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Roseomonas aestuarii sp. nov., a bacteriochlorophyll-a containing alphaproteobacterium isolated from an estuarine habitat of India.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Systematic and Applied Microbiology - October 24, 2009 Category: Microbiology Authors: Venkata Ramana V, Sasikala C, Takaichi S, Ramana CV Tags: Syst Appl Microbiol Source Type: journals

Phenotypic and genotypic characterization of rhizobia associated with Acacia saligna (Labill.) Wendl. in nurseries from Algeria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Systematic and Applied Microbiology - October 13, 2009 Category: Microbiology Authors: Amrani S, Noureddine NE, Bhatnagar T, Argandoña M, Nieto JJ, Vargas C Tags: Syst Appl Microbiol Source Type: journals

Classification of Bacteria and Archaea: Past, present and future.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 polyp...
Source: Systematic and Applied Microbiology - October 8, 2009 Category: Microbiology Authors: Schleifer KH Tags: Syst Appl Microbiol Source Type: journals

Hymenobacter tibetensis sp. nov., a UV-resistant bacterium isolated from Qinghai-Tibet plateau.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 norwic...
Source: Systematic and Applied Microbiology - September 15, 2009 Category: Microbiology Authors: Dai J, Wang Y, Zhang L, Tang Y, Luo X, An H, Fang C Tags: Syst Appl Microbiol Source Type: journals

Proposal of Xanthomonas translucens pv. pistaciae pv. nov., pathogenic to pistachio (Pistacia vera).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 t...
Source: Systematic and Applied Microbiology - September 10, 2009 Category: Microbiology Authors: Giblot-Ducray D, Marefat A, Gillings MR, Parkinson NM, Bowman JP, Ophel-Keller K, Taylor C, Facelli E, Scott ES Tags: Syst Appl Microbiol Source Type: journals

Isolation and characterization of fructophilic lactic acid bacteria from fructose-rich niches.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 iso...
Source: Systematic and Applied Microbiology - September 3, 2009 Category: Microbiology Authors: Endo A, Futagawa-Endo Y, Dicks LM Tags: Syst Appl Microbiol Source Type: journals

Water column anammox and denitrification in a temperate permanently stratified lake (Lake Rassnitzer, Germany).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 a...
Source: Systematic and Applied Microbiology - August 25, 2009 Category: Microbiology Authors: Robert Hamersley M, Woebken D, Boehrer B, Schultze M, Lavik G, Kuypers MM Tags: Syst Appl Microbiol Source Type: journals

Diversity of frankiae in soils from five continents.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 sequence...
Source: Systematic and Applied Microbiology - August 16, 2009 Category: Microbiology Authors: Mirza BS, Welsh A, Rieder JP, Paschke MW, Hahn D Tags: Syst Appl Microbiol Source Type: journals

Genotypic and phenotypic characterization of rhizobia that nodulate snap bean (Phaseolus vulgaris L.) in Egyptian soils.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 16...
Source: Systematic and Applied Microbiology - August 11, 2009 Category: Microbiology Authors: Elbanna K, Elbadry M, Gamal-Eldin H Tags: Syst Appl Microbiol Source Type: journals

"Candidatus Paraholospora nucleivisitans", an intracellular bacterium in Paramecium sexaurelia shuttles between the cytoplasm and the nucleus of its host.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 infectious to P. sexaurelia or other species of Paramecium and appeared to be an obligate intracellular bacterium, while bacteria-free host cells w...
Source: Systematic and Applied Microbiology - August 10, 2009 Category: Microbiology Authors: Eschbach E, Pfannkuchen M, Schweikert M, Drutschmann D, Brümmer F, Fokin S, Ludwig W, Görtz HD Tags: Syst Appl Microbiol Source Type: journals

Candidatus Monilibacter spp., common bulking filaments in activated sludge, are members of Cluster III Defluviicoccus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 gr...
Source: Systematic and Applied Microbiology - August 10, 2009 Category: Microbiology Authors: Nittami T, McIlroy S, Seviour EM, Schroeder S, Seviour RJ Tags: Syst Appl Microbiol Source Type: journals

Isolation of a new butanol-producing Clostridium strain: High level of hemicellulosic activity and structure of solventogenesis genes of a new Clostridium saccharobutylicum isolate.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. sacc...
Source: Systematic and Applied Microbiology - August 9, 2009 Category: Microbiology Authors: Berezina OV, Brandt A, Yarotsky S, Schwarz WH, Zverlov VV Tags: Syst Appl Microbiol Source Type: journals

