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. Thu, 18 Mar 2010 16:38:26 +0100 http://www.medworm.com/index.php?rid=3362760&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%3D20221594%26dopt%3DAbstract Authors: Ortega-Retuerta E, Duarte CM, Reche I The study of transparent exopolymer particles (TEP) in the Mediterranean Sea is particularly relevant as they can be promoters of mucilage events, a frequent phenomenon there. We assessed the influence of bacterioplankton on TEP distribution and dynamics across the west-east axis of the Mediterranean Sea. We performed an extensive study of TEP, dissolved carbohydrates, and their relationships with bacterial abundance and bacterial production (BP). A significant and positive relationship was observed between BP and TEP in the study region (r (2) = 0.51, p < 0.001). The direct release of TEP by bacteria was experimentally corroborated using regrowth cultures where increases in TEP tracked bacterial growth in abundance and production. Thes... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3362760 Wed, 10 Mar 2010 00:00:00 +0100 3362760 http://www.medworm.com/index.php?rid=3354968&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%3D20217404%26dopt%3DAbstract Authors: Laque T, Farjalla VF, Rosado AS, Esteves FA Bacterial community composition (BCC) has been extensively related to specific environmental conditions. Tropical coastal lagoons present great temporal and spatial variation in their limnological conditions, which, in turn, should influence the BCC. Here, we sought for the limnological factors that influence, in space and time, the BCC in tropical coastal lagoons (Rio de Janeiro State, Brazil). The Visgueiro lagoon was sampled monthly for 1 year and eight lagoons were sampled once for temporal and spatial analysis, respectively. BCC was evaluated by bacteria-specific PCR-DGGE methods. Great variations were observed in limnological conditions and BCC on both temporal and spatial scales. Changes in the BCC of Visgueiro lagoon througho... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3354968 Tue, 09 Mar 2010 00:00:00 +0100 3354968 http://www.medworm.com/index.php?rid=3354967&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%3D20217405%26dopt%3DAbstract In this study, we explore the carriage rates and disease associations of adenovirus, enterovirus, rhinovirus, Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis in military recruits using high-density resequencing microarrays. The results showed that rhinoviruses, adenoviruses, S. pneumoniae, H. influenzae, and N. meningitidis were widely distributed in recruits. Of these five agents, only adenovirus showed significant correlation with illness. Among the samples tested, only pathogens associated with FRI, such as adenovirus 4 and enterovirus 68, revealed strong temporal and spatial clustering of specific strains, indicating that they are transmitted primarily within sites. The results showed a strong negative association between adenoviral FRI and the presence of ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3354967 Tue, 09 Mar 2010 00:00:00 +0100 3354967 http://www.medworm.com/index.php?rid=3354966&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%3D20217406%26dopt%3DAbstract Authors: Seyfried EE, Newton RJ, Rubert KF, Pedersen JA, McMahon KD The contribution of human activities to environmental reservoirs of antibiotic resistance is poorly understood. The purpose of this study was to determine if oxytetracycline (OTC) use in aquaculture facilities increased the detection frequency (i.e., prevalence) of tetracycline resistance (tet(R)) genes relative to facilities with no recent OTC treatment. We used polymerase chain reaction to screen water and sediment from four noncommercial fish farms in northwestern Wisconsin for the presence of ten tet(R) determinants: tet(A), tet(B), tet(D), tet(E), tet(G), tet(M), tet(O), tet(Q), tet(S), and tet(W). Water from farms with recent OTC use had significantly higher tet(R) detection frequencies than did water from farms ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3354966 Tue, 09 Mar 2010 00:00:00 +0100 3354966 http://www.medworm.com/index.php?rid=3336219&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%3D20204349%26dopt%3DAbstract Authors: Taketani RG, Tsai SM Soil from the Amazonian region is usually regarded as unsuitable for agriculture because of its low organic matter content and low pH; however, this region also contains extremely rich soil, the Terra Preta Anthrosol. A diverse archaeal community usually inhabits acidic soils, such as those found in the Amazon. Therefore, we hypothesized that this community should be sensitive to changes in the environment. Here, the archaeal community composition of Terra Preta and adjacent soil was examined in four different sites in the Brazilian Amazon under different anthropic activities. The canonical correspondence analysis of terminal restriction fragment length polymorphisms has shown that the archaeal community structure was mostly influenced by soil attributes t... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3336219 Fri, 05 Mar 2010 00:00:00 +0100 3336219 http://www.medworm.com/index.php?rid=3328505&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%3D20198369%26dopt%3DAbstract Authors: Hutalle-Schmelzer KM, Zwirnmann E, Krüger A, Grossart HP In many limnetic systems, the input of allochthonous organic matter, e.g., leaf litter, is a substantial source of dissolved organic carbon (DOC) for pelagic bacteria, especially in fall and winter when autochthonous DOC production is low. However, relatively little is known about community changes of pelagic lake bacteria due to leaf litter input which includes both the release of leaf leachates and microorganisms from the leaf litter into the surrounding water. Therefore, we have experimentally studied the effects of different types of leaf litter (Betula pendula, Fagus silvatica, and Pinus silvestris) on the pelagic bacterial community composition by adding leaves to different treatments of epilimnic water sample... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3328505 Wed, 03 Mar 2010 00:00:00 +0100 3328505 http://www.medworm.com/index.php?rid=3328506&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%3D20195591%26dopt%3DAbstract Authors: Faeth SH, Hayes CJ, Gardner DR Neotyphodium endophytes are asexual, seed-borne fungal symbionts that are thought to interact mutualistically with their grass hosts. Benefits include increased growth, reproduction, and resistance to herbivores via endophytic alkaloids. Although these benefits are well established in infected introduced, agronomic grasses, little is known about the cost and benefits of endophyte infection in native grass populations. These populations exist as mosaics of uninfected and infected plants, with the latter often comprised of plants that vary widely in alkaloid content. We tested the costs and benefits of endophyte infections with varying alkaloids in the native grass Achnatherum robustum (sleepygrass). We conducted a 4-year field experiment, where he... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3328506 Tue, 02 Mar 2010 00:00:00 +0100 3328506 http://www.medworm.com/index.php?rid=3316362&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%3D20186408%26dopt%3DAbstract Authors: de La Cochetière MF, Montassier E, Hardouin JB, Carton T, Le Vacon F, Durand T, Lalande V, Petit JC, Potel G, Beaugerie L Antibiotic-associated diarrhea (AAD) is associated with altered intestinal microflora and other symptoms that may lead to possibly death. In critically ill patients, diarrhea increases rates of morbimortality. Assessing diarrhea risks is thus important for clinicians. For this reason, we conducted a hypothesis-generating study focused on AAD to provide insight into methods of prevention. We evaluated the hypothesis of predisposing factors within the resident intestinal microbiota in a cohort of outpatients receiving antibiotherapy. Among the pool of tested variables, only those related to bacterial 16S rRNA genes were found to be relevant. Complex stat... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3316362 Fri, 26 Feb 2010 00:00:00 +0100 3316362 http://www.medworm.com/index.php?rid=3316364&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%3D20179918%26dopt%3DAbstract Authors: Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M 16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3316364 Wed, 24 Feb 2010 00:00:00 +0100 3316364 http://www.medworm.com/index.php?rid=3316363&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%3D20179919%26dopt%3DAbstract This study addresses the issues of spatial distribution, dispersal, and genetic heterogeneity in social groups of the cellular slime molds (CSMs). The CSMs are soil amoebae with an unusual life cycle that consists of alternating solitary and social phases. Because the social phase involves division of labor with what appears to be an extreme form of "altruism", the CSMs raise interesting evolutionary questions regarding the origin and maintenance of sociality. Knowledge of the genetic structure of social groups in the wild is necessary for answering these questions. We confirm that CSMs are widespread in undisturbed forest soil from South India. They are dispersed over long distances via the dung of a variety of large mammals. Consistent with this mode of dispersal, most social groups in t... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3316363 Wed, 24 Feb 2010 00:00:00 +0100 3316363 http://www.medworm.com/index.php?rid=3303239&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%3D20174790%26dopt%3DAbstract Authors: Chouari R, Le Paslier D, Daegelen P, Dauga C, Weissenbach J, Sghir A A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anoxic activated sludge from a municipal wastewater treatment plant. Two 16S rRNA gene libraries were constructed using total genomic DNA and amplified by polymerase chain reaction using primers specific for archaeal or bacterial domains. Phylogenetic analysis of 132 and 249 almost full-length 16S rRNA genes for Archaea and Bacteria, respectively, was done using the ARB software package. Phylogenetic groups affiliated with the Archaea belong to Euryarchaeota (93.8% of the operational taxonomic units [OTUs]) and Crenarchaeota (6.2% of the OTUs). Within the bacterial library, 84.8% of the OTUs represent novel put... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3303239 Sat, 20 Feb 2010 00:00:00 +0100 3303239 http://www.medworm.com/index.php?rid=3255332&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%3D20140610%26dopt%3DAbstract In this study, we evaluated the efficiency of three different on-farm waste treatment systems in reducing AR. Three classes of erythromycin resistance genes (erm) genes (B, F, and X) conferring resistances to macrolide-lincosamides-streptogramin B (MLS(B)) and one class of tetracycline resistance genes (tet) gene (G) conferring resistance to tetracyclines were used as models. Real-time polymerase chain reaction assays were used to determine the reservoir sizes of these AR genes present in the entire microbiome. These classes of AR genes varied considerably in abundance, with erm(B) being more predominant than erm(F), erm(X), and tet(G). These AR genes also varied in persistence in different waste treatment systems. Aerobic biofiltration reduced erm(X) more effectively than other AR genes, ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3255332 Sat, 06 Feb 2010 00:00:00 +0100 3255332 http://www.medworm.com/index.php?rid=3236847&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%3D20127086%26dopt%3DAbstract We examined the ultrastructure of extracellular matter from five Antarctic bacteria (Shewanella livingstonensis NF22(T), Shewanella vesiculosa M7(T), Pseudoalteromonas sp. M4.2, Psychrobacter fozii NF23(T), and Marinobacter guineae M3B(T)) by transmission electron microscopy after high-pressure freezing and freeze substitution. All analyzed extracellular matter appeared as a netlike mesh composed of a capsular polymer around cells and large numbers of membrane vesicles (MVs), which have not yet been described for members of the genera Psychrobacter and Marinobacter. MVs showed the typical characteristics described for these structures, and seemed to be surrounded by the same capsular polymer as that found around the cells. The analysis of MV proteins from Antarctic strains by SDS-PAGE show... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3236847 Tue, 02 Feb 2010 00:00:00 +0100 3236847 http://www.medworm.com/index.php?rid=3225056&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%3D20112014%26dopt%3DAbstract Authors: Polo A, Cappitelli F, Brusetti L, Principi P, Villa F, Giacomucci L, Ranalli G, Sorlini C The study was conducted on alterations found on stone artwork and integrates microbial control and a biotechnological method for the removal of undesirable chemical substances. The Demetra and Cronos sculptures are two of 12 stone statues decorating the courtyard of the Buonconsiglio Castle in Trento (Italy). An initial inspection of the statues revealed putative black crusts and highlighted the microbial contamination causing discoloration. In 2006, the Cultural Heritage Superintendence of Trento commissioned us to study and remove these chemical and biological stains. Stereomicroscopy characterised the stone of the sculptures as oolitic limestone, and infrared analyses confirmed the pre... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3225056 Sat, 30 Jan 2010 00:00:00 +0100 3225056 http://www.medworm.com/index.php?rid=3220927&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%3D20107780%26dopt%3DAbstract Authors: Yutthammo C, Thongthammachat N, Pinphanichakarn P, Luepromchai E Phyllosphere bacteria on ornamental plants were characterized based on their diversity and activity towards the removal of polycyclic aromatic hydrocarbons (PAHs), the major air pollutants in urban area. The amounts of PAH-degrading bacteria were about 1-10% of the total heterotrophic phyllosphere populations and consisted of diverse bacterial species such as Acinetobacter, Pseudomonas, Pseudoxanthomonas, Mycobacterium, and uncultured bacteria. Bacterial community structures analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis from each plant species showed distinct band patterns. The uniqueness of these phyllosphere bacterial communities was partly due to the variation in leaf morphology... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3220927 Thu, 28 Jan 2010 00:00:00 +0100 3220927 http://www.medworm.com/index.php?rid=3220926&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%3D20107781%26dopt%3DAbstract Epilithic Algae Distribution Along a Chemical Gradient in a Naturally Acidic River, Río Agrio (Patagonia, Argentina). Microb Ecol. 2010 Jan 28; Authors: Baffico GD The epilithic algae distribution along a pH gradient and the relationship between the chemical gradient and biomass development were studied in Río Agrio, a naturally acidic river located in Patagonia (Argentina). The epilithic community was monitored during the summer of three consecutive years in sites located above and below the entrance of tributaries. The epilithic community showed differences between sites based on the chemical composition of the water and the precipitates that appear on the streambed of the river. The lowest biomass, diversity, and number of species were found at the most extreme par... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3220926 Thu, 28 Jan 2010 00:00:00 +0100 3220926 http://www.medworm.com/index.php?rid=3201174&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%3D20091406%26dopt%3DAbstract Authors: Ren Y, Strobel G, Sears J, Park M Geobacillus, a bacterial genus, is represented by over 25 species of Gram-positive isolates from various man-made and natural thermophilic areas around the world. An isolate of this genus (M-7) has been acquired from a thermal area near Yellowstone National Park, MT and partially characterized. The cells of this organism are globose (ca. 0.5 mu diameter), and they are covered in a matrix capsule which gives rise to elongate multicelled bacilliform structures (ranging from 3 to 12 mum) as seen by light and atomic force microscopy, respectively. The organism produces unique petal-shaped colonies (undulating margins) on nutrient agar, and it has an optimum pH of 7.0 and an optimum temperature range of 55-65 degrees C. The partial 16S rRNA sequenc... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3201174 Fri, 22 Jan 2010 00:00:00 +0100 3201174 http://www.medworm.com/index.php?rid=3186804&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%3D20082070%26dopt%3DAbstract Authors: Yang C, Hamel C, Schellenberg MP, Perez JC, Berbara RL Septate endophytes proliferating in the roots of grasslands' plants shed doubts on the importance of arbuscular mycorrhizal (AM) symbioses in dry soils. The functionality and diversity of the AM symbioses formed in four replicates of three adjacent plant communities (agricultural, native, and restored) in Grasslands National Park, Canada were assessed in periods of moisture sufficiency and deficiency typical of early and late summer in the region. The community structure of AM fungi, as determined by polymerase chain reaction-denaturing gradient gel electrophoresis, varied with sampling time and plant community. Soil properties other than soil moisture did not change significantly with sampling time. The DNA sequences domi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3186804 Fri, 15 Jan 2010 00:00:00 +0100 3186804 http://www.medworm.com/index.php?rid=3186803&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%3D20082071%26dopt%3DAbstract In this study, the mixture of mono- and di-rhamnolipids produced by Pseudomonas aeruginosa DS10-129 was characterized for its toxicity and modulatory effects on Cd availability to different bacteria. Gram-negative naturally bioluminescent Vibrio fischeri and recombinant bioluminescent Pseudomonas fluorescens, P. aeruginosa, Escherichia coli, and Gram-positive Bacillus subtilis were used as model organisms. Rhamnolipids reduced the bioluminescence of these bacteria in less than a second of exposure even in relatively low concentrations (30-min EC(50) 45-167 mg l(-1)). Toxicity of Cd to Gram-negative bacteria (30-min EC(50) values 0.16 mg l(-1) for E. coli, 0.96 mg l(-1) for P. fluorescens, and 4.4 mg l(-1) for V. fischeri) was remarkably (up to 10-fold) reduced in the presence of 50 mg l(-1... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3186803 Fri, 15 Jan 2010 00:00:00 +0100 3186803 http://www.medworm.com/index.php?rid=3186802&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%3D20082072%26dopt%3DAbstract Authors: Pleydell E, Rogers L, Kwan E, French N From July to December 2006, a panel of 401 enterococci was isolated from carcass rinse samples collected in five poultry processing plants in New Zealand. Agar diffusion assays for nine antibacterial drugs were used to obtain a resistance phenotype for each isolate. Hierarchical clustering techniques and diversity indices showed a high diversity of resistance phenotypes within each plant, with populations of Enterococcus faecalis showing greater heterogeneity than Enterococcus faecium. Bayesian modelling identified three clusters of phenotype patterns within the panel: the E. faecium isolates showed a high probability of containing two distinct clusters, whilst the E. faecalis isolates all grouped together to form the third cluster. The v... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3186802 Fri, 15 Jan 2010 00:00:00 +0100 3186802 http://www.medworm.com/index.php?rid=3130133&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%3D20037795%26dopt%3DAbstract Authors: Pitta DW, Pinchak WE, Dowd SE, Osterstock J, Gontcharova V, Youn E, Dorton K, Yoon I, Min BR, Fulford JD, Wickersham TA, Malinowski DP Rumen bacterial communities in forage-fed and grazing cattle continually adapt to a wide range of changing dietary composition, nutrient density, and environmental conditions. We hypothesized that very distinct community assemblages would develop between the fiber and liquid fractions of rumen contents in animals transitioned from bermudagrass hay diet to a grazed wheat diet. To address this hypothesis, we designed an experiment utilizing a 16S-based bTEFAP pyrosequencing technique to characterize and elucidate changes in bacterial diversity among the fiber and liquid rumen fractions and whole rumen contents of 14 (Angus x Hereford) ruminally c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3130133 Tue, 29 Dec 2009 00:00:00 +0100 3130133 http://www.medworm.com/index.php?rid=3115411&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%3D20024684%26dopt%3DAbstract We examined the archaeal community inhabiting the rhizoplane of two contrasting vascular plants, Dulichium arundinaceum and Sarracenia purpurea, from an acidic bog in upstate NY. Multiple archaeal 16S rRNA gene libraries showed that methanogenic Archaea were dominant in the rhizoplane of both plants. In addition, the community structure (evenness) of the rhizoplane was found markedly different from the bulk peat. The archaeal community in peat from the same site has been found dominated by the E2 group, meanwhile the rhizoplane communities on both plants were co-dominated by Methanosarcinaceae (MS), rice cluster (RC)-I, and E2. Complementary T-RFLP analysis confirmed the difference between bulk peat and rhizoplane, and further characterized the dominance pattern of MS, RC-I, and E2. In the... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3115411 Tue, 22 Dec 2009 00:00:00 +0100 3115411 http://www.medworm.com/index.php?rid=3115410&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%3D20024685%26dopt%3DAbstract Authors: Bretschger O, Osterstock JB, Pinchak WE, Ishii S, Nelson KE Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3115410 Tue, 22 Dec 2009 00:00:00 +0100 3115410 http://www.medworm.com/index.php?rid=3105601&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%3D20020121%26dopt%3DAbstract Authors: Gross CA, Reddy CK, Dazzo FB Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance o... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3105601 Sat, 19 Dec 2009 00:00:00 +0100 3105601 http://www.medworm.com/index.php?rid=3105603&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%3D20016980%26dopt%3DAbstract Authors: Lewis DE, White JR, Wafula D, Athar R, Dickerson T, Williams HN, Chauhan A Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3105603 Fri, 18 Dec 2009 00:00:00 +0100 3105603 http://www.medworm.com/index.php?rid=3105602&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%3D20016981%26dopt%3DAbstract The objective of this study was to compare the microbial community composition and biomass associated with the rhizosphere of a perennial gramineous species (Lygeum spartum L.) with that of an annual (Piptatherum miliaceum L.), both growing in semiarid mine tailings. We also established their relationship with the contents of potentially toxic metals as well as with indicators of soil quality. The total phospholipid fatty acid (PLFA) amount was significantly higher in the rhizosphere soil of the annual species than in the rhizosphere soil of the perennial species. The fungal/bacterial PLFA ratio was significantly greater in the perennial species compared to the annual species. The fatty acid 16:1omega5c, the fungal/bacterial PLFA ratio and monounsaturated/saturated PLFA ratio were correlat... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3105602 Fri, 18 Dec 2009 00:00:00 +0100 3105602 http://www.medworm.com/index.php?rid=3057370&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%3D19956939%26dopt%3DAbstract Authors: Yang J, Smith HG, Sherratt TN, Wilkinson DM A long-standing debate in microbial ecology is the extent to which free-living microorganisms exhibit cosmopolitan distributions. We use a comparison of testate amoebae communities in cold "polar" locations (Arctic, Antarctic, and Tibet) to investigate how a microorganism's size affects its probability of having a cosmopolitan distribution. We show that the probability a given taxa being reported in all three locations increases as testate size decreases. Likewise, excluding those testates found only in Tibet, very small testates (<20 mum) are more likely to occur in both the Arctic and Antarctic than in either of these poles alone. Attempting to correct for phylogeny reduces the number of statistically significant relationships-b... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3057370 Fri, 04 Dec 2009 00:00:00 +0100 3057370 http://www.medworm.com/index.php?rid=3057373&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%3D19953239%26dopt%3DAbstract Authors: Lamentowicz M, Lamentowicz L, van der Knaap WO, Gąbka M, Mitchell EA We studied the vegetation, testate amoebae and abiotic variables (depth of the water table, pH, electrical conductivity, Ca and Mg concentrations of water extracted from mosses) along the bog to extremely rich fen gradient in sub-alpine peatlands of the Upper Engadine (Swiss Alps). Testate amoeba diversity was correlated to that of mosses but not of vascular plants. Diversity peaked in rich fen for testate amoebae and in extremely rich fen for mosses, while for testate amoebae and mosses it was lowest in bog but for vascular plants in extremely rich fen. Multiple factor and redundancy analyses (RDA) revealed a stronger correlation of testate amoebae than of vegetation to water table and hydrochemical va... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3057373 Thu, 03 Dec 2009 00:00:00 +0100 3057373 http://www.medworm.com/index.php?rid=3057372&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%3D19953240%26dopt%3DAbstract Authors: Miletto M, Loeb R, Antheunisse AM, Bodelier PL, Laanbroek HJ We studied the response of the sulfate-reducing prokaryote (SRP) communities to the experimental variation of salinity and tide in an outdoor mesocosm setup. Intact soil monoliths were collected at two areas of the Haringvliet lagoon (The Netherlands): one sampling location consisted of agricultural grassland, drained and fertilized for at least the last century; the other of a freshwater marshland with more recent sea influence. Two factors, i.e., "salinity" (freshwater/oligohaline) and "tide" (nontidal/tidal), were tested in a full-factorial design. Soil samples were collected after 5 months (June-October). Dissimilatory (bi)sulfite reductase beta subunit-based denaturing gradient gel electrophoresis (dsrB-DGGE) an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3057372 Thu, 03 Dec 2009 00:00:00 +0100 3057372 http://www.medworm.com/index.php?rid=3057371&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%3D19953241%26dopt%3DAbstract Authors: Tourlomousis P, Kemsley EK, Ridgway KP, Toscano MJ, Humphrey TJ, Narbad A Denaturing gradient gel electrophoresis (DGGE) is widely used in microbial ecology to profile complex microbial communities over time and in response to different stimuli. However, inherent gel-to-gel variability has always been a barrier toward meaningful interpretation of DGGE profiles obtained from multiple gels. To address this problem, we developed a two-step methodology to align DGGE profiles across a large dataset. The use of appropriate inter-gel standards was of vital importance since they provided the basis for efficient within- and between-gel alignment and a reliable means to evaluate the final outcome of the process. Pretreatment of DGGE profiles by a commercially available image analysis so... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3057371 Thu, 03 Dec 2009 00:00:00 +0100 3057371 http://www.medworm.com/index.php?rid=3040410&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%3D19946683%26dopt%3DAbstract Authors: Iasur-Kruh L, Hadar Y, Milstein D, Gasith A, Minz D The idea of using constructed wetlands for the treatment and improving of wastewater emerged in the second half of the last century. Despite relatively wide use of this environmentally friendly technology, relatively little is known about the microbial populations involved in biotransformation and removal of contaminants in this system. The aim of the current study was to investigate the assembly and function of microbial populations in vertical-flow constructed wetland microcosms designed to improve the quality of wastewater after activated sludge treatment. Also, the performance of 3-year-old wetland ponds was investigated. Even though the quality of the influent water was relatively high, improvement in water parameters su... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3040410 Sat, 28 Nov 2009 00:00:00 +0100 3040410 http://www.medworm.com/index.php?rid=3033933&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%3D19937324%26dopt%3DAbstract Authors: Wong FK, Lau MC, Lacap DC, Aitchison JC, Cowan DA, Pointing SB The morphology of endolithic colonization in a limestone escarpment and surrounding rocky debris (termed float) at a high-altitude arid site in central Tibet was documented using scanning electron microscopy. Putative lichenized structures and extensive coccoid bacterial colonization were observed. Absolute and relative abundance of rRNA gene signatures using real-time quantitative polymerase chain reaction and phylogenetic analysis of environmental phylotypes were used to characterize community structure across all domains. Escarpment endoliths were dominated by eukaryotic phylotypes suggestive of lichenised associations (a Trebouxia lichen phycobiont and Leptodontidium lichen mycobiont), whereas float endoliths w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3033933 Wed, 25 Nov 2009 00:00:00 +0100 3033933 http://www.medworm.com/index.php?rid=3033934&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%3D19936822%26dopt%3DAbstract Authors: Freese HM, Eggert A, Garland JL, Schumann R Bacteria are very important degraders of organic substances in aquatic environments. Despite their influential role in the carbon (and many other element) cycle(s), the specific genetic identity of active bacteria is mostly unknown, although contributing phylogenetic groups had been investigated. Moreover, the degree to which phenotypic potential (i.e., utilization of environmentally relevant carbon substrates) is related to the genomic identity of bacteria or bacterial groups is unclear. The present study compared the genomic fingerprints of 27 bacterial isolates from the humic River Warnow with their ability to utilize 14 environmentally relevant substrates. Acetate was the only substrate utilized by all bacterial strains. Only 60%... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3033934 Fri, 20 Nov 2009 00:00:00 +0100 3033934 http://www.medworm.com/index.php?rid=3015799&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%3D19924466%26dopt%3DAbstract Authors: Koike S, Aminov RI, Yannarell AC, Gans HD, Krapac IG, Chee-Sanford JC, Mackie RI RNA methylase genes are common antibiotic resistance determinants for multiple drugs of the macrolide, lincosamide, and streptogramin B (MLS(B)) families. We used molecular methods to investigate the diversity, distribution, and abundance of MLS(B) methylases in waste lagoons and groundwater wells at two swine farms with a history of tylosin (a macrolide antibiotic structurally related to erythromycin) and tetracycline usage. Phylogenetic analysis guided primer design for quantification of MLS(B) resistance genes found in tylosin-producing Streptomyces (tlr(B), tlr(D)) and commensal/pathogenic bacteria (erm(A), erm(B), erm(C), erm(F), erm(G), erm(Q)). The near absence of tlr genes at these sites s... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3015799 Thu, 19 Nov 2009 00:00:00 +0100 3015799 http://www.medworm.com/index.php?rid=3015798&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%3D19924467%26dopt%3DAbstract In this study, we use 16S ribosomal RNA gene sequences to describe variation among bacterial communities in the midguts of cabbage white butterfly (Pieris rapae) larvae and examine the influence of community structure on susceptibility to invasion. We compared communities in larvae experiencing the same conditions at different times (temporal variation) or fed different diets (perturbation). The most highly represented phylum was Proteobacteria, which was present in all midgut communities. The observed species richness ranged from six to 15, and the most abundant members affiliated with the genera Methylobacteria, Asaia, Acinetobacter, Enterobacter, and Pantoea. Individual larvae subjected to the same conditions at the same time harbored communities that were highly similar in structure an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3015798 Thu, 19 Nov 2009 00:00:00 +0100 3015798 http://www.medworm.com/index.php?rid=3009225&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%3D19921327%26dopt%3DAbstract Authors: Hamilton CE, Dowling TE, Faeth SH When a host organism is infected by a symbiont, the resulting symbiotum has a phenotype distinct from uninfected hosts. Genotypic interactions between the partners may increase phenotypic variation of the host at the population level. Neotyphodium is an asexual, vertically transmitted endophytic symbiont of grasses often existing in hybrid form. Hybridization in Neotyphodium rapidly increases the symbiotum's genomic content and is likely to increase the phenotypic variation of the host. This phenotypic variation is predicted to enhance host performance, especially in stressful environments. We tested this hypothesis by comparing the growth, survival, and resource allocation of hybrid and nonhybrid infected host plants exposed to controlled var... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=3009225 Tue, 17 Nov 2009 00:00:00 +0100 3009225 http://www.medworm.com/index.php?rid=2985442&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%3D19904569%26dopt%3DAbstract Authors: Wu QL, Xing P, Liu WT Planktonic picocyanobacteria abundance and diversity were investigated in nine lakes on the East Tibetan Plateau spanning a salinity gradient of 0.4-22.6 g l(-1). The investigation was conducted using epifluorescence microscopy (EFM) and terminal restriction fragment polymorphism analysis of 16S-23S rRNA internal transcribed spacer (ITS) PCR amplicons followed by sequence analyses of large ITS clone libraries of seven selected samples. EFM showed that picocyanobacteria comprised 7-19% of the total prokaryotic cells found in surface water. Most of the clones were classified into six clusters and grouped within the "picocyanobacterial clade", which consists exclusively of freshwater Synechococcus. Four new phylogenetic clusters and one new subcluster of Syn... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2985442 Thu, 12 Nov 2009 00:00:00 +0100 2985442 http://www.medworm.com/index.php?rid=2968192&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%3D19888625%26dopt%3DAbstract In this study, we analyzed the susceptibility to antibiotics (ampicillin, streptomycin, tetracycline, or co-trimoxazole = mix of sulfamethoxazole and trimetoprim) of Vibrio sp. AO1 growing in pure culture or in association with its hydroid host by using microcosm experiments. The results of minimum inhibitory concentration (MIC) experiments demonstrated that Vibrio sp. AO1 was highly resistant to ampicillin and streptomycin in pure culture. Nevertheless, these antibiotics, when used at sub-MIC values, significantly reduced the hydroid fluorescence. Co-trimoxazole showed the highest inhibitory effect on fluorescence of A. octodonta. However, in all treatments, the fluorescence was reduced after 48 h, but never disappeared completely around the folds along the hydrocaulus and at the base of ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2968192 Wed, 04 Nov 2009 00:00:00 +0100 2968192 http://www.medworm.com/index.php?rid=2968191&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%3D19888626%26dopt%3DAbstract In conclusion, our results suggest that some specific bacterial taxonomic groups maintain their diversity and even increase their relative numbers during transit through the gastrointestinal tract of earthworms. PMID: 19888626 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2968191 Wed, 04 Nov 2009 00:00:00 +0100 2968191 http://www.medworm.com/index.php?rid=2968190&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%3D19888627%26dopt%3DAbstract Authors: Rastogi G, Osman S, Vaishampayan PA, Andersen GL, Stetler LD, Sani RK Microbial diversity was characterized in mining-impacted soils collected from two abandoned uranium mine sites, the Edgemont and the North Cave Hills, South Dakota, using a high-density 16S microarray (PhyloChip) and clone libraries. Characterization of the elemental compositions of soils by X-ray fluorescence spectroscopy revealed higher metal contamination including uranium at the Edgemont than at the North Cave Hills mine site. Microarray data demonstrated extensive phylogenetic diversity in soils and confirmed nearly all clone-detected taxonomic levels. Additionally, the microarray exhibited greater diversity than clone libraries at each taxonomic level at both the mine sites. Interestingly, the PhyloChi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2968190 Wed, 04 Nov 2009 00:00:00 +0100 2968190 http://www.medworm.com/index.php?rid=2968189&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%3D19888628%26dopt%3DAbstract Authors: Vadasz P, Vadasz AS The analysis and results presented in this paper provide conclusive evidence to distinguish between the delay effect and the lag as two biologically distinct phenomena. It therefore dispels the incorrect notion that delay effects represented by delay differential equations are the biological reason behind the lag phase in microorganism growth. The resulting consequence so far is that the only other reason for the lag phase is the existence of unstable stationary states. The latter are a result of accounting for the microbial metabolic mass transfer in the population growth process. PMID: 19888628 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2968189 Wed, 04 Nov 2009 00:00:00 +0100 2968189 http://www.medworm.com/index.php?rid=2924127&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%3D19851805%26dopt%3DAbstract In this study, the contribution of the two substances to methanogenesis and the conversion in Zoige wetland were analyzed. It was determined that methanol supported the highest CH(4) formation rate in the enrichments of the soil grown with Eleocharis valleculosa, and even higher at 15 degrees C than at 30 degrees C; while hydrogenotrophic methanogenesis was higher at 30 degrees C. Both methanol- and acetate-using methanogens were counted at the highest (10(7) g(-1)) in the soil, whereas methanol-using acetogens (10(8) g(-1)) were ten times more abundant than either methanol- or acetate-using methanogens. Both methanol and acetate were detected in the methanogenesis-inhibited soil samples, so that both could be the primary methanogenic precursors in E. valleculosa soil. However, the levels ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2924127 Fri, 23 Oct 2009 00:00:00 +0100 2924127 http://www.medworm.com/index.php?rid=2919051&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%3D19847475%26dopt%3DAbstract Authors: Berg N, Steinberger Y Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a long-term research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinit... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919051 Wed, 21 Oct 2009 23:00:00 +0100 2919051 http://www.medworm.com/index.php?rid=2919048&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%3D19847476%26dopt%3DAbstract Authors: Fujii M, Takano Y, Kojima H, Hoshino T, Tanaka R, Fukui M "Red snow" refers to red-colored snow, caused by bloom of cold-adapted phototrophs, so-called snow algae. The red snow found in Langhovde, Antarctica, was investigated from several viewpoints. Various sizes of rounded red cells were observed in the red snow samples under microscopy. Pigment analysis demonstrated accumulation of astaxanthin in the red snow. Community structure of microorganisms was analyzed by culture-independent methods. In the analyses of small subunit rRNA genes, several species of green algae, fungus, and various phylotypes of bacteria were detected. The detected bacteria were closely related to psychrophilic or psychrotolerant heterotrophic strains, or sequences detected from low-temperature environ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919048 Wed, 21 Oct 2009 23:00:00 +0100 2919048 http://www.medworm.com/index.php?rid=2919067&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%3D19844647%26dopt%3DAbstract We report changes in the structure and function of Enterococcus communities in pig feces sampled from individual animals at three times, from suckling through to maturity. Enterococcus faecalis was largely replaced by Enterococcus hirae between suckling and 9 weeks of age, and a shift from one sub-species group of E. hirae to another was observed in all animals between 9 and 15 weeks. Conversely, E. faecalis strains remained consistent throughout the study period. Our results demonstrate that cpn60 sequences can be used to detect strain level changes in Enterococcus populations during succession in the fecal microbiota of growing pigs. PMID: 19844647 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919067 Tue, 20 Oct 2009 23:00:00 +0100 2919067 http://www.medworm.com/index.php?rid=2919066&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%3D19844648%26dopt%3DAbstract In this study, the mechanisms of complement activation responsible for killing Salmonella O48 serum-sensitive rods by NHS were established. Four of such mechanisms involving pathways, which are important in the bactericidal mechanism of complement activation, were distinguished: only the classical/lectin pathways, independent activation of the classical/lectin or alternative pathway, parallel activation of the classical/lectin and alternative pathways, and only the alternative pathway important in the bactericidal action of human serum. To further study the role of NeuAc, its content in bacterial cells was determined by gas-liquid chromatography-mass spectrometry in relation to 3-deoxy-D-manno-2-octulosonic acid (Kdo), an inherent constituent of LPS. The results indicate that neither the p... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919066 Tue, 20 Oct 2009 23:00:00 +0100 2919066 http://www.medworm.com/index.php?rid=2919065&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%3D19844649%26dopt%3DAbstract Authors: Burr G, Hume M, Ricke S, Nisbet D, Gatlin D Two separate experiments were conducted with hybrid striped bass to evaluate four potential prebiotics: GroBiotic(R)-A (partially autolyzed brewer's yeast, dairy ingredient components, and fermentation products), mannanoligosaccharide (MOS), galactooligosaccharide (GOS), and inulin. In the in vitro experiment, intestinal contents were incubated with the individual prebiotics (0.5% by weight) at 25 degrees C for 24 and 48 h. Analysis of volatile fatty acids in the supernatant showed that GroBiotic(R)-A, MOS, and GOS tended to produce lower acetate levels but higher butyrate levels at 48 h compared to diet alone. However, denaturing gradient gel electrophoresis (DGGE) analysis failed to detect any differences in the composition of the ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919065 Tue, 20 Oct 2009 23:00:00 +0100 2919065 http://www.medworm.com/index.php?rid=2919055&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%3D19844650%26dopt%3DAbstract Authors: Taylor EB, Williams MA The capacity to study the content and resolve the dynamics of the proteome of diverse microbial communities would help to revolutionize the way microbiologists study the function and activity of microorganisms in soil. To better understand the limitations of a proteomic approach to studying soil microbial communities, we characterized extractable soil microbial proteins using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Two methods were utilized to extract proteins from microorganisms residing in a Quitman and Benfield soil: (1) direct extraction of bulk protein from soil and (2) separation of the microorganisms from soil using density gradient centrifugation and subsequent extraction (DGC-EXT) of microbial protein. In addition, ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2919055 Tue, 20 Oct 2009 23:00:00 +0100 2919055 http://www.medworm.com/index.php?rid=2902147&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%3D19834639%26dopt%3DAbstract Authors: Wornik S, Grube M Dispersal of symbiotic partners by joint propagules is considered as an efficient strategy to maintain successful associations and to circumvent low symbiont availability. Joint dispersal is widespread in diverse symbioses and a particularly common reproductive mode in lichens. We were interested in the implications of joint symbiont dispersal on population genetic structure and investigated patterns of symbiont association in populations of two closely related lichen species in the genus Physconia, with similar range of compatible algal partners. One of the lichen species is characterized by joint dispersal of both symbionts, whereas the other species propagates by meiotic fungal spores alone. The latter species must re-establish the symbiotic stage with app... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2902147 Thu, 15 Oct 2009 23:00:00 +0100 2902147 http://www.medworm.com/index.php?rid=2902150&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%3D19830476%26dopt%3DAbstract Authors: Vesth T, Wassenaar TM, Hallin PF, Snipen L, Lagesen K, Ussery DW Thirty-two genome sequences of various Vibrionaceae members are compared, with emphasis on what makes V. cholerae unique. As few as 1,000 gene families are conserved across all the Vibrionaceae genomes analysed; this fraction roughly doubles for gene families conserved within the species V. cholerae. Of these, approximately 200 gene families that cluster on various locations of the genome are not found in other sequenced Vibrionaceae; these are possibly unique to the V. cholerae species. By comparing gene family content of the analysed genomes, the relatedness to a particular species is identified for two unspeciated genomes. Conversely, two genomes presumably belonging to the same species have suspiciously dissi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2902150 Wed, 14 Oct 2009 23:00:00 +0100 2902150 http://www.medworm.com/index.php?rid=2902149&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%3D19830477%26dopt%3DAbstract Authors: Goodenough AE, Stallwood B Although interest in the relationship between birds and microorganisms is increasing, few studies have compared nest microbial assemblages in wild passerines to determine variation within and between species. Culturing microorganisms from blue tit (Cyanistes caeruleus) and great tit (Parus major) nests from the same study site demonstrated diverse microbial communities with 32 bacterial and 13 fungal species being isolated. Dominant bacteria were Pseudomonas fluorescens, Pseudomonas putida, and Staphylococcus hyicus. Also common in the nests were the keratinolytic bacteria Pseudomonas stutzeri and Bacillus subtilis. Dominant fungi were Cladosporium herbarum and Epicoccum purpurascens. Aspergillus flavous, Microsporum gallinae, and Candida albicans (c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2902149 Wed, 14 Oct 2009 23:00:00 +0100 2902149 http://www.medworm.com/index.php?rid=2902148&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%3D19830478%26dopt%3DAbstract Authors: Dimitriu PA, Grayston SJ Productivity gradients in the boreal forest are largely determined by regional-scale changes in soil conditions, and bacterial communities are likely to respond to these changes. Few studies, however, have examined how variation in specific edaphic properties influences the composition of soil bacterial communities along environmental gradients. We quantified bacterial compositional diversity patterns in ten boreal forest sites of contrasting fertility. Bulk soil (organic and mineral horizons) was sampled from sites representing two extremes of a natural moisture-nutrient gradient and two distinct disturbance types, one barren and the other vegetation-rich. We constructed 16S rRNA gene clone libraries to characterize the bacterial communities under phy... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2902148 Wed, 14 Oct 2009 23:00:00 +0100 2902148 http://www.medworm.com/index.php?rid=2856144&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%3D19789909%26dopt%3DAbstract Authors: Obernosterer I, Lami R, Larcher M, Batailler N, Catala P, Lebaron P The temporal dynamics in bulk bacterial parameters and in the richness of the total and active bacterial community, determined from CE-SSCP fingerprints of 16S rRNA genes and 16S rRNA transcripts, respectively, were followed weekly to bimonthly at an oligotrophic coastal site in the NW Mediterranean Sea. Bacterial abundance, bacterial heterotrophic production, and bacterial and community respiration determined over two seasonal cycles displayed large short-term variability and no pronounced temporal pattern was detectable for these parameters. Concentrations in inorganic nutrients, salinity, or concentrations of chlorophyll a could not significantly explain the temporal variability of the bacterial parameters ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2856144 Tue, 29 Sep 2009 23:00:00 +0100 2856144 http://www.medworm.com/index.php?rid=2856143&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%3D19789910%26dopt%3DAbstract Authors: Ben Said O, Goñi-Urriza M, El Bour M, Aissa P, Duran R In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted stations related to the pollution revealed sequences affiliated to alpha, beta, g... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2856143 Tue, 29 Sep 2009 23:00:00 +0100 2856143 http://www.medworm.com/index.php?rid=2847351&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%3D19787390%26dopt%3DAbstract Authors: Kennedy PG, Schouboe JL, Rogers RH, Weber MG, Nadkarni NM The ecological importance of microbial symbioses in terrestrial soils is widely recognized, but their role in soils that accumulate in forest canopies is almost entirely unknown. To address this gap, this study investigated the Frankia-Alnus rubra symbiosis in canopy and forest floor roots at Olympic National Park, WA, USA. Sixteen mature A. rubra trees were surveyed and Frankia genetic diversity in canopy and forest floor nodules was assessed with sequence-based nifH analyses. A seedling bioassay experiment was conducted to determine Frankia propagule availability in canopy and forest floor soils. Total soil nitrogen from both environments was also quantified. Nodules were present in the canopies of nine of the 16 tree... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2847351 Tue, 29 Sep 2009 23:00:00 +0100 2847351 http://www.medworm.com/index.php?rid=2810310&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%3D19763680%26dopt%3DAbstract Authors: Durham-Colleran MW, Verhoeven AB, van Hoek ML Francisella tularensis is associated with water and waterways and infects many species of animals, insects, and protists. The mechanism Francisella utilizes to persist in the environment and in tick vectors is currently unknown. We have demonstrated for the first time that Francisella novicida, a model organism of F. tularensis, forms a biofilm in vitro. Selected F. novicida transposon mutants were tested for their ability to form biofilm compared to the wildtype F. novicida strain. Mutation of the putative qseB gene led to an impairment in the ability to form biofilm with no impairment in bacterial growth. A qseC mutant had impaired growth but demonstrated a marked impairment in biofilm production. Mutation in capC affected both b... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2810310 Fri, 18 Sep 2009 23:00:00 +0100 2810310 http://www.medworm.com/index.php?rid=2804940&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%3D19760448%26dopt%3DAbstract Authors: Shade A, Chiu CY, McMahon KD Yuan Yang Lake (YYL), Taiwan, experiences both winter and typhoon-initiated mixing, and each type of mixing event is characterized by contrasting environmental conditions. Previous work suggested that after typhoon mixing, bacterial communities in YYL reset to a pioneer composition and then follow a predictable trajectory of change until the next typhoon. Our goal was to continue this investigation by observing bacterial community change after a range of mixing intensities, including seasonal winter mixing. We fingerprinted aquatic bacterial communities in the epilimnion and hypolimnion using automated ribosomal intergenic spacer analysis and then assessed community response using multivariate statistics. We found a significant linear relationship ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2804940 Thu, 17 Sep 2009 23:00:00 +0100 2804940 http://www.medworm.com/index.php?rid=2804944&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%3D19756847%26dopt%3DAbstract Authors: Beauregard MS, Hamel C, Atul-Nayyar , St-Arnaud M Soil function may be affected by cropping practices impacting the soil microbial community. The effect of different phosphorus (P) fertilization rates (0, 20, or 40 kg P(2)O(5) ha(-1)) on soil microbial diversity was studied in 8-year-old alfalfa monocultures. The hypothesis that P fertilization modifies soil microbial community was tested using denaturing gradient gel electrophoresis and phospholipids fatty acid (PLFA) profiling to describe soil bacteria, fungi, and arbuscular mycorrhizal (AM) fungi diversity. Soil parameters related to fertility (soil phosphate flux, soluble P, moisture, phosphatase and dehydrogenase assays, and carbon and nitrogen content of the light fraction of soil organic matter) were also monitored and ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2804944 Tue, 15 Sep 2009 23:00:00 +0100 2804944 http://www.medworm.com/index.php?rid=2804943&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%3D19756848%26dopt%3DAbstract Authors: Cooney TJ, Simon KS PMID: 19756848 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2804943 Tue, 15 Sep 2009 23:00:00 +0100 2804943 http://www.medworm.com/index.php?rid=2804942&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%3D19756849%26dopt%3DAbstract Authors: Ayarza JM, Guerrero LD, Erijman L The aim of this work was to investigate the dynamics of assembly of bacterial populations in activated sludge flocs. We approached this question by following the development of active bacterial populations during floc development in four replicated lab-scale activated sludge reactors, in which solid retention time (SRT) was set at 4 days. The null hypothesis was that the similarities in community composition could be accounted for by the probability that the same organisms occur in more than one replicated reactor. Microscopic imaging showed that the size of flocs in reactors with biomass retention increased during the first few days until a steady-state size was reached. The diversity and community structure of the sludge in all reactors were... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2804942 Tue, 15 Sep 2009 23:00:00 +0100 2804942 http://www.medworm.com/index.php?rid=2804941&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%3D19756850%26dopt%3DAbstract Authors: Meyer C, Gilbert D, Gaudry A, Franchi M, Nguyen-Viet H, Fabure J, Bernard N Atmospheric pollution has become a major problem for modern societies owing to its fatal effects on both human health and ecosystems. We studied the relationships of nitrogen dioxide atmospheric pollution and metal trace elements contained in atmospheric particles which were accumulated in bryophytes to microbial communities of bryophytes at three differently polluted sites in France (rural, urban, and industrial) over an 8-month period. The analysis of bryophytes showed an accumulation of Cr and Fe at the rural site; Cr, Fe, Zn, Cu, Al, and Pb at the urban site; and Fe, Cr, Pb, Al, Sr, Cu, and Zn at the industrial site. During this study, the structure of the microbial communities which is characteriz... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2804941 Tue, 15 Sep 2009 23:00:00 +0100 2804941 http://www.medworm.com/index.php?rid=2767024&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%3D19730765%26dopt%3DAbstract Authors: Han TX, Tian CF, Wang ET, Chen WX The associations among rhizobia chromosomal background, nodulation genes, legume plants, and geographical regions are very attractive but still unclear. To address this question, we analyzed the interactions among rhizobia rDNA genotypes, nodC genotypes, legume genera, as well as geographical regions in the present study. Complex relationships were observed among them, which may be the genuine nature of their associations. The statistical analyses indicate that legume plant is the key factor shaping both rhizobia genetic and symbiotic diversity. In the most cases of our results, the nodC lineages are clearly associated with rhizobial genomic species, demonstrating that nodulation genes have co-evolved with chromosomal background, though the la... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2767024 Thu, 03 Sep 2009 23:00:00 +0100 2767024 http://www.medworm.com/index.php?rid=2767023&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%3D19730766%26dopt%3DAbstract In this report, we characterized a number of environmental isolates of M. luteus, including several recovered from amber. There was substantial variation in the predicted rpf gene product. While the lysozyme-like and LysM domains showed little variation, the linker region was elongated from ten amino acid residues in the laboratory strains to as many as 120 residues in one isolate. The genes encoding these Rpf proteins have been characterized, and a possible role for the Rpf linker in environmental adaptation is proposed. The environmental isolates show enhanced resistance to lysozyme as compared with the laboratory strains and this correlates with increased peptidoglycan acetylation. In strains that make a protein with an elongated linker, Rpf was bound to the cell wall, rather than being... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2767023 Wed, 02 Sep 2009 23:00:00 +0100 2767023 http://www.medworm.com/index.php?rid=2767027&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%3D19727928%26dopt%3DAbstract Authors: Inoue K, Kabeya H, Kosoy MY, Bai Y, Smirnov G, McColl D, Artsob H, Maruyama S PMID: 19727928 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2767027 Tue, 01 Sep 2009 23:00:00 +0100 2767027 http://www.medworm.com/index.php?rid=2767026&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%3D19727929%26dopt%3DAbstract Authors: Grimes DJ, Johnson CN, Dillon KS, Flowers AR, Noriea NF, Berutti T To date, the genomes of eight Vibrio strains representing six species and three human pathogens have been fully sequenced and reported. This review compares genomic information revealed from these sequencing efforts and what we can infer about Vibrio biology and ecology from this and related genomic information. The focus of the review is on those attributes that allow the Vibrios to survive and even proliferate in their ocean habitats, which include seawater, plankton, invertebrates, fish, marine mammals, plants, man-made structures (surfaces), and particulate matter. Areas covered include general information about the eight genomes, each of which is distributed over two chromosomes; a discussion of expected a... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2767026 Tue, 01 Sep 2009 23:00:00 +0100 2767026 http://www.medworm.com/index.php?rid=2767025&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%3D19727930%26dopt%3DAbstract Authors: Lin YT, Huang YJ, Tang SL, Whitman WB, Coleman DC, Chiu CY The diversity and composition of soil bacterial communities in three topographic sites (summit, foot slope, and lakeshore) from subtropical montane forest ecosystem in Taiwan were examined by using 16S rRNA gene clone library analysis. This locality is temperate, perhumid, and has low soil acidity (pH < 4), which is an uncommon ecosystem in a monsoonal part of Southeast Asia. A total of 481 clones were sequenced and placed into ten phylogenetic groups according to their similarities to type strains of described organisms. Toposequence of the transect was investigated from summit to foot slope and at the lakeshore. More than 86% of the clones were affiliated with members of the Proteobacteria, Acidobacteria, and Acti... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2767025 Tue, 01 Sep 2009 23:00:00 +0100 2767025 http://www.medworm.com/index.php?rid=2735233&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%3D19705193%26dopt%3DAbstract Authors: Ikenaga M, Guevara R, Dean AL, Pisani C, Boyer JN Community structure of sediment bacteria in the Everglades freshwater marsh, fringing mangrove forest, and Florida Bay seagrass meadows were described based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) patterns of 16S rRNA gene fragments and by sequencing analysis of DGGE bands. The DGGE patterns were correlated with the environmental variables by means of canonical correspondence analysis. There was no significant trend in the Shannon-Weiner index among the sediment samples along the salinity gradient. However, cluster analysis based on DGGE patterns revealed that the bacterial community structure differed according to sites. Not only were these salinity/vegetation regions distinct but the se... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2735233 Tue, 25 Aug 2009 23:00:00 +0100 2735233 http://www.medworm.com/index.php?rid=2735235&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%3D19705191%26dopt%3DAbstract Authors: Charpy L, Palinska KA, Casareto B, Langlade MJ, Suzuki Y, Abed RM, Golubic S Dinitrogen-fixing organisms in cyanobacterial mats were studied in two shallow coral reef ecosystems: La Reunion Island, southwestern Indian Ocean, Sesoko (Okinawa) Island, and northwestern Pacific Ocean. Rapidly expanding benthic miniblooms, frequently dominated by a single cyanobacterial taxon, were identified by microscopy and molecular tools. In addition, nitrogenase activity by these blooms was measured in situ. Dinitrogen fixation and its contribution to mat primary production were calculated using (15)N(2) and (13)C methods. Dinitrogen-fixing cyanobacteria from mats in La Reunion and Sesoko showed few differences in taxonomic composition. Anabaena sp. among heterocystous and Hydrocoleum majus a... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2735235 Mon, 24 Aug 2009 23:00:00 +0100 2735235 http://www.medworm.com/index.php?rid=2735234&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%3D19705192%26dopt%3DAbstract Authors: Thomson BC, Ostle N, McNamara N, Bailey MJ, Whiteley AS, Griffiths RI Plant-derived organic matter inputs are thought to be a key driver of soil bacterial community composition and associated soil processes. We sought to investigate the role of acid grassland vegetation on soil bacterial community structure by assessing bacterial diversity in combination with other soil variables in temporally and spatially distinct samples taken from a field-based plant removal experiment. Removal of aboveground vegetation resulted in reproducible differences in soil properties, soil respiration and bacterial diversity. Vegetated soils had significantly increased carbon and nitrogen concentrations and exhibited higher rates of respiration. Molecular analyses revealed that the soils were broad... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2735234 Mon, 24 Aug 2009 23:00:00 +0100 2735234 http://www.medworm.com/index.php?rid=2725381&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%3D19697077%26dopt%3DAbstract Authors: Wilson MK, Lane AB, Law BF, Miller WG, Joens LA, Konkel ME, White BA Campylobacter jejuni is one of the leading bacterial causes of food-borne illness in the USA. Molecular typing methods are often used in food safety for identifying sources of infection and pathways of transmission. Moreover, the identification of genetically related isolates (i.e., clades) may facilitate the development of intervention strategies for control and prevention of food-borne diseases. We analyzed the pan genome (i.e., core and variable genes) of 63 C. jejuni isolates recovered from chickens raised in conventional, organic, and free-range poultry flocks to gain insight into the genetic diversity of C. jejuni isolates recovered from different environments. We assessed the discriminatory power of th... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2725381 Thu, 20 Aug 2009 23:00:00 +0100 2725381 http://www.medworm.com/index.php?rid=2692054&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%3D19669828%26dopt%3DAbstract Authors: Berrada ZL, Telford SR We determined whether Francisella spp. are present in water, sediment, and soil from an active tularemia natural focus on Martha's Vineyard, Massachusetts, during a multiyear outbreak of pneumonic tularemia. Environmental samples were tested by polymerase chain reaction (PCR) targeting Francisella species 16S rRNA gene and succinate dehydrogenase A (sdhA) sequences; evidence of the agent of tularemia was sought by amplification of Francisella tularensis-specific sequences for the insertion element ISFTu2, 17-kDa protein gene tul4, and the 43-kDa outer membrane protein gene fopA. Evidence of F. tularensis subsp. tularensis, the causative agent of the human infections in this outbreak, was not detected from environmental samples despite its active transmis... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2692054 Tue, 11 Aug 2009 23:00:00 +0100 2692054 http://www.medworm.com/index.php?rid=2692055&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%3D19669227%26dopt%3DAbstract Authors: Li CH, Zhao MW, Tang CM, Li SP The antagonistic potentials of endophytic bacteria isolated from the roots of six cotton cultivars at different developmental stages were determined in vitro toward three pathogens: Verticillium dahliae Kleb V107 and V396 and Fusarium oxysporum f.sp. vasinfectum (F108). The populations of antagonistic endophytic bacteria (AEB) toward V107, V396, and F108 at the flowering and maturation stages were significantly higher than those at the seedling stage were. More AEB were found to be antagonistic toward pathogens V396 and F108 than V107. Results from the multivariate analysis of variance showed that the populations of AEB were significantly different for the main factors of cultivars, stages, and their interactions. Based on 16S rDNA sequence analy... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2692055 Fri, 07 Aug 2009 23:00:00 +0100 2692055 http://www.medworm.com/index.php?rid=2682534&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%3D19662454%26dopt%3DAbstract Authors: Ikeda S, Kaneko T, Okubo T, Rallos LE, Eda S, Mitsui H, Sato S, Nakamura Y, Tabata S, Minamisawa K A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacter... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2682534 Thu, 06 Aug 2009 23:00:00 +0100 2682534 http://www.medworm.com/index.php?rid=2675333&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%3D19655080%26dopt%3DAbstract Authors: Chan YF, Tsai AY, Chiang KP, Hsieh CH We investigated seasonal variation of grazing impact of the pigmented nanoflagellates (PNF) with different sizes upon Synechococcus in the subtropical western Pacific coastal waters using grazing experiments with fluorescently labeled Synechococcus (FLS). For total PNF, conspicuous seasonal variations of ingestion rates on Synechococcus were found, and a functional response was observed. To further investigate the impact of different size groups, we separated the PNF into four categories (<3, 3-5, 5-10, and >10 mum). Our results indicated that the smallest PNF (<3 mum PNF) did not ingest FLS and was considered autotrophic. PNF of 3-5 mum in size made up most of the PNF community; however, their ingestion on Synechococcus was too l... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2675333 Tue, 04 Aug 2009 23:00:00 +0100 2675333 http://www.medworm.com/index.php?rid=2661008&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%3D19641948%26dopt%3DAbstract Authors: Ponnusamy L, Wesson DM, Arellano C, Schal C, Apperson CS In the container habitats of immature mosquitoes, catabolism of plant matter and other organic detritus by microbial organisms produces metabolites that mediate the oviposition behavior of Aedes aegypti and Aedes albopictus. Public health agencies commonly use oviposition traps containing plant infusions for monitoring populations of these mosquito species, which are global vectors of dengue viruses. In laboratory experiments, gravid females exhibited significantly diminished responses to experimental infusions made with sterilized white oak leaves, showing that attractive odorants were produced through microbial metabolic activity. We evaluated effects of infusion concentration and fermentation time on attraction of gra... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2661008 Wed, 29 Jul 2009 23:00:00 +0100 2661008 http://www.medworm.com/index.php?rid=2646149&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%3D19633806%26dopt%3DAbstract Authors: Santos A, Cerrada A, García S, San Andrés M, Abrusci C, Marquina D This paper uses molecular techniques to describe the microstructure and microbiological communities of sixteenth century artwork and their relationships. The microbiological populations, analysed by denaturing gradient gel electrophoresis (DGGE), were highly influenced by the chemical composition of the pictorial layers detected by energy-dispersive X-ray analysis. DGGE revealed that the diversity of microbial communities was lower in pictorial layers composed of pigments with metals, such as Pb, Cu and Hg, than in those found in pictorial layers without such compounds. The number of cultivable microorganisms, mainly fungi and bacteria, was very low in comparison to those found by DGGE, revealing the ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2646149 Fri, 24 Jul 2009 23:00:00 +0100 2646149 http://www.medworm.com/index.php?rid=2646148&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%3D19633807%26dopt%3DAbstract Authors: Thomas P, Soly TA A cultivation-based assessment of endophytic bacteria present in deep-seated shoot tips of banana suckers was made with a view to generate information on the associated organisms, potential endophytic contaminants in tissue-cultured bananas and to assess if the endophytes shared a beneficial relationship with the host. Plating the tissue homogenate from the central core of suckers showed colony growth on nutrient agar from just 75% and 42% of the 12 stocks during May and November, respectively (average 58%; 6 x 10(3) colony-forming units per gram), yielding diverse organisms belonging to firmicutes (Bacillus, Brevibacillus, Paenibacillus, Virgibacillus, Staphylococcus spp.), actinobacteria (Cellulomonas, Micrococcus, Corynebacterium, Kocuria spp.), alpha-prot... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2646148 Fri, 24 Jul 2009 23:00:00 +0100 2646148 http://www.medworm.com/index.php?rid=2640305&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%3D19629577%26dopt%3DAbstract Authors: Pascoal C, Cássio F, Nikolcheva L, Bärlocher F Freshwaters include some of the most impaired systems on Earth with high rates of species loss, underscoring the significance of investigating whether ecosystems with fewer species will be able to maintain ecological processes. The environmental context is expected to modulate the effects of declining diversity. We conducted microcosm experiments manipulating fungal inoculum diversity and zinc concentration to test the hypothesis that fungal diversity determines the susceptibility of leaf litter decomposition to Zn stress. Realized fungal diversity was estimated by counting released spores and by measuring species-specific biomasses via denaturing gradient gel electrophoresis. In the absence of Zn, positive diversity eff... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2640305 Thu, 23 Jul 2009 23:00:00 +0100 2640305 http://www.medworm.com/index.php?rid=2640306&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%3D19626265%26dopt%3DAbstract Authors: Gamble MD, Bagwell CE, Larocque J, Bergholz PW, Lovell CR Nitrogen fixation is the primary N source in the highly productive but N-limited North Inlet, SC, USA salt marsh system. The diverse assemblages of nitrogen-fixing (diazotrophic) bacteria associated with the rhizospheres of the short and tall growth forms of Spartina alterniflora were analyzed at two sites, Crab Haul Creek and Goat Island, which are in different tidal creek drainage systems in this marsh. The sites differed in proximity to the main channel for tidal intrusion and in several edaphic parameters. We hypothesized that either the differing abiotic environmental regimes of the two sites or the variation due to seasonal effects result in differences in the diazotroph assemblage. Rhizosphere samples were collec... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2640306 Tue, 21 Jul 2009 23:00:00 +0100 2640306 http://www.medworm.com/index.php?rid=2640304&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%3D19629578%26dopt%3DAbstract Authors: Edmonds JW, Weston NB, Joye SB, Mou X, Moran MA Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical chan... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2640304 Tue, 21 Jul 2009 23:00:00 +0100 2640304 http://www.medworm.com/index.php?rid=2627531&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%3D19618099%26dopt%3DAbstract Authors: Muthukumarasamy R, Revathi G PMID: 19618099 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2627531 Fri, 17 Jul 2009 23:00:00 +0100 2627531 http://www.medworm.com/index.php?rid=2615568&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%3D19609598%26dopt%3DAbstract Authors: Coppotelli BM, Ibarrolaza A, Dias RL, Del Panno MT, Berthe-Corti L, Morelli IS The present study describes the phenanthrene-degrading activity of Sphingomonas paucimobilis 20006FA and its ability to promote the bioavailability of phenanthrene. S. paucimobilis 20006FA was isolated from a phenanthrene-contaminated soil microcosm. The strain was able to grow in liquid mineral medium saturated with phenanthrene as the sole carbon source, showing high phenanthrene elimination (52.9% of the supplied phenanthrene within 20 days). The accumulation of 1-hydroxy-2-naphthoic acid and salicylic acid as major phenanthrene metabolites and the capacity of the strain to grow with sodium salicylate as the sole source of carbon and energy indicated that the S. paucimobilis 20006FA possesses a c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2615568 Thu, 16 Jul 2009 23:00:00 +0100 2615568 http://www.medworm.com/index.php?rid=2615567&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%3D19609599%26dopt%3DAbstract Authors: Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE, PMID: 19609599 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2615567 Thu, 16 Jul 2009 23:00:00 +0100 2615567 http://www.medworm.com/index.php?rid=2603031&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%3D19597862%26dopt%3DAbstract Authors: Kaszab E, Kriszt B, Atzél B, Szabó G, Szabó I, Harkai P, Szoboszlay S The main aim of this paper was the comprehensive estimation of the occurrence rate and the antibiotic-resistance conditions of opportunistic pathogen Pseudomonas aeruginosa in hydrocarbon-contaminated environments. From 2002 to 2007, 26 hydrocarbon-contaminated sites of Hungary were screened for the detection of environmental isolates. Altogether, 156 samples were collected and examined for the determination of appearance, representative cell counts, and antibiotic-resistance features of P. aeruginosa. The detected levels of minimal inhibitory concentrations of ten different drugs against 36 environmental strains were compared to the results of a widely used reference strain ATCC 27853 and fou... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2603031 Mon, 13 Jul 2009 23:00:00 +0100 2603031 http://www.medworm.com/index.php?rid=2603032&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%3D19593555%26dopt%3DAbstract Authors: Angel R, Asaf L, Ronen Z, Nejidat A Levels of inorganic nitrogen species (ammonia, nitrite, and nitrate), ammonia oxidation potential (AOP), and diversity of ammonia-oxidizing bacteria (AOB) were studied in the sediments of a 50-km-long segment of an ephemeral stream in the Negev desert, receiving untreated wastewater. Water analysis in downstream sampling points showed reductions of 91.7% in biological oxygen demand, 87.7% in chemical oxygen demand, 73.9% in total nitrogen, and 72.8% in total ammonia nitrogen. Significant AOP levels in the sediment were detected mainly in the fall and spring seasons. Denaturing gradient gel electrophoresis of AOB 16S rRNA gene fragments showed that in most sampling points, the streambed was dominated by Nitrosospira cluster 3 strains similar ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2603032 Fri, 10 Jul 2009 23:00:00 +0100 2603032 http://www.medworm.com/index.php?rid=2592235&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%3D19590809%26dopt%3DAbstract This study emphasizes the diverse and unique abilities of actinomycetes inhabiting rock surfaces which could be of potential biotechnological applications, such as in the bioremediation of metal-contaminated environments and metal biorecovery. PMID: 19590809 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2592235 Thu, 09 Jul 2009 23:00:00 +0100 2592235 http://www.medworm.com/index.php?rid=2592236&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%3D19588186%26dopt%3DAbstract Authors: Gerçe B, Schwartz T, Voigt M, Rühle S, Kirchen S, Putz A, Proksch P, Obst U, Syldatk C, Hausmann R The aim of this study was to analyze successional changes in the bacterial community over a period of 6 months of cultivation of Aplysina aerophoba sponges under different artificial cultivation conditions by use of denaturing gradient gel electrophoresis (DGGE). The cultivation conditions varied concerning the water temperature (20 +/- 2 degrees C and 25 +/- 2 degrees C) of the aquaria, additional illumination of one aquarium, and feeding of the sponges. Amplicons from DGGE separation of dominant colonizing or variably appearing bacteria were sequenced and aligned for taxonomical identification. In addition, secondary metabolites typically found in A. aerophoba were an... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2592236 Wed, 08 Jul 2009 23:00:00 +0100 2592236 http://www.medworm.com/index.php?rid=2580688&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%3D19582501%26dopt%3DAbstract Authors: Odić D, Budič B, Mandić-Mulec I, Stopar D All physico-chemical parameters that affect bacterial growth rate will also affect bacterial molecular composition, which in turn influences the chemical composition of bacterial lysate and its turnover rate in the ecosystem. To produce qualitatively different lysates, Vibrio sp. cells were grown under different pH, salt, or temperature conditions in rich growth media and then washed and lysed by autoclaving. Both the absolute concentrations and the ratios between elements in the lysates varied with different growth conditions, implying differences in lysate quality. Either Pseudoalteromonas sp. or Vibrio sp. was grown on the lysates at non-limiting lysate concentrations. Different lysates supported growth rates of Ps... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2580688 Mon, 06 Jul 2009 23:00:00 +0100 2580688 http://www.medworm.com/index.php?rid=2573390&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%3D19572164%26dopt%3DAbstract Authors: Li M, Yang H, Gu JD The phylogenetic diversity and axial distribution of microorganisms in three sections of the gastrointestinal tracts of the polychaete Neanthes glandicincta was evaluated using both most probable number method and cloning analyses of 16S rRNA genes in this study. Quantification of the density of microorganisms in the gut showed that aerobic microorganisms decreased from anterior to posterior, while anaerobic ones showed a reverse trend. The total numbers of microorganisms decreased significantly (p < 0.05, analysis of variance) but more rapidly from the anterior to the middle segment. Phylogenetic analysis showed that the dominating phylogenetic groups included Methanomicrobiales I: Methanosaetaceae (up to 66% of archaeal clones), delta-Proteobacteria (u... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2573390 Wed, 01 Jul 2009 23:00:00 +0100 2573390 http://www.medworm.com/index.php?rid=2474016&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%3D19381712%26dopt%3DAbstract Authors: O'Neill B, Grossman J, Tsai MT, Gomes JE, Lehmann J, Peterson J, Neves E, Thies JE Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared fro... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474016 Sun, 14 Jun 2009 07:08:51 +0100 2474016 http://www.medworm.com/index.php?rid=2473965&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%3D19517158%26dopt%3DAbstract In this study, we investigated the role of biotic interactions (e.g., competition, facilitation) in fungal endophyte community assembly by examining endophyte species co-occurrences within communities using null models. We used recombinant inbred lines (genotypes) of maize (Zea mays) to examine community assembly at multiple habitat levels, at the individual plant and host genotype levels. Both culture-dependent and culture-independent approaches were used to assess endophyte communities. Communities were analyzed using the complete fungal operational taxonomic unit (OTU) dataset or only the dominant (most abundant) OTUs in order to ascertain whether species co-occurrences were different for dominant members compared to when all members were included. In the culture-dependent approach, we ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473965 Fri, 12 Jun 2009 04:00:00 +0100 2473965 http://www.medworm.com/index.php?rid=2473967&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%3D19504148%26dopt%3DAbstract Authors: Pontes DS, Pinheiro FA, Lima-Bittencourt CI, Guedes RL, Cursino L, Barbosa F, Santos FR, Chartone-Souza E, Nascimento AM The aim of this study was to evaluate the resistance to ten antimicrobial agents and the presence of bla ( TEM1 ) gene of Gram-negative bacteria isolated from three natural oligotrophic lakes with varying degrees of anthropogenic influence. A total of 272 indigenous bacteria were recovered on eosin methylene blue medium; they were characterized for antimicrobial resistance and identified taxonomically by homology search and phylogenetic comparisons. Based on 16S ribosomal RNA sequences analysis, 97% of the isolates were found to be Gram-negative bacteria; they belonged to 11 different genera. Members of the genera Acinetobacter, Enterobacter, and Pseudomonas... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473967 Sat, 06 Jun 2009 04:00:00 +0100 2473967 http://www.medworm.com/index.php?rid=2473974&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%3D19495853%26dopt%3DAbstract Authors: Alguacil MD, Kohler J, Caravaca F, Roldán A Arbuscular mycorrhizal (AM) symbiosis and plant-growth-promoting rhizobacterium (PGPR) can alleviate the effects of water stress in plants, but it is unknown whether these benefits can be maintained at elevated CO(2). Therefore, we carried out a study where seedlings of Lactuca sativa were inoculated with the AM fungus (AMF) Glomus intraradices N.C. Schenk & G.S. Sm. or the PGPR Pseudomonas mendocina Palleroni and subjected to two levels of watering and two levels of atmospheric CO(2) to ascertain their effects on plant physiological parameters and gene expression of one PIP aquaporin in roots. The inoculation with PGPR produced the greatest growth in lettuce plants under all assayed treatments as well as the highest foliar ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473974 Thu, 04 Jun 2009 04:00:00 +0100 2473974 http://www.medworm.com/index.php?rid=2473971&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%3D19495854%26dopt%3DAbstract Authors: Poll C, Brune T, Begerow D, Kandeler E Transport of litter carbon in the detritusphere might determine fungal abundance and diversity at the small scale. Rye residues were applied to the surface of soil cores with two different water contents and incubated at 10 degrees C for 2 and 12 weeks. Fungal community structure was analysed by constructing clone libraries of 18S rDNA and subsequent sequencing. Litter addition induced fungal succession in the adjacent soil and decreased detectable fungal diversity mainly due to the huge supply of substrates. Ergosterol content and N-acetyl-glucosaminidase activity indicated fungal growth after 2 weeks. Simultaneously, the structure of the fungal community changed, with Mortierellaceae proliferating during the initial phase of litter deco... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473971 Thu, 04 Jun 2009 04:00:00 +0100 2473971 http://www.medworm.com/index.php?rid=2473969&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%3D19495855%26dopt%3DAbstract Authors: Ordoñez OF, Flores MR, Dib JR, Paz A, Farías ME A total of 88 bacterial strains were isolated from six Andean lakes situated at altitudes ranging from 3,400 to 4,600 m above sea level: L. Aparejos (4,200 m), L. Negra (4,400 m), L. Verde (4,460 m), L. Azul (4,400 m), L. Vilama (4,600 m), and Salina Grande (3,400 m). Salinity ranged from 0.4 to 117 ppm. General diversity was determined by denaturing gradient gel electrophoresis (DGGE) analysis. From the excised DGGE bands, 182 bacterial sequences of good quality were obtained. Gammaproteobacteria and Cytophaga/Flavobacterium/Bacteroides (CFB) were the most abundant phylogenetic groups with 42% and 18% of identified bands, respectively. The isolated strains were identified by sequence analysis. Isolated bacteria were su... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473969 Thu, 04 Jun 2009 04:00:00 +0100 2473969 http://www.medworm.com/index.php?rid=2473977&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%3D19479305%26dopt%3DAbstract Authors: Langhans TM, Storm C, Schwabe A In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 x 18 plots, each 20 x 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473977 Sat, 30 May 2009 04:00:00 +0100 2473977 http://www.medworm.com/index.php?rid=2473979&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%3D19479304%26dopt%3DAbstract Authors: Mengoni A, Pini F, Huang LN, Shu WS, Bazzicalupo M Bacteria associated with tissues of metal-hyperaccumulating plants are of great interest due to the multiple roles they may play with respect to plant growth and resistance to heavy metals. The variability of bacterial communities associated with plant tissues of three populations of Alyssum bertolonii, a Ni hyperaccumulator endemic of serpentine outcrops of Central Italy, was investigated. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes was applied to DNA extracted from leaf tissues of 30 individual plants from three geographically separated serpentine outcrops. Moreover, T-RFLP fingerprinting was also performed on DNA extracted from the same soils from which the plants were col... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473979 Fri, 29 May 2009 04:00:00 +0100 2473979 http://www.medworm.com/index.php?rid=2473986&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%3D19475444%26dopt%3DAbstract This study presents a depth-related survey of virioplankton abundance in Lake Pavin (Massif Central, France), in relation to the abundances of heterotrophic prokaryotes, picocyanobacteria (Pcy), autotrophic picoeukaryotes (Peu), and of autotrophic (ANF) and heterotrophic (HNF) nanoflagellates. The sampling strategy was designed to be representative of the physico-chemical gradients of the whole water column of the lake, and the seasonal variability as well. In mixolimnic surface waters, all communities were present and viral abundance peaked in summer and autumn. Viral abundance was significantly correlated (p < 0.001) with Pcy, Peu, and ANF, indicating that cyanophages and perhaps other phytoplankton viruses represent a significant pool of viral standing stocks in the mixolimnion of La... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473986 Thu, 28 May 2009 04:00:00 +0100 2473986 http://www.medworm.com/index.php?rid=2473984&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%3D19475445%26dopt%3DAbstract Authors: Akhtar M, Hirt H, Zurek L The house fly (Musca domestica L.) alimentary canal was evaluated for the potential of horizontal transfer of tetM on plasmid pCF10 among Enterococcus faecalis. Two sets of experiments were conducted: (1) house flies without surface sterilization and (2) surface-sterilized flies. Both sets of flies were exposed to E. faecalis OG1RF:pCF10 as donor for 12 h and then E. faecalis OG1SSp as recipient for 1 h. Another group of flies received the recipient first for 12 h followed by exposure to the donor strain for 1 h. House flies were screened daily to determine the donor, recipient, and transconjugant bacterial load for up to 5 days. In addition, the sponge-like mouth parts used for food uptake (labellum) of surface-sterilized house flies were removed and... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473984 Thu, 28 May 2009 04:00:00 +0100 2473984 http://www.medworm.com/index.php?rid=2473981&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%3D19475446%26dopt%3DAbstract Authors: Fontes ML, Abreu PC PMID: 19475446 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473981 Thu, 28 May 2009 04:00:00 +0100 2473981 http://www.medworm.com/index.php?rid=2473988&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%3D19471996%26dopt%3DAbstract Authors: Sipkema D, Holmes B, Nichols SA, Blanch HW We have characterised the northern Pacific undescribed sponge Haliclona (?gellius) sp. based on rDNA of the sponge and its associated microorganisms. The sponge is closely related to Amphimedon queenslandica from the Great Barrier Reef as the near-complete 18S rDNA sequences of both sponges were identical. The microbial fingerprint of three specimens harvested at different times and of a transplanted specimen was compared to identify stably associated microorganisms. Most bacterial phyla were detected in each sample, but only a few bacterial species were determined to be stably associated with the sponge. A sponge-specific beta- and gamma-Proteobacterium were abundant clones and both of them were present in three of the four specimens... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473988 Wed, 27 May 2009 04:00:00 +0100 2473988 http://www.medworm.com/index.php?rid=2473992&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%3D19468700%26dopt%3DAbstract Authors: Alexandre A, Brígido C, Laranjo M, Rodrigues S, Oliveira S Several Mesorhizobium species are able to induce effective nodules in chickpea, one of the most important legumes worldwide. Our aims were to examine the biogeography of chickpea rhizobia, to search for a predominant species, and to identify the most efficient microsymbiont, considering Portugal as a case study. One hundred and ten isolates were obtained from continental Portugal and Madeira Island. The 16S ribosomal RNA gene phylogeny revealed that isolates are highly diverse, grouping with most Mesorhizobium type strains, in four main clusters (A-D). Interestingly, only 33% of the isolates grouped with Mesorhizobium ciceri (cluster B) or Mesorhizobium mediterraneum (cluster D), the formerly described specific ch... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473992 Tue, 26 May 2009 04:00:00 +0100 2473992 http://www.medworm.com/index.php?rid=2473996&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%3D19466478%26dopt%3DAbstract The objectives of this greenhouse study with tomato were to determine (1) if reduced rates of inorganic fertilizer coupled with microbial inoculants will produce plant growth, yield, and nutrient uptake levels equivalent to those with full rates of the fertilizer and (2) the minimum level to which fertilizer could be reduced when inoculants were used. The microbial inoculants used in the study were a mixture of plant growth-promoting rhizobacteria (PGPR) strains Bacillus amyloliquefaciens IN937a and Bacillus pumilus T4, a formulated PGPR product, and the arbuscular mycorrhiza fungus (AMF), Glomus intraradices. Results showed that supplementing 75% of the recommended fertilizer rate with inoculants produced plant growth, yield, and nutrient (nitrogen and phosphorus) uptake that were statist... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473996 Sat, 23 May 2009 04:00:00 +0100 2473996 http://www.medworm.com/index.php?rid=2473994&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%3D19466479%26dopt%3DAbstract This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473994 Sat, 23 May 2009 04:00:00 +0100 2473994 http://www.medworm.com/index.php?rid=2473998&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%3D19462196%26dopt%3DAbstract Authors: Lowell JL, Gordon N, Engstrom D, Stanford JA, Holben WE, Gannon JE The Nyack floodplain is located on the Middle Fork of the Flathead River, an unregulated, pristine, fifth-order stream in Montana, USA, bordering Glacier National Park. The hyporheic zone is a nutritionally heterogeneous floodplain component harboring a diverse array of microbial assemblages essential in fluvial biogeochemical cycling, riverine ecosystem productivity, and trophic interactions. Despite these functions, microbial community structure in pristine hyporheic systems is not well characterized. The current study was designed to assess whether physical habitat heterogeneity within the hyporheic zone of the Nyack floodplain was sufficient to drive bacterial beta diversity between three different hyporhei... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473998 Fri, 22 May 2009 04:00:00 +0100 2473998 http://www.medworm.com/index.php?rid=2474000&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%3D19452199%26dopt%3DAbstract Authors: Baschien C, Rode G, Böckelmann U, Götz P, Szewzyk U We investigated microbial interactions of aquatic bacteria associated with hyphae (the hyphosphere) of freshwater fungi on leaf litter. Bacteria were isolated directly from the hyphae of fungi from sedimented leaves of a small stream in the National Park "Lower Oder," Germany. To investigate interactions, bacteria and fungi were pairwise co-cultivated on leaf-extract medium and in microcosms loaded with leaves. The performance of fungi and bacteria was monitored by measuring growth, enzyme production, and respiration of mono- and co-cultures. Growth inhibition of the fungus Cladosporium herbarum by Ralstonia pickettii was detected on leaf extract agar plates. In microcosms, the presence of Chryseobacterium sp. lower... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474000 Tue, 19 May 2009 04:00:00 +0100 2474000 http://www.medworm.com/index.php?rid=2474006&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%3D19444496%26dopt%3DAbstract Authors: Wu QL, Chatzinotas A, Wang J, Boenigk J Eukaryotic plankton assemblages in 11 high-mountain lakes located at altitudes of 2,817 to 5,134 m and over a total area of ca. one million square kilometers on the Eastern Tibet Plateau, spanning a salinity gradient from 0.2 (freshwater) to 187.1 g l(-1) (hypersaline), were investigated by cultivation independent methods. Two 18S rRNA gene-based fingerprint approaches, i.e., the terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing were applied. Samples of the same lake type (e.g., freshwater) generally shared more of the same bands or T-RFs than samples of different types (e.g., freshwater versus saline). However, a certain number of bands or T-RFs among the... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474006 Sat, 16 May 2009 04:00:00 +0100 2474006 http://www.medworm.com/index.php?rid=2474004&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%3D19444497%26dopt%3DAbstract Authors: Cooney TJ, Simon KS Microbial films play a central role in mediating energy flux in groundwater ecosystems. The activity of these microbes is likely to be influenced by the availability of resources, especially dissolved organic matter (DOM), and also by consumers, such as invertebrates that feed on microbial films. We used microcosm experiments to examine how bacterial production and extracellular enzyme activity on rocks and fine sediments from cave streams responded to amendments of DOM of varying form and to cave amphipods (Gammarus minus) that feed on microbial films. Glucose and mixtures of DOM extracted from soils and leaves stimulated bacterial production on rocks by 89-166% relative to unamended controls. In contrast, tannic acid amendment did not influence production... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474004 Fri, 15 May 2009 04:00:00 +0100 2474004 http://www.medworm.com/index.php?rid=2474008&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%3D19440648%26dopt%3DAbstract Authors: Spyrou IM, Karpouzas DG, Menkissoglu-Spiroudi U The effects of synthetic pesticides on the soil microbial community have been thoroughly investigated in the past mostly by culture-dependent methods and only few recent studies have used culture-independent approaches for this purpose. However, it should be noted that most of these studies have been conducted in microcosms where the soil microbial community is exposed to unrealistic concentrations of the pesticides, providing an unrealistic exposure scheme for soil microorganism. On the other hand, little is known regarding the potential impact of botanical pesticides on the soil microbial community. Therefore, a laboratory study and a field study were conducted to investigate the effects of synthetic (metham sodium [MS], sodium... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474008 Thu, 14 May 2009 04:00:00 +0100 2474008 http://www.medworm.com/index.php?rid=2474002&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%3D19444498%26dopt%3DAbstract Authors: Persson Y, Vasaitis R, Långström B, Ohrn P, Ihrmark K, Stenlid J The bark beetle Ips typographus has different hibernation environments, under the bark of standing trees or in the forest litter, which is likely to affect the beetle-associated fungal flora. We isolated fungi from beetles, standing I. typographus-attacked trees, and forest litter below the attacked trees. Fungal identification was done using cultural and molecular methods. The results of the two methods in detecting fungal species were compared. Fungal communities associated with I. typographus differed considerably depending on the hibernation environment. In addition to seven taxa of known ophiostomoid I. typographus-associated fungi, we detected 18 ascomycetes and anamorphic fungi, five wood-decayin... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474002 Tue, 12 May 2009 04:00:00 +0100 2474002 http://www.medworm.com/index.php?rid=2473990&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%3D19468701%26dopt%3DAbstract The objective of this study was to investigate the regrowth potential of Salmonella spp., Escherichia coli O157:H7, and Listeria monocytogenes in dairy-based composts under different environmental conditions. Water extract of commercially available dairy compost was used as a model system. Cocktails of five rifampin-resistant strains of each pathogen previously grown in reduced nutrient media (1/2 or 1/10 strength of tryptic soy broth, TSB) were inoculated into water extract of compost of different ratios (1:2,1:5, and 1:10, w/v), and then stored at 35 degrees C or 22 degrees C for 7 days. The strains exhibiting greatest survival or regrowth were identified by pulsed-field gel electrophoresis (PFGE). At 22 degrees C, both E. coli O157:H7 and L. monocytogenes multiplied in all compost extra... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2473990 Tue, 12 May 2009 04:00:00 +0100 2473990 http://www.medworm.com/index.php?rid=2474012&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%3D19418091%26dopt%3DAbstract Authors: Azúa-Bustos A, González-Silva C, Mancilla RA, Salas L, Palma RE, Wynne JJ, McKay CP, Vicuña R PMID: 19418091 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474012 Thu, 07 May 2009 04:00:00 +0100 2474012 http://www.medworm.com/index.php?rid=2474010&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%3D19418092%26dopt%3DAbstract Authors: Ki JS, Zhang R, Zhang W, Huang YL, Qian PY In the present study, we sequenced the RNA polymerase beta subunit (rpoB) gene of marine Vibrio species and assessed its discriminative power in identifying vibrios. Both the rpoB and 16S rRNA sequences of 29 phenotypically different Vibrio strains isolated from coastal waters were determined. Molecular and phylogenetic comparisons of the sequences of these two genes classified the 29 strains into 11 different species. The resolution of the Vibrio spp. on the rpoB phylogenetic tree was approximately three times greater than that on the 16S rRNA phylogenetic tree. Moreover, by comparing the rpoB sequences of 98 marine gamma-Proteobacteria, including 38 marine Vibrio species, Vibrio-specific primers were developed to amplify a 730-bp fr... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474010 Thu, 07 May 2009 04:00:00 +0100 2474010 http://www.medworm.com/index.php?rid=2474014&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%3D19387721%26dopt%3DAbstract Authors: Trifonova R, Postma J, Schilder MT, van Elsas JD The quality of torrefied grass fibers (TGF) as a new potting soil ingredient was tested in a greenhouse experiment. TGF was colonized with previously selected microorganisms. Four colonization treatments were compared: (1) no inoculants, (2) the fungus Coniochaeta ligniaria F/TGF15 alone, (3) the fungus followed by inoculation with two selected bacteria, and (4) the fungus with seven selected bacteria. Cultivation-based and DNA-based methods, i.e., PCR-DGGE and BOX-PCR, were applied to assess the bacterial and fungal communities established in the TGF. Although colonization was not performed under sterile conditions, all inoculated strains were recovered from TGF up to 26 days incubation. Stable fungal and bacterial populations ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474014 Thu, 23 Apr 2009 04:00:00 +0100 2474014 http://www.medworm.com/index.php?rid=2474019&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%3D19367430%26dopt%3DAbstract Authors: Männistö MK, Tiirola M, Häggblom MM The effect of freeze-thaw (FT) cycles on Arctic tundra soil bacterial community was studied in laboratory microcosms. FT-induced changes to the bacterial community were followed over a 60-day period by terminal restriction fragment length polymorphism (T-RFLP) profiles of amplified 16S rRNA genes and reverse transcribed 16S rRNA. The main phylotypes of the active, RNA-derived bacterial community were identified using clone analysis. Non-metric multidimensional scaling ordination of the T-RFLP profiles indicated some shifts in the bacterial communities after three to five FT cycles at -2, -5, and -10 degrees C as analyzed both from the DNA and rRNA. The dominating T-RFLP peaks remained the same, however, and only slight variati... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474019 Wed, 15 Apr 2009 04:00:00 +0100 2474019 http://www.medworm.com/index.php?rid=2474022&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%3D19365668%26dopt%3DAbstract Authors: Taylor M, Ross K, Bentham R Currently, the investigation of Legionella ecology falls into two distinct areas of research activity: (1) that Legionella multiply within water sources by parasitizing amoebic or ciliate hosts or (2) that Legionella grows extracellularly within biofilms. Less focus has been given to the overlaps that may occur between these two areas or the likelihood that Legionella employs multiple survival strategies to persist in water sources. It is likely that Legionella interacts with protozoa, bacteria, algae, fungi, etc., and biofilm components in a more complex fashion than multiplication or death due to the presence or absence of single components of these complex microbial systems. This paper addresses gaps that exist in the understanding of Legionella ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474022 Tue, 14 Apr 2009 04:00:00 +0100 2474022 http://www.medworm.com/index.php?rid=2474026&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%3D19352770%26dopt%3DAbstract We examined 23 soils collected from across North America and used sequence-based analyses to compare the AOB communities in each of the distinct soils. Using 97% 16S rRNA sequence similarity groups, we identified only 24 unique AOB phylotypes across all of the soils sampled. The majority of the sequences collected were in the Nitrosospira lineages (representing 80% of all the sequences collected), and AOB belonging to Nitrosospira cluster 3 were particularly common in our clone libraries and ubiquitous across the soil types. Community composition was highly variable across the collected soils, and similar ecosystem types did not always harbor similar AOB communities. We did not find any significant correlations between AOB community composition and measures of N availability. From the suit... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474026 Wed, 08 Apr 2009 04:00:00 +0100 2474026 http://www.medworm.com/index.php?rid=2474024&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%3D19352771%26dopt%3DAbstract Authors: Long T, Or D The high degree of microbial diversity found in soils is attributed to the highly heterogeneous pore space and the dynamic aqueous microenvironments. Previous studies have shown that spatial and temporal variations in aqueous diffusion pathways play an important role in shaping microbial habitats and biological activity in unsaturated porous media. A new modeling framework was developed for the quantitative description of diffusion-dominated microbial interactions focusing on competitive growth of two microbial species inhabiting partially saturated rough surfaces. Surface heterogeneity was represented by patches with different porosities and water retention properties, yielding heterogeneous distribution of water contents that varies with changes in relative humi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474024 Wed, 08 Apr 2009 04:00:00 +0100 2474024 http://www.medworm.com/index.php?rid=2474030&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%3D19330550%26dopt%3DAbstract Authors: Mirza BS, Welsh A, Rasul G, Rieder JP, Paschke MW, Hahn D The potential role of host plant species in the selection of symbiotic, nitrogen-fixing Frankia strains belonging to the Elaeagnus host infection group was assessed in bioassays with two Morella, three Elaeagnus, and one Shepherdia species as capture plants, inoculated with soil slurries made with soil collected from a mixed pine/grassland area in central Wisconsin, USA. Comparative sequence analysis of nifH gene fragments amplified from homogenates of at least 20 individual lobes of root nodules harvested from capture plants of each species confirmed the more promiscuous character of Morella cerifera and Morella pensylvanica that formed nodules with frankiae of the Alnus and the Elaeagnus host infection groups, while f... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474030 Tue, 31 Mar 2009 04:00:00 +0100 2474030 http://www.medworm.com/index.php?rid=2474028&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%3D19330551%26dopt%3DAbstract In this study, we investigated the differences in the stability (resistance and resilience) of microbial community composition and enzyme activities in adjacent soils under either native tropical forest (FST) or in agricultural cropping use for 14 years (AGR). Mineral soil samples (0 to 5 cm) from both areas were incubated at 40 degrees C, 50 degrees C, 60 degrees C, or 70 degrees C for 15 min in order to successively reduce the microbial biomass. Three and 30 days after the heat shocks, fluorescein diacetate (FDA) hydrolysis, cellulase and laccase activities, and phospholipid-derived fatty acids-based microbial community composition were measured. Microbial biomass was reduced up to 25% in both soils 3 days after the heat shocks. The higher initial values of microbial biomass, enzyme acti... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2474028 Tue, 31 Mar 2009 04:00:00 +0100 2474028 http://www.medworm.com/index.php?rid=2297628&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%3D19322604%26dopt%3DAbstract This study investigates the microbial diversity and population changes of a single-stage sulfidogenic gas-lift bioreactor treating synthetic zinc-rich waste water at pH 5.5 by denaturing gradient gel electrophoresis of 16S rRNA gene fragments and quantitative polymerase chain reaction. The results indicate the presence of a diverse range of phylogenetic groups with the predominant microbial populations belonging to the Desulfovibrionaceae from delta-Proteobacteria. Desulfovibrio desulfuricans-like populations were the most abundant among the SRB during the three stable phases of varying sulfide and zinc concentrations and increased from 13% to 54% of the total bacterial populations over time. The second largest group was Desulfovibrio marrakechensis-like SRB that increased from 1% to about... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2297628 Fri, 27 Mar 2009 04:00:00 +0100 2297628 http://www.medworm.com/index.php?rid=2297630&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%3D19319588%26dopt%3DAbstract This study is the first to use geostatistical analyses to analyze landscape patterns of microbial activity on decomposing leaf litter and in conjunction with studies of the microbial community composition and/or substrate characteristics, should provide key insights into the function of these processes. PMID: 19319588 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2297630 Thu, 26 Mar 2009 04:00:00 +0100 2297630 http://www.medworm.com/index.php?rid=2297629&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%3D19319589%26dopt%3DAbstract Authors: Vyas P, Rahi P, Gulati A Nineteen efficient phosphate-solubilizing fluorescent Pseudomonas from the cold deserts of the trans-Himalayas were screened for stress tolerance against temperature, alkalinity, salinity, calcium salts, and desiccation. Phylogenetic analysis based on 16S rRNA gene sequencing placed these bacteria under three groups with fourteen strains in Group I including Pseudomonas trivialis and P. poae, two strains in Group II together with Pseudomonas kilonensis and P. corrugata, and three strains in Group III along with Pseudomonas jessenii and P. moraviensis. Genetic diversity assessed by ERIC and BOX-PCR revealed variability among strains belonging to the same phylogenetic groups. Cluster analysis based on the growth characteristics under regimes of different... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2297629 Thu, 26 Mar 2009 04:00:00 +0100 2297629 http://www.medworm.com/index.php?rid=2297631&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%3D19306116%26dopt%3DAbstract Authors: Caton TM, Caton IR, Witte LR, Schneegurt MA The Great Salt Plains of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described the bacterial community through the characterization of 105 isolates from 46 phylotypes. The current report describes the archaeal community through both microbial isolation and culture-independent techniques. Nineteen distinct archaea were isolated, and ten were characterized phenetically. Included were isolates phylogenetically related to Haloarcula, Haloferax, Halorubrum, Haloterrigena, and Natrinema. The isolates were aerobic, non-motile, Gram-negative organisms and exhibited little capacity for fermentation. All of the isolates were halophilic, with most requiring at least ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2297631 Tue, 24 Mar 2009 04:00:00 +0100 2297631 http://www.medworm.com/index.php?rid=2284208&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%3D19301066%26dopt%3DAbstract Authors: Zhou MY, Chen XL, Zhao HL, Dang HY, Luan XW, Zhang XY, He HL, Zhou BC, Zhang YZ Protease-producing bacteria are known to play an important role in degrading sedimentary particular organic nitrogen, and yet, their diversity and extracellular proteases remain largely unknown. In this paper, the diversity of the cultivable protease-producing bacteria and their extracellular proteases in the sediments of the South China Sea was investigated. The richness of the cultivable protease-producing bacteria reached 10(6) cells/g in all sediment samples. Analysis of the 16S rRNA gene sequences revealed that the predominant cultivated protease-producing bacteria are Gammaproteobacteria affiliated with the genera Pseudoalteromonas, Alteromonas, Marinobacter, Idiomarina, Halomonas, Vibrio, Sh... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2284208 Fri, 20 Mar 2009 04:00:00 +0100 2284208 http://www.medworm.com/index.php?rid=2284209&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%3D19294463%26dopt%3DAbstract In this study, ten strains of serotype O48 Salmonella, mainly associated with warm-blooded vertebrates and clinically important causing diarrhea in infants and children, were tested. The results demonstrated that the most efficient killing of Salmonella O48 occurred when all the components of normal bovine serum (NBS) and normal human serum (NHS) cooperated. To prove the role of lysozyme in the bactericidal activity of bovine and human serum, the method of serum adsorption onto bentonite (montmorillonite, MMT) was used. In order to investigate structural transitions accompanying the adsorption of serum components, we applied X-ray diffraction methods. The results of this investigation suggested that apart from lysozyme, other proteins (as, e.g., C3 protein or IgG immunoglobulin) were adsor... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2284209 Wed, 18 Mar 2009 04:00:00 +0100 2284209 http://www.medworm.com/index.php?rid=2274411&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%3D19290566%26dopt%3DAbstract Authors: Hamilton CE, Faeth SH, Dowling TE Most asexual fungal symbionts of grasses in the genus Neotyphodium occurring in nature are of hybrid origin. Most hybrid Neotyphodium species result from interspecific hybridization events between pathogenic Epichloë species or co-occurring non-hybrid Neotyphodium species. Current hypotheses for the prevalence of hybrid Neotyphodium species include reduction of mutation accumulation and increased adaptive response to environmental extremes. We tested the adaptive response hypothesis by characterizing the distribution of uninfected, hybrid, and non-hybrid Neotyphodium endophytes in 24 native Arizona fescue host populations and abiotic parameters at each locality. Infection was high in all host populations (>70%), but the majority of hos... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2274411 Wed, 18 Mar 2009 04:00:00 +0100 2274411 http://www.medworm.com/index.php?rid=2259713&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%3D19277769%26dopt%3DAbstract Authors: Porsch K, Meier J, Kleinsteuber S, Wendt-Potthoff K Iron- and sulfate-reducing microorganisms play an important role for alkalinity-generating processes in mining lakes with low pH. In the acidic mining lake 111 in Lusatia, Germany, a passive in situ remediation method was tested in a large scale experiment, in which microbial iron and sulfate reduction are stimulated by addition of Carbokalk (a mixture of the nonsugar compounds of sugar beets and lime) and straw. The treated surface sediment consisted of three layers of different pH and geochemical composition. The top layer was acidic and rich in Fe(III), the second and third layer both showed moderately acidic to circum-neutral pH values, but only the second was rich in organics, strongly reduced and sulfidic. Aim of the st... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2259713 Wed, 11 Mar 2009 04:00:00 +0100 2259713 http://www.medworm.com/index.php?rid=2259712&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%3D19277770%26dopt%3DAbstract In this study, we examined acquisition of gut microbiota by the wood-feeding beetle, Anoplophora glabripennis, by identifying and comparing microbial community members among different life stages of the insect and with microbes it encounters in the environment. Automated ribosomal intergenic spacer analysis was employed to compare bacterial communities present in the egg and larval stages of A. glabripennis as well as with microbes found in the oviposition site and the surrounding woody tissue. Multivariate analyses were used to identify relationships between sample type and specific bacterial types (operational taxonomic units). From this analysis, bacteria that were derived from the environment, the oviposition site, and/or the egg were identified and compared with taxa found in larvae. ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2259712 Wed, 11 Mar 2009 04:00:00 +0100 2259712 http://www.medworm.com/index.php?rid=2259715&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%3D19267150%26dopt%3DAbstract Authors: Garbeva P, de Boer W Recent publications indicate that inter-specific interactions between soil bacteria may strongly affect the behavior of the strains involved, e.g., by increased production of antibiotics or extracellular enzymes. This may point at an enhanced competitive ability due to inter-specific triggering of gene expression. However, it is not known if such inter-specific interactions also occur during competition for carbon which is the normal situation in soil. Here, we report on competitive interactions between two taxonomically non-related bacterial strains, Pseudomonas sp. A21 and Pedobacter sp. V48, that were isolated from a dune soil. The strains showed strong effects on each other's behavior and gene expression patterns when growing together under carbon-limi... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2259715 Sat, 07 Mar 2009 05:00:00 +0100 2259715 http://www.medworm.com/index.php?rid=2259714&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%3D19267151%26dopt%3DAbstract Authors: Williams HN, Turng BF, Kelley JI The Bacteriovorax, previously in the genus Bdellovibrio, are prokaryotes that prey upon many Gram-negative bacteria. They are ubiquitous in salt-water environments and have been reported to have a strong association with biofilms. The purpose of this study was to test the hypothesis that this association affords protection for the Bacteriovorax and enhances their survival in nature when exposed to extreme environmental conditions. Experiments were designed to compare their survival in biofilms versus in suspension when exposed to extremes in salinity and temperature. Natural mixed-population biofilms generated in moderate-salinity (16 per thousand) Patuxent River water and containing Bacteriovorax were exposed to drastic changes in salinity by ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2259714 Sat, 07 Mar 2009 05:00:00 +0100 2259714 http://www.medworm.com/index.php?rid=2242229&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%3D19259626%26dopt%3DAbstract Authors: Azúa-Bustos A, González-Silva C, Mancilla RA, Salas L, Palma RE, Wynne JJ, McKay CP, Vicuña R Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all th... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2242229 Thu, 05 Mar 2009 05:00:00 +0100 2242229 http://www.medworm.com/index.php?rid=2242228&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%3D19259627%26dopt%3DAbstract This study was conducted to identify an indicator organism(s) in evaluating the pathogen-reducing capacity of biogas plants. Fresh cow manure containing 10(4) to 10(5) colony forming unit (CFU) per milliliter of Escherichia coli and Enterococcus faecalis along with an inoculated Clostridium perfringens strain were exposed to 37 degrees C for 15 days, 55 degrees C for 48 h, and 70 degrees C for 24 h. C. perfringens was the most heat-resistant organism followed by E. faecalis, while E. coli was the most heat-sensitive organism. E. coli was reduced below detection limit at all temperatures with log(10) reductions of 4.94 (10 s), 4.37 (40 min), and 2.6 (5 days) at 70 degrees C, 55 degrees C, and 37 degrees C, respectively. Maximum log(10) reductions for E. faecalis were 1.77 at 70 degrees C (1... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2242228 Thu, 05 Mar 2009 05:00:00 +0100 2242228 http://www.medworm.com/index.php?rid=2242227&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%3D19262973%26dopt%3DAbstract Authors: PMID: 19262973 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2242227 Thu, 05 Mar 2009 05:00:00 +0100 2242227 http://www.medworm.com/index.php?rid=2234801&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%3D19252940%26dopt%3DAbstract Authors: Bascom-Slack CA, Ma C, Moore E, Babbs B, Fenn K, Greene JS, Hann BD, Keehner J, Kelley-Swift EG, Kembaiyan V, Lee SJ, Li P, Light DY, Lin EH, Schorn MA, Vekhter D, Boulanger LA, Hess WM, Vargas PN, Strobel GA, Strobel SA Microbial biodiversity provides an increasingly important source of medically and industrially useful compounds. We have isolated 14 actinomycete species from a collection of approximately 300 plant stem samples from the upper Amazonian rainforest in Peru. All of the cultured isolates produce substances with inhibitory activity directed at a range of potential fungal and bacterial pathogens. For some organisms, this activity is very broad in spectrum while other organisms show specific activity against a limited number of organisms. Two of these organisms pref... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2234801 Sat, 28 Feb 2009 05:00:00 +0100 2234801 http://www.medworm.com/index.php?rid=2223978&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%3D19242746%26dopt%3DAbstract Authors: Gerbersdorf SU, Westrich B, Paterson DM Microbially produced extracellular polymeric substances (EPS) have been linked with many important ecological functions in natural sediments; yet, most information has been derived from marine systems. The present paper is the first comprehensive study on EPS (i.e., carbohydrates and proteins) dynamics in riverine sediments addressing spatial (six reservoirs and four groyne fields across three European rivers), temporal (all seasons in 2003-2005), and vertical (over a 50-cm sediment depth transect) pattern. The variation in hydrodynamic regime found in the reservoirs and groyne fields was reflected in the biomass and composition of the benthic microorganisms that produce EPS. The microphytobenthic communities consisted mainly of diatoms ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2223978 Thu, 26 Feb 2009 05:00:00 +0100 2223978 http://www.medworm.com/index.php?rid=2218065&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%3D19238477%26dopt%3DAbstract Authors: Jayakumar A, O'Mullan GD, Naqvi SW, Ward BB Denitrification in the ocean is a major sink for fixed nitrogen in the global N budget, but the process is geographically restricted to a few oceanic regions, including three oceanic oxygen minimum zones (OMZ) and hemipelagic sediments worldwide. Here, we describe the diversity and community composition of microbes responsible for denitrification in the OMZ using polymerase chain reaction, sequence and fragment analysis of clone libraries of the signature genes (nirK and nirS) that encode the enzyme nitrite reductase, responsible for key denitrification transformation steps. We show that denitrifying assemblages vary in space and time and exhibit striking changes in diversity associated with the progression of denitrification from in... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2218065 Tue, 24 Feb 2009 05:00:00 +0100 2218065 http://www.medworm.com/index.php?rid=2201924&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%3D19225830%26dopt%3DAbstract Authors: Duan J, Müller KM, Charles TC, Vesely S, Glick BR PMID: 19225830 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2201924 Thu, 19 Feb 2009 05:00:00 +0100 2201924 http://www.medworm.com/index.php?rid=2201927&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%3D19224269%26dopt%3DAbstract Authors: Han J, Xia D, Li L, Sun L, Yang K, Zhang L The distribution of culturable bacteria in the rhizosphere, rhizoplane, and interior root tissues of moso bamboo plants was investigated in this study. Of the 182 isolates showing different colony characteristics on Luria-Bertani and King B plates, 56 operational taxonomic units of 22 genera were identified by 16S ribosomal RNA gene sequence analysis. The majority of root endophytic bacteria were Proteobacteria (67.5%), while the majority of rhizospheric and rhizoplane bacteria were Firmicutes (66.3% and 70.4%, respectively). The most common genus in both the rhizosphere and on the rhizoplane was Bacillus (42.4% and 44.4%, respectively), while Burkholderia was the most common genus inside the roots, comprising 35.0% of the isolates fr... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2201927 Wed, 18 Feb 2009 05:00:00 +0100 2201927 http://www.medworm.com/index.php?rid=2201926&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%3D19224270%26dopt%3DAbstract Authors: Fließbach A, Winkler M, Lutz MP, Oberholzer HR, Mäder P Pseudomonas fluorescens strains are used in agriculture as plant growth-promoting rhizobacteria (PGPR). Nontarget effects of released organisms should be analyzed prior to their large-scale use, and methods should be available to sensitively detect possible changes in the environments the organism is released to. According to ecological theory, microbial communities with a greater diversity should be less susceptible to disturbance by invading organisms. Based on this principle, we laid out a pot experiment with field-derived soils different in their microbial biomass and activity due to long-term management on similar parent geological material (loess). We investigated the survival of P. fluorescens CHA0 that c... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2201926 Wed, 18 Feb 2009 05:00:00 +0100 2201926 http://www.medworm.com/index.php?rid=2201925&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%3D19224271%26dopt%3DAbstract Authors: Jha P, Kumar A Nine diazotrophic bacteria were isolated from surface-sterilized roots and culms of wheat variety Malviya-234, which is grown with very low or no inputs of nitrogen fertilizer. Out of the nine bacteria, four showed indole acetic acid (IAA) production, and five were positive for P solubilization. One isolate, WM234C-3, showed appreciable level of nitrogenase activity, IAA production, and P solubilization ability, and was further characterized with a view to exploiting its plant growth promoting activity. Based on 16S rDNA sequence analysis, this isolate was identified as Achromobacter xylosoxidans. Diazotrophic nature of this particular isolate was confirmed by Western blot analysis of dinitrogenase reductase and amplification of nifH. Analysis of the nifH sequen... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2201925 Wed, 18 Feb 2009 05:00:00 +0100 2201925 http://www.medworm.com/index.php?rid=2195875&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%3D19221834%26dopt%3DAbstract We examined the species-time relationship, a measure of species turnover rate, and found that the relationship was fundamentally similar to that observed in plant and invertebrate communities, just on a shorter time scale. The temporal dynamics we observed suggest that although phyllosphere bacterial communities have high levels of phylogenetic diversity and rapid turnover rates, these communities follow predictable successional patterns from season to season. PMID: 19221834 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2195875 Tue, 17 Feb 2009 05:00:00 +0100 2195875 http://www.medworm.com/index.php?rid=2195874&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%3D19221835%26dopt%3DAbstract Authors: Val G, Marín S, Mellado RP PMID: 19221835 [PubMed - as supplied by publisher] (Source: Microbial Ecology) Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2195874 Tue, 17 Feb 2009 05:00:00 +0100 2195874 http://www.medworm.com/index.php?rid=2191764&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%3D19219487%26dopt%3DAbstract Authors: Inoue K, Kabeya H, Kosoy MY, Bai Y, Smirnov G, McColl D, Artsob H, Maruyama S To clarify the relationship between Bartonella grahamii strains and both the rodent host species and the geographic location of the rodent habitat, we have investigated 31 B. grahamii strains from ten rodent host species from Asia (Japan and China), North America (Canada and the USA), and Europe (Russia and the UK). On the basis of multi-locus sequencing analysis of 16S rRNA, ftsZ, gltA, groEL, ribC, and rpoB, the strains were classified into two large groups, an Asian group and an American/European group. In addition, the strains examined were clearly clustered according to the geographic locations where the rodents had been captured. In the phylogenetic analysis based on gltA, the Japanese strains ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2191764 Sat, 14 Feb 2009 05:00:00 +0100 2191764 http://www.medworm.com/index.php?rid=2188563&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%3D19214623%26dopt%3DAbstract Authors: Ostermaier V, Kurmayer R The filamentous cyanobacterium Planktothrix rubescens frequently occurs in deep and stratified lakes in the temperate region of the northern hemisphere and is a known producer of the hepatotoxic secondary metabolite microcystin. These cyclic heptapeptides are synthesized nonribosomally via large enzyme complexes encoded by the microcystin (mcy) synthetase gene cluster. The occurrence of cyanobacterial strains lacking microcystin, but containing the mcy gene cluster has been reported repeatedly; it was shown that this inactivation is due to mutations such as gene deletion events and the insertion of transposable elements. In the present study, 12 lakes in Austria, Germany, and Switzerland were sampled from July 2005 to October 2007, and the proportion o... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2188563 Fri, 13 Feb 2009 05:00:00 +0100 2188563 http://www.medworm.com/index.php?rid=2184343&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%3D19212698%26dopt%3DAbstract Authors: Bisson IA, Marra PP, Burtt Jr EH, Sikaroodi M, Gillevet PM Migratory birds can be efficient dispersers of pathogens, yet we know little about the effect of migration and season on the microbial community in avian plumage. This is the first study to describe and compare the microbial plumage community of adult and juvenile migratory birds during the annual cycle and compare the plumage community of migrants to that of resident birds at both neotropical and nearctic locations. We used length heterogeneity PCR (16S rRNA) to describe the microbial assemblage sampled from the plumage of 66 birds in two age classes and from 16 soil samples. Resident birds differed significantly in plumage microbial community composition from migrants (R >/= 0.238, P < 0.01). Nearctic resident ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2184343 Wed, 11 Feb 2009 05:00:00 +0100 2184343 http://www.medworm.com/index.php?rid=2184342&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%3D19212699%26dopt%3DAbstract Authors: Lasher C, Dyszynski G, Everett K, Edmonds J, Ye W, Sheldon W, Wang S, Joye SB, Moran MA, Whitman WB The phylogenetic diversity and composition of the bacterial community in anaerobic sediments from Sapelo Island, GA, USA were examined using 16S rRNA gene libraries. The diversity of this community was comparable to that of soil, and 1,186 clones formed 817 OTUs at 99% sequence similarity. Chao1 estimators for the total richness were also high, at 3,290 OTUs at 99% sequence similarity. The program RDPquery was developed to assign clones to taxonomic groups based upon comparisons to the RDP database. While most clones could be assigned to describe phyla, fewer than 30% of the clones could be assigned to a described order. Similarly, nearly 25% of the clones were only distantly re... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2184342 Wed, 11 Feb 2009 05:00:00 +0100 2184342 http://www.medworm.com/index.php?rid=2157484&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%3D19184185%26dopt%3DAbstract Authors: Grover JP, Chrzanowski TH Ingestion and growth rates of the nanoflagellate predator Ochromonas danica feeding on the bacterium Pseudomonas fluorescens were quantified in laboratory cultures. Bacterial prey were grown under four nutritional conditions with respect to macronutrient elements: C-limited, N-limited, P-limited, and balanced. Ingestion and growth rates were saturating functions of prey abundance when preying upon nutritionally balanced, C-limited, and P-limited bacteria but were unimodal functions of abundance when preying on N-limited bacteria. At saturating prey concentrations, the ingestion rate of C-limited prey was about twice that of prey in other nutritional states, while at subsaturating prey concentrations, the ingestion rates of both C- and N-limited prey w... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2157484 Fri, 30 Jan 2009 05:00:00 +0100 2157484 http://www.medworm.com/index.php?rid=2145117&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%3D19172216%26dopt%3DAbstract Authors: Horath T, Bachofen R Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the e... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2145117 Wed, 28 Jan 2009 05:00:00 +0100 2145117 http://www.medworm.com/index.php?rid=2138615&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%3D19169740%26dopt%3DAbstract This study is among the first to explore intra-lake horizontal heterogeneity of organic-aggregate-associated bacterial community composition (OABC) in the large, shallow, and eutrophic Lake Taihu. During November 2006, samples were collected at four locations representing different trophic states and food web structures. Regional variability of OABC and diversity were studied by amplified ribosomal DNA restriction analysis and comparative analysis of four large 16S ribosomal RNA clone libraries. Our results demonstrate that OABC were numerically dominated by members of the beta-proteobacteria (19.2-38.6%), Bacteroidetes (3.6-20.0%), and alpha-proteobacteria (11.5-19.2%) groups. The dominance of the Bacteroidetes group was related to algae-based aggregates. Horizontal heterogeneity of OABC ... Microbial Ecology journals http://www.medworm.com/rss/comments.php?id=2138615 Sat, 24 Jan 2009 05:00:00 +0100 2138615