial Neural Network (ANN) Analysis modelling techniques. Seven key ions identified by the ANNs that were predictive of MRSA and MSSA were validated by incorporation into a model. This model exhibited an area under the ROC curve value of 0.9147 indicating the potential application of this approach for rapidly characterising MRSA and MSSA isolates. Nearly all strains (n=97) were correctly assigned to the correct group, w... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399977 Fri, 21 Jan 2011 00:00:00 +0100 4399977 http://www.medworm.com/index.php?rid=4399981&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21247714%26dopt%3DAbstract Authors: Vasileuskaya-Schulz Z, Kaiser S, Maier T, Kostrzewa M, Jonas D The genus Stenotrophomonas is genetically and phenotypically heterogeneous. Of the nine species now accepted, only S. maltophilia is of clinical importance. Based on DNA-sequences of seven house keeping genes, it encompasses genogroups of DNA-similarity below 97% that predominantly comprise strains of environmental origin. Therefore, in order to unravel the uneven distribution of environmental isolates within genogroups and reveal genetic relationships within the genus, there is need for an easy and reliable approach for the identification and delineation of Stenotrophomonas spp. In this first study, a multi-locus sequence analysis (MLSA) with seven housekeeping genes (atpD, gapA, guaA, mutM, nuoD, ppsA and recA) w... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399981 Mon, 17 Jan 2011 00:00:00 +0100 4399981 http://www.medworm.com/index.php?rid=4399980&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21247715%26dopt%3DAbstract Authors: Hinse D, Vollmer T, Erhard M, Welker M, Moore ER, Kleesiek K, Dreier J The Streptococcus bovis/equinus complex is a heterogeneous group within the group D streptococci with important clinical relevance regarding infective endocarditis, sepsis and colon carcinoma. The taxonomic identification of species and sub-species of this complex, by the standard methods remains difficult. In the present study, we compared the cluster analysis of 88 strains of species of the S. bovis/equinus complex by sequence analysis of the manganese-dependent superoxide dismutase gene (sodA) and by Matrix Assisted Laser Desorption/Ionization-Time Of Flight Mass Spectrometry (MALDI-TOF MS). We observed a high congruence of strain grouping by MALDI-TOF MS in comparison with sodA sequence analyses, demons... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399980 Mon, 17 Jan 2011 00:00:00 +0100 4399980 http://www.medworm.com/index.php?rid=4399979&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21247716%26dopt%3DAbstract Authors: Gaia V, Casati S, Tonolla M A set of reference strains representing 38 different Legionella species were submitted to Whole Cell Mass Spectrometry (WCMS) with MALDI-TOF. The dendrogram computed from strain mass spectral patterns obtained by WCMS was compared to the phylogenetic tree obtained from macrophage infectivity potentiator (mip) sequences. The trees inferred from these two methods revealed significant homologies. Using 453 Legionella isolates previously characterized by genotyping, it was possible to create species-specific SuperSpectra, using appropriate sets of spectral masses, allowing unambiguous differentiation and identification of the most frequently isolated Legionella species. These SuperSpectra were tested for their suitability to identify Legionella strains ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399979 Mon, 17 Jan 2011 00:00:00 +0100 4399979 http://www.medworm.com/index.php?rid=4399983&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21242046%26dopt%3DAbstract Authors: Munoz R, López-López A, Urdiain M, Moore ER, Rosselló-Móra R The moderately halophilic, cultivable fraction of prokaryotes thriving in hypersaline sediments of a solar saltern in Mallorca, Spain, has been studied by means of different cultivation media. A set of 374 isolates retrieved with six different culture conditions was screened, using whole-cell MALDI-TOF MS analysis to classify them into 25 phenotypic clusters at 52% similarity. The phylogenetic inference, made from comparative sequence analyses of the 16S rRNA genes of selected strains, indicated that each phenotypic cluster was comprised of a genealogically homogeneous set of strains. DNA-DNA hybridization (DDH) results among selected strains confirmed that each MALDI-TOF cluster encompassed members of the same s... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399983 Sat, 15 Jan 2011 00:00:00 +0100 4399983 http://www.medworm.com/index.php?rid=4399982&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21242047%26dopt%3DAbstract Authors: Hahn D, Mirza B, Benagli C, Vogel G, Tonolla M Matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry (MS) was evaluated as a technique to characterize strains of the nitrogen-fixing actinomycete Frankia. MALDI-TOF MS reliably distinguished 37 isolates within the genus Frankia and assigned them to their respective host infection groups, i.e., the Alnus/Casuarina and the Elaeagnus host infection groups. The assignment of individual strains to sub-groups within the respective host infection groups was consistent with classification based on comparative sequence analysis of nifH gene fragments, confirming the usefulness of MALDI-TOF MS as a rapid and reliable tool for the characterization of Frankia strains. PMID: 21242047 [PubMed - as suppli... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399982 Sat, 15 Jan 2011 00:00:00 +0100 4399982 http://www.medworm.com/index.php?rid=4399984&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21239132%26dopt%3DAbstract Authors: Wittwer M, Heim J, Schär M, Dewarrat G, Schürch N In the everyday routine of an analytic lab, one is often confronted with the challenge to identify an unknown microbial sample lacking prior information to set the search limits. In the present work, we propose a workflow, which uses the spectral diversity of a commercial database (SARAMIS) to narrow down the search field at a certain taxonomic level, followed by a refined classification by supervised modelling. As supervised learning algorithm, we have chosen a shrinkage discriminant analysis approach, which takes collinearity of the data into account and provides a scoring system for biomarker ranking. This ranking can be used to tailor specific biomarker subsets, which optimize discrimination between subgroups, allowing a ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399984 Fri, 14 Jan 2011 00:00:00 +0100 4399984 http://www.medworm.com/index.php?rid=4399985&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21237605%26dopt%3DAbstract Authors: Sedo O, Voráč A, Zdráhal Z The influence of the matrix solution, sample form and deposition technique on the quality MALDI-TOF mass spectra was examined and assessed with the aim to improve MALDI-TOF MS performance for the identification of microorganisms and to enable automatic spectra acquisition. It was observed that the use of matrix compounds ferulic and sinapinic acid may result in improved mass spectral features, in terms of signal resolution and S/N ratio, as compared to alpha-cyano-4-hydroxycinnamic acid, which was, on the other hand, found to be the only matrix compound that enabled fully automatic mass spectra acquisition. The robustness of the whole sample preparation procedure was then assessed on a set of 25 strains of four Acinetobacter species. Results showe... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4399985 Thu, 13 Jan 2011 00:00:00 +0100 4399985 http://www.medworm.com/index.php?rid=4331310&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21194866%26dopt%3DAbstract Authors: Makk J, Homonnay ZG, Kéki Z, Lejtovicz Z, Márialigeti K, Spröer C, Schumann P, Tóth EM Three Gram-stain negative, aerobic, non-motile, non-spore-forming, rod-shaped bacterial strains, PYM5-11(T), RaM5-2 and PYM5-8, were isolated from the drinking water supply system of Budapest (Hungary) and their taxonomic positions were investigated by a polyphasic approach. All three strains grew optimally at 20-28°C and pH 5-7 without NaCl. The G+C content of the DNA of the type strain was 65.4mol%. On the basis of 16S rRNA gene sequence analysis, the isolates showed 94.5-94.9% sequence similarity to the type strain of Dokdonella koreensis and a similarity of 93.0-94.1% to the species of the genera Aquimonas and Arenimonas. The major isoprenoid quinone of the strains was ubiquinone Q-... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4331310 Wed, 29 Dec 2010 00:00:00 +0100 4331310 http://www.medworm.com/index.php?rid=4331309&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21194867%26dopt%3DAbstract Authors: Degefu T, Wolde-Meskel E, Frostegård A Leguminous trees play an important role in agroforestry in Ethiopia, but studies of their rhizobial symbionts are scarce. In earlier studies, we surveyed natural nodulation of native leguminous trees growing in different agro-ecological zones in Southern Ethiopia, isolated 400 rhizobia, and characterized them based on different phenotypic and genotypic methods. In the present study we characterized 18 strains belonging to the genus Mesorhizobium, isolated from nodules of Acacia abyssinica, A. senegal, A. tortilis and Sesbania sesban. Phylogenetic analysis of nearly full-length 16S rRNA gene grouped the test strains into three distinct clades separated from all currently recognized Mesorhizobium species. Three divergent strains formed sep... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4331309 Wed, 29 Dec 2010 00:00:00 +0100 4331309 http://www.medworm.com/index.php?rid=4331311&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21193279%26dopt%3DAbstract Authors: Fargier E, Saux MF, Manceau C Previous classification of Xanthomonas campestris has defined six pathovars (aberrans, armoraciae, barbareae, campestris, incanae, and raphani) that cause diseases on cruciferous plants. However, pathogenicity assays with a range of strains and different hosts identifies only three types of symptom: black rot, leaf spot and bacterial blight. These findings raise the question of the genetic relatedness between strains assigned to different pathovars or symptom phenotypes. Here we have addressed this issue by multilocus sequence analysis of 42 strains. The X. campestris species was polymorphic at the 8 loci analysed and had a high genetic diversity; 23 sequence types were identified of which 16 were unique. All strains that induce black rot (pathova... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4331311 Tue, 28 Dec 2010 00:00:00 +0100 4331311 http://www.medworm.com/index.php?rid=4331312&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21185143%26dopt%3DAbstract Authors: Figueras MJ, Collado L, Levican A, Perez J, Solsona MJ, Yustes C Nineteen bacteria isolates recovered from shellfish samples (mussels and oysters) showed a new and specific 16S rDNA-RFLP pattern with an Arcobacter identification method designed to recognize all species described up to 2008. These results suggested that they could belong to a new species. ERIC-PCR revealed that the 19 isolates belonged to 3 different strains. The sequence of the 16S rRNA gene of a representative strain (F98-3(T)) showed 97.6% similarity with the closest species Arcobacter marinus followed by Arcobacter halophilus (95.6%) and Arcobacter mytili (94.7%). The phylogenetic analysis with the16S rRNA, rpoB, gyrB and hsp60 genes placed the shellfish strains within the same cluster as the three species ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4331312 Wed, 22 Dec 2010 00:00:00 +0100 4331312 http://www.medworm.com/index.php?rid=4216874&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21095084%26dopt%3DAbstract Authors: Farfán M, Miñana-Galbis D, Garreta A, Lorén JG, Fusté MC The reconstruction of correct genealogies among biological entities, the estimation of the divergence time between organisms or the study of the different events that occur along evolutionary lineages are not always based on suitable genes. For reliable results, it is necessary to look at full-length sequences of genes under stabilizing selection (neutral or purifying) and behaving as good molecular clocks. In bacteria it has been proved that the malate dehydrogenase gene (mdh) can be used to determine the inter- and intraspecies divergence, and hence this gene constitutes a potential marker for phylogeny and bacterial population genetics. We have sequenced the full-length mdh gene in 36 type and reference strains of... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4216874 Sat, 20 Nov 2010 00:00:00 +0100 4216874 http://www.medworm.com/index.php?rid=4216873&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21095085%26dopt%3DAbstract Authors: Cappello MS, Zapparoli G, Stefani D, Logrieco A The diversity of indigenous Oenococcus oeni strains was investigated by molecular and biochemical characterization of isolates from Malvasia Nera wine, an economically important red wine of the Salento Region (Apulia, Italy), during spontaneous malolactic fermentation (MLF). A total of 82 isolates of this species, identified by species-specific PCR and 16S rDNA sequence analysis, was molecularly characterized by the amplified fragment length polymorphism (AFLP) technique. Three main groups resulted from cluster analysis and showed intraspecific homology higher than 50%, and a total of seven subgroups, with similarity values ranged from 80% to 98%, were obtained within these groups. Enzymatic activities, such as esterase, β-gluco... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4216873 Sat, 20 Nov 2010 00:00:00 +0100 4216873 http://www.medworm.com/index.php?rid=4216872&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21095086%26dopt%3DAbstract Authors: Svec P, Pantůček R, Petráš P, Sedláček I, Nováková D A group of 212 type and reference strains deposited in the Czech Collection of Microorganisms (Brno, Czech Republic) and covering 41 Staphylococcus species comprising 21 subspecies was characterised using rep-PCR fingerprinting with the (GTG)(5) primer in order to evaluate this method for identification of staphylococci. All strains were typeable using the (GTG)(5) primer and generated PCR products ranging from 200 to 4500bp. Numerical analysis of the obtained fingerprints revealed (sub)species-specific clustering corresponding with the taxonomic position of analysed strains. Taxonomic position of selected strains representing the (sub)species that were distributed over multiple rep-PCR clusters was verified and conf... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4216872 Sat, 20 Nov 2010 00:00:00 +0100 4216872 http://www.medworm.com/index.php?rid=4216871&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21115313%26dopt%3DAbstract Authors: Brady C, Denman S, Kirk S, Venter S, Rodríguez-Palenzuela P, Coutinho T Gram-negative, facultatively anaerobic bacterial strains were consistently isolated from oak trees displaying symptoms of extensive stem bleeding. In Britain, this disorder is called Acute Oak Decline (AOD). A similar condition has been noted on species of Mediterranean oak in Spain. The identity of bacterial isolates from symptomatic trees in both countries was investigated using molecular techniques and phenotypic assays. 16S rRNA gene sequencing indicated that the strains were most closely related to the genera Serratia, Kluyvera, Klebsiella and Raoultella (all>97%). Phylogenetic analysis revealed that the strains formed a distinct lineage within the family Enterobacteriaceae, which was confirmed by... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4216871 Thu, 04 Nov 2010 00:00:00 +0100 4216871 http://www.medworm.com/index.php?rid=4152388&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21051170%26dopt%3DAbstract Authors: Chung AP, Lopes A, Nobre MF, Morais PV Three red-pink pigmented strains, designated A1-12(T), A2-50A(T) and A2-91(T), were recovered from two different sites in a uranium mine. For all strains, the optimum growth temperature was 25°C, the optimum pH was 6.0-6.5 and the DNA G+C contents were between 60 and 63.4mol%. The major respiratory quinone was menaquinone 7 (MK-7) and the fatty acid profiles contained iso- and anteiso-branched C15 fatty acids, summed feature 3 (16:1 ω6c and/or ω7c and/or 15:0 iso 2-OH), summed feature 4 (17:1 anteiso B and/or iso I) and the unsaturated fatty acid 16:1 ω5c as the major components. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented three distinct branches within the family Flexibacteraceae most ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4152388 Tue, 02 Nov 2010 00:00:00 +0100 4152388 http://www.medworm.com/index.php?rid=4107722&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20970941%26dopt%3DAbstract Authors: Hauschild T, Sliżewski P, Masiewicz P A total of 197 isolates of Staphylococcus from small wild animals (insectivores and rodents) were identified by partial sequencing of the rpoB and dnaJ genes. Among the identified isolates the predominant species was S. succinus (28%), followed by S. xylosus (20.8%) and S. stepanovicii (18.3%). The other 14 Staphylococcus species were occasionally isolated. PCR-RFLP of the rpoB gene digested by Hpy8I was a fast and simple method to distinguish the two subspecies of S. succinus. More than 90% of the 55 S. succinus strains isolated belonged to S. succinus subsp. casei and only 9% to S. succinus subsp. succinus. Moreover, the present study describes the first ever isolation of S. fleurettii from healthy animals. PMID: 20970941 [PubMed - ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4107722 Wed, 20 Oct 2010 23:00:00 +0100 4107722 http://www.medworm.com/index.php?rid=4107721&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20970942%26dopt%3DAbstract In this study, we investigated the diversity and distribution of Comamonadaceae family (Betaproteobacteria) related catechol 2,3-dioxygenase genes, which belong to the I.2.C subfamily of extradiol dioxygenase genes. These catabolic genes encode enzymes supposed to function under hypoxic conditions as well, and may play a notable role in BTEX degradation in oxygen limited environments. Therefore, their diversity was analyzed in oxygen limited, petroleum hydrocarbon contaminated groundwater by terminal restriction fragment length polymorphism and cloning. Subfamily I.2.C related catechol 2,3-dioxygenase genes were detected in every investigated groundwater sample and a dynamic change was observed in the case of the structure of C23O gene possessing bacterial communities. To link the metaboli... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4107721 Wed, 20 Oct 2010 23:00:00 +0100 4107721 http://www.medworm.com/index.php?rid=4107723&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20965680%26dopt%3DAbstract Authors: Zhao L, Deng Z, Yang W, Cao Y, Wang E, Wei G A total of seventy-five symbiotic bacterial strains isolated from root nodules of wild Sophora alopecuroides grown in different regions of China's Loess Plateau were characterized. Based on the combined RFLP patterns, thirty-five genotypes were defined among the rhizobia and they were classified into nine genomic species, including Mesorhizobium alhagi and M. gobiense as the main groups, as well as Agrobacterium tumefaciens, M. amorphae, Phyllobacterium trifolii, Rhizobium giardinii, R. indigoferae, Sinorhizobium fredii and S. meliloti as the minor groups according to the 16S rRNA and recA gene analyses. Five and three lineages of nodA and nifH were found, respectively, in these strains, implying that the symbiotic genes of the S. a... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4107723 Mon, 18 Oct 2010 23:00:00 +0100 4107723 http://www.medworm.com/index.php?rid=4088157&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20956064%26dopt%3DAbstract In this study, a marine laboratory model system was developed. Cooperation between marine nitrifiers and anammox bacteria was induced by incremental exposure of a marine anammox community dominated by Scalindua species to oxygen in a bioreactor set-up under high ammonium (40mM influent) conditions. Changes in the activities of the relevant functional groups (anammox bacteria, aerobic ammonia oxidizers and nitrite oxidizers) were monitored by batch tests. Changes in community composition were followed by Fluorescence in situ Hybridization (FISH) and by amplification and sequencing of 16S rRNA and amoA genes. A co-culture of Scalindua sp., an aerobic ammonia-oxidizing Nitrosomonas-like species, and an aerobic (most likely Nitrospira sp.) nitrite oxidizer was obtained. Aerobic ammonia oxidize... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4088157 Fri, 15 Oct 2010 23:00:00 +0100 4088157 http://www.medworm.com/index.php?rid=4088158&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20950979%26dopt%3DAbstract Authors: Killer J, Kopečný J, Mrázek J, Havlík J, Koppová I, Benada O, Rada V, Kofroňová O One hundred and eighty-seven fructose-6-phosphate phosphoketolase positive strains were isolated from the digestive tract of three different bumblebee species. Analyses of the partial 16S rRNA gene sequences of the representative strains showed only 92.8% and 92.5% similarity to Bifidobacterium coryneforme YIT 4092(T) and Bifidobacterium indicum JCM 1302(T), 92.2% similarity to Alloscardovia omnicolens CCUG 18650 and slightly reduced similarity of 91% to other members of the family Bifidobacteriaceae. On the other hand, analyses of the partial heat-shock protein 60 (hsp60) gene sequence revealed that the proposed type strain BLAPIII-AGV(T) was affiliated only to the 60kDa chaperonin sequen... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=4088158 Tue, 12 Oct 2010 23:00:00 +0100 4088158 http://www.medworm.com/index.php?rid=3988016&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851546%26dopt%3DAbstract Authors: Aoki S, Kondo T, Prévost D, Nakata S, Kajita T, Ito M Sixty-one rhizobial strains from Lathyrus japonicus nodules growing on the seashore in Japan were characterized and compared to two strains from Canada. The PCR-based method was used to identify test strains with novel taxonomic markers that were designed to discriminate between all known Lathyrus rhizobia. Three genomic groups (I, II, and III) were finally identified using RAPD, RFLP, and phylogenetic analyses. Strains in genomic group I (related to Rhizobium leguminosarum) were divided into two subgroups (Ia and Ib) and subgroup Ia was related to biovar viciae. Strains in subgroup Ib, which were all isolated from Japanese sea pea, belonged to a distinct group from other rhizobial groups in the recA phylogeny and PCR-ba... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3988016 Thu, 16 Sep 2010 23:00:00 +0100 3988016 http://www.medworm.com/index.php?rid=3988015&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20851547%26dopt%3DAbstract In this study, the genetic diversity of native soybean bradyrhizobia isolated from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal was explored. Soil samples were collected from three different topographical regions with contrasting climates. A local soybean cultivar, Cobb, was used as a trap plant to isolate bradyrhizobia. A total of 24 isolates selected on the basis of their colony morphology were genetically characterized. For each isolate, the full nucleotide sequence of the 16S rRNA gene and ITS region, and partial sequences of the nifD and nodD1 genes were determined. Two lineages were evident in the conserved gene phylogeny; one representing Bradyrhizobium elkanii (71% of isolates), and the other representing Bradyrhizobium japonicum (21... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3988015 Thu, 16 Sep 2010 23:00:00 +0100 3988015 http://www.medworm.com/index.php?rid=3988017&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20828962%26dopt%3DAbstract Authors: Sato H, Teramoto K, Ishii Y, Watanabe K, Benno Y The taxonomic positions of the subspecies of Bifidobacterium longum (B. longum subsp. longum, subsp. infantis, and subsp. suis) have been controversial. A current proposal is that the former two species "B. infantis" and "B. suis" be unified with B. longum and all three reclassified as three subspecies. To test this proposal, ribosomal protein profiling as observed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was applied to the classification of 17 strains of B. longum, including three subspecies. Among 41 different kinds of ribosomal proteins selected as biomarkers whose masses were calculated from their amino acid sequences, 31-41 ribosomal proteins were observed in sample stra... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3988017 Mon, 06 Sep 2010 23:00:00 +0100 3988017 http://www.medworm.com/index.php?rid=3955232&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20822874%26dopt%3DAbstract Authors: López-López A, Rogel MA, Ormeño-Orrillo E, Martínez-Romero J, Martínez-Romero E The bacterial endophytic community present in different Phaseolus vulgaris (bean) cultivars was analyzed by 16S ribosomal RNA gene sequences of cultured isolates derived from surface disinfected roots and immature seeds. Isolated endophytes from tissue-macerates belonged to over 50 species in 24 different genera and some isolates from Acinetobacter, Bacillus, Enterococcus, Nocardioides, Paracoccus, Phyllobacterium, and Sphingomonas seem to correspond to new lineages. Phytate solubilizing bacteria were identified among Acinetobacter, Bacillus and Streptomyces bean isolates, phytate is the most abundant reserve of phosphorus in bean and in other seeds. Endophytic rhizobia were not capa... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3955232 Thu, 02 Sep 2010 23:00:00 +0100 3955232 http://www.medworm.com/index.php?rid=3955231&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20822875%26dopt%3DAbstract This study characterized a glycoside hydrolase family 42 (GH42) beta-galactosidase of Lactobacillus acidophilus (LacA) and compared lactose hydrolysis, hydrolysis of oNPG, pNPG and pNPG-analogues and galactooligosaccharides (GOSs) formation to GH2 beta-galactosidases of Streptococcus thermophilus (LacZ type), Lactobacillus plantarum and Leuconostoc mesenteroides subsp. cremoris (both LacLM type). Beta-galactosidases were heterologously expressed in Lactococcus lactis using a p170 derived promoter; experiments were performed with L. lactis crude cell extract (CCE). The novel GH42 beta-galactosidase of Lb. acidophilus had lower activity on lactose, oNPG and pNPG but higher relative activity on pNP analogues compared to GH2 beta-galactosidases, and did not transgalactosylate at high lactose c... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3955231 Thu, 02 Sep 2010 23:00:00 +0100 3955231 http://www.medworm.com/index.php?rid=3955233&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20817437%26dopt%3DAbstract Authors: Yarza P, Ludwig W, Euzéby J, Amann R, Schleifer KH, Glöckner FO, Rosselló-Móra R The "All-Species Living Tree Project" (LTP) provides the scientific community with a useful taxonomic tool consisting of a curated database of type strain sequences, a universal and optimized alignment and a single phylogenetic tree harboring all the type strains of the hitherto classified species [33]. On the website http://www.arb-silva.de/projects/living-tree an update has been regularly maintained by including the 1301 new descriptions that have appeared in the validation and notification lists of the IJSEM journal. The topology of the 16S rRNA-based tree was validated with a detailed comparison against a collection of taxa-specific and broad-range trees made using different approa... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3955233 Tue, 31 Aug 2010 23:00:00 +0100 3955233 http://www.medworm.com/index.php?rid=3955234&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20813476%26dopt%3DAbstract Authors: Behrendt U, Schumann P, Stieglmeier M, Pukall R, Augustin J, Spröer C, Schwendner P, Moissl-Eichinger C, Ulrich A In the course of studying the influence of N-fertilization on N(2) and N(2)O flux rates in relation to soil bacterial community composition of a long-term fertilization experiment in fen peat grassland, a strain group was isolated that was related to a strain isolated from a spacecraft assembly clean room during diversity studies of microorganisms, which withstood cleaning and bioburden reduction strategies. Both the fen soil isolates and the clean room strain revealed versatile physiological capacities in N-transformation processes by performing heterotrophic nitrification, respiratory ammonification and denitrification activity. Phylogenetic analysis based on ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3955234 Mon, 30 Aug 2010 23:00:00 +0100 3955234 http://www.medworm.com/index.php?rid=3915836&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20801595%26dopt%3DAbstract Authors: Gallego S, Vila J, Nieto JM, Urdiain M, Rosselló-Móra R, Grifoll M A Gram-negative bacterium designated UBF-P1(T) was isolated from an enrichment culture established in nutrient supplemented artificial sea water with pyrene as a carbon source, and inoculated with a marine fuel oil-degrading consortium obtained from a sand sample collected from the beach of Corrubedo (A Coruña, Galicia, Spain) after the Prestige accidental oil spill. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence affiliated strain UBF-P1(T) with the family Cohaesibacteraceae, Cohaesibacter gelatinilyticus (DSM 18289(T)) being the closest relative species with 92% sequence similarity. Cells were irregular rods, motile, strictly aerobic, catalase and oxidase positive. Ubiquinon... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3915836 Thu, 26 Aug 2010 23:00:00 +0100 3915836 http://www.medworm.com/index.php?rid=3890805&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20724091%26dopt%3DAbstract Authors: Beaz-Hidalgo R, Diéguez AL, Cleenwerck I, Balboa S, Doce A, de Vos P, Romalde JL A group of four motile facultative anaerobic marine isolates (Rd 8.15(T) [=CECT 7224(T), =LMG 23850(T)], Rd 16.13, Rd 6.8 [=LMG 25696] and Rd2L5) were obtained from cultured clams (Ruditapes philippinarum and Venerupis pullastra) in Galicia, north-western Spain. They formed a tight phylogenetic group based on sequences of the 16S rRNA gene and the four housekeeping genes rpoA (encoding the alpha-chain of RNA polymerase), rpoD (encoding the sigma factor of RNA polymerase), recA (encoding RecA protein), and atpA (encoding the alpha-subunit of bacterial ATP synthase). The phylogenies based on these sequences indicated that the four isolates represented a novel species in the genus Vibrio, and more... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3890805 Mon, 16 Aug 2010 23:00:00 +0100 3890805 http://www.medworm.com/index.php?rid=3855173&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20688447%26dopt%3DAbstract Authors: Moreno MD, García MT, Ventosa A, Iglesias-Guerra F, Mellado E The extremely halophilic bacterium strain IC10 was isolated from a solar saltern on Isla Cristina (southern Spain). Phylogenetic, genotypic and phenotypic data supported the inclusion of this strain in the species Salicola marasensis. An analysis of intracellular organic osmotic solutes showed glycine betaine to be present, contributing to the overall osmotic balance, and this was the only compatible solute accumulated when S. marasensis IC10 was grown over a wide range of external NaCl concentrations (10-25%, w/v). PMID: 20688447 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3855173 Mon, 02 Aug 2010 23:00:00 +0100 3855173 http://www.medworm.com/index.php?rid=3824162&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20675088%26dopt%3DAbstract In this study, denitrifiers were cultured using a strategy to generally enrich soil microorganisms. Of 490 colonies screened, eight nirK-containing isolates were phylogenetically identified (16S rRNA genes) as members of the Rhizobiales. A nirK gene related to a large cluster of sequences from uncultured bacteria mainly retrieved from soil was found in three isolates classified as Bradyrhizobium sp. Additional isolates were classified as Bradyrhizobium japonicum and Bosea sp. that contained nirK genes also closely related to the nirK from these strains. These isolates denitrified, albeit with different efficiencies. In Devosia sp., nirK was the only denitrification gene detected. Two Mesorhizobium sp. isolates contained a nirK gene also related to nirK from cultured Mesorhizobia and uncult... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3824162 Thu, 29 Jul 2010 23:00:00 +0100 3824162 http://www.medworm.com/index.php?rid=3804312&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20655680%26dopt%3DAbstract In this study, sequences from the V2 region of the small subunit ribosomal RNA gene were targeted in the development of qPCR assays to quantify DNA from six Bacteroides and one Prevotella species. In silico and experimental analyses suggested that each of the assays was highly discriminatory in detecting DNA from the intended species. Analytical sensitivity, precision and ranges of quantification were demonstrated for each assay by coefficients of variation of less than 2% for cycle threshold measurements over a range from 10 to 4x10(4) target sequence copies. The assays were applied to assess the occurrence and relative abundance of their target sequences in feces from humans and five animal groups as well as in 14 sewage samples from 13 different treatment facilities. Sequences from each... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3804312 Wed, 21 Jul 2010 23:00:00 +0100 3804312 http://www.medworm.com/index.php?rid=3786368&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20650590%26dopt%3DAbstract Authors: Krishnamurthi S, Ruckmani A, Pukall R, Chakrabarti T The taxonomic status of three Bacillus species, Bacillus insolitus, B. psychrodurans and B. psychrotolerans was reexamined using a polyphasic approach. In our analysis, these three Bacillus species formed a cluster separate from other members of Bacillus rRNA group 2 [5] and from Bacillus sensu stricto. These three species shared high 16S rRNA gene sequence similarities between them (97.8-99.7%) and showed closest sequence similarity (95.3-96.3%) to Paenisporosarcina quisquiliarum gen. nov., sp. nov. [18]. Sequence similarities with other related genera ranged between 90.9% and 94.5%. Phylogenetic coherence of the three species was supported by phenotypic characteristics, such as growth at low temperatures, negative oxidatio... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3786368 Mon, 19 Jul 2010 23:00:00 +0100 3786368 http://www.medworm.com/index.php?rid=3710904&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20580507%26dopt%3DAbstract Authors: Schäfer J, Jäckel U, Kämpfer P Mould-colonized water damaged building materials are frequently co-colonized by actinomycetes. Here, we report the results of the analyses of Actinobacteria on different wall materials from water damaged buildings obtained by both cultivation-dependent and cultivation-independent methods. Actinobacteria were detected in all but one of the investigated materials by both methods. The detected concentrations of Actinobacteria ranged between 1.8x10(4) and 7.6x10(7)CFUg(-1) of investigated material. A total of 265 isolates from 17 materials could be assigned to 31 different genera of the class Actinobacteria on the basis of 16S rRNA gene sequence analyses. On the basis of the cultivation-independent approach, 16S rRNA gene inserts of 800 clon... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3710904 Thu, 24 Jun 2010 23:00:00 +0100 3710904 http://www.medworm.com/index.php?rid=3659865&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20542651%26dopt%3DAbstract Authors: Shiraishi A, Matsushita N, Hougetsu T Nodulation abilities of bacteria in the subclasses Gammaproteobacteria and Betaproteobacteria on black locust (Robinia pseudoacacia) were tested. Pseudomonas sp., Burkholderia sp., Klebsiella sp., and Paenibacillus sp. were isolated from surface-sterilized black locust nodules, but their nodulation ability is unknown. The aims of this study were to determine if these bacteria are symbiotic. The species and genera of the strains were determined by RFLP analysis and DNA sequencing of 16S rRNA gene. Inoculation tests and histological studies revealed that Pseudomonas sp. and Burkholderia sp. formed nodules on black locust and also developed differentiated nodule tissue. Furthermore, a phylogenetic analysis of nodA and a BLASTN analysis of the... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3659865 Sun, 06 Jun 2010 23:00:00 +0100 3659865 http://www.medworm.com/index.php?rid=3570301&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20466501%26dopt%3DAbstract Authors: Lorén JG, Farfán M, Miñana-Galbis D, Fusté MC Different methods are available to determine the G+C content (e.g. thermal denaturation temperature or high performance liquid chromatography, HPLC), but obtained values may differ significantly between strains, as well as between laboratories. Recently, several authors have demonstrated that the genomic DNA G+C content of prokaryotes can be reliably estimated from one or several protein coding gene nucleotide sequences. Few G+C content values have been published for the Aeromonas species described and the data, when available, are often incomplete or provide only a range of values. Our aim in this current work was twofold. First, the genomic G+C content of the type or reference strains of all species and subspecies of ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3570301 Mon, 10 May 2010 23:00:00 +0100 3570301 http://www.medworm.com/index.php?rid=3556686&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20452160%26dopt%3DAbstract Authors: Kalita M, Małek W The phylogeny and taxonomic position of slow-growing Genista tinctoria rhizobia from Poland, Ukraine and England were estimated by comparative 16S rDNA, atpD, and dnaK sequence analyses, PCR-RFLP of 16S rDNA, DNA G+C content, and DNA-DNA hybridization. Each core gene studied placed the G. tinctoria rhizobia in the genus Bradyrhizobium cluster with unequivocal bootstrap support. G. tinctoria symbionts and bradyrhizobial strains shared 96-99% similarity in 16S rDNA sequences. Their similarity for atpD and dnaK sequences was 93-99% and 89-99%, respectively. These data clearly showed that G. tinctoria rhizobia belonged to the genus Bradyrhizobium. 16S rDNA sequence analysis was in good agreement with the results of the PCR-RFLP of the 16S rRNA gene. Although t... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3556686 Wed, 05 May 2010 23:00:00 +0100 3556686 http://www.medworm.com/index.php?rid=3556687&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20451341%26dopt%3DAbstract Authors: Albuquerque L, Rainey FA, Nobre MF, da Costa MS Two red-pigmented isolates, with optimum growth temperatures between 45 and 50 degrees C, were recovered from a hot spring in the Furnas, Area da Fonte 1825 on the Island of São Miguel in the Azores. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. These new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the fatty acid composition and polar lipid pattern, since they did not possess 2-OH fatty acids or glycolipid variant GL-1a. Moreover, the two new isolates had the lowest growth temperature range of any of the known species of the genus Meiothermus. On the basis of the results presented h... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3556687 Tue, 04 May 2010 23:00:00 +0100 3556687 http://www.medworm.com/index.php?rid=3545945&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20447791%26dopt%3DAbstract Authors: Lorite MJ, Donate-Correa J, Del Arco-Aguilar M, Pérez Galdona R, Sanjuán J, León-Barrios M Genetic and symbiotic characterization of 34 isolates from several Lotus species endemic to the Canary Islands showed extraordinary diversity, with bacteria belonging to different species of the genera Mesorhizobium (17 isolates), Sinorhizobium (12 isolates) and Rhizobium/Agrobacterium (5 isolates). In a previous report, we showed that the Sinorhizobium isolates mostly belonged to S. meliloti. Here, we focused on the remaining isolates. The Lotus mesorhizobial strains were distributed in the rrs tree within six poorly resolved branches. Partial sequences from atpD and recA genes produced much better resolved phylogenies that were, with some exceptions, congruent with the ribosom... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3545945 Mon, 03 May 2010 23:00:00 +0100 3545945 http://www.medworm.com/index.php?rid=3545941&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20447792%26dopt%3DAbstract Authors: Martin PA, Gundersen-Rindal DE, Blackburn MB An extensive collection of Bacillus thuringiensis isolates from around the world were phenotypically profiled using standard biochemical tests. Six phenotypic traits occurred in 20-86% of the isolates and were useful in distinguishing isolates: production of urease (U; 20.5% of isolates), hydrolysis of esculin (E; 32.3% of isolates), acid production from salicin (A; 37.4% of isolates), acid production from sucrose (S; 34.0% of isolates), production of phospholipase C or lecithinase (L; 79.7% of isolates), and hydrolysis of starch (T; 85.8% of isolates). With the exception of acid production from salicin and hydrolysis of esculin, which were associated, the traits assorted independently. Of the 64 possible combinations of these six p... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3545941 Mon, 03 May 2010 23:00:00 +0100 3545941 http://www.medworm.com/index.php?rid=3530814&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20435421%26dopt%3DAbstract Authors: Martin E, Fallschissel K, Kämpfer P, Jäckel U Investigations of bioaerosols collected from turkey, chicken and duck houses, as well as from a duck slaughterhouse, each in triplicate, revealed that 4-18% of 16S rRNA gene sequences in investigated 16S rRNA gene clone libraries were closely related to Jeotgalicoccus spp. J. halotolerans- and J. psychrophilus-related sequences were obtained in all investigated bioaerosol samples and formed a distinct group with sequences of both species type strains, which were collectively entitled Jeot-cluster-I. For a quantification of Jeot-cluster-I bacteria, a group specific PCR primer combination targeting the 16S rRNA genes was developed. Estimated concentrations by quantitative real-time PCR analyses revealed cell numbers between 10(... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3530814 Thu, 29 Apr 2010 23:00:00 +0100 3530814 http://www.medworm.com/index.php?rid=3508517&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20418037%26dopt%3DAbstract Authors: Hauschild T, Stepanović S, Zakrzewska-Czerwińska J Five novobiocin-resistant and oxidase-positive staphylococcal strains were isolated from wild small mammals. Phenotypic studies and phylogenetic analysis based on 16S rRNA, rpoB and dnaJ gene sequences revealed that these strains were members of the Staphylococcus sciuri cluster group and were similar to Staphylococcus fleurettii. DNA-DNA hybridisation with closely related staphylococcal species suggested that the strains represented a novel species. The name Staphylococcus stepanovicii is proposed, and the type strain is 196(T) (=PCM 2693(T) =CCM 7717(T)). PMID: 20418037 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3508517 Thu, 22 Apr 2010 23:00:00 +0100 3508517 http://www.medworm.com/index.php?rid=3399858&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20303688%26dopt%3DAbstract Authors: Cavalca L, Zanchi R, Corsini A, Colombo M, Romagnoli C, Canzi E, Andreoni V A rhizobacterial community, associated with the roots of wild thistle Cirsium arvense (L.) growing in an arsenic polluted soil, was studied by fluorescence in situ hybridization (FISH) analysis in conjunction with cultivation-based methods. In the bulk, rhizosphere, and rhizoplane fractions of the soil, the qualitative picture obtained by FISH analysis of the main phylogenetic bacterial groups was similar and was predominantly comprised of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The arsenic-resistant isolates belonged to 13 genera, the most abundant being those of Bacillus, Achromobacter, Brevundimonas, Microbacterium, and Ochrobactrum. Most bacteria grew in the presence of hi... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3399858 Thu, 18 Mar 2010 00:00:00 +0100 3399858 http://www.medworm.com/index.php?rid=3373006&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227843%26dopt%3DAbstract In this study, the 16S rRNA approach was used to investigate the bacterial diversity and community composition within the southern basin of the Lagoon of Venice and at one inlet in October 2007 and June 2008. Comparative sequence analysis of 645 mostly partial 16S rRNA gene sequences indicated high diversity and dominance of Alphaproteobacteria, Gammaproteobacteria and Bacteroidetes at the lagoon as well as at the inlet station, therefore pointing to significant mixing. Many of these sequences were close to the 16S rRNA of marine, often coastal, bacterioplankton, such as the Roseobacter clade, the family Vibrionaceae, and class Flavobacteria. Sequences of Actinobacteria were indicators of a freshwater input. The composition of the bacterioplankton was quantified by catalyzed reporter depos... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3373006 Fri, 12 Mar 2010 00:00:00 +0100 3373006 http://www.medworm.com/index.php?rid=3373005&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227844%26dopt%3DAbstract Authors: Beaz-Hidalgo R, Alperi A, Buján N, Romalde JL, Figueras MJ Phenotypicaly identified Aeromonas strains (n=119) recovered mainly from diseased fish were genetically re-identified and the concordance between the results was analysed. Molecular characterization based on the GCAT genus specific gene showed that only 90 (75.6%) strains belonged to the genus Aeromonas. The 16S rDNA-RFLP method identified correctly most of the strains with the exception of a few that belonged to A. bestiarum, A. salmonicida or A. piscicola. Separation of these 3 species was correctly assessed with the rpoD gene sequences, which revealed that 5 strains with the RFLP pattern of A. salmonicida belonged to A. piscicola, as did 1 strain with the pattern of A. bestiarum. Correct phenotypic identificati... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3373005 Fri, 12 Mar 2010 00:00:00 +0100 3373005 http://www.medworm.com/index.php?rid=3373007&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227217%26dopt%3DAbstract Authors: Bull CT, Manceau C, Lydon J, Kong H, Vinatzer BA, Fischer-Le Saux M Sequence similarity in the 16S rDNA gene confirmed that crucifer pathogen Pseudomonas syringae pv. alisalensis belongs to P. syringae sensu lato. In reciprocal DNA/DNA hybridization experiments, DNA relatedness was high (69-100%) between P. syringae pv. alisalensis strains and the type strain of P. cannabina (genomospecies 9). In contrast, DNA relatedness was low (below 48%) between P. syringae pv. alisalensis and reference strains from the remaining genomospecies of P. syringae including the type strain of P. syringae and reference strain of genomospecies 3 (P. syringae pv. tomato) although the well-known crucifer pathogen, P. syringae pv. maculicola, also belongs to genomospecies 3. Additional evidence that ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3373007 Thu, 11 Mar 2010 00:00:00 +0100 3373007 http://www.medworm.com/index.php?rid=3373008&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20226613%26dopt%3DAbstract Authors: Arnds J, Knittel K, Buck U, Winkel M, Amann R Members of the highly diverse bacterial phylum Verrucomicrobia are globally distributed in various terrestrial and aquatic habitats. They are key players in soils, but little is known about their role in aquatic systems. Here, we report on the design and evaluation of a 16S rRNA-targeted probe set for the identification of Verrucomicrobia and of clades within this phylum. Subsequently, the probe set was applied to a study concerning the seasonal abundance of Verrucomicrobia in waters of the humic lake Grosse Fuchskuhle (Germany) by catalyzed reporter deposition fluorescence in situ hybridization. The lake hosted diverse Verrucomicrobia clades in all seasons. Either Spartobacteria (up to 19%) or Opitutus spp. (up to 7%) dominated th... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3373008 Wed, 10 Mar 2010 00:00:00 +0100 3373008 http://www.medworm.com/index.php?rid=3347326&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206455%26dopt%3DAbstract Authors: Bælum J, Jacobsen CS, Holben WE 31 different bacterial strains isolated using the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) as the sole source of carbon, were investigated for their ability to mineralize 2,4-D and the related herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA). Most of the strains mineralize 2,4-D considerably faster than MCPA. Three novel primer sets were developed enabling amplification of full-length coding sequences (CDS) of the three known tfdA gene classes, known to be involved in phenoxy acid degradation. 16S rRNA genes were also sequenced and in order to investigate possible linkage between tfdA gene classes and bacterial species, tfdA and 16S rRNA gene phylogeny was compared. Three distinctly different classes of tfdA genes were observed,... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3347326 Wed, 03 Mar 2010 00:00:00 +0100 3347326 http://www.medworm.com/index.php?rid=3336217&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20202776%26dopt%3DAbstract Authors: Filteau M, Lagacé L, Lapointe G, Roy D An arbitrary primed community PCR fingerprinting technique based on capillary electrophoresis was developed to study maple sap microbial community characteristics among 19 production sites in Québec over the tapping season. Presumptive fragment identification was made with corresponding fingerprint profiles of bacterial isolate cultures. Maple sap microbial communities were subsequently compared using a representative subset of 13 16S rRNA gene clone libraries followed by gene sequence analysis. Results from both methods indicated that all maple sap production sites and flow periods shared common microbiota members, but distinctive features also existed. Changes over the season in relative abundance of predominant populations sh... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3336217 Tue, 02 Mar 2010 00:00:00 +0100 3336217 http://www.medworm.com/index.php?rid=3316361&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20185262%26dopt%3DAbstract Authors: Cho SH, Lee KS, Shin DS, Han JH, Park KS, Lee CH, Park KH, Kim SB The taxonomic positions of five Gram-negative, non-spore-forming and non-motile bacterial strains isolated from the rhizosphere of sand dune plants were examined using a polyphasic approach. The analysis of the 16S rRNA gene sequence indicated that all of the isolates fell into four distinct phylogenetic clusters belonging to the genus Chryseobacterium of the family Flavobacteriaceae. The 16S rRNA gene sequence similarities of isolates to mostly related type strains of Chryseobacterium ranged from 97.5% to 98.5%. All strains contained MK-6 as the predominant menaquinone, and iso-C(15:0), iso-C(17:0) 3-OH and a summed feature of iso-C(15:0) 2-OH and/or C(16:1) omega7c as the dominant fatty acids. Combined phenoty... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3316361 Tue, 23 Feb 2010 00:00:00 +0100 3316361 http://www.medworm.com/index.php?rid=3277246&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153592%26dopt%3DAbstract Authors: Heindl H, Wiese J, Thiel V, Imhoff JF To date, only a small number of investigations covering microbe-bryozoa associations have been carried out. Most of them have focused on a few bryozoan species and none have covered the antibacterial activities of associated bacteria. In the current study, the proportion and phylogenetic classification of Bryozoan-associated bacteria with antimicrobial properties were investigated. Twenty-one specimens of 14 different bryozoan species were collected from several sites in the Baltic and the Mediterranean Sea. A total of 340 associated bacteria were isolated, and 101 displayed antibiotic activities. While antibiosis was predominantly directed against Gram-positive test strains, 16S rRNA gene sequencing revealed affiliation of the isolates to... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3277246 Thu, 11 Feb 2010 00:00:00 +0100 3277246 http://www.medworm.com/index.php?rid=3277245&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153593%26dopt%3DAbstract Authors: Serrano W, Amann R, Rossello-Mora R, Fischer U Four species of marine purple sulfur bacteria of the genus Marichromatium have been validly described. A recent re-analysis of the 16S rRNA-based similarity and genomic DNA-DNA hybridizations (DDH) of the type strains [33] suggested that some of them are so closely related that they can be considered heterotypic synonyms. Here, we report on the evaluation of the multilocus sequence analysis approach (MLSA) for nine Marichromatium strains in order to resolve their intrageneric genealogical relationships. MLSA was based on six protein-coding genes (gyrB, recA, fusA, dnaK, pufM, and soxB), and the results were comparable to DDH. The phylogenetic tree constructed with the concatenated sequences, which also included the 16S rRNA gene a... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3277245 Thu, 11 Feb 2010 00:00:00 +0100 3277245 http://www.medworm.com/index.php?rid=3230246&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20116192%26dopt%3DAbstract Authors: Albuquerque L, Rainey FA, Pena A, Tiago I, Veríssimo A, Fernanda Nobre M, da Costa MS Two isolates, with an optimum growth temperature of about 45-50 degrees C and an optimum pH for growth between 7.5 and 8.5, were recovered from a hot spring in the Furnas area on the Island of São Miguel in the Azores. Strains form irregular rod-shaped cells are motile and stain Gram negative. The cells multiply by budding. These strains are non-pigmented, strictly aerobic, catalase and oxidase positive. These organisms assimilated carbohydrates, organic acids and amino acids. The major fatty acids are 19:0(cyclo omega8c) and 18:0. Ubiquinone 10 is the major respiratory quinone. The major polar lipids are diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethano... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3230246 Wed, 27 Jan 2010 00:00:00 +0100 3230246 http://www.medworm.com/index.php?rid=3220925&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20106623%26dopt%3DAbstract Authors: González-Domenech CM, Martínez-Checa F, Béjar V, Quesada E We have made a comprehensive study of the denitrifying species of the genus Halomonas, evaluating both the phylogenetic and phenotypic relationships amongst them and other species of Halomonas. The phylogenetic analysis was based on the 16S rRNA gene sequence as well as those of the three genes essential to a complete denitrification process: narH, nirS and nosZ. The main aim of the phenotypic study was to improve our knowledge of some of the species in question. To this end we investigated the type strain of each species, although in the case of Halomonas cerina we also studied strains R53 and 15CR. In addition to this we investigated some other strains phylogenetically related to Halomonas ventosae, Ha... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3220925 Mon, 25 Jan 2010 00:00:00 +0100 3220925 http://www.medworm.com/index.php?rid=3213143&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20097027%26dopt%3DAbstract In this study, the phylogenetic affiliation of seahorse-associated bacteria was assessed by 16S rRNA gene sequencing of cloned DNA fragments. Fluorescence in situ hybridization (FISH) was used to confirm the presence of the predominant groups indicated by 16S rRNA analysis. Both methods revealed that Vibrionaceae was the dominant population in Artemia sp. (live prey) and intestinal content of the seahorses, while Rhodobacteraceae was dominant in water samples from the aquaculture system and cutaneous mucus of the seahorses. To our knowledge, this is the first time that bacterial communities associated with healthy seahorses in captivity have been described. PMID: 20097027 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3213143 Thu, 21 Jan 2010 00:00:00 +0100 3213143 http://www.medworm.com/index.php?rid=3213142&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20097028%26dopt%3DAbstract In conclusion, for extraction of high amounts of microbial DNA with high purity from samples of biogas plants, a combined lysozyme/SDS-based cell lysis followed by a purification step with sephacryl columns is recommended. PMID: 20097028 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3213142 Thu, 21 Jan 2010 00:00:00 +0100 3213142 http://www.medworm.com/index.php?rid=3146882&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20047814%26dopt%3DAbstract Authors: Shen FT, Young LS, Hsieh MF, Lin SY, Young CC The alkB gene encodes for alkane 1-monooxygenase, which is a key enzyme responsible for the initial oxidation of inactivated alkanes. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. In the present study, a pair of primers was designed based on the conserved regions of the AlkB amino acid sequences of Actinobacteria, for amplifying the alkB gene from the genus Gordonia (20 Gordonia strains representing 13 species). The amplified alkB genes were then sequenced and analyzed. In the phylogenetic tree based on the translated AlkB amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence identity of the alkB gene in Gordonia rang... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3146882 Sat, 02 Jan 2010 00:00:00 +0100 3146882 http://www.medworm.com/index.php?rid=3067556&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19962263%26dopt%3DAbstract Authors: Grünwald S, Pilhofer M, Höll W Using fluorescence in situ hybridization (FISH) techniques and PCR-based rDNA sequencing, gut microflora in the larvae of bark- and wood-inhabiting cerambycid beetles (Rhagium inquisitor, Tetropium castaneum, Plagionotus arcuatus and Leptura rubra [Coleoptera: Cerambycidae]) was investigated. A total of 12 novel ascomycetous yeast strains were isolated from the gut content. Panfungal and strain-specific oligonucleotide probes identified two yeast strains as Candida rhagii and Candida shehatae, which were colonizing specialized organs (mycetomes) adhering to the gut of R. inquisitor and L. rubra larvae, respectively. Fragments containing these organisms were constantly being released from the mycetomes into the gut lumen. Whereas the myc... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3067556 Wed, 02 Dec 2009 00:00:00 +0100 3067556 http://www.medworm.com/index.php?rid=3040411&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19945811%26dopt%3DAbstract In this study, PCR species-specific primers based on the 16S rRNA gene were designed, which allowed rapid, easy, and correct identification of most known N(2)-fixing Burkholderia. With this approach, type and reference strains of Burkholderia kururiensis, B. unamae, B. xenovorans, B. tropica, and B. silvatlantica, as well as the legume-nodulating B. phymatum, B. tuberum, B. mimosarum, and B. nodosa, were unambiguously identified. In addition, the PCR species-specific primers allowed the diversity of the diazotrophic Burkholderia associated with field-grown tomato and sorghum plants to be determined. B. tropica and B. xenovorans were the predominant species found in association with tomato, but the occurrence of B. tropica with sorghum plants was practically exclusive. The efficiency of the... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3040411 Fri, 27 Nov 2009 00:00:00 +0100 3040411 http://www.medworm.com/index.php?rid=3040412&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19945242%26dopt%3DAbstract Authors: Debruyne L, Houf K, Douidah L, De Smet S, Vandamme P Arcobacter cryaerophilus is a heterogeneous species in which two distinct subgroups have been reported. In the present study, the taxonomic status of these subgroups was reassessed using amplified fragment length polymorphism and heat shock protein 60 gene sequence analysis. The results demonstrated that A. cryaerophilus has a complex taxonomic structure, which consists of multiple cores of strains that share intermediate levels of DNA-DNA hybridisation and exhibit low levels of DNA-DNA hybridisation towards other Arcobacter species. One of these cores consisted of the majority of strains and included most subgroup 2 strains from previous studies. A. cryaerophilus subgroup 1 strains represented three distinct cores, among wh... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3040412 Thu, 26 Nov 2009 00:00:00 +0100 3040412 http://www.medworm.com/index.php?rid=3033940&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19932578%26dopt%3DAbstract Authors: Shahram M, Nicholas RA, Wood AP, Kelly DP Analysis, using the polymerase chain reaction (PCR), restriction enzyme endonuclease analysis (REA), protein profile patterns, random amplification of polymorphic DNA (RAPD) fingerprinting, 16S rRNA gene sequencing and antisera growth inhibition tests, of 22 strains of Mycoplasma mycoides subsp. mycoides Large Colony type (MmmLC) and eight strains of M. mycoides subsp. capri (Mmc) are presented, along with a summary of comparative data from the literature for over 100 strains, all of which supports the reclassification of the MmmLC and Mmc strains into the single subspecies, M. mycoides subspecies capri. PMID: 19932578 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology) Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=3033940 Fri, 20 Nov 2009 00:00:00 +0100 3033940 http://www.medworm.com/index.php?rid=2935590&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19857940%26dopt%3DAbstract Authors: Venkata Ramana V, Sasikala C, Takaichi S, Ramana CV Two strains (JC17(T) and JC19a) of orange pigmented bacteria were isolated from an estuarine sample. Cells of both the strains were Gram-negative coccobacilli, non-motile, non-spore forming and strictly aerobic. Chemo-organoheterotrophy was the growth mode for both strains and was possible on a wide range of organic compounds. Strains were non-hemolytic and contained low levels of BChl-a and carotenoids. Iso-C(17:1)omega9c and C(20:1)omega9c were the major fatty acids. The genomic DNA G+C content of strain JC17(T) was 66.2mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strains JC17(T) and JC19a had the highest similarity to members of the genus Roseomonas and were closely related to Roseomonas c... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2935590 Sat, 24 Oct 2009 00:00:00 +0100 2935590 http://www.medworm.com/index.php?rid=2912734&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19836181%26dopt%3DAbstract Authors: Amrani S, Noureddine NE, Bhatnagar T, Argandoña M, Nieto JJ, Vargas C Twenty seven rhizobial strains associated with Acacia saligna grown in northern and southern Algeria were characterized, including generation time, host-range, the 16S rRNA gene and 16S-23S rRNA intergenic spacer restriction patterns, 16S rRNA gene sequence analysis and tolerance to salinity and drought. Cross inoculation tests indicated that 11 slow-growing isolates from northern nurseries were able to nodulate introduced Australian acacias exclusively, whereas 16 fast-growing isolates, mainly from southern nurseries, were capable of also nodulating native acacias. Restriction patterns and sequence analysis of the 16S rRNA gene showed that strains of the first group belonged to Bradyrhizobium while str... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2912734 Tue, 13 Oct 2009 23:00:00 +0100 2912734 http://www.medworm.com/index.php?rid=2887534&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19819658%26dopt%3DAbstract Authors: Schleifer KH The late 19th century was the beginning of bacterial taxonomy and bacteria were classified on the basis of phenotypic markers. The distinction of prokaryotes and eukaryotes was introduced in the 1960s. Numerical taxonomy improved phenotypic identification but provided little information on the phylogenetic relationships of prokaryotes. Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977. The current classification of Bacteria and Archaea is based on an operational-based model, the so-called polyphasic approach, comprised of phenotypic, chemotaxonomic and genotypic data, as well as phylogenetic information. The provisional status Candidatus h... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2887534 Thu, 08 Oct 2009 23:00:00 +0100 2887534 http://www.medworm.com/index.php?rid=2824635&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19765933%26dopt%3DAbstract Authors: Dai J, Wang Y, Zhang L, Tang Y, Luo X, An H, Fang C A brick-red-pigmented strain (XTM003(T)) isolated from the Qinghai-Tibet plateau was investigated using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequence indicated that the organism belonged to the genus Hymenobacter. The predominant menaquinone was MK7. The major fatty acids included iso-15:0, 16:1w5c and summed feature 3 (C(16: 1)omega7c and/or C(16: 1)omega6c). The G+C content of the DNA was 55.8%. In addition, DNA-DNA hybridization studies demonstrated that strain XTM003(T) had a relatedness value of 50.7% with the phylogenetically most closely related species Hymenobacter norwichensis DSM 15439(T). Based on the results of phenotypic characteristics and DNA-DNA hybridization studies, st... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2824635 Tue, 15 Sep 2009 23:00:00 +0100 2824635 http://www.medworm.com/index.php?rid=2797673&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19748753%26dopt%3DAbstract Authors: Giblot-Ducray D, Marefat A, Gillings MR, Parkinson NM, Bowman JP, Ophel-Keller K, Taylor C, Facelli E, Scott ES Strains of Xanthomonas translucens have caused dieback in the Australian pistachio industry for the last 15 years. Such pathogenicity to a dicotyledonous woody host contrasts with that of other pathovars of X. translucens, which are characterized by their pathogenicity to monocotyledonous plant families. Further investigations, using DNA-DNA hybridization, gyrB gene sequencing and integron screening, were conducted to confirm the taxonomic status of the X. translucens pathogenic to pistachio. DNA-DNA hybridization provided a clear classification, at the species level, of the pistachio pathogen as a X. translucens. In the gyrB-based phylogeny, strains of the pistachio... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2797673 Thu, 10 Sep 2009 23:00:00 +0100 2797673 http://www.medworm.com/index.php?rid=2775316&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19733991%26dopt%3DAbstract Authors: Endo A, Futagawa-Endo Y, Dicks LM Fourteen strains of fructophilic lactic acid bacteria were isolated from fructose-rich niches, flowers, and fruits. Phylogenetic analysis and BLAST analysis of 16S rDNA sequences identified six strains as Lactobacillus kunkeei, four as Fructobacillus pseudoficulneus, and one as Fructobacillus fructosus. The remaining three strains grouped within the Lactobacillus buchneri phylogenetic subcluster, but shared low sequence similarities to other known Lactobacillus spp. The fructophilic strains fermented only a few carbohydrates and fermented d-fructose faster than d-glucose. Based on the growth characteristics, the 14 isolates were divided into two groups. Strains in the first group containing L. kunkeei, F. fructosus, and F. pseudoficulneus grew... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2775316 Thu, 03 Sep 2009 23:00:00 +0100 2775316 http://www.medworm.com/index.php?rid=2752578&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19716251%26dopt%3DAbstract Authors: Robert Hamersley M, Woebken D, Boehrer B, Schultze M, Lavik G, Kuypers MM We studied microbial N(2) production via anammox and denitrification in the anoxic water column of a restored mining pit lake in Germany over an annual cycle. We obtained high-resolution hydrochemical profiles using a continuous pumping sampler. Lake Rassnitzer is permanently stratified at ca. 29m depth, entraining anoxic water below a saline density gradient. Mixed-layer nitrate concentrations averaged ca. 200mumolL(-1), but decreased to zero in the anoxic bottom waters. In contrast, ammonium was <5mumolL(-1) in the mixed layer but increased in the anoxic waters to ca. 600mumolL(-1) near the sediments. In January and October, (15)N tracer measurements detected anammox activity (maximum 504nmolN(2)L(-... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2752578 Tue, 25 Aug 2009 23:00:00 +0100 2752578 http://www.medworm.com/index.php?rid=2720871&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19692194%26dopt%3DAbstract Authors: Mirza BS, Welsh A, Rieder JP, Paschke MW, Hahn D Clone libraries of nifH gene fragments specific for the nitrogen-fixing actinomycete Frankia were generated from six soils obtained from five continents using a nested PCR. Comparative sequence analyses of all libraries (n=247 clones) using 96 to 97% similarity thresholds revealed the presence of three and four clusters of frankiae representing the Elaeagnus and the Alnus host infection groups, respectively. Diversity of frankiae was represented by fewer clusters (i.e., up to four in total) within individual libraries, with one cluster generally harboring the vast majority of sequences. Meta-analysis including sequences previously published for cultures (n=48) and for uncultured frankiae in root nodules of Morella pensylvanica f... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2720871 Sun, 16 Aug 2009 23:00:00 +0100 2720871 http://www.medworm.com/index.php?rid=2713342&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19682816%26dopt%3DAbstract Authors: Elbanna K, Elbadry M, Gamal-Eldin H Snap bean fields in 12 of the 25 governorates of Egypt were surveyed to determine the distribution and taxonomy of snap bean-nodulating rhizobia. Nodulation rates in the field were very low, indicating that Egyptian soils do not have sufficient numbers of snap bean-compatible Rhizobium spp. A total of 87 rhizobial isolates were assayed on the most commonly grown cultivars in order to identify the most effective strains. The five most effective isolates (R11, R13, R28, R49 and R52) were fast-growing and utilized a wide range of carbon and nitrogen sources. A phylogenetic assignment of these strains by analysis of the 16S ribosomal RNA gene suggested that all fell within the Rhizobium etli-Rhizobium leguminosarum group. Strains R11, R49 and R5... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2713342 Tue, 11 Aug 2009 23:00:00 +0100 2713342 http://www.medworm.com/index.php?rid=2703217&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19679418%26dopt%3DAbstract "Candidatus Paraholospora nucleivisitans", an intracellular bacterium in Paramecium sexaurelia shuttles between the cytoplasm and the nucleus of its host. Syst Appl Microbiol. 2009 Aug 11; Authors: Eschbach E, Pfannkuchen M, Schweikert M, Drutschmann D, Brümmer F, Fokin S, Ludwig W, Görtz HD An intracellular bacterium was discovered in two isolates of Paramecium sexaurelia from an aquarium with tropical fish in Münster (Germany) and from a pond in the Wilhelma zoological-botanical garden, Stuttgart (Germany). The bacteria were regularly observed in the cytoplasm of the host, but on some occasions they were found in the macronucleus of the host cell. In these cases, only a few, if any, bacteria were observed remaining in the cytoplasm. The bacterium was not infect... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2703217 Mon, 10 Aug 2009 23:00:00 +0100 2703217 http://www.medworm.com/index.php?rid=2703216&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19679419%26dopt%3DAbstract Authors: Nittami T, McIlroy S, Seviour EM, Schroeder S, Seviour RJ Two alphaproteobacterial Neisser negative 'Nostocoida limicola' morphotypes differing slightly in their trichome diameter and filament regularity were dominant populations in the Bendigo, Victoria, Australia activated sludge community removing phosphorus (P). Neither responded to the FISH probes available for any of the other alphaproteobacterial 'N. limicola' morphotypes. Instead both fluoresced with the DF988 FISH probe designed originally to target alphaproteobacterial cluster II Defluviicoccus tetrad forming organisms. A 16S rRNA based clone library from this biomass revealed that the alphaproteobacterial clones grouped closely with Candidatus 'Monilibacter batavus' and Defluviicoccus clones in a cluster separate fr... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2703216 Mon, 10 Aug 2009 23:00:00 +0100 2703216 http://www.medworm.com/index.php?rid=2703218&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19674858%26dopt%3DAbstract Authors: Berezina OV, Brandt A, Yarotsky S, Schwarz WH, Zverlov VV New isolates of solventogenic bacteria exhibited high hemicellulolytic activity. They produced butanol and acetone with high selectivity for butanol (about 80% of butanol from the total solvent yield). Their 16S rDNA sequence was 99% identical to that of Clostridium saccharobutylicum. The genes responsible for the last steps of solventogenesis and encoding crotonase, butyryl-CoA dehydrogenase, electron-transport protein subunits A and B, 3-hydroxybutyryl-CoA dehydrogenase, alcohol dehydrogenase, CoA-transferase (subunits A and B), acetoacetate decarboxylase, and aldehyde dehydrogenase were identified in the new C. saccharobutylicum strain Ox29 and cloned into Escherichia coli. The genes for crotonase, butyryl-CoA dehydr... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2703218 Sun, 09 Aug 2009 23:00:00 +0100 2703218 http://www.medworm.com/index.php?rid=2692059&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19665858%26dopt%3DAbstract Authors: Mnasri B, Badri Y, Saïdi S, de Lajudie P, Mhamdi R Ensifer meliloti (formerly Sinorhizobium meliloti) was first considered as a specific microsymbiont of Medicago, Melilotus and Trigonella. However, strains of E. meliloti were recovered from root nodules of various legume species and their symbiotic status still remains unclear. Here, we further investigate the specificity of these strains. A collection of 47 E. meliloti strains isolated in Tunisia from root nodules of Medicago truncatula, Medicago sativa, Medicago ciliaris, Medicago laciniata, Medicago marina, Medicago scutellata, Phaseolus vulgaris, Cicer arietinum, Argyrolobium uniflorum, Lotus creticus, Lotus roudairei, Ononis natrix, Retama raetam, Genista saharae, Acacia tortilis, Hedysarum carnosum and Hippocrepis ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2692059 Thu, 06 Aug 2009 23:00:00 +0100 2692059 http://www.medworm.com/index.php?rid=2640309&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19625150%26dopt%3DAbstract The objective of this work was to investigate the occurrence of Enterococcus gilvus in cheese. For this purpose, a real-time PCR protocol using phenylalanyl-tRNA synthase (pheS) as a target gene was optimized to evaluate the presence and abundance of this microorganism in Italian artisan cheeses. The real-time assay unequivocally distinguished E. gilvus from 25 non-target LAB and non-LAB species, demonstrating its absolute specificity. The assay performed well not only with purified DNA but also with DNA extracted from cheese samples artificially contaminated with E. gilvus. The dynamic range of target determination of the method in the cheese matrix (from 10(7) to 10(4)cfu/ml, covering three orders of magnitude) was lower and the detection limit higher than in vitro conditions, but still ... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2640309 Sun, 19 Jul 2009 23:00:00 +0100 2640309 http://www.medworm.com/index.php?rid=2640308&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19625151%26dopt%3DAbstract Authors: Taborda M, Antunes A, Tiago I, Veríssimo A, Nobre MF, da Costa MS A halophilic, aerobic Gram-negative bacterium, designated strain CVS-6(T), was isolated from a sea salt evaporation pond on the Island of Sal in the Cape Verde Archipelago. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation of the organism with members of the family Idiomarinaceae. Sequence similarities between CVS-6(T) and the type strains of the species of the genera Pseudidiomarina and Idiomarina ranged from 93.7% to 96.9%. The major isoprenoid quinone was ubiquinone 8 (Q-8). The major cellular fatty acids were 15:0 iso (21.8%), 17:0 iso (12.5%), 17:1 iso omega9c (10.7%), and 16:1 omega7c (10.6%). The DNA G+C content was 51.6mol%. The species represented by strain CVS-6(T) c... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2640308 Sun, 19 Jul 2009 23:00:00 +0100 2640308 http://www.medworm.com/index.php?rid=2580690&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19577874%26dopt%3DAbstract Authors: Albuquerque L, Ferreira C, Tomaz D, Tiago I, Veríssimo A, da Costa MS, Nobre MF Four red-pigmented isolates, with optimum growth temperatures of approximately 55-60 degrees C and an optimum pH for growth between 7.5 and 8.5, were recovered from hot springs in Central France. Phylogenetic analysis of the 16S rRNA gene sequences showed that these organisms represented a new species of the genus Meiothermus. The new isolates could be distinguished from other strains of the species of the genus Meiothermus primarily by the glycolipid profile and fatty acid composition because these organisms lacked the hydroxy fatty acids and the glycolipid variant GL-1a found in all other isolates of the species of Meiothermus examined. On the basis of the results presented here we propose t... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2580690 Thu, 02 Jul 2009 23:00:00 +0100 2580690 http://www.medworm.com/index.php?rid=2474052&cid=s_36255_77_f&fid=36255&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19346095%26dopt%3DAbstract Authors: Firsova J, Doronina N, Lang E, Spröer C, Vuilleumier S, Trotsenko Y A novel aerobic facultative methylotroph was isolated from contaminated soil. The organism (strain DM16) is a Gram-negative asporogenous non-motile curved rod multiplying by binary fission. Cells are neutrophilic and mesophilic. This strain utilized dichloromethane, methanol, formate and formaldehyde along with a variety of polycarbon compounds. Strain DM16 employs the ribulosebisphosphate pathway for C(1) assimilation. The DNA G+C content is 64.5mol%. The major ubiquinone is Q-10. The dominant cellular fatty acids are 18:1omega7c (58.6%), cyclo-19:0omega8c (34.8%) and 16:0 (3.2%). Sequencing of the 16S rRNA gene and DNA-DNA hybridization experiments clearly indicated that this methylotroph should be clas... Systematic and Applied Microbiology journals http://www.medworm.com/rss/comments.php?id=2474052 Sun, 14 Jun 2009 07:39:16 +0100 2474052