Symbiotic diversity of Ensifer meliloti strains recovered from various legume species in Tunisia.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 rouda...
Source: Systematic and Applied Microbiology - August 6, 2009 Category: Microbiology Authors: Mnasri B, Badri Y, Saïdi S, de Lajudie P, Mhamdi R Tags: Syst Appl Microbiol Source Type: journals

Detection and quantification of Enterococcus gilvus in cheese by real-time PCR.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Systematic and Applied Microbiology - July 19, 2009 Category: Microbiology Authors: Zago M, Bonvini B, Carminati D, Giraffa G Tags: Syst Appl Microbiol Source Type: journals

Description of Idiomarina insulisalsae sp. nov., isolated from the soil of a sea salt evaporation pond, proposal to transfer the species of the genus Pseudidiomarina to the genus Idiomarina and emended description of the genus Idiomarina.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 omega...
Source: Systematic and Applied Microbiology - July 19, 2009 Category: Microbiology Authors: Taborda M, Antunes A, Tiago I, Veríssimo A, Nobre MF, da Costa MS Tags: Syst Appl Microbiol Source Type: journals

Meiothermus rufus sp. nov., a new slightly thermophilic red-pigmented species and emended description of the genus Meiothermus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 M...
Source: Systematic and Applied Microbiology - July 2, 2009 Category: Microbiology Authors: Albuquerque L, Ferreira C, Tomaz D, Tiago I, Veríssimo A, da Costa MS, Nobre MF Tags: Syst Appl Microbiol Source Type: journals

Ancylobacter dichloromethanicus sp. nov. - a new aerobic facultatively methylotrophic bacterium utilizing dichloromethane.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 D...
Source: Systematic and Applied Microbiology - June 14, 2009 Category: Microbiology Authors: Firsova J, Doronina N, Lang E, Spröer C, Vuilleumier S, Trotsenko Y Tags: Syst Appl Microbiol Source Type: journals

The bacterial diversity in an anaerobic ammonium-oxidizing (anammox) reactor community.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An anaerobic ammonium-oxidation (anammox) reactor was operated for more than 500 days and the anammox activity of the biomass in the reactor reached 0.58kg N(total)/kg VSSd. The removal ratios of NO(2)(-)-N to NH(4)(+)-N in both reactor and activity tests were nearly 1.1. The bacterial diversity in the reactor was investigated by analysis of 16S rRNA gene clone libraries and quantitative real-time PCR (qPCR). The analysis showed that more than half of the clones in the library were affiliated to recognized filamentous bacteria. The previously recognized anammox bacterium (AnAOB) Candidatus Kuenenia stuttgartiensis was ...
Source: Systematic and Applied Microbiology - June 14, 2009 Category: Microbiology Authors: Li XR, Du B, Fu HX, Wang RF, Shi JH, Wang Y, Jetten MS, Quan ZX Tags: Syst Appl Microbiol Source Type: journals

Phylogenetic classification of heterotrophic bacteria associated with filamentous marine cyanobacteria in culture.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Fifty-one heterotrophic bacterial strains were isolated from the marine cyanobacterial cultures of heterocystous Nodularia harveyana strain Bo53 and non-heterocystous Oscillatoria brevis strain Bo10. Fluorescence in situ hybridisation and fingerprinting methods were used for a preliminary taxonomical classification of 44 of the 51 isolates. The strains obtained from Bo53 were mostly Alphaproteobacteria (10/24), followed by Bacteroidetes (7/24), and Gammaproteobacteria (3/24). The affiliation of the isolates originating from Bo10 was dominated by Alphaproteobacteria (8/20) and Bacteroidetes (7/20), followed by Gammaprot...
Source: Systematic and Applied Microbiology - June 14, 2009 Category: Microbiology Authors: Hube AE, Heyduck-Söller B, Fischer U Tags: Syst Appl Microbiol Source Type: journals

Effects of seawater ozonation on biofilm development in aquaculture tanks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study investigated the effects of seawater ozonation on biofilm development on microscope glass slides placed in small-scale aquaculture tanks containing the live feed organism Artemia. Fluorescence in situ hybridization (FISH) demonstrated that ozonation accelerated the biofilm formation cycle, while it delayed the establishment of filamentous bacteria. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial groups in the biofilm for both water types, but ozonation influenced their dynamics. With ozonation, the bacterial community structure was relatively stable and dominated by Gammaproteobacter...
Source: Systematic and Applied Microbiology - June 14, 2009 Category: Microbiology Authors: Wietz M, Hall MR, Høj L Tags: Syst Appl Microbiol Source Type: journals

