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 'Microbial Ecology' source. Mon, 06 Feb 2012 21:32:18 +0100 http://www.medworm.com/index.php?rid=5638415&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22281804%26dopt%3DAbstract Authors: Jackson SA, Kennedy J, Morrissey JP, O'Gara F, Dobson AD Abstract Marine sponges are host to numerically vast and phylogenetically diverse bacterial communities, with 26 major phyla to date having been found in close association with sponge species worldwide. Analyses of these microbial communities have revealed many sponge-specific novel genera and species. These endosymbiotic microbes are believed to play significant roles in sponge physiology including the production of an array of bioactive secondary metabolites. Here, we report on the use of culture-based and culture-independent (pyrosequencing) techniques to elucidate the bacterial community profiles associated with the marine sponges Raspailia ramosa and Stelligera stuposa sampled from a single geographical location... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5638415 Sat, 28 Jan 2012 05:00:00 +0100 5638415 http://www.medworm.com/index.php?rid=5620104&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22252223%26dopt%3DAbstract Authors: Zhao JY, Dang H Abstract Diversity and prevalence of plasmid-mediated quinolone resistance determinants were investigated in environmental bacteria isolated from surface seawater of Jiaozhou Bay, China. Five qnr gene alleles were identified in 34 isolates by PCR amplification, including qnrA3 gene in a Shewanella algae isolate, qnrB9 gene in a Citrobacter freundii isolate, qnrD gene in 22 Proteus vulgaris isolates, qnrS1 gene in 1 Enterobacter sp. and 4 Klebsiella spp. isolates, and qnrS2 gene in 1 Pseudomonas sp. and 4 Pseudoalteromonas sp. isolates. The qnrC, aac(6')-Ib-cr, and qepA genes could not be detected in this study. The 22 qnrD-positive Proteus vulgaris isolates could be differentiated into four genotypes based on ERIC-PCR assay. The qnrS1 and qnrD genes could b... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5620104 Wed, 18 Jan 2012 05:00:00 +0100 5620104 http://www.medworm.com/index.php?rid=5598283&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234510%26dopt%3DAbstract Authors: Kuhnert R, Oberkofler I, Peintner U Abstract Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We f... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5598283 Thu, 12 Jan 2012 05:00:00 +0100 5598283 http://www.medworm.com/index.php?rid=5598282&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234511%26dopt%3DAbstract Authors: Morales-Jiménez J, Zúñiga G, Ramírez-Saad HC, Hernández-Rodríguez C Abstract Dendroctonus rhizophagus Thomas and Bright (Curculionidae: Scolytinae) is an endemic economically important insect of the Sierra Madre Occidental in Mexico. This bark beetle has an atypical behavior within the genus because just one beetle couple colonizes and kills seedlings and young trees of 11 pine species. In this work, the bacteria associated with the Dendroctonus rhizophagus gut were analyzed by culture-dependent and culture-independent methods. Analysis of 16S rRNA sequences amplified directly from isolates of gut bacteria suggests that the bacterial community associated with Dendroctonus rhizophagus, like that of other Dendroctonus spp. and Ips pini, is limited in number. Nine bacte... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5598282 Thu, 12 Jan 2012 05:00:00 +0100 5598282 http://www.medworm.com/index.php?rid=5577826&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22214994%26dopt%3DAbstract Authors: Urbieta MS, González Toril E, Aguilera A, Giaveno MA, Donati E Abstract Two acidic hot springs close to the crater of Copahue Volcano (Neuquén, Argentina) are the source of the Río Agrio. The river runs several kilometres before flowing into Caviahue Lake. Along the river, temperature, iron, other metal and proton concentrations decrease gradually with distance downstream. From the source to the lake and depending on the season, pH can rise from 1.0 (or even less) to about 4.0, while temperature values decrease from 70°C to 15°C. Water samples were taken from different stations on the river selected according to their physicochemical parameters. In order to assess prokaryotic biodiversity throughout the water column, different and complementary molecular biology techn... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5577826 Wed, 04 Jan 2012 05:00:00 +0100 5577826 http://www.medworm.com/index.php?rid=5559295&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22213055%26dopt%3DAbstract Authors: Ransom-Jones E, Jones DL, McCarthy AJ, McDonald JE Abstract The phylum Fibrobacteres currently comprises one formal genus, Fibrobacter, and two cultured species, Fibrobacter succinogenes and Fibrobacter intestinalis, that are recognised as major bacterial degraders of lignocellulosic material in the herbivore gut. Historically, members of the genus Fibrobacter were thought to only occupy mammalian intestinal tracts. However, recent 16S rRNA gene-targeted molecular approaches have demonstrated that novel centres of variation within the genus Fibrobacter are present in landfill sites and freshwater lakes, and their relative abundance suggests a potential role for fibrobacters in cellulose degradation beyond the herbivore gut. Furthermore, a novel subphylum within the Fibroba... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5559295 Tue, 03 Jan 2012 05:00:00 +0100 5559295 http://www.medworm.com/index.php?rid=5559301&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202886%26dopt%3DAbstract In this study, we focus on community integration of F. nucleatum. We demonstrated using an established in vitro mice oral microbiota (O-mix) that the viability of F. nucleatum was significantly reduced upon addition to the O-mix due to cell contact-dependent induction of hydrogen peroxide (H(2)O(2)) production by oral community. Interestingly, this inhibitory effect was significantly alleviated when F. nucleatum was allowed to adhere to its known interacting partner species (such as Streptococcus sanguinis) prior to addition. Furthermore, this aggregate formation-dependent protection was absent in the F. nucleatum mutant strain ΔFn1526 that is unable to bind to a number of Gram-positive species. More importantly, this protective effect was also observed during integration of F. nucleatum ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5559301 Wed, 28 Dec 2011 05:00:00 +0100 5559301 http://www.medworm.com/index.php?rid=5559299&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202887%26dopt%3DAbstract In this study a quantification of Vibrio in the North Sea and their response to biotic and abiotic parameters were assessed. Between January and December 2009, Vibrio at Helgoland Roads (North Sea, Germany) were quantified using fluorescence in situ hybridization. Vibrio numbers up to 3.4 × 10(4) cells × mL(-1) (2.2% of total microbial counts) were determined in summer, but their abundance was significantly lower in winter (5 × 10(2) cells × mL(-1)). Correlations between Vibrio and nutrients (SiO(2), PO(4) (3-), DIN), Secchi depth, temperature, salinity, and chlorophyll a were calculated using Spearman rank analysis. Multiple stepwise regression analysis was carried out to analyze the additive influence of multiple factors on Vibrio. Based on these calcul... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5559299 Wed, 28 Dec 2011 05:00:00 +0100 5559299 http://www.medworm.com/index.php?rid=5559296&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202889%26dopt%3DAbstract Authors: Goberna M, García C, Insam H, Hernández MT, Verdú M Abstract Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the l... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5559296 Wed, 28 Dec 2011 05:00:00 +0100 5559296 http://www.medworm.com/index.php?rid=5559297&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22202888%26dopt%3DAbstract Authors: Murdock JN, Wetzel DL Abstract Pollutant effects on biofilm physiology are difficult to assess due to differential susceptibility of species and difficulty separating individual species for analysis. Also, measuring whole assemblage responses such as metabolism can mask species-specific responses, as some species may decrease and others increase metabolic activity. Physiological responses can add information to compositional data, and may be a more sensitive indicator of effect. It is difficult, however, to separate individual species for biochemical analyses. Agricultural runoff often contains multiple pollutants that may alter algal assemblages in receiving waters. It is unclear how mixtures containing potential algal growth stimulators and inhibitors (e.g., nutrients an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5559297 Sat, 24 Dec 2011 05:00:00 +0100 5559297 http://www.medworm.com/index.php?rid=5548162&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22198685%26dopt%3DAbstract Authors: Goudar CT Abstract The Lambert W function was used to explicitly relate substrate concentration S, to time t, and the kinetic parameters V (m), K (m), and R in the modified Michaelis-Menten equation that accounts for endogenous substrate production. The applicability of this explicit formulation for kinetic parameter estimation by progress curve analysis was demonstrated using a combination of synthetic and experimental substrate depletion data. Synthetic substrate depletion data were generated using S (0) values of 1, 2, and 3 μM and V (m), K (m), and R values of 1.0 μM h(-1), 1.0 μM, and 0.1 μM h(-1), respectively, and contained 5% normally distributed error. Experimental data were obtained from two previously publish... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5548162 Sat, 24 Dec 2011 05:00:00 +0100 5548162 http://www.medworm.com/index.php?rid=5548163&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22193925%26dopt%3DAbstract Authors: Resat H, Bailey V, McCue LA, Konopka A Abstract We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by lo... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5548163 Fri, 23 Dec 2011 05:00:00 +0100 5548163 http://www.medworm.com/index.php?rid=5531733&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22183046%26dopt%3DAbstract Authors: Goodenough AE, Stallwood B Abstract Although bird-microbial interactions have become a topic of increasing research, the influence of nest-site characteristics, such as cavity orientation, on nest microbial communities in free-living passerines has not, to our knowledge, been investigated. This is despite the possibility of microbial differences explaining non-random patterns in nest-site selection and offspring quality, such as those exhibited by great tits (Parus major). We swabbed great tit nestboxes that faced either south-southwest (180-269°) or north-northeast (0-89°). Overall, 28 bacterial species and 11 fungal species were isolated, but the culturable microbial community differed substantially between different orientations-indeed nestboxes could be classified to... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531733 Tue, 20 Dec 2011 05:00:00 +0100 5531733 http://www.medworm.com/index.php?rid=5531732&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22183047%26dopt%3DAbstract Authors: Carbonero F, Oakley BB, Hawkins RJ, Purdy KJ Abstract A reductionist ecological approach of using a model genus was adopted in order to understand how microbial community structure is driven by metabolic properties. The distribution along an estuarine gradient of the highly specialised genus Methanosaeta was investigated and compared to the previously determined distribution of the more metabolically flexible Desulfobulbus. Methanosaeta genotypic distribution along the Colne estuary (Essex, UK) was determined by DNA- and RNA-based denaturing gradient gel electrophoresis and 16S rRNA gene sequence analyses. Methanosaeta distribution was monotonic, with a consistently diverse community and no apparent niche partitioning either in DNA or RNA analyses. This distribution patter... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531732 Tue, 20 Dec 2011 05:00:00 +0100 5531732 http://www.medworm.com/index.php?rid=5531734&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22173371%26dopt%3DAbstract We describe the first discovery of an assembly of antibiotic-producing Actinobacteria occurring in fungus-growing termite nests. However, due to the diversity found, and the lack of both phylogenetic and bioactivity specificity, further work is necessary for a better understanding of the putative role of antibiotic-producing bacteria in the fungus-growing termite mutualistic system. PMID: 22173371 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531734 Fri, 16 Dec 2011 05:00:00 +0100 5531734 http://www.medworm.com/index.php?rid=5531735&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22167078%26dopt%3DAbstract In this study, we analyzed the presence of Acidobacteria in freshwater ponds at Doñana National Park (southwestern Spain). Nucleic acid sequence analysis, quantitative, real-time RT-PCR, and fluorescence in situ hybridization (FISH) were carried out. Acidobacteria in these aquatic environments were investigated using their 16S and 23S rDNA sequences and acidobacterial specific primer pairs through phylogenetic approaches. The presence of up to five subdivisions of Acidobacteria was detected during this study. The analyzed ponds exhibited distinctive patterns of acidobacterial clades. In order to detect their role in ecosystem functions, metabolically active Acidobacteria were detected based upon rRNA analyses. Quantitative, real-time RT-PCR showed a low percentage of metabolically active ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531735 Thu, 15 Dec 2011 05:00:00 +0100 5531735 http://www.medworm.com/index.php?rid=5531736&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22159526%26dopt%3DAbstract Authors: Zumsteg A, Luster J, Göransson H, Smittenberg RH, Brunner I, Bernasconi SM, Zeyer J, Frey B Abstract Glacier forefield chronosequences, initially composed of barren substrate after glacier retreat, are ideal locations to study primary microbial colonization and succession in a natural environment. We characterized the structure and composition of bacterial, archaeal and fungal communities in exposed rock substrates along the Damma glacier forefield in central Switzerland. Soil samples were taken along the forefield from sites ranging from fine granite sand devoid of vegetation near the glacier terminus to well-developed soils covered with vegetation. The microbial communities were studied with genetic profiling (T-RFLP) and sequencing of clone libraries. According to the ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531736 Tue, 13 Dec 2011 05:00:00 +0100 5531736 http://www.medworm.com/index.php?rid=5531738&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22159497%26dopt%3DAbstract In this study, methanotrophs with respect to community structure, abundance, and activity were investigated in peat soils collected in the vicinity of different marshland plants that dominate different regions of the wetland, including Polygonum amphibium, Carex muliensis, and Eleocharis valleculosa (EV). 16S rRNA gene and particulate methane monooxygenase gene (pmoA) clone library sequence data indicated the presence of methanotrophs with two genera, Methylobacter and Methylocystis. Methylococcus, like pmoA gene sequences, were also retrieved and showed low similarity to those from Methylococcus spp. and thus indicates the existence of novel methanotrophs in the Zoige wetland. Quantitative polymerase chain reaction (qPCR) assays were used to measure the abundance of methantrophs and detec... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531738 Sat, 10 Dec 2011 05:00:00 +0100 5531738 http://www.medworm.com/index.php?rid=5531737&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22159498%26dopt%3DAbstract In this study, we investigated the influence of different plant species, fertilisation and L. perenne ingression on microbial communities in soils from three semi-natural Irish grasslands. Bacterial and fungal community compositions were determined by automated ribosomal intergenic spacer analysis, and community changes were linked to environmental factors by multivariate statistical analysis. Soil type had a strong effect on bacterial and fungal communities, mainly correlated to soil pH, as well as soil carbon and nitrogen status. Within each soil type, plant species composition was the main influencing factor followed by nitrogen fertilisation and finally Lolium ingression in the acidic upland and mesotrophic grassland. In the alkaline grassland, however, Lolium ingression had a stronger... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531737 Sat, 10 Dec 2011 05:00:00 +0100 5531737 http://www.medworm.com/index.php?rid=5531739&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138964%26dopt%3DAbstract Authors: Arakawa Y, Akiyama Y, Furukawa H, Suda W, Amachi S Abstract α-Proteobacteria that can oxidize iodide (I(-)) to molecular iodine (I(2)) have only been isolated from iodide-rich natural and artificial environments, i.e., natural gas brine waters and seawaters supplemented with iodide, respectively. To understand the growth characteristics of such iodide-oxidizing bacteria (IOB) under iodide-rich environments, microcosms comprising natural seawater and 1 mM iodide were prepared, and the succession of microbial communities was monitored by culture-independent techniques. PCR-denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis showed that bacteria closely related with known IOB were predominant in the microcosms after several weeks of incubation. Quant... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531739 Sat, 03 Dec 2011 05:00:00 +0100 5531739 http://www.medworm.com/index.php?rid=5531740&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22134599%26dopt%3DAbstract Authors: Evans TN, Seviour RJ Abstract Fungal diversity of communities in several activated sludge plants treating different influent wastes was determined by comparative sequence analyses of their 18S rRNA genes. Methods for DNA extraction and choice of primers for PCR amplification were both optimised using denaturing gradient gel electrophoresis profile patterns. Phylogenetic analysis revealed that the levels of fungal biodiversity in some communities, like those treating paper pulp wastes, were low, and most of the fungi detected in all communities examined were novel uncultured representatives of the major fungal subdivisions, in particular, the newly described clade Cryptomycota. The fungal populations in activated sludge revealed by these culture-independent methods were mar... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531740 Fri, 02 Dec 2011 05:00:00 +0100 5531740 http://www.medworm.com/index.php?rid=5531742&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22124570%26dopt%3DAbstract Authors: Burgess EA, Unrine JM, Mills GL, Romanek CS, Wiegel J Abstract Arkashin Schurf (Arkashin) and Zavarzin Spring (Zavarzin), two active thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied for geochemical and microbiological characterization. Arkashin, the smaller of the two pools, had broader temperature and pH ranges, and the sediments had higher concentrations of total As (4,250 mg/kg) relative to Zavarzin (48.9 mg/kg). Glycerol dialkyl glycerol tetraether profiles represented distinct archaeal communities in each pool and agreed well with previous studies of these pools. Although no archaeal 16S rRNA sequences were recovered from Arkashin, sequences recovered from Zavarzin were mostly representatives of the Crenarchaeota and "Korarchaeota," and 13% of the ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531742 Tue, 29 Nov 2011 05:00:00 +0100 5531742 http://www.medworm.com/index.php?rid=5531741&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22124571%26dopt%3DAbstract Authors: Sereda JM, Vandergucht DM, Hudson JJ Abstract We investigated the effect of ultraviolet radiation (UVR) on the uptake and partitioning of radiophosphate ((33)PO (4) (3-) ) in size-fractionated plankton assemblages (0.2-0.8, 0.8-2.0 and >2.0 μm) collected from nine freshwater lakes located in Saskatchewan, Canada. A significant (p < 0.05) reduction in (33)PO (4) (3-) uptake by plankton was observed in seven of the nine lakes. Plankton >2.0 μm were generally unaffected by UVR, whereas the 0.2-0.8 μm size fraction exhibited severe photoinhibition. The effect of UVR on the 0.8-2.0 μm size fraction was variable, ranging from significant reductions to significant increases in (33)... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531741 Tue, 29 Nov 2011 05:00:00 +0100 5531741 http://www.medworm.com/index.php?rid=5531745&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22109095%26dopt%3DAbstract Authors: Ormeño-Orrillo E, Rogel-Hernández MA, Lloret L, López-López A, Martínez J, Barois I, Martínez-Romero E Abstract Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531745 Wed, 23 Nov 2011 05:00:00 +0100 5531745 http://www.medworm.com/index.php?rid=5531744&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22109096%26dopt%3DAbstract We report the isolation and chemical characterization of small molecules belonging to class of diketopiperazines (DKPs) in Haloterrigena hispanica, an extremely halophilic archaeon. One of the DKPs isolated, the compound cyclo-(L: -prolyl-L: -valine) activated N-acyl homoserine lactone (AHL) bioreporters, indicating that Archaea may have the ability to interact with AHL-producing bacteria within mixed communities. PMID: 22109096 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531744 Wed, 23 Nov 2011 05:00:00 +0100 5531744 http://www.medworm.com/index.php?rid=5531743&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22109097%26dopt%3DAbstract Authors: Fujii M, Kojima H, Iwata T, Urabe J, Fukui M Abstract Relationships between environmental factors and bacterial communities were investigated in 41 freshwater lakes located in mountainous regions of eastern Japan. Bacterioplankton community composition (BCC) was determined by polymerase chain reaction-denaturing gradient gel electrophoresis of the 16S rRNA gene and then evaluated on the basis of physicochemical and biological variables of the lakes. Canonical correspondence analysis revealed that BCC of oligotrophic lakes was significantly influenced by dissolved organic carbon (DOC) content, but its effect was not apparent in the analysis covering all lakes including mesotrophic and eutrophic ones. The generalized linear model showed the negative association of DOC on the... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531743 Wed, 23 Nov 2011 05:00:00 +0100 5531743 http://www.medworm.com/index.php?rid=5531747&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22105516%26dopt%3DAbstract Authors: Lapanje A, Wimmersberger C, Furrer G, Brunner I, Frey B Abstract Colonisation and weathering of freshly deglaciated granite are key processes in initial soil formation and development. We have obtained 438 isolates from granite sand covering glacial toe, 284 isolates at 22°C and 154 at 4°C incubation temperatures, respectively, to obtain cultures for the investigation of their weathering capabilities under laboratory conditions. The isolation of bacteria from granite sand was performed on rich-, intermediate- and low-nutrient-content solid media. Isolates were identified by 16S rRNA gene sequencing. According to the genera-associated weathering capabilities described in the literature and according to their abundance in our culture collection, we selected eight strains t... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531747 Tue, 22 Nov 2011 05:00:00 +0100 5531747 http://www.medworm.com/index.php?rid=5531746&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22105517%26dopt%3DAbstract Authors: Chaudhary HJ, Peng G, Hu M, He Y, Yang L, Luo Y, Tan Z Abstract Thirty-three endophytic diazotrophs were isolated from surface-sterilized leaves, stem, and roots of wild rice Oryza alta. The SDS-PAGE profile of total protein and insertion sequence-based polymerase chain reaction (IS-PCR) fingerprinting grouped the isolates into four clusters (I-IV). The 16S rRNA gene sequence homology of the representative strains B21, B31, B1, and B23 of clusters I, II, III, and IV were assigned to Pseudomonas oleovorans (99.2% similarity), Burkholderia fungorum (99.4% similarity), Enterobacter cloacae (98.9% similarity), and Acinetobacter johnsonii (98.4% similarity), respectively. The results showed wide genetic diversity of the putative diazotrophic strains of the wild rice, O. alta, a... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5531746 Tue, 22 Nov 2011 05:00:00 +0100 5531746 http://www.medworm.com/index.php?rid=5418645&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22083250%26dopt%3DAbstract Authors: García-Amado MA, Godoy-Vitorino F, Piceno YM, Tom LM, Andersen GL, Herrera EA, Domínguez-Bello MG Abstract The capybara (Hydrochoerus hydrochaeris) is the world's largest living rodent. Native to South America, this hindgut fermenter is herbivorous and coprophagous and uses its enlarged cecum to digest dietary plant material. The microbiota of specialized hindgut fermenters has remained largely unexplored. The aim of this work was to describe the composition of the bacterial community in the fermenting cecum of wild capybaras. The analysis of bacterial communities in the capybara cecum is a first step towards the functional characterization of microbial fermentation in this model of hindgut fermentation. We sampled cecal contents from five wild adult capybaras (three mal... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418645 Tue, 15 Nov 2011 05:00:00 +0100 5418645 http://www.medworm.com/index.php?rid=5418648&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22080256%26dopt%3DAbstract Authors: McGuire KL, Fierer N, Bateman C, Treseder KK, Turner BL Abstract Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20 cm) and leaf litter (O horizons) were collected from six established 1-ha forest c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418648 Sat, 12 Nov 2011 05:00:00 +0100 5418648 http://www.medworm.com/index.php?rid=5418647&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22080257%26dopt%3DAbstract We examined the distribution of the yeast, Metschnikowia reukaufii, and other fungal species found in the floral nectar of the sticky monkey flower, Mimulus aurantiacus, a hummingbird-pollinated shrub, at a California site. We found that the frequency of nectar-inhabiting microfungi on a given host plant was not significantly correlated with light availability, nectar volume, or the percent cover of M. aurantiacus around the plant, but was significantly correlated with the location of the host plant and loosely correlated with the density of flowers on the plant. These results suggest that dispersal limitation caused by spatially nonrandom foraging by pollinators may be a primary factor driving the observed distribution pattern. PMID: 22080257 [PubMed - as supplied by publisher] (Sourc... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418647 Sat, 12 Nov 2011 05:00:00 +0100 5418647 http://www.medworm.com/index.php?rid=5418646&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22080258%26dopt%3DAbstract Authors: Bohorquez LC, Delgado-Serrano L, López G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM PMID: 22080258 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418646 Sat, 12 Nov 2011 05:00:00 +0100 5418646 http://www.medworm.com/index.php?rid=5418649&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22076694%26dopt%3DAbstract Authors: Fernández DA, Roldán A, Azcón R, Caravaca F, Bååth E Abstract Our aim was to examine the effect of water stress on plant growth and development of two native plant species (Tetraclinis articulata and Crithmum maritimum) and on microbial community composition and activity in the rhizosphere soil, following the addition of an organic amendment, namely sugar beet residue (SBR), and/or the inoculation with an arbuscular mycorrhizal (AM) fungus, namely Glomus mosseae, in a non-sterile heavy metal-polluted soil. The AM inoculation did not have any significant effect on plant growth of both species. In T. articulata, SBR increased shoot growth, foliar P, total phospholipid fatty acids (PLFA), fungi-related PLFA, AM fungi-related neutral lipid fatty acid, bacterial gram-posit... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418649 Fri, 11 Nov 2011 05:00:00 +0100 5418649 http://www.medworm.com/index.php?rid=5418650&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22072124%26dopt%3DAbstract Authors: Oishi R, Tada C, Asano R, Yamamoto N, Suyama Y, Nakai Y Abstract A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418650 Thu, 10 Nov 2011 05:00:00 +0100 5418650 http://www.medworm.com/index.php?rid=5418651&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22057471%26dopt%3DAbstract Authors: Mohlin M, Roleda MY, Pattanaik B, Tenne SJ, Wulff A Abstract The cyanobacterial blooms in the Baltic Sea are dominated by diazotrophic cyanobacteria, the potentially toxic species Aphanizomenon sp. and the toxic species Nodularia spumigena. The seasonal succession with peaks of Aphanizomenon sp., followed by peaks of N. spumigena, has been explained by the species-specific niches of the two species. In a three-factorial outdoor experiment, we tested if nutrient and radiation conditions may impact physiological and biochemical responses of N. spumigena and Aphanizomenon sp. in the presence or absence of the other species. The two nutrient treatments were f/2 medium without NO (3) (-) (-N) and f/2 medium without PO (4) ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418651 Sun, 06 Nov 2011 04:00:00 +0100 5418651 http://www.medworm.com/index.php?rid=5418652&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22057398%26dopt%3DAbstract Authors: Hubert J, Kopecký J, Perotti MA, Nesvorná M, Braig HR, Ságová-Marečková M, Macovei L, Zurek L Abstract Internal bacterial communities of synanthropic mites Acarus siro, Dermatophagoides farinae, Lepidoglyphus destructor, and Tyrophagus putrescentiae (Acari: Astigmata) were analyzed by culturing and culture-independent approaches from specimens obtained from laboratory colonies. Homogenates of surface-sterilized mites were used for cultivation on non-selective agar and DNA extraction. Isolated bacteria were identified by sequencing of the 16S rRNA gene. PCR amplified 16S rRNA genes were analyzed by terminal restriction fragment length polymorphism analysis (T-RFLP) and cloning sequencing. Fluorescence in situ hybridization using universal bacterial probes was used for... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5418652 Sat, 05 Nov 2011 04:00:00 +0100 5418652 http://www.medworm.com/index.php?rid=5379122&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22052370%26dopt%3DAbstract In conclusion, it was shown that BrdU immunocapture was applicable to detect shifts in community composition among replicating β-AOB populations in soil. However, this was not reflected by the soils' ammonia oxidation capacity to resist to or recover from the induced perturbation suggesting that rapid population shifts may not influence soil functioning in a short-term perspective. PMID: 22052370 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379122 Fri, 04 Nov 2011 04:00:00 +0100 5379122 http://www.medworm.com/index.php?rid=5379125&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038034%26dopt%3DAbstract Authors: Bachar A, Soares MI, Gillor O Abstract Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample's origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379125 Sat, 29 Oct 2011 04:00:00 +0100 5379125 http://www.medworm.com/index.php?rid=5379126&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22031452%26dopt%3DAbstract This study illustrates how over 80 genomes can be broadly compared using simple bioinformatic tools, leading to both confirmation of known information as well as novel observations. PMID: 22031452 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379126 Thu, 27 Oct 2011 04:00:00 +0100 5379126 http://www.medworm.com/index.php?rid=5379124&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038035%26dopt%3DAbstract Authors: Neave MJ, Streten-Joyce C, Glasby CJ, McGuinness KA, Parry DL, Gibb KS Abstract Tolerant species of polychaete worms can survive in polluted environments using various resistance mechanisms. One aspect of resistance not often studied in polychaetes is their association with symbiotic bacteria, some of which have resistance to metals and may help the organism to survive. We used "next generation" 454 sequencing of bacterial 16S rRNA sequences associated with polychaetes from a copper- and zinc-polluted harbor and from a reference site to determine bacterial community structure. We found changes in the bacteria at the polluted site, including increases in the abundance of bacteria from the order Alteromonadales. These changes in the bacteria associated with polychaetes may b... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379124 Thu, 27 Oct 2011 04:00:00 +0100 5379124 http://www.medworm.com/index.php?rid=5379123&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22038036%26dopt%3DAbstract Authors: Becklin KM, Hertweck KL, Jumpponen A Abstract Fungal diversity and composition are still relatively unknown in many ecosystems; however, host identity and environmental conditions are hypothesized to influence fungal community assembly. To test these hypotheses, we characterized the richness, diversity, and composition of rhizosphere fungi colonizing three alpine plant species, Taraxacum ceratophorum, Taraxacum officinale, and Polemonium viscosum. Roots were collected from open meadow and willow understory habitats at treeline on Pennsylvania Mountain, Colorado, USA. Fungal small subunit ribosomal DNA was sequenced using fungal-specific primers, sample-specific DNA tags, and 454 pyrosequencing. We classified operational taxonomic units (OTUs) as arbuscular mycorrhizal (AMF... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379123 Thu, 27 Oct 2011 04:00:00 +0100 5379123 http://www.medworm.com/index.php?rid=5379128&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22015683%26dopt%3DAbstract Authors: Renault D, Vallance J, Déniel F, Wery N, Godon JJ, Barbier G, Rey P Abstract In recent years, increasing the level of suppressiveness by the addition of antagonistic bacteria in slow filters has become a promising strategy to control plant pathogens in the recycled solutions used in soilless cultures. However, knowledge about the microflora that colonize the filtering columns is still limited. In order to get information on this issue, the present study was carried out over a 4-year period and includes filters inoculated or not with suppressive bacteria at the start of the filtering process (two or three filters were used each year). After 9 months of filtration, polymerase chain reaction (PCR)-single strand conformation polymorphism analyses point out that, for the same... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379128 Fri, 21 Oct 2011 04:00:00 +0100 5379128 http://www.medworm.com/index.php?rid=5379127&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22015684%26dopt%3DAbstract Authors: Kobune S, Kajimura H, Masuya H, Kubono T Abstract We investigated the association between a gall midge, Illiciomyia yukawai, and its symbiotic fungi on Japanese star anise, Illicium anisatum. The number of fungal species isolated from the galls increased with development of the galls, whereas those from the leaves showed a different trend. Botryosphaeria dothidea was dominant in the galls from June to October, and after that Phomopsis sp. 1, Colletotrichum sp., and Pestalotiopsis sp. became dominant. Although B. dothidea was not isolated from the leaves, it was detected from mycangia (abdominal sternite VII) of egg-laying adults at a high isolation frequency (>90%). However, B. dothidea was not isolated from mycangia of adults emerging from galls that were enclosed by p... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379127 Fri, 21 Oct 2011 04:00:00 +0100 5379127 http://www.medworm.com/index.php?rid=5379129&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22006549%26dopt%3DAbstract Authors: Auclair J, Parent S, Villemur R Abstract Nitrate is a serious problem in closed-circuit public aquariums because its accumulation rapidly becomes toxic to many lifeforms. A moving bed biofilm denitrification reactor was installed at the Montreal Biodome to treat its 3,250-m(3) seawater system. Naturally occurring microorganisms from the seawater affluent colonized the reactor carriers to form a denitrifying biofilm. Here, we investigated the functional diversity of this biofilm by retrieving gene sequences related to narG, napA, nirK, nirS, cnorB, and nosZ. A total of 25 sequences related to these genes were retrieved from the biofilm. Among them, the corresponding napA1, nirK1, cnorB9, and nosZ3 sequences were identical to the corresponding genes found in Hyphomicrobium s... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379129 Tue, 18 Oct 2011 04:00:00 +0100 5379129 http://www.medworm.com/index.php?rid=5379131&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22001997%26dopt%3DAbstract In this study, we developed a multiplex PCR method to simultaneously detect these two bacterial species and allow for pathotype discrimination. The detection limits of this assay, that includes an internal amplification control to eliminate any false-negative results, were determined at 10 pg purified DNA and 200 cfu/ml. After confirming the effectiveness of our method using experimentally infected animals, its accuracy was compared to standard biochemical methods during a field survey using 94 samples collected over 3 years from shrimp farms encountering mortality events. The multiplex PCR showed very high specificity for the detection of V. penaeicida and V. nigripulchritudo (inclusivity and exclusivity 100%) and allowed us to detect the spreading of highly pathogenic isolates of V. n... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379131 Sat, 15 Oct 2011 04:00:00 +0100 5379131 http://www.medworm.com/index.php?rid=5379130&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22001998%26dopt%3DAbstract Authors: Pierre G, Graber M, Rafiliposon BA, Dupuy C, Orvain F, De Crignis M, Maugard T Abstract The main goal of this work was to study the dynamics and biochemical composition of extracellular polysaccharides (ECPS), a fraction of the extracellular polymeric substances (EPS) produced during the development of a microphytobenthic biofilm in a European intertidal mudflat (Marennes-Oléron Bay, France) during winter. Microphytobenthic biomass was surveyed during four consecutive emersion periods to confirm the biofilm growth. Bacteria abundance was also checked considering the importance of heterotrophic bacteria observed by various authors in the dynamics of EPS. Various colorimetric assays, coupled to biochemical chromatographic analysis, were used to characterize the three main f... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379130 Sat, 15 Oct 2011 04:00:00 +0100 5379130 http://www.medworm.com/index.php?rid=5379132&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21997543%26dopt%3DAbstract The objective of this study was to assess the occurrence of resistance to chlortetracycline and tylosin among bacterial populations at the Swine Complex of McGill University (Province of Quebec, Canada) in the absence of antibiotic administration to pigs for 2.5 years prior to the beginning of this study. Feces from ten pigs born from the same sow and provided feed without antibiotic were sampled during suckling (n = 6 for enumerations, n = 10 for PCR), weanling (n = 10 both for PCR and enumerations), growing (n = 10 both for PCR and enumerations), and finishing (n = 10 both for PCR and enumerations). The percentage of chlortetracycline-resistant anaerobic bacterial populations (Tet(R)) was higher than that of tylosin-resistant anaerobic bacterial populations (Tyl(R)) ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379132 Fri, 14 Oct 2011 04:00:00 +0100 5379132 http://www.medworm.com/index.php?rid=5379135&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21994033%26dopt%3DAbstract Authors: Hill PG, Heywood JL, Holland RJ, Purdie DA, Fuchs BM, Zubkov MV Abstract Microbial community structure in the subtropical north-east Atlantic Ocean was compared between 2 years and variation attributed to environmental variables. Surface seawater communities were analysed by flow cytometry and fluorescence in situ hybridisation. Probes specific to Alphaproteobacteria, Cyanobacteria, Gammaproteobacteria and Bacteroidetes identified 67-100% of cells. Due to natural variation in the study region due to the occurrence of major currents and islands, data could not be pooled but were instead divided between distinct water masses. Community structure did not differ greatly around the Cape Verde Islands between sampling periods but varied substantially in the open ocean, suggesti... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379135 Thu, 13 Oct 2011 04:00:00 +0100 5379135 http://www.medworm.com/index.php?rid=5379134&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21994034%26dopt%3DAbstract Authors: Oliveira I, Pereira JA, Lino-Neto T, Bento A, Baptista P Abstract Olive production is one of the main agricultural activities in Portugal. In the region of Trás-os-Montes, this crop has been considerably affected by Prays oleae. In order to evaluate the diversity of fungi on Prays oleae population of Trás-os-Montes olive orchards, larvae and pupae of the three annual generations (phyllophagous, antophagous and carpophagous) were collected and evaluated for fungal growth on their surface. From the 3,828 larvae and pupae, a high percentage of individuals exhibited growth of a fungal agent (40.6%), particularly those from the phyllophagous generation. From all the moth generations, a total of 43 species from 24 genera were identified, but the diversity and abundance of fung... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379134 Thu, 13 Oct 2011 04:00:00 +0100 5379134 http://www.medworm.com/index.php?rid=5379133&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21994035%26dopt%3DAbstract In this study, both the uptake of exogenous BMAA by and the effect of exogenous BMAA on the growth of Synechocystis PCC6803 were investigated. BMAA was rapidly taken up by the non-diazotrophic cyanobacterium Synechocystis PCC6803 in a concentration dependent manner. The presence of exogenous BMAA resulted in a substantial and concentration-dependent decrease in cell growth and the substantial loss of photosynthetic pigmentation. Similar effects were seen in the presence of the non-proteinogenic amino acid, 2,4-diaminobutyric acid but to a lesser degree than that of BMAA. The effects were reversed when light was decreased from 16 to 10 μmol m(-2) s(-1). Control cultures grown in the presence of L: -arginine, L: -asparagine, L: -glutamate and glycine showed normal or slightly increased g... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379133 Thu, 13 Oct 2011 04:00:00 +0100 5379133 http://www.medworm.com/index.php?rid=5379137&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21990015%26dopt%3DAbstract Authors: Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, A N A, Chun J, Adams JM Abstract Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leave... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379137 Wed, 12 Oct 2011 04:00:00 +0100 5379137 http://www.medworm.com/index.php?rid=5379136&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21990016%26dopt%3DAbstract Authors: Crotty FV, Adl SM, Blackshaw RP, Murray PJ Abstract Protozoa are one of the most abundant groups of bacterivores within the soil and are responsible for mineralisation of bacterial biomass, having a large impact on C and N cycling. Little is known of their contribution to soil nutrient transfers or the identity of their consumers. Here, for the first time indigenous flagellates and ciliates, enriched to 83 atom% for (13)C and 10 atom% for (15)N, were introduced to soil cores from two different land managements, grassland and woodland with the same soil type, to trace the flow of protozoan C and N through the soil food web. Nematodes, Collembola, earthworms and insect larvae obtained the greatest amounts of C and N of protozoan origin, either through direct consumption or u... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379136 Wed, 12 Oct 2011 04:00:00 +0100 5379136 http://www.medworm.com/index.php?rid=5379139&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21984347%26dopt%3DAbstract Authors: Kvennefors EC, Sampayo E, Kerr C, Vieira G, Roff G, Barnes AC Abstract Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379139 Sat, 08 Oct 2011 04:00:00 +0100 5379139 http://www.medworm.com/index.php?rid=5379138&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21984348%26dopt%3DAbstract Authors: Jaiswal SK, Anand A, Dhar B, Vaishampayan A Abstract Analysis of genetic diversity among indigenous rhizobia and its symbiotic effectiveness with soybean cultivar is important for development of knowledge about rhizobial ecology. In India, little is known about the genetic resources and diversity of rhizobia nodulating soybean. Indigenous bradyrhizobia isolated from root nodules of soybean plants, collected from traditional cultivating regions of two states (Madhya Pradesh and Uttar Pradesh) of India, were screened for bacteriophage sensitivity to identify successful broad host range symbiotic effectivity. Of 172 rhizobial isolates, 91 showed sensitivities to eight lytic phages and form ten groups on the basis of sensitivity patterns. The genetic diversity of 23 isolates b... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5379138 Sat, 08 Oct 2011 04:00:00 +0100 5379138 http://www.medworm.com/index.php?rid=5296163&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21968611%26dopt%3DAbstract Authors: Savage D, Barbetti MJ, Macleod WJ, Salam MU, Renton M Abstract Many of the fungal pathogens that threaten agricultural and natural systems undergo wind-assisted dispersal. During turbulent wind conditions, long-distance dispersal can occur, and airborne spores are carried over distances greater than the mean. The occurrence of long-distance dispersal is an important ecological process, as it can drastically increase the extent to which pathogen epidemics spread across a landscape, result in rapid transmission of disease to previously uninfected areas, and influence the spatial structure of pathogen populations in fragmented landscapes. Since the timing of spore release determines the wind conditions that prevail over a dispersal event, this timing is likely to affect the p... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5296163 Tue, 04 Oct 2011 04:00:00 +0100 5296163 http://www.medworm.com/index.php?rid=5296164&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21965156%26dopt%3DAbstract This study aims to provide an overview of the diversity of intestinal Lactobacillus among Chinese patients with hepatitis B virus (HBV)-related decompensated cirrhosis and who received liver transplant for hepatitis B cirrhosis. Fecal samples were collected from 38 healthy volunteers, 61 patients with HBV-related decompensated cirrhosis (group LC) and 74 patients who had liver transplant for hepatitis B cirrhosis (group LT). Quantitative polymerase chain reaction technology with species-specific primers was applied to investigate lactobacilli 16S rDNA in crude DNA, extracted from fecal samples. Software package Statistical Package for the Social Sciences and Palaeontological Statistics for Windows was used to analyze the data. Lactobacilli population of the two patient groups was different... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5296164 Sat, 01 Oct 2011 04:00:00 +0100 5296164 http://www.medworm.com/index.php?rid=5276423&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21960435%26dopt%3DAbstract Authors: Kojima Y, Toki T, Morimoto T, Yoshiyama M, Kimura K, Kadowaki T Abstract Invasion of alien species has been shown to cause detrimental effects on habitats of native species. Insect pollinators represent such examples; the introduction of commercial bumble bee species for crop pollination has resulted in competition for an ecological niche with native species, genetic disturbance caused by mating with native species, and pathogen spillover to native species. The European honey bee, Apis mellifera, was first introduced into Japan for apiculture in 1877, and queen bees have been imported from several countries for many years. However, its effects on Japanese native honey bee, Apis cerana japonica, have never been addressed. We thus conducted the survey of honey bee viruses an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276423 Fri, 30 Sep 2011 04:00:00 +0100 5276423 http://www.medworm.com/index.php?rid=5276425&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947461%26dopt%3DAbstract Authors: Bohorquez LC, Delgado-Serrano L, López G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM Abstract The microbial community of a Colombian high mountain hot spring, El Coquito, was analyzed using three different culture-independent assessments of 16S ribosomal RNA genes: clone libraries, pyrosequencing of the V5-V6 hypervariable region, and microarray. This acidic spring had a diverse community composed mainly of Bacteria that shared characteristics with those from other hot springs and extreme acidic environments. The microbial community was dominated by Proteobacteria, Firmicutes, and Planctomycetes and contained chemotrophic bacteria potentially involved in cycling of ferrous and sulfur-containing minerals and phototrophic organisms, most of whi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276425 Tue, 27 Sep 2011 04:00:00 +0100 5276425 http://www.medworm.com/index.php?rid=5276424&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947462%26dopt%3DAbstract In this study, we described the isolation and preliminary characterization of bacteriophage IHQ1 (family Myoviridae) active against the Gram-negative bacterial strain A. punctata. This virulent bacteriophage was isolated from stream water sample. Genome analysis indicated that phage IHQ1 was a double-stranded DNA virus with an approximate genome size of 25-28 kb. The initial characterization of this newly isolated phage showed that it has a narrow host range and infects only A. punctata as it failed to infect seven other clinically isolated pathogenic strains, i.e., methicillin-resistant Staphylococcus aureus 6403, MRSA 17644, Acinetobacter 33408, Acinetobacter 1172, Pseudomonas aeruginosa 22250, P. aeruginosa 11219, and Escherichia coli. Proteomic pattern of phage IHQ1, generated by SDS-... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276424 Tue, 27 Sep 2011 04:00:00 +0100 5276424 http://www.medworm.com/index.php?rid=5276427&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947429%26dopt%3DAbstract Authors: Leão PN, Ramos V, Vale M, Machado JP, Vasconcelos VM Abstract An increasing body of evidence points out that allelopathy may be an important process shaping microbial communities in aquatic ecosystems. Cyanobacteria have well-documented allelopathic properties, mainly derived from the evaluation of the activity of allelopathic extracts or pure compounds towards monocultures of selected target microorganisms. Consequently, little is known regarding the community dynamics of microorganisms associated with allelopathic interactions. In this laboratory-based study, a Microcystis spp.-dominated microbial community from a freshwater lake was exposed, for 15 days, to exudates from the cyanobacterium Oscillatoria sp. strain LEGE 05292 in laboratory conditions. This cyanobacteriu... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276427 Fri, 23 Sep 2011 04:00:00 +0100 5276427 http://www.medworm.com/index.php?rid=5276426&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21947430%26dopt%3DAbstract Authors: Fürnkranz M, Lukesch B, Müller H, Huss H, Grube M, Berg G Abstract Recent and substantial yield losses of Styrian oil pumpkin (Cucurbita pepo L. subsp. pepo var. styriaca Greb.) are primarily caused by the ascomycetous fungus Didymella bryoniae but bacterial pathogens are frequently involved as well. The diversity of endophytic microbial communities from seeds (spermosphere), roots (endorhiza), flowers (anthosphere), and fruits (carposphere) of three different pumpkin cultivars was studied to develop a biocontrol strategy. A multiphasic approach combining molecular, microscopic, and cultivation techniques was applied to select a consortium of endophytes for biocontrol. Specific community structures for Pseudomonas and Bacillus, two important plant-associated genera, were... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276426 Fri, 23 Sep 2011 04:00:00 +0100 5276426 http://www.medworm.com/index.php?rid=5276428&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21938508%26dopt%3DAbstract Authors: Rojas JD, Sette LD, de Araujo WL, Lopes MS, da Silva LF, Furlan RL, Padilla G Abstract The chemical ecology and biotechnological potential of metabolites from endophytic and rhizosphere fungi are receiving much attention. A collection of 17 sugarcane-derived fungi were identified and assessed by PCR for the presence of polyketide synthase (PKS) genes. The fungi were all various genera of ascomycetes, the genomes of which encoded 36 putative PKS sequences, 26 shared sequence homology with β-ketoacyl synthase domains, while 10 sequences showed homology to known fungal C-methyltransferase domains. A neighbour-joining phylogenetic analysis of the translated sequences could group the domains into previously established chemistry-based clades that represented non-reducing, part... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5276428 Thu, 22 Sep 2011 04:00:00 +0100 5276428 http://www.medworm.com/index.php?rid=5245976&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21935609%26dopt%3DAbstract We present primers targeting a family of termite gut [FeFe] hydrogenases and provide results that are consistent with a pivotal role for hydrogen in the termite gut ecosystem and point toward unique evolutionary adaptations to the gut ecosystem. PMID: 21935609 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5245976 Wed, 21 Sep 2011 04:00:00 +0100 5245976 http://www.medworm.com/index.php?rid=5245975&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21935610%26dopt%3DAbstract Authors: Burge CA, Friedman CS Abstract Understanding the pathogenic potential of a new pathogen strain or a known pathogen in a new locale is crucial for management of disease in both wild and farmed animals. The Ostreid herpesvirus-1 (OsHV-1), a known pathogen of early-life-stage Pacific oysters, Crassostrea gigas, has been associated with mortalities of juvenile oysters in many locations around the world including Tomales Bay, California. In two trials, the California OsHV-1 strain was transmitted from infected juvenile C. gigas to naïve C. gigas larvae. Survival of control larvae was high throughout both trials (97-100%) and low among those exposed to OsHV-1. No OsHV-1-exposed larvae survived to day 9 in trial 1, while trial 2 was terminated at day 7 when survival was 36.9... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5245975 Wed, 21 Sep 2011 04:00:00 +0100 5245975 http://www.medworm.com/index.php?rid=5228304&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21915631%26dopt%3DAbstract Authors: Olapade OA Abstract The diel change in abundance and community diversity of the bacterioplankton assemblages within the Pacific Ocean at a fixed location in Monterey Bay, California (USA) were examined with several culture-independent (i.e., nucleic acid staining, fluorescence in situ hybridization {FISH}, and 16S ribosomal RNA gene libraries) approaches over a tidal cycle. FISH analyses revealed the quantitative predominance of bacterial members belonging to the Cytophaga-Flavobacterium cluster as well as two Proteobacteria (α- and γ-) subclasses within the bacterioplankton assemblages, especially during high tide (HT) and outgoing tide (OT) than the other tidal events. While the clone libraries showed that majority of the sequences were similar to the 16S rRNA gene seq... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5228304 Wed, 14 Sep 2011 04:00:00 +0100 5228304 http://www.medworm.com/index.php?rid=5228303&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21915632%26dopt%3DAbstract In this study, the intestinal bacterial communities of juvenile P. monodon (70 individuals) from eight commercial farms in Thailand were examined using 16S rDNA PCR-DGGE, and seven 16S rDNA clone libraries from representative DGGE profiles were constructed. Bacteria in the γ-Proteobacteria class were the only common bacteria group found in the intestinal tracts of shrimp from all farms. The dominant bacterial genera in the intestinal population of each shrimp varied among different farms, and these genera were Vibrio, Photobacterium, Aeromonas, or Propionigenium (phylum Fusobacteria). Other commonly found genera included Actinomyces, Anaerobaculum, Halospirulina, Pseudomonas, Mycoplasma, and Shewanella. Twelve phyla of bacteria including Proteobacteria, Firmicutes, Fusobacteria, Actinobac... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5228303 Wed, 14 Sep 2011 04:00:00 +0100 5228303 http://www.medworm.com/index.php?rid=5218171&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21904954%26dopt%3DAbstract Authors: Di Giuseppe G, Cervia D, Vallesi A Abstract Ultraviolet (UV) radiation has detrimental effects on marine ecosystems, in particular in the polar regions where stratospheric ozone reduction causes higher levels of solar radiation. We analyzed two polar species of Euplotes, Euplotes focardii and Euplotes nobilii, for the sensitivity to UV radiation in comparison with two akin species from mid-latitude and tropical waters. Results showed that they face UV radiation much more efficiently than the non-polar species by adopting alternative strategies that most likely reflect different times of colonization of the polar waters. While E. focardii, which is endemic to the Antarctic, survives for longer exposed to UV radiation, E. nobilii, which inhabits both the Antarctic and Arctic... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5218171 Fri, 09 Sep 2011 04:00:00 +0100 5218171 http://www.medworm.com/index.php?rid=5218173&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21898102%26dopt%3DAbstract Authors: Stibal M, Telling J, Cook J, Mak KM, Hodson A, Anesio AM Abstract Microbes in supraglacial ecosystems have been proposed to be significant contributors to regional and possibly global carbon cycling, and quantifying the biogeochemical cycling of carbon in glacial ecosystems is of great significance for global carbon flow estimations. Here we present data on microbial abundance and productivity, collected along a transect across the ablation zone of the Greenland ice sheet (GrIS) in summer 2010. We analyse the relationships between the physical, chemical and biological variables using multivariate statistical analysis. Concentrations of debris-bound nutrients increased with distance from the ice sheet margin, as did both cell numbers and activity rates before reaching a pea... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5218173 Wed, 07 Sep 2011 04:00:00 +0100 5218173 http://www.medworm.com/index.php?rid=5218172&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21898103%26dopt%3DAbstract Authors: Inceoğlu O, Falcão Salles J, van Elsas JD Abstract The rhizospheres of five different potato cultivars (including a genetically modified cultivar) obtained from a loamy sand soil and two from a sandy peat soil, next to corresponding bulk soils, were studied with respect to their community structures and potential function. For the former analyses, we performed bacterial 16S ribosomal RNA gene-based PCR denaturing gradient gel electrophoresis (PCR-DGGE) on the basis of soil DNA; for the latter, we extracted microbial communities and subjected these to analyses in phenotype arrays (PM1, PM2, and PM4, Biolog), with a focus on the use of different carbon, sulfur and phosphorus sources. In addition, we performed bacterial PCR-DGGE on selected wells to assess the structures of... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5218172 Wed, 07 Sep 2011 04:00:00 +0100 5218172 http://www.medworm.com/index.php?rid=5218174&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21892672%26dopt%3DAbstract In this study, we define the specific localization of an Arsenophonus bacterium pathogenic to sugar beet and strawberry plants within the plant hosts and the insect vector, Pentastiridius leporinus (Hemiptera: Cixiidae), using fluorescence in situ hybridization assays. Phylogenetic analysis on 16S rRNA and nucleotide coding sequences, using both maximum likelihood and Bayesian criteria, revealed that this bacterium is not a sister taxon to "Candidatus Phlomobacter fragariae," a previously characterized Arsenophonus bacterium pathogenic to strawberry plants in France and Japan. Ancestral state reconstruction analysis indicated that the adaptation to a plant pathogenic lifestyle likely evolved from an arthropod-associated lifestyle and showed that within the genus Arsenophonus, the plant pat... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5218174 Sat, 03 Sep 2011 04:00:00 +0100 5218174 http://www.medworm.com/index.php?rid=5192443&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21887519%26dopt%3DAbstract Authors: Laghdass M, Catala P, Caparros J, Oriol L, Lebaron P, Obernosterer I Abstract We investigated the abundance and activity of SAR11 on a monthly time scale between January 2008 and October 2008 in the oligotrophic NW Mediterranean Sea. Applying MICRO-CARD-FISH, we observed that SAR11 had a large contribution to bulk abundance (37 ± 6% of DAPI-stained cells) and to bulk bacterial heterotrophic production (BHP), as estimated from leucine incorporation (55 ± 15% of DAPI-cells assimilating leucine) in surface waters (5 m) throughout the study period. SAR11 contributed also substantially to the assimilation of glucose, ATP, and a combination of amino acids (44 ± 17%, 37 ± 14%, and 43 ± 12% of DAPI cells assimilating these compounds, respectively), organi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5192443 Thu, 01 Sep 2011 23:00:00 +0100 5192443 http://www.medworm.com/index.php?rid=5192445&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21881943%26dopt%3DAbstract Authors: Soto E, Revan F Abstract Francisella noatunensis subsp. orientalis (syn. Francisella asiatica), the causative agent of franciselliosis in warm-water fish, is a Gram-negative facultative intracellular bacterium. Although it has been characterized as one of the most pathogenic bacteria in fish, the water conditions that allow for its survival and infectious capacities outside the fish host are not known. Data obtained in this project indicate that both temperature and salinity are important factors in the culturability and persistence of F. noatunensis subsp. orientalis in both sea- and freshwater microcosms. These results indicate that culturable F. noatunensis subsp. orientalis persist for longer periods of time and at higher numbers in seawater, and its persistence is inv... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5192445 Wed, 31 Aug 2011 23:00:00 +0100 5192445 http://www.medworm.com/index.php?rid=5192444&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21881944%26dopt%3DAbstract Authors: Chaban B, Links MG, Hill JE Abstract Members of the rare microbiome can be important components of complex microbial communities. For example, pet dog ownership is a known risk factor for human campylobacteriosis, and Campylobacter is commonly detected in dog feces by targeted assays. However, these organisms have not been detected by metagenomic methods. The goal of this study was to characterize fecal microbiota from healthy and diarrheic pet dogs using two different levels of molecular detection. PCR amplification and pyrosequencing of the universal cpn60 gene target was used to obtain microbial profiles from each dog. To investigate the relatively rare epsilon-proteobacteria component of the microbiome, a molecular enrichment was carried out using a PCR that first ampl... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5192444 Wed, 31 Aug 2011 23:00:00 +0100 5192444 http://www.medworm.com/index.php?rid=5141006&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21850446%26dopt%3DAbstract Authors: Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V Abstract The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkh... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141006 Wed, 17 Aug 2011 23:00:00 +0100 5141006 http://www.medworm.com/index.php?rid=5141005&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21850447%26dopt%3DAbstract Authors: Chen H, Fu L, Luo L, Lu J, White WL, Hu Z Abstract The viable but nonculturable (VBNC) state has been found to be a growth strategy used by many aquatic pathogens; however, few studies have focused on VBNC state on other aquatic bacterial groups. The purpose of this study was to explore the VBNC state of cyanobacteria-lysing bacteria and the conditions that regulate their VBNC state transformation. Three cyanobacteria-lysing heterotrophic bacterial strains (F1, F2 and F3) were isolated with liquid infection method from a lake that has experienced a cyanobacterial bloom. According to their morphological, physiological and biochemical characteristics and results of 16SrDNA sequence analysis, F1, F2 and F3 were identified as strains of Staphylococcus sp., Stappia sp. and Micr... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141005 Wed, 17 Aug 2011 23:00:00 +0100 5141005 http://www.medworm.com/index.php?rid=5141007&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21845446%26dopt%3DAbstract Authors: Kahlisch L, Henne K, Gröbe L, Brettar I, Höfle MG Abstract The question which bacterial species are present in water and if they are viable is essential for drinking water safety but also of general relevance in aquatic ecology. To approach this question we combined propidium iodide/SYTO9 staining ("live/dead staining" indicating membrane integrity), fluorescence-activated cell sorting (FACS) and community fingerprinting for the analysis of a set of tap water samples. Live/dead staining revealed that about half of the bacteria in the tap water had intact membranes. Molecular analysis using 16S rRNA and 16S rRNA gene-based single-strand conformation polymorphism (SSCP) fingerprints and sequencing of drinking water bacteria before and after FACS sorting revealed: (1) the D... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141007 Mon, 15 Aug 2011 23:00:00 +0100 5141007 http://www.medworm.com/index.php?rid=5141008&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21837472%26dopt%3DAbstract This study used a multiphasic approach, characterized by the simultaneous use of culture-dependent and culture-independent methods, to investigate endophytic bacterial communities in strawberry (Fragaria ananassa) fruit. A total of 92 bacterial endophytes were isolated and initially grouped by their repetitive extragenic palindromic (rep)-PCR banding pattern and biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of 45 representatives showed that the isolates belonged to the species Bacillus subtilis (eight isolates), Bacillus sp. (seven isolates), Enterobacter sp. (seven isolates), Enterobacter ludwigii (six isolates), Lactobacillus plantarum (six isolates), Pseudomonas sp. (five isolates), Pantoea punctata (three isolates), and Curtobacterium citreum (three isolate... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141008 Thu, 11 Aug 2011 23:00:00 +0100 5141008 http://www.medworm.com/index.php?rid=5141010&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21833539%26dopt%3DAbstract Authors: Chochlakis D, Ioannou I, Sandalakis V, Dimitriou T, Kassinis N, Papadopoulos B, Tselentis Y, Psaroulaki A Abstract In two surveys conducted from March 1999 to March 2001 and from January 2004 to December 2006, a total of 3,950 ticks (belonging to ten different species) were collected from seven domestic and wild animals (goat, sheep, cattle, dog, fox, hare, and mouflon) from different localities throughout Cyprus. In order to establish their infection rate with Spotted Fever Rickettsiae (SFG), ticks were pooled and tested by polymerase chain reaction targeting gltA and ompA genes, followed by sequencing analysis. When tick pools tested positive, individual ticks were then tested one by one, and of the 3,950 ticks screened, rickettsial DNA was identified in 315 ticks (infec... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141010 Wed, 10 Aug 2011 23:00:00 +0100 5141010 http://www.medworm.com/index.php?rid=5141009&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21833540%26dopt%3DAbstract We report the isolation of 17 yeast strains from Paxillus and Xerocomus, 16 of which were obtained from the surface tissue, the primary site of Sepedonium infection. Phylogenetic analyses with the D1/D2 region of the 28S ribosomal gene and the internal transcribed spacers placed the yeasts as Rhodotorula, Rhodosporidium, and Mastigobasidium from the Pucciniomycotina, Cryptococcus, Cystofilobasidium, Holtermanniella, and Trichosporon from the Agaricomycotina, and Kluyveromyces from the Saccharomycotina including the first isolation of Rhodotorula graminis from Europe. To investigate the influence of the yeast strains on the mycoparasite and the host fungus, in vitro assays were conducted with Sepedonium chrysospermum and Paxillus involutus. Both S. chrysospermum growth inhibitory and stimul... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141009 Wed, 10 Aug 2011 23:00:00 +0100 5141009 http://www.medworm.com/index.php?rid=5141012&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21826490%26dopt%3DAbstract We present an approach aimed at improving reliability by studying the relevance and implications of an important concept from theoretical ecology in the context of a bacterial system: conditional dispersal denoting that the dispersal strategy depends on environmental conditions. Different dispersal strategies, which either incorporate or neglect this concept, are implemented in a bacterial model and results are compared to data obtained from laboratory experiments with Pseudomonas putida colonies growing on glucose agar. Our results show that, with respect to the condition of resource uptake, the model's correspondence to experimental data is significantly higher for conditional than for unconditional bacterial dispersal. In particular, these results support the hypothesis that bacteria di... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141012 Mon, 08 Aug 2011 23:00:00 +0100 5141012 http://www.medworm.com/index.php?rid=5141011&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21826491%26dopt%3DAbstract In this study, an integrated approach was used to identify key parameters determining the abundance of Vibrio spp in marine samples from the Venetian Lagoon in Italy, which is an important area for fish farming and tourism. Multivariate techniques have been adopted to analyze the dataset: using PCA, it was shown that a relatively high proportion of the total variance in this area was mainly due to two independent variables, namely salinity and temperature. Using cluster analysis, it was possible to categorize different groups with homogeneous features as regards space ("stations") and time ("seasons") distribution, as well as to quantify the values of environmental variables and the Vibrio abundances in each category. Furthermore, integrating key environmental factors and bacterial concent... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5141011 Mon, 08 Aug 2011 23:00:00 +0100 5141011 http://www.medworm.com/index.php?rid=5097481&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21814872%26dopt%3DAbstract Authors: Xu M, Wang B, Fu Y, Chen Y, Yang F, Lu H, Chen Y, Xu J, Li L The beneficial effects of Bifidobacteria on health have been widely accepted. Patients with chronic liver disease have varying degrees of intestinal microflora imbalance with a decrease of total Bifidobacterial counts. Since different properties have been attributed to different Bifidobacterium species and there is no information available for the detailed changes in the genus Bifidobacterium in patients with chronic liver disease heretofore, it is meaningful to investigate the structure of this bacterium at the species level in these patients. The aim of this study was to characterize the composition of intestinal Bifidobacterium in patients with hepatitis B virus-induced chronic liver disease. Nested-PCR-based dena... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097481 Wed, 03 Aug 2011 23:00:00 +0100 5097481 http://www.medworm.com/index.php?rid=5097615&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811791%26dopt%3DAbstract Authors: Karsten U, Holzinger A Members of the cosmopolitan green algal genus Klebsormidium (Klebsormidiales, Streptophyta) are typical components of terrestrial microbiotic communities such as biological soil crusts, which have many important ecological functions. In the present study, Klebsormidium dissectum (Gay) Ettl & Gärtner was isolated from a high alpine soil crust in the Tyrolean Alps, Austria. Physiological performance in terms of growth and photosynthesis was investigated under different controlled abiotic conditions and compared with ultrastructural changes under the treatments applied. K. dissectum showed very low light requirements as reflected in growth patterns and photosynthetic efficiency. Increasing temperatures from 5°C to 40°C led to different effects on res... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097615 Tue, 02 Aug 2011 23:00:00 +0100 5097615 http://www.medworm.com/index.php?rid=5097589&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811792%26dopt%3DAbstract Authors: Ballor NR, Paulsen I, Leadbetter JR We have completed a bioinformatic analysis of the hydrogenases encoded in the genomes of three termite gut treponeme isolates: hydrogenotrophic, homoacetogenic Treponema primitia strains ZAS-1 and ZAS-2, and the hydrogen-producing, sugar-fermenting Treponema azotonutricium ZAS-9. H(2) is an important free intermediate in the breakdown of wood by termite gut microbial communities, reaching concentrations in some species exceeding those measured for any other biological system. The spirochetes encoded 4, 8, and 5 [FeFe] hydrogenase-like proteins, identified by their H domains, respectively, but no other recognizable hydrogenases. The [FeFe] hydrogenases represented many sequence families previously proposed in an analysis of termite gut metage... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097589 Tue, 02 Aug 2011 23:00:00 +0100 5097589 http://www.medworm.com/index.php?rid=5097573&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811793%26dopt%3DAbstract In this study, temporal changes in AMR carried by both cultivated and uncultivated bacteria present in swine manure during simulated composting and lagoon storage were analyzed. Treatments were designed to simulate the environmental conditions of composting (55°C with modest aeration) and lagoon storage (ambient temperature with modest aeration). As determined by selective plate counting, over a 48-day period, cultivated aerobic heterotrophic erythromycin-resistant bacteria and tetracycline-resistant bacteria decreased by more than 4 and 7 logs, respectively, in the simulated composting treatment while only 1 to 2 logs for both resistant bacterial groups in the simulated lagoon treatment. Among six classes each of erm and tet genes quantified by class-specific real-time PCR assays, the ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097573 Tue, 02 Aug 2011 23:00:00 +0100 5097573 http://www.medworm.com/index.php?rid=5097552&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811794%26dopt%3DAbstract Authors: Wang P, Shen H, Xie P Diatom blooms occur in many water bodies worldwide, causing significant ecological and social concerns. In order to understand the mechanisms of diatom blooms formation, the effects of varying phosphorus (P) concentration and hydrodynamics on the growth of diatoms were studied by combining results from field observations and laboratory experiments. The field investigation showed that spring diatom blooms (Cyclotella meneghiniana and Stephanodiscus hantzschii) occurred in Lake Taihu and Hanjiang River with similar environmental factors such as water temperature, pH, and dissolved oxygen in 2008. Concentrations of total phosphorus (TP), total nitrogen, and ammonia nitrogen (NH(4)-N) in Lake Taihu were significantly higher than the concentrations in the Hanj... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097552 Tue, 02 Aug 2011 23:00:00 +0100 5097552 http://www.medworm.com/index.php?rid=5097512&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811795%26dopt%3DAbstract Authors: Ozen AI, Ussery DW The genus Pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. The relationship of the Pseudomonas genus to Azotobacter vinelandii is examined using three genomic sequence-based methods. First, using 16S rRNA trees, it is shown that A. vinelandii groups within the Pseudomonas close to Pseudomonas aeruginosa. Genomes from other related organisms (Acinetobacter, Psychrobacter, and Cellvibrio) are outside the Pseudomonas cluster. Second, pan genome family trees based on conserved gene families also show A. vinelandii to be more closely related to Pseudomonas than other related organisms. Third, exhaustive BLAST... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097512 Tue, 02 Aug 2011 23:00:00 +0100 5097512 http://www.medworm.com/index.php?rid=5097492&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21811796%26dopt%3DAbstract Authors: Chen Z, Liu J, Wu M, Xie X, Wu J, Wei W The impact of fertilization regimes on sequential denitrifying communities was investigated in a rice paddy field with 17 years continuous fertilization, located in Taoyuan Agro-ecosystem Research Station (110°72″ E, 28°52″ N), China. The diversity, community composition, and size of denitrifying genes of narG, qnorB, and nosZ were determined using molecular tools including terminal restriction fragment length polymorphism, quantitative polymerase chain reaction (qPCR), cloning, and sequencing analysis. Soil samples were collected from the plots with no fertilizer (NF), urea (UR), balanced mineral fertilizers (BM), and BM combined with rice straw (BMR). UR and BM caused marked increase in the community size of the denitrifying gen... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097492 Tue, 02 Aug 2011 23:00:00 +0100 5097492 http://www.medworm.com/index.php?rid=5097632&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21805083%26dopt%3DAbstract In this study, we examined the temporal fluctuations of freshwater fungi, including chytrids, in Lake Inba by using molecular techniques of denaturing gradient gel electrophoresis (DGGE). DGGE profiles, and associated sequence analysis, indicated that chytrids were present on all sampling dates from May to October (n = 12). In addition, analysis showed that a large proportion of the sequences belonged to chytrids of both parasitic and saprotrophic species. This finding was supported by microscopic observations using Calcofluor white to stain chytrids infecting various phytoplankton species. The percentages of infection by chytrids on two dominant diatom species, Aulacoseira granulata and Aulacoseira ambigua, showed a similar seasonal pattern in the DGGE band profiles. From the phylogen... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5097632 Fri, 29 Jul 2011 23:00:00 +0100 5097632 http://www.medworm.com/index.php?rid=5051448&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21766218%26dopt%3DAbstract Authors: Postec A, Tapia N, Bernadac A, Joseph M, Davidson S, Wu LF, Ollivier B, Pradel N Magnetotactic bacteria (MTB) mineralize nanosized magnetite or greigite crystals within cells and thus play an important role in the biogeochemical process. Despite decades of research, knowledge of MTB distribution and ecology, notably in areas subjected to oil industry activities, is still limited. In the present study, we investigated the presence of MTB in the Gulf of Fos, French Mediterranean coast, which is subjected to intensive oil industry activities. Microcosms containing sediments/water (1:2, v/v) from several sampling sites were monitored over several weeks. The presence of MTB was revealed in five of eight sites. Diverse and numerous MTB were revealed particularly from one site (named... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051448 Fri, 15 Jul 2011 23:00:00 +0100 5051448 http://www.medworm.com/index.php?rid=5051449&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21755290%26dopt%3DAbstract Authors: Graças DA, Miranda PR, Baraúna RA, McCulloch JA, Ghilardi R, Schneider MP, Silva A Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 a... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051449 Wed, 13 Jul 2011 23:00:00 +0100 5051449 http://www.medworm.com/index.php?rid=5051451&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21748267%26dopt%3DAbstract Authors: Lo Giudice A, Caruso C, Mangano S, Bruni V, De Domenico M, Michaud L The bacterial community inhabiting the water column at Terra Nova Bay (Ross Sea, Antarctica) was examined by the fluorescent in situ hybridization (FISH) technique and the genotypic and phenotypic characterization of 606 bacterial isolates. Overall, the FISH analysis revealed a bacterioplankton composition that was typical of Antarctic marine environments with the Cytophaga/Flavobacter (CF) group of Bacteroidetes that was equally dominant with the Actinobacteria and Gammaproteobacteria. As sampling was performed during the decay of sea-ice, it is plausible to assume the origin of Bacteroidetes from the sea-ice compartment where they probably thrive in high concentration of DOM which is efficiently remineraliz... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051451 Mon, 11 Jul 2011 23:00:00 +0100 5051451 http://www.medworm.com/index.php?rid=5051450&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21748268%26dopt%3DAbstract Authors: Cao H, Hong Y, Li M, Gu JD The phylogenetic diversity of ammonia-oxidizing archaea (AOA) was surveyed in the surface sediments from the northern part of the South China Sea (SCS). The distribution pattern of AOA in the western Pacific was discussed through comparing the SCS with other areas in the western Pacific including Changjiang Estuary and the adjacent East China Sea where high input of anthropogenic nitrogen was evident, the tropical West Pacific Continental Margins close to the Philippines, the deep-sea methane seep sediments in the Okhotsk Sea, the cold deep sea of Northeastern Japan Sea, and the hydrothermal field in the Southern Okinawa Trough. These various environments provide a wide spectrum of physical and chemical conditions for a better understanding of the di... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051450 Mon, 11 Jul 2011 23:00:00 +0100 5051450 http://www.medworm.com/index.php?rid=5051452&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21744159%26dopt%3DAbstract Authors: Polizzi V, Fazzini L, Adams A, Picco AM, De Saeger S, Van Peteghem C, De Kimpe N A Penicillium decumbens strain was collected from a water-damaged building, and the production of microbial volatile organic compounds (MVOCs) was investigated by means of headspace solid-phase microextraction, followed by GC-MS analysis. The strain was characterized by a high production of (+)-thujopsene. The influence of various temperatures, relative humidity (RH) values, substrates, and inoculum concentrations on fungal growth and (+)-thujopsene production was studied. The optimal temperature and relative humidity for P. decumbens growth were 30°C and 100% RH, respectively. In general, the more favourable the incubation parameters were for growth, the faster maximum (+)-thujopsene production ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051452 Fri, 08 Jul 2011 23:00:00 +0100 5051452 http://www.medworm.com/index.php?rid=5051455&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21735152%26dopt%3DAbstract Authors: Sercu B, Van De Werfhorst LC, Murray JL, Holden PA PMID: 21735152 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051455 Wed, 06 Jul 2011 23:00:00 +0100 5051455 http://www.medworm.com/index.php?rid=5051454&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21735153%26dopt%3DAbstract Authors: Ferrer M, Guazzaroni ME, Richter M, García-Salamanca A, Yarza P, Suárez-Suárez A, Solano J, Alcaide M, van Dillewijn P, Molina-Henares MA, López-Cortés N, Al-Ramahi Y, Guerrero C, Acosta A, de Eugenio LI, Martínez V, Marques S, Rojo F, Santero E, Genilloud O, Pérez-Pérez J, Rosselló-Móra R, Ramos JL The phylogenetic and functional structure of the microbial community residing in a Ca(2+)-rich anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, initially operated as a gypsum (CaSO(4) × 2 H(2)O) mine) was estimated by analyzing the diversity of 16S rRNA amplicons and a 3.1 Mb of consensus metagenome sequence. The lake has about half the salinity of seawater and possesses an unusual relative concentration of ions, with Ca(2+) and SO (4) (2-) being dom... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051454 Wed, 06 Jul 2011 23:00:00 +0100 5051454 http://www.medworm.com/index.php?rid=5051453&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21735154%26dopt%3DAbstract Authors: Singh D, Takahashi K, Kim M, Chun J, Adams JM Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system. Samples were taken at elevational intervals, between the base of the mountain at 1,000 m and its summit at 3,700 m. Polymerase chain reaction-amplified soil DNA for the bacterial 16S gene targeting V1-V3 region was pyrosequenced using the 454 Roche machine, and taxonomically classified with reference to a bioinformatic database. There was a significant "peak" in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051453 Wed, 06 Jul 2011 23:00:00 +0100 5051453 http://www.medworm.com/index.php?rid=5051456&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21732020%26dopt%3DAbstract This study is first to show that immature I. ricinus ticks feeding on free-living lizards in a Central European region could be infected with gammaherpesvirus (MHV-68), naturally infecting free-living murid rodents. Our results provide evidence supporting the hypothesis that ticks may play a mediating role in circulation of MHV-68 in nature. PMID: 21732020 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5051456 Tue, 05 Jul 2011 23:00:00 +0100 5051456 http://www.medworm.com/index.php?rid=5000912&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728037%26dopt%3DAbstract Authors: Gupta V, Smemo KA, Yavitt JB, Basiliko N The active methanotroph community was investigated in two contrasting North American peatlands, a nutrient-rich sedge fen and nutrient-poor Sphagnum bog using in vitro incubations and (13)C-DNA stable-isotope probing (SIP) to measure methane (CH(4)) oxidation rates and label active microbes followed by fingerprinting and sequencing of bacterial and archaeal 16S rDNA and methane monooxygenase (pmoA and mmoX) genes. Rates of CH(4) oxidation were slightly, but significantly, faster in the bog and methanotrophs belonged to the class Alphaproteobacteria and were similar to other methanotrophs of the genera Methylocystis, Methylosinus, and Methylocapsa or Methylocella detected in, or isolated from, European bogs. The fen had a greater phyloge... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000912 Mon, 04 Jul 2011 23:00:00 +0100 5000912 http://www.medworm.com/index.php?rid=5000911&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728038%26dopt%3DAbstract This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges. PMID: 21728038 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000911 Mon, 04 Jul 2011 23:00:00 +0100 5000911 http://www.medworm.com/index.php?rid=5000910&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21728039%26dopt%3DAbstract Authors: Lelong A, Haberkorn H, Le Goïc N, Hégaret H, Soudant P The allelopathic effects of Alexandrium minutum, a toxic dinoflagellate, on the diatom Chaetoceros neogracile were evaluated using unialgal cultures evaluated by flow cytometry (FCM) and photosynthetic-performance analysis. Using FCM, we demonstrated that red chlorophyll fluorescence, relative cell size (Forward scatter of blue laser light, FSC) and cell complexity (Side scatter, 90°-angle scatter of blue laser light, SSC) significantly and rapidly decreased in C. neogracile cells exposed to A. minutum. Cells of C. neogracile exposed to A. minutum had fewer active photosynthetic reaction centers and sharply decreased photosynthetic efficiency. These effects were intensified with advancing A. minutum batch culture age an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000910 Mon, 04 Jul 2011 23:00:00 +0100 5000910 http://www.medworm.com/index.php?rid=5000913&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21720829%26dopt%3DAbstract Authors: Harke MJ, Berry DL, Ammerman JW, Gobler CJ Cyanobacteria blooms caused by species such as Microcystis have become commonplace in many freshwater ecosystems. Although phosphorus (P) typically limits the growth of freshwater phytoplankton populations, little is known regarding the molecular response of Microcystis to variation in P concentrations and sources. For this study, we examined genes involved in P acquisition in Microcystis including two high-affinity phosphate-binding proteins (pstS and sphX) and a putative alkaline phosphatase (phoX). Sequence analyses among ten clones of Microcystis aeruginosa and one clone of Microcystis wesenbergii indicates that these genes are present and conserved within the species, but perhaps not the genus, as phoX was not identified in M. we... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000913 Thu, 30 Jun 2011 23:00:00 +0100 5000913 http://www.medworm.com/index.php?rid=5000915&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21713434%26dopt%3DAbstract Authors: Fan F, Yang Q, Li Z, Wei D, Cui X, Liang Y The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the oppos... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000915 Tue, 28 Jun 2011 23:00:00 +0100 5000915 http://www.medworm.com/index.php?rid=5000914&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21713435%26dopt%3DAbstract Authors: Wang Y, Boyd E, Crane S, Lu-Irving P, Krabbenhoft D, King S, Dighton J, Geesey G, Barkay T The distribution and phylogeny of extant protein-encoding genes recovered from geochemically diverse environments can provide insight into the physical and chemical parameters that led to the origin and which constrained the evolution of a functional process. Mercuric reductase (MerA) plays an integral role in mercury (Hg) biogeochemistry by catalyzing the transformation of Hg(II) to Hg(0). Putative merA sequences were amplified from DNA extracts of microbial communities associated with mats and sulfur precipitates from physicochemically diverse Hg-containing springs in Yellowstone National Park, Wyoming, using four PCR primer sets that were designed to capture the known diversity of mer... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000914 Tue, 28 Jun 2011 23:00:00 +0100 5000914 http://www.medworm.com/index.php?rid=5000916&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21710225%26dopt%3DAbstract Authors: Krüger T, Hölzel N, Luckas B Microcystis aeruginosa isolated in 2005 from the shallow eutrophic Lake Chao (Anhui, China) was investigated in terms of growth parameters and microcystin production under varying nutrient concentrations (P, N) and pH values (abiotic factors) as well as under the influence of spent medium of the non-toxic cyanobacterium Synechocystis sp. (biotic factors). Stimulating effects on growth were observed at the alkaline pH value (10.5), whereas toxin production was significantly increased under phosphate-P limitation (0.6 mg L(-1) medium). Within a broad range of nitrate-N concentrations (41.2-247.2 mg L(-1) medium), no significant influence on cell growth and microcystin production was observed; however, N-starvation resulted in a typical decrease... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000916 Mon, 27 Jun 2011 23:00:00 +0100 5000916 http://www.medworm.com/index.php?rid=5000917&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21706196%26dopt%3DAbstract This study investigated the abundance of archaeal (AOA) and bacterial (ammonia-oxidizing bacteria (AOB)) amoA genes in eight of Bangkok's municipal WWTPs. AOA amoA genes (3.28 × 10(7) ± 1.74 × 10(7)-2.23 × 10(11) ± 1.92 × 10(11) copies l(-1) sludge) outnumbered AOB amoA genes in most of the WWTPs even though the plants' treatment processes, influent and effluent characteristics, removal efficiencies, and operation varied. An estimation of the ammonia-oxidizing activity of AOA and AOB suggests that AOA involved in autotrophic ammonia oxidation in the WWTPs. Statistical analysis shows that the numbers of AOA amoA genes correlated negatively to the ammonium levels in effluent wastewater, while no correlation was found between the AOA amoA gene numbers and the ox... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000917 Fri, 24 Jun 2011 23:00:00 +0100 5000917 http://www.medworm.com/index.php?rid=5000918&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21701871%26dopt%3DAbstract This study examined the effects of different light conditions (intensity, incident direction, time of illumination) on the settling behavior of the marine diatom Navicula sp. on glass surfaces. The density of this diatom's settlement on glass was strongly influenced by light conditions. Moreover, very weak light emitted on the bottom of the culture dish could also rapidly inhibit diatom settlement. These phenomena were explained by spatial interference between chloroplast and holdfast-like structures inside the thecae. The holdfast-like structure is observed to be responsible for diatom locomotion and hence the settlement behavior. It was proposed that the interrelation of illumination and attachment of diatoms allowed them to better adapt to the habitat with higher efficiency of attachmen... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000918 Thu, 23 Jun 2011 23:00:00 +0100 5000918 http://www.medworm.com/index.php?rid=5000921&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21698401%26dopt%3DAbstract Authors: Feng Y, Lin X, Yu Y, Zhu J The knowledge of the impact of elevated ground-level O(3) below ground the agro-ecosystem is limited. A field experiment in China Ozone Free-Air Concentration Enrichment (FACE-O(3)) facility on a rice-wheat rotation system was carried out to investigate responses of anoxygenic phototrophic purple bacteria (AnPPB) to elevated ground-level O(3). AnPPB community structures and sizes in paddy soil were monitored by molecular approaches including PCR-DGGE and real-time quantitative PCR based upon the pufM gene on three typical rice growth stages. Repetitive sequence-based PCR (rep-PCR) in combination with culture-reliant method was conducted to reveal changes in genotypic diversity. Elevated ground-level O(3) statistically reduce AnPPB abundance and perce... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000921 Wed, 22 Jun 2011 23:00:00 +0100 5000921 http://www.medworm.com/index.php?rid=5000920&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21698402%26dopt%3DAbstract In this study, to explore the microbial community structure and its functionality in the deep-sea environments, we initially performed a 16S ribosomal RNA (rRNA)-based community structure analyses for microbial communities in the sea water collected from sites of 765-790 m in depth in the Pacific Ocean. Interestingly, in the clone library we detected the presence of both photoautotrophic bacteria such as cyanobacteria and photoheterotrophic bacteria, such as Chloroflexus sp. To further explore the existence and diversity of possible light-utilizing microorganisms, we then constructed and analyzed a 23S rRNA plastid gene cloning library. The results showed that the majority of this cloning library was occupied by oxygenic photoautotrophic organisms, such as diatoms Thalassiosira spp. and c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000920 Wed, 22 Jun 2011 23:00:00 +0100 5000920 http://www.medworm.com/index.php?rid=5000919&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21698403%26dopt%3DAbstract Authors: Boucher D, Laffaire JB, Jaziri F, David C, Biderre-Petit C, Duquenne P, Peyretaillade E, Peyret P Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=5000919 Wed, 22 Jun 2011 23:00:00 +0100 5000919 http://www.medworm.com/index.php?rid=4955488&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21681548%26dopt%3DAbstract Authors: Park SJ, Park BJ, Jung MY, Kim SJ, Chae JC, Roh Y, Forwick M, Yoon HI, Rhee SK PMID: 21681548 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4955488 Thu, 16 Jun 2011 23:00:00 +0100 4955488 http://www.medworm.com/index.php?rid=4955490&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21667195%26dopt%3DAbstract Authors: Freese HM, Schink B Small filter-feeding zooplankton organisms like the cladoceran Daphnia spp. are key members of freshwater food webs. Although several interactions between Daphnia and bacteria have been investigated, the importance of the microbial communities inside Daphnia guts has been studied only poorly so far. In the present study, we characterised the bacterial community composition inside the digestive tract of a laboratory-reared clonal culture of Daphnia magna using 16S rRNA gene libraries and terminal-restriction length polymorphism fingerprint analyses. In addition, the diversity and stability of the intestinal microbial community were investigated over time, with different food sources as well as under starvation stress and death, and were compared to the commu... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4955490 Fri, 10 Jun 2011 23:00:00 +0100 4955490 http://www.medworm.com/index.php?rid=4955489&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21667196%26dopt%3DAbstract Authors: Otten TG, Paerl HW Blooms of the toxin-producing cyanobacterium, Microcystis spp., are an increasingly prevalent water quality problem and health hazard worldwide. China's third largest lake, Lake Taihu, has been experiencing progressively more severe Microcystis blooms over the past three decades. In 2009 and 2010, individual Microcystis colonies, consisting of four different morphospecies, were isolated and genotyped using a whole-cell multiplex PCR assay. The 16S-23S rDNA-ITS sequences were aligned based on Bayesian inference and indicated that one morphospecies was genetically unique (Microcystis wesenbergii) and three were indistinguishable (Microcystis aeruginosa, Microcystis flos-aquae, and Microcystis ichthyoblabe). Microcystin (mcyB) genes were detected intermittently... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4955489 Fri, 10 Jun 2011 23:00:00 +0100 4955489 http://www.medworm.com/index.php?rid=4906094&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21647696%26dopt%3DAbstract Authors: Rokni-Zadeh H, Mangas-Losada A, De Mot R Bacterial lipopeptides (LPs) are a diverse group of secondary metabolites synthesized through one or more non-ribosomal peptide synthetases (NRPSs). In certain genera, such as Pseudomonas and Bacillus, these enzyme systems are often involved in synthesizing biosurfactants or antimicrobial compounds. Several different types of LPs have been reported for non-pathogenic plant-associated Pseudomonas. Focusing on this group of bacteria, we devised and validated a PCR method to detect novel LP-synthesizing NRPS genes by targeting their lipoinitiation and tandem thioesterase domains, thus avoiding amplification of genes for non-LP metabolites, such as the pyoverdine siderophores present in all fluorescent Pseudomonas. This approach enabled det... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906094 Mon, 06 Jun 2011 23:00:00 +0100 4906094 http://www.medworm.com/index.php?rid=4906096&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21643699%26dopt%3DAbstract Authors: Jacobsen A, Hendriksen RS, Aaresturp FM, Ussery DW, Friis C Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed p... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906096 Fri, 03 Jun 2011 23:00:00 +0100 4906096 http://www.medworm.com/index.php?rid=4906095&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21643700%26dopt%3DAbstract Authors: Reháková K, Chlumská Z, Doležal J Although phototrophic microbial communities are important components of soils in arid and semi-arid ecosystems around the world, the knowledge of their taxonomic composition and dependency on soil chemistry and vegetation is still fragmentary. We studied the abundance and the diversity of cyanobacteria and eukaryotic microalgae along altitudinal gradients (3,700-5,970 m) at four sites in the dry mountains of Ladakh (Little Tibet, Zanskar Mountains, and Eastern Karakoram), using epifluorescence. The effects of environmental factors (altitude, mountain range, and vegetation type) on soil physico-chemical parameters (pH; texture; organic matter, nitrogen, ammonia, and phosphorus contents; and concentration of chlorophylls and carotenoids) an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906095 Fri, 03 Jun 2011 23:00:00 +0100 4906095 http://www.medworm.com/index.php?rid=4906099&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21625971%26dopt%3DAbstract In this study, endophytes colonizing flowers as well as berries and seeds of grapevine plants grown under natural conditions were investigated by cultivation as well as by fluorescence in situ hybridization. For comparison, bacteria were additionally isolated from other plant parts and the rhizosphere and characterized. Flowers, fruits, and seeds hosted various endophytic bacteria. Some taxa were specifically isolated from plant reproductive organs, whereas others were also detected in the rhizosphere, endorhiza or grape inflo/infructescence stalk at the flowering or berry harvest stage. Microscopic analysis by fluorescence in situ hybridization of resin-embedded samples confirmed the presence of the isolated taxa in plant reproductive organs and enabled us to localize them within the plan... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906099 Mon, 30 May 2011 23:00:00 +0100 4906099 http://www.medworm.com/index.php?rid=4906098&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21625972%26dopt%3DAbstract Authors: Hook SE, Steele MA, Northwood KS, Wright AD, McBride BW Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906098 Mon, 30 May 2011 23:00:00 +0100 4906098 http://www.medworm.com/index.php?rid=4906097&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21625973%26dopt%3DAbstract The objective of this study was to assess the potential influence of short-term environmental variability on the composition of testate amoeba communities in Sphagnum-dominated peatlands. Testate amoebae and environmental conditions, including hourly measurements of relative humidity within the upper centimeter of the peatland surface, were examined throughout the 2008 growing season at 72 microsites within 11 peatlands of Pennsylvania and Wisconsin, USA. Relationships among testate amoeba communities, vegetation, depth to water table, pH, and an index of short-term environmental variability (EVI), were examined using nonmetric multidimensional scaling and correlation analysis. Results suggest that EVI influences testate amoeba communities, with some taxa more abundant under highly variabl... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906097 Mon, 30 May 2011 23:00:00 +0100 4906097 http://www.medworm.com/index.php?rid=4906101&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21617895%26dopt%3DAbstract Authors: Passy SI, Larson CA The century-long research on succession has bestowed us with a number of theories, but little agreement on what causes species replacements through time. The majority of studies has explored the temporal trends of individual species in plant and much less so in microbial communities, arguing that interspecific interactions, especially competition, play a key role in community organization throughout succession. In this experimental investigation of periphytic succession in re-circulating laboratory streams, we examined the density and the relative abundance of diatoms and soft algae for 35 days across gradients of low to high nutrient supply (nitrogen + phosphorus) and low to intermediate current velocity (10 vs. 30 cm·s(-1)). All algal species were clas... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906101 Thu, 26 May 2011 23:00:00 +0100 4906101 http://www.medworm.com/index.php?rid=4906100&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21617896%26dopt%3DAbstract This study quantified fecal indicator bacteria and compared the distributions of human-specific genetic markers and bacterial community composition during dry and wet weather in urban creeks draining two neighboring watersheds in Santa Barbara, CA. In a prior study conducted during exclusively dry weather, the creeks were contaminated with human waste as indicated by elevated numbers of the human-specific Bacteroidales marker HF183 (Sercu et al. in Environ Sci Technol 43:293-298, 2009). During the storm, fecal indicator bacterial numbers and loads increased orders of magnitude above dry weather conditions. Moreover, bacterial community composition drastically changed during rainfall and differed from dry weather flow by (1) increased bacterial diversity, (2) reduced spatial heterogeneity w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906100 Thu, 26 May 2011 23:00:00 +0100 4906100 http://www.medworm.com/index.php?rid=4906103&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21614459%26dopt%3DAbstract Authors: Gutierrez-Zamora ML, Zemb O, Manefield M In the past decade, an increasing number of methods in microbial ecology have been developed that address the questions of which microbes exist in the environment, what their roles are and, to some extent, what their abundance is. In the present paper, we propose and describe the proof of principle of a novel method for analysing shifts in microbial community composition that uses small RNA fragments directly derived from 16S rRNA. Community fingerprints are generated on the basis of sequence-dependent conformational differences of rRNA fragments. We applied this method to profile artificial and natural communities and to detect changes in community structure in enrichment cultures. This method constitutes a PCR-free alternative to micr... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906103 Wed, 25 May 2011 23:00:00 +0100 4906103 http://www.medworm.com/index.php?rid=4906102&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21614460%26dopt%3DAbstract Authors: Villa F, Pitts B, Stewart PS, Giussani B, Roncoroni S, Albanese D, Giordano C, Tunesi M, Cappitelli F Candida albicans is the most notorious and the most widely studied yeast biofilm former. Design of experiments (DoE) showed that 10 mg/L zosteric acid sodium salt reduced C. albicans adhesion and the subsequent biofilm formation by at least 70%, on both hydrophilic and hydrophobic surfaces of 96-well plates. Indeed, biofilm imaging revealed the dramatic impact of zosteric acid sodium salt on biofilm thickness and morphology, due to the inability of the cells to form filamentous structures while remaining metabolically active. In the same way, 10 mg/L zosteric acid sodium salt inhibited C. albicans biofilm formation when added after the adhesion phase. Contrary to zosteric ac... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906102 Wed, 25 May 2011 23:00:00 +0100 4906102 http://www.medworm.com/index.php?rid=4906106&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21611687%26dopt%3DAbstract Authors: Xiao Y, Zeng GM, Yang ZH, Ma YH, Huang C, Shi WJ, Xu ZY, Huang J, Fan CZ The method of continuous thermophilic composting (CTC) remarkably shortened the active composting cycle and enhanced the compost stability. Effects of CTC on the quantities of bacteria, with a comparison to the traditional composting (TC) method, were explored by plate count with incubation at 30, 40 and 50°C, respectively, and by quantitative PCR targeting the universal bacterial 16S rRNA genes and the Bacillus 16S rRNA genes. The comparison of cultivatable or uncultivatable bacterial numbers indicated that CTC might have increased the biomass of bacteria, especially Bacillus spp., during the composting. Denaturing gradient gel electrophoresis (DGGE) analysis was employed to investigate the effects of C... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906106 Tue, 24 May 2011 23:00:00 +0100 4906106 http://www.medworm.com/index.php?rid=4906105&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21611688%26dopt%3DAbstract Authors: Tiquia SM The potential effects of urbanization on the bioavailability of dissolved organic carbon (DOC) were tested by determining the extracellular enzyme activities of the heterotrophic microbial communities of the Rouge River. The activities of 19 enzymes were monitored across two water samples (river water and groundwater) at different spatial and temporal scales. High phosphatase, esterase, and aminopeptidase activities was observed in site 9 (site most exposed to anthropogenic sources) showed higher concentrations of DOC compared to sites 1 and 8 (sites exposed to less anthropogenic sources), where moderate activities of diverse range of enzymes were observed. High relative contributions of phosphatase, esterase, and aminopeptidase activities to the overall enzyme activ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906105 Tue, 24 May 2011 23:00:00 +0100 4906105 http://www.medworm.com/index.php?rid=4906104&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21611689%26dopt%3DAbstract Authors: Machado-Ferreira E, Dietrich G, Hojgaard A, Levin M, Piesman J, Zeidner NS, Soares CA Members of the Coxiella genus are intracellular bacteria that can infect a variety of animals including humans. A symbiotic Coxiella was recently described in Amblyomma americanum ticks in the Northern Hemisphere with no further investigations of other Amblyomma species in other geographic regions. These ixodid ticks represent a group of important vectors for human infectious agents. In the present work, we have demonstrated that symbiotic Coxiella (SCox) are widespread, occurring in South America and infecting 100% of all life stages and eggs of the Cayenne ticks Amblyomma cajennense from Brazil and the USA. Using light microscopy, in situ hybridization, and PCR, we demonstrated SCox in sali... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4906104 Tue, 24 May 2011 23:00:00 +0100 4906104 http://www.medworm.com/index.php?rid=4855968&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21607876%26dopt%3DAbstract Authors: Pelz-Stelinski K, Kaufman MG, Walker ED Container-breeding mosquitoes, such as Aedes triseriatus, ingest biofilms and filter water column microorganisms directly to obtain the bulk of their nutrition. Scirtid beetles often co-occur with A. triseriatus and may facilitate the production of mosquito adults under low-resource conditions. Using molecular genetic techniques and quantitative assays, we observed changes in the dynamics and composition of bacterial and fungal communities present on leaf detritus and in the water column when scirtid beetles co-occur with A. triseriatus. Data from terminal restriction fragment polymorphism analysis indicated scirtid presence alters the structure of fungal communities in the water column but not leaf-associated fungal communities. Similar... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855968 Mon, 23 May 2011 23:00:00 +0100 4855968 http://www.medworm.com/index.php?rid=4855969&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21597940%26dopt%3DAbstract Authors: Hu A, Jiao N, Zhang CL Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO(2) fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rR... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855969 Thu, 19 May 2011 23:00:00 +0100 4855969 http://www.medworm.com/index.php?rid=4855970&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21594594%26dopt%3DAbstract Authors: Pieja AJ, Rostkowski KH, Criddle CS Methanotrophs are known to produce poly-3-hydroxybutyrate (PHB), but there is conflicting evidence in the literature as to which genera produce the polymer. We screened type I and II proteobacterial methanotrophs that use the ribulose monophosphate and serine pathways for carbon assimilation, respectively, for both phaC, which encodes for PHB synthase, and the ability to produce PHB under nitrogen-limited conditions. Twelve strains from six different genera were evaluated. All type I strains tested negative for phaC and PHB production; all Type II strains tested positive for phaC and PHB production. In order to identify conditions that favor PHB production, we also evaluated a range of selection conditions using a diverse activated sludge in... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855970 Wed, 18 May 2011 23:00:00 +0100 4855970 http://www.medworm.com/index.php?rid=4855971&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21590300%26dopt%3DAbstract Authors: van Heerden A, van Zyl WH, Cruywagen CW, Mouton M, Botha A The yeast-like fungus Coniochaeta pulveracea was studied with regard to its novel lignocellulolytic activities and the possible effect thereof on yeasts from the woody phylloplane. An enrichment procedure was used to isolate C. pulveracea from a decaying Acacia tree, and the identity of the isolate was confirmed using morphology, as well as molecular and phylogenetic techniques. This isolate, as well as strains representing C. pulveracea from different geographical regions, were compared with regard to optimum growth temperature and enzyme activity to representatives of closely related species. These include strains of Coniochaeta boothii, Coniochaeta rhopalochaeta, and Coniochaeta subcorticalis. Plate assays for cellu... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855971 Tue, 17 May 2011 23:00:00 +0100 4855971 http://www.medworm.com/index.php?rid=4855974&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584754%26dopt%3DAbstract Authors: Elifantz H, Kautsky L, Mor-Yosef M, Tarchitzky J, Bar-Tal A, Chen Y, Minz D The global changes in rainfall frequency and quantity have subjected arid and semi-arid regions to long periods of drought. As this phenomenon corresponds to increasing trend of water shortage, the use of treated wastewater (TWW) has been suggested as an alternative for irrigation of agricultural crops in these areas. The aim of the study was to investigate the short- and middle-term effects of TWW irrigation on the soil microbial activities and organic carbon content. The microbial community activity was measured every 1-3 months for 4 years in a persimmon (Diospyros kaki) orchard. These activities were used here as an indicator for the soil health. The hydrolysis activity (detected by fluorescein d... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855974 Mon, 16 May 2011 23:00:00 +0100 4855974 http://www.medworm.com/index.php?rid=4855973&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584755%26dopt%3DAbstract Authors: Meisterhans G, Raymond N, Lebreton S, Salin F, Bourasseau L, de Montaudouin X, Garabetian F, Jude-Lemeilleur F The bacterial communities associated with the cockle (Cerastoderma edule) were investigated at the individual level through a 10-month monitoring programme. Temporal changes and those changes associated with a common parasite of the cockle, Bucephalus minimus, were investigated by monthly sampling of individuals, selected based on their shell length (cohort monitoring). Cockle bacterial community abundance (CBCA) and diversity (CBCD) were estimated by epifluorescence microscopy counts and automated ribosomal intergenic spacer analysis, respectively. CBCA showed a temporal pattern peaking at 30 × 10(6) cells per gram of cockle flesh and intervalval liquid in Octob... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855973 Mon, 16 May 2011 23:00:00 +0100 4855973 http://www.medworm.com/index.php?rid=4855972&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21584756%26dopt%3DAbstract Authors: Kelly LC, Cockell CS, Herrera-Belaroussi A, Piceno Y, Andersen G, Desantis T, Brodie E, Thorsteinsson T, Marteinsson V, Poly F, Leroux X Bacteria inhabiting crystalline rocks from two terrestrial Icelandic volcanic lava flows of similar age and from the same geographical region, but differing in porosity and mineralogy, were characterised. Microarray (PhyloChip) and clone library analysis of 16S rRNA genes revealed the presence of a diverse assemblage of bacteria in each lava flow. Both methods suggested a more diverse community at the Dómadalshraun site (rhyolitic/andesitic lava flow) than that present at the Hnausahraun site (basaltic lava flow). Proteobacteria dominated the clone library at the Dómadalshraun site, while Acidobacteria was the most abundant phylum in the Hn... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855972 Mon, 16 May 2011 23:00:00 +0100 4855972 http://www.medworm.com/index.php?rid=4855975&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21573760%26dopt%3DAbstract In this study, Gram-negative bacterium Vibrio sp. DSM14379, isolated from the estuarine waters of the northern Adriatic Sea, was grown aerobically in a peptone-yeast extract medium with different salt concentrations (ranging from 0.3% to 10% (w/v) NaCl). Carbon flux through the central metabolic pathways was determined at low and high salt concentrations. At low salt concentrations, total endogenous respiration, dehydrogenase activity, and net intracellular adenosine triphosphate (ATP) concentration significantly increased, the phosphofructokinase and pyruvate kinase activity decreased, whereas glucose-6-phosphate dehydrogenase activity remained unchanged. The carrying capacity of bacterial culture decreased dramatically, indicating a severe metabolic imbalance at low salt concentrations. ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855975 Sat, 14 May 2011 23:00:00 +0100 4855975 http://www.medworm.com/index.php?rid=4855976&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21567188%26dopt%3DAbstract Authors: Pérez-de-Mora A, Engel M, Schloter M Unraveling functional genes related to biodegradation of organic compounds has profoundly improved our understanding of biological remediation processes, yet the ecology of such genes is only poorly understood. We used a culture-independent approach to assess the abundance and diversity of bacteria catalyzing the degradation of n-alkanes with a chain length between C(5) and C(16) at a forest site co-contaminated with mineral oil hydrocarbons and metals for nearly 60 years. The alkB gene coding for a rubredoxin-dependent alkane monooxygenase enzyme involved in the initial activation step of aerobic aliphatic hydrocarbon metabolism was used as biomarker. Within the area of study, four different zones were evaluated: one highly contaminated,... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855976 Thu, 12 May 2011 23:00:00 +0100 4855976 http://www.medworm.com/index.php?rid=4855980&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21556882%26dopt%3DAbstract Authors: Papadopoulou ES, Karpouzas DG, Menkissoglu-Spiroudi U Phospholipid fatty acid (PLFA) analysis is a robust method for characterizing soil microbial communities. We determined the effects of extraction solvent (chloroform vs dichloromethane) and buffer (phosphate vs citrate) on the yield and the profile of PLFAs extracted from an acidic (pH 5.5) and an alkaline (pH 8.6) soil following two 2-h sequential extractions. The yield and the profile of the PLFAs obtained separately by the first and the second 2-h extraction were compared to identify the impact of sequential extractions on the PLFA extraction efficiency. Chloroform-citrate and a 2 × 2-h extraction maximized PLFA yields in both soils. Multivariate analysis of the data showed that the choice of the extraction mixtur... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855980 Mon, 09 May 2011 23:00:00 +0100 4855980 http://www.medworm.com/index.php?rid=4855979&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21556883%26dopt%3DAbstract Authors: Bouvier T, Maurice CF Culture studies of phage-host systems have shown that phage proliferation strongly depends on the physiological state of the host, but it is still unclear to what extent this holds true within aquatic ecosystems. We used a combination of flow sorting and electron microscopy to explore how the frequency of bacterial cells with attached viruses (FCAV), of visibly infected cells, and the number of intracellular viruses are distributed within five physiologic categories: cells with high (HNA) and low (LNA) nucleic acid content, with a compromised membrane, in division, and with an intact-looking morphology. FCAV was not different between the cellular physiologic categories, suggesting low influence of host physiology on viral adsorption. Infected cells were f... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855979 Mon, 09 May 2011 23:00:00 +0100 4855979 http://www.medworm.com/index.php?rid=4855978&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21556884%26dopt%3DAbstract Authors: Park SJ, Park BJ, Jung MY, Kim SJ, Chae JC, Roh Y, Forwick M, Yoon HI, Rhee SK Increases in global temperatures have been shown to enhance glacier melting in the Arctic region. Here, we have evaluated the effects of meltwater runoff on the microbial communities of coastal marine sediment located along a transect of Temelfjorden, in Svalbard. As close to the glacier front, the sediment properties were clearly influenced by deglaciation. Denaturing gradient gel electrophoresis profiles showed that the sediment microbial communities of the stations of glacier front (stations 188-178) were distinguishable from that of outer fjord region (station 176). Canonical correspondence analysis indicated that total carbon and calcium carbonate in sediment and chlorophyll a in bottom water w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855978 Mon, 09 May 2011 23:00:00 +0100 4855978 http://www.medworm.com/index.php?rid=4855977&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21556885%26dopt%3DAbstract Authors: Koch H, Schmid-Hempel P Recent studies on the microbial flora of the honeybee gut have revealed an apparently highly specific community of resident bacteria that might play a role in immune defence and food preservation for their hosts. However, at present, very little is known about the diversity and ecology of bacteria occurring in non-domesticated bees like bumblebees, which are of similar importance as honeybees for the pollination of agricultural and wild flowers. To fill this gap in knowledge, we examined six of the most common bumblebee species in Central Europe from three locations in Germany and Switzerland for their bacterial communities. We used a culture-independent molecular approach based on sequencing the 16S rRNA gene from a selection of individuals and examini... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4855977 Mon, 09 May 2011 23:00:00 +0100 4855977 http://www.medworm.com/index.php?rid=4804055&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21553058%26dopt%3DAbstract Authors: Pradhan A, Seena S, Pascoal C, Cássio F The extensive use of nanometal-based products increases the chance of their release into aquatic environments, raising the question whether they can pose a risk to aquatic biota and the associated ecological processes. Aquatic microbes, namely fungi and bacteria, play a key role in forested streams by decomposing plant litter from terrestrial vegetation. Here, we investigated the effects of nanocopper oxide and nanosilver on leaf litter decomposition by aquatic microbes, and the results were compared with the impacts of their ionic precursors. Alder leaves were immersed in a stream of Northwest Portugal to allow microbial colonization before being exposed in microcosms to increased nominal concentrations of nanometals (CuO, 100, 200 and... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804055 Fri, 06 May 2011 23:00:00 +0100 4804055 http://www.medworm.com/index.php?rid=4804056&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21547449%26dopt%3DAbstract Authors: Borić M, Danevčič T, Stopar D Pigments such as melanin, scytonemin and carotenoids protect microbial cells against the harmful effects of ultraviolet (UV) radiation. The role in UV protection has never been assigned to the prodigiosin pigment. In this work, we demonstrate that prodigiosin provides a significant level of protection against UV stress in Vibrio sp. DSM 14379. In the absence of pigment production, Vibrio sp. was significantly more susceptible to UV stress, and there was no difference in UV survival between the wild-type strain and non-pigmented mutant. The pigment's protective role was more important at higher doses of UV irradiation and correlated with pigment concentration in the cell. Pigmented cells survived high UV exposure (324 J/m(2)) around 1,000-fold ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804056 Thu, 05 May 2011 23:00:00 +0100 4804056 http://www.medworm.com/index.php?rid=4804057&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21538105%26dopt%3DAbstract Authors: Pachiadaki MG, Kallionaki A, Dählmann A, De Lange GJ, Kormas KA We investigated the top 30-cm sediment prokaryotic community structure in 5-cm spatial resolution, at an active site of the Amsterdam mud volcano, East Mediterranean Sea, based on the 16S rRNA gene diversity. A total of 339 and 526 sequences were retrieved, corresponding to 25 and 213 unique (≥98% similarity) phylotypes of Archaea and Bacteria, respectively, in all depths. The Shannon-Wiener diversity index H was higher for Bacteria (1.92-4.03) than for Archaea (0.99-1.91) and varied differently between the two groups. Archaea were dominated by anaerobic methanotrophs ANME-1, -2 and -3 groups and were related to phylotypes involved in anaerobic oxidation of methane from similar habitats. The much more complex B... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804057 Mon, 02 May 2011 23:00:00 +0100 4804057 http://www.medworm.com/index.php?rid=4804058&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21523464%26dopt%3DAbstract Authors: Golberg K, Eltzov E, Shnit-Orland M, Marks RS, Kushmaro A Marine environment habitats, such as the coral mucus layer, are abundant in nutrients and rich with diverse populations of microorganisms. Since interactions among microorganisms found in coral mucus can be either mutualistic or competitive, understanding quorum sensing-based acyl homoserine lactone (AHL) language may shed light on the interaction between coral-associated microbial communities in the native host. More than 100 bacterial isolates obtained from different coral species were screened for their ability to produce AHL. When screening the isolated coral bacteria for AHL induction activity using the reporter strains Escherichia coli K802NR-pSB1075 and Agrobacterium tumefaciens KYC55, we found that approximately... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804058 Tue, 26 Apr 2011 23:00:00 +0100 4804058 http://www.medworm.com/index.php?rid=4804059&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21519913%26dopt%3DAbstract This study extended our knowledge of sponge-associated fungal phylogenetic diversity and their potential roles in the chemical defense. PMID: 21519913 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804059 Mon, 25 Apr 2011 23:00:00 +0100 4804059 http://www.medworm.com/index.php?rid=4804060&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21509607%26dopt%3DAbstract Authors: Hewson I, Brown JM, Gitlin SA, Doud DF Viruses in aquatic ecosystems comprise those produced by both autochthonous and allochthonous host taxa. However, there is little information on the diversity and abundance of viruses of allochthonous origin, particularly from non-anthropogenic sources, in freshwater and marine ecosystems. We investigated the presence of nucleopolyhedroviruses (NPV) (Baculovirus), which commonly infect terrestrial lepidopteran taxa, across the landscape of Appledore Island, Gulf of Maine. PCR and qPCR primers were developed around a 294-bp fragment of the polyhedrin (polH) gene, which is the major constituent protein of NPV multivirion polyhedral occlusion bodies. polH was successfully amplified from several aquatic habitats, and recovered polH sequences ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804060 Wed, 20 Apr 2011 23:00:00 +0100 4804060 http://www.medworm.com/index.php?rid=4804062&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21503775%26dopt%3DAbstract Authors: Mandal SK, Singh RP, Patel V Extracellular polymeric substances (EPS) produced by a toxic dinoflagellate Amphidinium carterae Hulburt 1957 was isolated and characterized. Molecular masses of the EPS were about 233 and 1,354 kDa. Spectral analyses by (1)H nuclear magnetic resonance and Fourier Transformed-Infrared Spectroscopy revealed the characteristic of the functional groups viz. primary amine, carboxyl, halide, and sulfate groups present in the EPS. However, five elements (C, O, Na, S, and Ca) were detected by scanning electron microscopy - energy dispersive X-ray spectroscopy (SEM-EDX) analysis. X-ray diffraction and differential scanning calorimetric analysis confirmed the amorphous nature of EPS, which was comprised of an average particle size of 13.969 μm (d 0.5) wi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804062 Mon, 18 Apr 2011 23:00:00 +0100 4804062 http://www.medworm.com/index.php?rid=4804061&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21503776%26dopt%3DAbstract Authors: Remold SK, Brown CK, Farris JE, Hundley TC, Perpich JA, Purdy ME Many species of Pseudomonas have the ability to use a variety of resources and habitats, and as a result Pseudomonas are often characterized as having broad fundamental niches. We questioned whether actual habitat use by Pseudomonas species is equally broad. To do this, we sampled extensively to describe the biogeography of Pseudomonas within the human home, which presents a wide variety of habitats for microbes that live in close proximity to humans but are not part of the human flora, and for microbes that are opportunistic pathogens, such as Pseudomonas aeruginosa. From 960 samples taken in 20 homes, we obtained 163 Pseudomonas isolates. The most prevalent based on identification using the SepsiTest BLAST anal... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804061 Mon, 18 Apr 2011 23:00:00 +0100 4804061 http://www.medworm.com/index.php?rid=4804063&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21491114%26dopt%3DAbstract In this study, the occurrence and diversity of anammox bacteria in the deep-sea subsurface sediments of the South China Sea (SCS) were investigated. Results indicated that the anammox bacterial sequences recovered from this habitat by amplifying both 16S rRNA gene and hydrazine oxidoreductase encoding hzo gene were all closely related to the Candidatus Scalindua genus. A total of 96 16S rRNA gene sequences from 346 clones were grouped into five subclusters: two subclusters affiliated with the brodae and arabica species, while three new subclusters named zhenghei-I, -II, and -III showed ≤97.4% nucleic acid sequence identity with other known Candidatus Scalindua species. Meanwhile, 88 hzo gene sequences from the sediments also formed five distant subclusters within hzo cluster 1c. Through ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804063 Wed, 13 Apr 2011 23:00:00 +0100 4804063 http://www.medworm.com/index.php?rid=4804064&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21484497%26dopt%3DAbstract This study probably represents the first one in which these functional models have been tested in subsurface systems. Results obtained in this study seem to suggest that microbial communities inhabiting groundwaters in Doñana are not dead or compromised cells. By contrast, these communities play relevant roles in carbon and nutrient cycling, continue with the decomposition process that begins in the sediments of the shallow lakes located in the area, provide remineralized carbon and nutrients to producers of these surface aquatic systems, and close energy and matter cycles. This study proposes that groundwater systems should be considered dynamic systems, comparable in functional complexity to surface systems. PMID: 21484497 [PubMed - as supplied by publisher] (Source: Microbial Ecolo... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804064 Mon, 11 Apr 2011 23:00:00 +0100 4804064 http://www.medworm.com/index.php?rid=4804065&cid=s_37317_77_f&fid=37317&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21475991%26dopt%3DAbstract Authors: Kernaghan G, Patriquin G Fungal root endophytes colonize root tissue concomitantly with mycorrhizal fungi, but their identities and host preferences are largely unknown. We cultured fungal endophytes from surface-sterilized Cenococcum geophilum ectomycorrhizae of Betula papyrifera, Abies balsamea, and Picea glauca from two boreal sites in eastern Canada. Isolates were initially grouped on the basis of cultural morphology and then identified by internal transcribed spacer ribosomal DNA sequencing or by PCR restriction fragment length polymorphism. Phylogenetic analysis of the sequence data revealed 31 distinct phylotypes among the isolates, comprising mainly members of the ascomycete families Helotiaceae, Dermateaceae, Myxotrichaceae, and Hyaloscyphaceae, although other fungi w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=4804065 Thu, 07 Apr 2011 23:00:00 +0100 4804065