Proposal to reclassify the Streptomyces albidoflavus clade on the basis of multilocus sequence analysis and DNA-DNA hybridization, and taxonomic elucidation of Streptomyces griseus subsp. solvifaciens.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Streptomyces albidoflavus 16S rRNA gene clade contains 10 species and subspecies with identical 16S rRNA gene sequences and very similar numerical taxonomic data, including Streptomyces griseus subsp. solvifaciens. Type strains of this clade, as well as three CGMCC strains which were received as Streptomyces galilaeus, Streptomyces sioyaensis and Streptomyces vinaceus, respectively, that shared the same 16S rRNA gene sequences with the clade, were subjected to multilocus sequence analysis (MLSA), DNA-DNA hybridization (DDH) and phenotypic characterization for a comprehensive reevaluation. The 13 strains still forme...
Source: Systematic and Applied Microbiology - June 8, 2009 Category: Microbiology Authors: Rong X, Guo Y, Huang Y Tags: Syst Appl Microbiol Source Type: journals

Genetic diversity and distribution of Bradyrhizobium and Azorhizobium strains associated with the herb legume Zornia glochidiata sampled from across Senegal.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Herb legumes have great potential for rehabilitation of semi-arid degraded soils in Sahelian ecosystems as they establish mutualistic symbiosis with N(2)-fixing rhizobia. A phylogenetic analysis was performed for 78 root nodule bacteria associated with the common Sahelian herb legume Zornia glochidiata Reichb ex DC in Senegal. Based on ITS (rDNA16S-23S) and recA sequences, these strains were shown to belong to the two genera Bradyrhizobium and Azorhizobium. Strains of this latter, although frequent, formed small and ineffective nodules and suggested a parasitism rather than a symbiotic association. A potential negative...
Source: Systematic and Applied Microbiology - June 1, 2009 Category: Microbiology Authors: Gueye F, Moulin L, Sylla S, Ndoye I, Béna G Tags: Syst Appl Microbiol Source Type: journals

Rice roots select for type I methanotrophs in rice field soil.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Methanotrophs are an important regulator for reducing methane (CH(4)) emissions from rice field soils. The type I group of the proteobacterial methanotrophs are generally favored at low CH(4) concentration and high O(2) availability, while the type II group lives better under high CH(4) and limiting O(2) conditions. Such physiological differences are possibly reflected in their ecological preferences. In the present study, methanotrophic compositions were compared between rice-planted soil and non-planted soil and between the rhizosphere and rice roots by using terminal restriction fragment length polymorphism (T-RFLP)...
Source: Systematic and Applied Microbiology - May 28, 2009 Category: Microbiology Authors: Wu L, Ma K, Lu Y Tags: Syst Appl Microbiol Source Type: journals

Multi-gene analysis reveals previously unrecognized phylogenetic diversity in Aliivibrio.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The "Vibrio fischeri species group" recently was reclassified as a new genus, Aliivibrio, comprising four species, Aliivibrio fischeri, Aliivibrio logei, Aliivibrio salmonicida, and Aliivibrio wodanis. Only limited phylogenetic analysis of strains within Aliivibrio has been carried out, however, and taxonomic ambiguity is evident within this group, especially for phenotypically unusual strains and certain strains isolated from bioluminescent symbioses. Therefore, to examine in depth the evolutionary relationships within Aliivibrio and redefine the host affiliations of symbiotic species, we examined several previously i...
Source: Systematic and Applied Microbiology - May 28, 2009 Category: Microbiology Authors: Ast JC, Urbanczyk H, Dunlap PV Tags: Syst Appl Microbiol Source Type: journals

Ensifer meliloti bv. lancerottense establishes nitrogen-fixing symbiosis with Lotus endemic to the Canary Islands and shows distinctive symbiotic genotypes and host range.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Eleven strains were isolated from root nodules of Lotus endemic to the Canary Islands and they belonged to the genus Ensifer, a genus never previously described as a symbiont of Lotus. According to their 16S rRNA and atpD gene sequences, two isolates represented minority genotypes that could belong to previously undescribed Ensifer species, but most of the isolates were classified within the species Ensifer meliloti. These isolates nodulated Lotus lancerottensis, Lotus corniculatus and Lotus japonicus, whereas Lotus tenuis and Lotus uliginosus were more restrictive hosts. However, effective nitrogen fixation only occur...
Source: Systematic and Applied Microbiology - May 22, 2009 Category: Microbiology Authors: León-Barrios M, Lorite MJ, Donate-Correa J, Sanjuán J Tags: Syst Appl Microbiol Source Type: journals

Acinetobacter strains IH9 and OCI1, two rhizospheric phosphate solubilizing isolates able to promote plant growth, constitute a new genomovar of Acinetobacter calcoaceticus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
During a screening of phosphate solubilizing bacteria (PSB) in agricultural soils, two strains, IH9 and OCI1, were isolated from the rhizosphere of grasses in Spain, and they showed a high ability to solubilize phosphate in vitro. Inoculation experiments in chickpea and barley were conducted with both strains and the results demonstrated their ability to promote plant growth. The 16S rRNA gene sequences of these strains were nearly identical to each other and to those of Acinetobacter calcoaceticus DSM 30006(T), as well as the strain CIP 70.29 representing genomospecies 3. Their phenotypic characteristics also coincide...
Source: Systematic and Applied Microbiology - May 19, 2009 Category: Microbiology Authors: Peix A, Lang E, Verbarg S, Spröer C, Rivas R, Santa-Regina I, Mateos PF, Martínez-Molina E, Rodríguez-Barrueco C, Velázquez E Tags: Syst Appl Microbiol Source Type: journals

In situ detection of antibiotic-resistance elements in single Bacillus cereus spores.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study presents permeabilization and in situ signal amplification protocols, using Bacillus cereus spores as a model, in order to detect antibiotic-resistance genes. The permeabilization protocol was designed based on the different layers of the Bacillus spore. Catalyzed reporter deposition (CARD)-FISH and in situ polymerase chain reaction (PCR) were used as signal amplification techniques. B. cereus was transformed with the high copy number pC194 and low copy number pMTL500Eres plasmids in order to induce resistance to chloramphenicol and erythromycin, respectively. In addition, a rifampicin-resistant B. cereus strain...
Source: Systematic and Applied Microbiology - May 13, 2009 Category: Microbiology Authors: Laflamme C, Gendron L, Turgeon N, Filion G, Ho J, Duchaine C Tags: Syst Appl Microbiol Source Type: journals

Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The C12O gene (catA gene) encodes for catechol 1,2-dioxygenase, which is a key enzyme involved in the first step catalysis of the aromatic ring in the ortho-cleavage pathway. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. C12OF and C12OR primers were designed based on the conserved regions of the CatA amino acid sequence of Actinobacteria for amplifying the catA gene from the genus Gordonia (16 Gordonia representing 11 species). The amplified catA genes (382bp) were sequenced and analyzed. In the phylogenetic tree based on the translated catA amino acid seq...
Source: Systematic and Applied Microbiology - May 8, 2009 Category: Microbiology Authors: Shen FT, Lin JL, Huang CC, Ho YN, Arun AB, Young LS, Young CC Tags: Syst Appl Microbiol Source Type: journals

Molecular diversity of Bacteroides spp. in human fecal microbiota as determined by group-specific 16S rRNA gene clone library analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, the molecular diversity of Bacteroides spp. in human fecal microbiota was analyzed from a seven-member, four-generation Chinese family using Bacteroides spp. group-specific 16S rRNA gene clone library analysis. A total of 549 partial 16S rRNA sequences amplified by Bacteroides spp.-specific primers were classified into 52 operational taxonomic units (OTUs) with a 99% sequence identity cut-off. Twenty-three OTUs, representing 83% of all clones, were related to 11 validly described Bacteroides species, dominated by Bacteroides coprocola, B. uniformis, and B. vulgatus. Most of the OTUs did not correspond to kno...
Source: Systematic and Applied Microbiology - March 19, 2009 Category: Microbiology Authors: Li M, Zhou H, Hua W, Wang B, Wang S, Zhao G, Li L, Zhao L, Pang X Tags: Syst Appl Microbiol Source Type: journals

A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new cloning system is described, which allows the construction of large-insert fosmid libraries in Escherichia coli and the transfer of the recombinant libraries to the extreme thermophile Thermus thermophilus via natural transformation. Libraries are established in the thermophilic host by site-specific chromosomal insertion of the recombinant fosmids via single crossover or double crossover recombination at the T. thermophilus pyr locus. Comparative screening of a fosmid library constructed from genomic DNA from the thermophilic spirochaete, Spirochaeta thermophila, for clones expressing thermoactive xylanase activ...
Source: Systematic and Applied Microbiology - March 11, 2009 Category: Microbiology Authors: Angelov A, Mientus M, Liebl S, Liebl W Tags: Syst Appl Microbiol Source Type: journals

Detection and persistence of fecal Bacteroidales as water quality indicators in unchlorinated drinking water.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The results of this study support the use of fecal Bacteroidales qPCR as a rapid method to complement traditional, culture-dependent, water quality indicators in systems where drinking water is supplied without chlorination or other forms of disinfection. A SYBR-green based, quantitative PCR assay was developed to determine the concentration of fecal Bacteroidales 16S rRNA gene copies. The persistence of a Bacteroides vulgatus pure culture and fecal Bacteroidales from a wastewater inoculum was determined in unchlorinated drinking water at 10 degrees C. B. vulgatus 16S rRNA gene copies persisted throughout the experimen...
Source: Systematic and Applied Microbiology - March 2, 2009 Category: Microbiology Authors: Saunders AM, Kristiansen A, Lund MB, Revsbech NP, Schramm A Tags: Syst Appl Microbiol Source Type: journals

Antifungal activity of strains of lactic acid bacteria isolated from a semolina ecosystem against Penicillium roqueforti, Aspergillus niger and Endomyces fibuliger contaminating bakery products.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Thirty samples of Italian durum wheat semolina and whole durum wheat semolina, generally used for the production of Southern Italy's traditional breads, were subjected to microbiological analysis in order to explore their lactic acid bacteria (LAB) diversity and to find strains with antifungal activity. A total of 125 presumptive LAB isolates (Gram-positive and catalase-negative) were characterized by repetitive extragenic palindromic-PCR (REP-PCR) and sequence analysis of the 16S rRNA gene, leading to the identification of the following species: Weissella confusa, Weissella cibaria, Leuconostoc citreum, Leuconostoc me...
Source: Systematic and Applied Microbiology - February 23, 2009 Category: Microbiology Authors: Valerio F, Favilla M, De Bellis P, Sisto A, de Candia S, Lavermicocca P Tags: Syst Appl Microbiol Source Type: journals

Diversity of frankiae in root nodules of Morella pensylvanica grown in soils from five continents.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bioassays with Morella pensylvanica as capture plant and comparative sequence analyses of nifH gene fragments of Frankia populations in nodules formed were used to investigate the diversity of Frankia in soils over a broad geographic range, i.e., from sites in five continents (Africa, Europe, Asia, North America, and South America). Phylogenetic analyses of 522-bp nifH gene fragments of 100 uncultured frankiae from root nodules of M. pensylvanica and of 58 Frankia strains resulted in a clear differentiation between frankiae of the Elaeagnus and the Alnus host infection groups, with sequences from each group found in al...
Source: Systematic and Applied Microbiology - February 23, 2009 Category: Microbiology Authors: Welsh A, Mirza BS, Rieder JP, Paschke MW, Hahn D Tags: Syst Appl Microbiol Source Type: journals

Towards large-scale FAME-based bacterial species identification using machine learning techniques.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have...
Source: Systematic and Applied Microbiology - February 21, 2009 Category: Microbiology Authors: Slabbinck B, De Baets B, Dawyndt P, De Vos P Tags: Syst Appl Microbiol Source Type: journals

Retama species growing in different ecological-climatic areas of northeastern Algeria have a narrow range of rhizobia that form a novel phylogenetic clade within the Bradyrhizobium genus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Sixty-seven isolates were isolated from nodules collected on roots of Mediterranean shrubby legumes Retama raetam and Retama sphaerocarpa growing in seven ecological-climatic areas of northeastern Algeria. Genetic diversity of the Retama isolates was analyzed based on genotyping by restriction fragment length polymorphism of PCR-amplified fragments of the 16S rRNA gene, the intergenic spacer (IGS) region between the 16S and 23S rRNA genes (IGS), and the symbiotic genes nifH and nodC. Eleven haplotypes assigned to the Bradyrhizobium genus were identified. Significant biogeographical differentiation of the rhizobial popu...
Source: Systematic and Applied Microbiology - February 19, 2009 Category: Microbiology Authors: Farida B, Géraldine D, Abdelghani B, Djellali B, Said B, Gisèle L Tags: Syst Appl Microbiol Source Type: journals

Fluorescence in situ hybridization for intracellular localization of nifH mRNA.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study reports a reliable approach for the in situ detection of nifH mRNA using fluorescence hybridization based on a previously described protocol for pmoA. nifH codes for a dinitrogenase reductase, a key enzyme in dinitrogen fixation. nifH mRNA was hybridized with a digoxigenin-labelled polynucleotide probe. The hybrid was detected with an anti-DIG-antibody labelled with horseradish peroxidase. Subsequently, the signal was amplified by catalyzed reporter deposition (CARD) with fluorochrome-labelled tyramides. Furthermore, the imaged organisms were identified using standard fluorescence in situ hybridization of rRNA. ...
Source: Systematic and Applied Microbiology - February 11, 2009 Category: Microbiology Authors: Pilhofer M, Pavlekovic M, Lee NM, Ludwig W, Schleifer KH Tags: Syst Appl Microbiol Source Type: journals

Diversity of aerobic and facultative alkalitolerant and halotolerant endospore formers in soil from the Alvord Basin, Oregon.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The objectives of this study were to develop new PCR primers that could target Bacillus or closely related 16S rRNA genes, to characterize the diversity of alkalitolerant, halotolerant, endospore-forming organisms in the soils surrounding Borax Lake, and to identify novel organisms that may ultimately provide new enzymes for applied use. A three-pronged approach was used to identify such bacteria in soil samples. Organisms were isolated using two different techniques. Finally, metagenomic DNA from soil samples was subjected to 16S rRNA gene amplification using the newly designed primers. Assays were performed to characteri...
Source: Systematic and Applied Microbiology - February 11, 2009 Category: Microbiology Authors: Smith SA, Benardini JN, Strap JL, Crawford RL Tags: Syst Appl Microbiol Source Type: journals

Stenotrophomonas chelatiphaga sp. nov., a new aerobic EDTA-degrading bacterium.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new ethylenediaminetetraacetic acid (EDTA)-utilizing gammaproteobacterial strain LPM-5(T) was isolated from municipal sewage sludge. Aerobic, gram-negative, motile rods multiply by binary fission. Neutrophilic and mesophilic, these are unable to grow in the presence of 3% NaCl (w/v), and unable to reduce nitrate to nitrite, and are oxidase and catalase positive, but lipase negative. The major cellular fatty acids are C(i15:0), C(a15:0) and C(16:1w7c). The dominant phospholipids are phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.3mol% (T(m)). The 16S ...
Source: Systematic and Applied Microbiology - February 10, 2009 Category: Microbiology Authors: Kaparullina E, Doronina N, Chistyakova T, Trotsenko Y Tags: Syst Appl Microbiol Source Type: journals

Biogeography and phylogeny of the NOR5/OM60 clade of Gammaproteobacteria.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The phylogeny, abundance, and biogeography of the NOR5/OM60 clade was investigated. This clade includes "Congregibacter litoralis" strain KT71, the first cultured representative of marine aerobic anoxygenic phototrophic Gammaproteobacteria. More than 500 16S rRNA sequences affiliated with this clade were retrieved from public databases. By comparative sequence analysis, 13 subclades could be identified, some of which are currently restricted to discrete habitat types. Almost all sequences in the largest subclade NOR5-1 and related subclade NOR5-4 originated from marine surface water samples. Overall, most of the NOR5/O...
Source: Systematic and Applied Microbiology - February 10, 2009 Category: Microbiology Authors: Yan S, Fuchs BM, Lenk S, Harder J, Wulf J, Jiao NZ, Amann R Tags: Syst Appl Microbiol Source Type: journals

Polyphasic taxonomic characterization of Lactobacillus rossiae isolates from Belgian and Italian sourdoughs reveals intraspecific heterogeneity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, this study has demonstrated that a polyphasic approach remains highly useful for identification of isolates belonging to genotypically heterogeneous species such as L. rossiae. PMID: 19201563 [PubMed - as supplied by publisher] (Source: Systematic and Applied Microbiology)
Source: Systematic and Applied Microbiology - February 6, 2009 Category: Microbiology Authors: Ilse S, Roel VD, Gino V, Luc DV, Luca S, Peter V, Geert H Tags: Syst Appl Microbiol Source Type: journals

Inter- and intra-genomic heterogeneity of the intervening sequence in the 23S ribosomal RNA gene of Campylobacter jejuni and Campylobacter coli.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An intervening sequence (IVS) can be present or absent in the 23S rRNA of Campylobacter jejuni and Campylobacter coli. As part of a survey, we used a polymerase chain reaction (PCR) assay to detect the presence of the IVS in 43 isolates of C. coli and 82 isolates of C. jejuni. An IVS was present in 40 (93.0%) of the C. coli and only 34 (41.5%) of the C. jejuni isolates. Twelve (27.9%) of the C. coli isolates and seven (8.5%) of the C. jejuni isolates resulted in two polymerase chain reaction products, indicating heterogeneity in the presence of the 23S rRNA IVS. Fourteen of the isolates with two products were evaluated...
Source: Systematic and Applied Microbiology - February 5, 2009 Category: Microbiology Authors: Meinersmann RJ, Phillips RW, Ladely SR Tags: Syst Appl Microbiol Source Type: journals

Multilocus sequence analysis of the genus Bradyrhizobium.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The use of multilocus sequence analysis (MLSA) for the taxonomy of Bradyrhizobium was assessed. We compared partial sequences for atpD, recA, gyrB, rpoB and dnaK for a set of reference strains representing named species and genospecies, and a number of new isolates from Lupinus albus, Arachis hypogaea and Ornithopus compressus from Spain. The phylogenies of the individual genes were compared with previous DNA-DNA hybridization results. High hybridization values were well reflected, but intermediary hybridization values were less clearly apparent. However, the phylogeny of a concatenated dataset of the five genes did re...
Source: Systematic and Applied Microbiology - February 5, 2009 Category: Microbiology Authors: Rivas R, Martens M, de Lajudie P, Willems A Tags: Syst Appl Microbiol Source Type: journals

Evolution of pathogenicity in the Bacillus cereus group.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Bacillus cereus group of bacteria comprises soil-dwelling saprophytes but on occasion these bacteria can cause a wide range of diseases in humans, including food poisoning, systemic infections and highly lethal forms of anthrax. While anthrax is almost invariably caused by strains from a single evolutionary lineage, Bacillus anthracis, variation in the virulence properties of strains from other lineages has not been fully addressed. Using multi-locus sequence data from 667 strains, we reconstructed the evolutionary history of the B. cereus group in terms of both clonal inheritance and recombination. The strains inc...
Source: Systematic and Applied Microbiology - February 4, 2009 Category: Microbiology Authors: Didelot X, Barker M, Falush D, Priest FG Tags: Syst Appl Microbiol Source Type: journals

Genetic diversity and biogeography of rhizobia associated with Caragana species in three ecological regions of China.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Twenty-two genospecies belonging mainly to Mesorhizobium, and occasionally to Rhizobium and Bradyrhizobium, were defined among the 174 rhizobia strains isolated from Caragana species. Highly similar nodC genes were found in the sole Bradyrhizobium strain and among all the detected Mesorhizobium strains. A clear correlation between rhizobial genospecies and the eco-regions where they were isolated was found using homogeneity analysis. All these results demonstrated that Caragana species had stringently selected the rhizobia symbiotic genotype, but not the genomic background; lateral transfer of symbiotic genes from Meso...
Source: Systematic and Applied Microbiology - February 3, 2009 Category: Microbiology Authors: Lu YL, Chen WF, Wang ET, Guan SH, Yan XR, Chen WX Tags: Syst Appl Microbiol Source Type: journals

Vibrio gallaecicus sp. nov. isolated from cultured clams in north-western Spain.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A group of three motile facultative anaerobic marine bacteria were isolated from cultured Manila clams (Ruditapes philippinarum) in Galicia, north-western Spain. The strains were characterized phenotypically and genotypically. Phylogenetic analysis of the 16S rRNA gene and four housekeeping genes, RNA polymerase alpha-chain (rpoA), RecA protein (recA), the alpha-subunit of bacterial ATP synthase (atpA) and the uridine monophosphate (UMP) kinase (pyrH), indicated that these strains were closely related to the Vibrio splendidus clade. The amplified fragment length polymorphism (AFLP) fingerprints, DNA-DNA hybridizations ...
Source: Systematic and Applied Microbiology - January 29, 2009 Category: Microbiology Authors: Beaz-Hidalgo R, Doce A, Pascual J, Toranzo AE, Romalde JL Tags: Syst Appl Microbiol Source Type: journals

Diversity analysis of magnetotactic bacteria in Lake Miyun, northern China, by restriction fragment length polymorphism.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Magnetotactic bacteria (MTB) synthesize intracellular nano-scale crystals of magnetite or greigite within magnetosomes. MTB are ubiquitous in limnic and marine environments. In order to understand the diversity of MTB better, sediment samples were examined from Lake Miyun near Beijing by restriction fragment length polymorphism (RFLP). First, in silico analysis was used to evaluate the effectiveness of 12 sets of restriction endonucleases for distinguishing MTB sequences retrieved from the GenBank database. It was found that the tested restriction endonucleases had different power in the ability to differentiate the op...
Source: Systematic and Applied Microbiology - January 23, 2009 Category: Microbiology Authors: Lin W, Li J, Schüler D, Jogler C, Pan Y Tags: Syst Appl Microbiol Source Type: journals

Description of Dietzia lutea sp. nov., isolated from a desert soil in Egypt.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An actinobacterial strain YIM 80766(T) was isolated from a soil sample collected from the eastern desert of Egypt, and its taxonomic position was investigated by a polyphasic approach. The organism was found to have a range of chemical and morphological properties consistent with its classification in the genus Dietzia. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between strain YIM 80766(T) and the other type strains of recognized members of the genus Dietzia were 97.0-98.9%. However, DNA-DNA hybridization values and phenotypic characteristics revealed that the strain differed f...
Source: Systematic and Applied Microbiology - January 19, 2009 Category: Microbiology Authors: Li J, Chen C, Zhao GZ, Klenk HP, Pukall R, Zhang YQ, Tang SK, Li WJ Tags: Syst Appl Microbiol Source Type: journals

Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Bacterial midrib rot of greenhouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) is an emerging disease in Flanders (Belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. Isolations from infected lettuces, collected from 14 commercial greenhouses in Flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, LOPAT characteristics, FAME analysis, BOX-PCR fingerprinting, 16S rRNA and rpoB gene sequencing, as well as DNA-DNA hybridization...
Source: Systematic and Applied Microbiology - January 19, 2009 Category: Microbiology Authors: Cottyn B, Heylen K, Heyrman J, Vanhouteghem K, Pauwelyn E, Bleyaert P, Van Vaerenbergh J, Höfte M, De Vos P, Maes M Tags: Syst Appl Microbiol Source Type: journals

Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RubisCO genotypes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A molecular approach, based on the detection of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes, was applied to investigate the distribution and diversity of autotrophic bacteria in groundwater systems. DNA extracts from 48 sampling stations, including a variety of pristine and polluted, shallow and deep-subsurface groundwater samples obtained from Germany and Austria, served as a template for the PCR amplification of form I (cbbL) and form II (cbbM) large subunit RubisCO genes. The majority of the samples (>80%) contained two different forms of RubisCO. In 17 samples, all three forms o...
Source: Systematic and Applied Microbiology - January 19, 2009 Category: Microbiology Authors: Alfreider A, Vogt C, Geiger-Kaiser M, Psenner R Tags: Syst Appl Microbiol Source Type: journals

Toxicity phenotype does not correlate with phylogeny of Cylindrospermopsis raciborskii strains.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cylindrospermopsis raciborskii is a species of freshwater, bloom-forming cyanobacterium. C. raciborskii produces toxins, including cylindrospermopsin (hepatotoxin) and saxitoxin (neurotoxin), although non toxin-producing strains are also observed. In spite of differences in toxicity, C. raciborskii strains comprise a monophyletic group, based upon 16S rRNA gene sequence identities (greater than 99%). We performed phylogenetic analyses; 16S rRNA gene and 16S-23S rRNA gene internally transcribed spacer (ITS-1) sequence comparisons, and genomic DNA restriction fragment length polymorphism (RFLP), resolved by pulsed-field ...
Source: Systematic and Applied Microbiology - December 30, 2008 Category: Microbiology Authors: Stucken K, Murillo AA, Soto-Liebe K, Fuentes-Valdés JJ, Méndez MA, Vásquez M Tags: Syst Appl Microbiol Source Type: journals