Bacterial diversity in the sediment from polymetallic nodule fields of the Clarion-Clipperton Fracture Zone

The Clarion-Clipperton Fracture Zone (CCFZ) is located in the northeastern equatorial Pacific and contains abundant polymetallic nodules. To investigate its bacterial diversity, four libraries of 16S rRNA genes were constructed from sediments of four stations in different areas of the CCFZ. In total, 313 clones sequenced from the 4 libraries were assigned into 14 phylogenetic groups and 1 group of 28 unclassified bacteria. High bacterial diversity was predicted by the rarefaction analysis. The most dominant group overall was Proteobacteria, but there was variation in each library: Gammaproteobacteria was the most dominant group in two libraries, E2005-01 and ES0502, while Alphaproteobacteria and Deltaproteobacteria were the most dominant groups in libraries EP2005-03 and WS0505, respectively. Seven groups, including Alphaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Betaproteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes, were common to all four libraries. The remaining minor groups were distributed in libraries with different patterns. Most clones sequenced in this study were clustered with uncultured bacteria obtained from the environment, such as the ocean crust and marine sediment, but only distantly related to isolates. Bacteria involved in the cycling of metals, sulfur and nitrogen were detected, and their relationship with their habitat was discussed. This study sheds light on the bacterial communities associated with polymetallic nodules in the CCFZ and provides primary data on the bacterial diversity of this area.     

Diversity and structure of bacterial communities in Fildes Peninsula, King George Island

To examine the bacterial community structure in the Fildes Peninsula, King George Island, Antarctica, we examined the bacterial diversity and community composition of samples collected from lacustrine sediment, marine sediment, penguin ornithogenic sediments, and soils using culture-dependent and culture-independent methods. The 70 strains fell into five groups: Actinobacteria, Bacteroidetes, Firmicutes, Gammaproteobacteria, and Betaproteobacteria. Bacterial diversity at the phylum level detected in Denaturing Gradient Gel Electrophoresis (DGGE) profiles comprised Proteobacteria (including the subphyla Alpha-, Beta-, Gamma-, Deltaproteobacteria), Bacteroidetes, Firmicutes, Chlorobi, and Deinococcus-Thermus. Gammaproteobacteria was identified to be the dominant bacterial subphylum by cultivation and DGGE method. By cluster analysis, the overall structure and composition of bacterial communities in the soil and lacustrine sediment were similar to one another but significantly different from bacterial communities in penguin ornithogenic sediment and marine sediment, which were similar to one another. The majority of 16S rDNA sequences from cultured bacteria were closely related to sequences found in cold environments. In contrast, a minority of 16S rDNA sequences from the DGGE approach were closely related to sequences found in cold environments.     

添加不同益生菌对草鱼养殖水体菌群结构的影响

为评价添加不同益生菌对草鱼养殖水体菌群结构的影响,研究采用454焦磷酸测序技术分析其水体菌群结构。结果表明:添加益生菌后的处理组（枯草芽孢杆菌BS、光合细菌PSB和复合菌CB）其微生物多样性高于对照组（Control）。在门的水平,Control和CB样品中变形菌（Proteobacteria）为优势菌,PSB和BS中变形菌（Proteobacteria）和放线菌（Actinobacteria）所占比例差别不大。与Control相比,其他三组中拟杆菌（Bacteroidetes）和放线菌（Actinobacteria）都增加。对变形菌深入分析发现,在PSB,BS和 CB 样品中,-变形杆菌为优势菌,接下来是-变形杆菌纲、-变形杆菌纲和-变形杆菌纲。对拟杆菌分析发现,除对照外,其他样品中黄杆菌纲（Flavobacteria）为优势菌。在对照和处理组中,-变形杆菌、-变形杆菌、-变形杆菌和拟杆菌门在目的水平组成也有差异。以上结果表明,水体中添加益生菌能增加水体菌群多样性,改变菌群结构。       

Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea)

Climate change is projected to cause increased inflow of terrestrial dissolved organic matter to coastal areas in northerly regions. Estuarine bacterial community will thereby receive larger loads of organic matter and inorganic nutrients available for microbial metabolism. The composition of the bacterial community and its ecological functions may thus be affected. We studied the responses of bacterial community to inflow of terrestrial dissolved organic matter in a subarctic estuary in the northern Baltic Sea, using a 16S rRNA gene metabarcoding approach. Betaproteobacteria dominated during the spring river flush, constituting ~ 60% of the bacterial community. Bacterial diversity increased as the runoff decreased during summer, when Verrucomicrobia, Betaproteobacteria, Bacteroidetes, Gammaproteobacteria and Planctomycetes dominated the community. Network analysis revealed that a larger number of associations between bacterial populations occurred during the summer than in spring. Betaproteobacteria and Bacteroidetes populations appeared to display similar correlations to environmental factors. In spring, freshly discharged organic matter favoured specialists, while in summer a mix of autochthonous and terrestrial organic matter promoted the development of generalists. Our study indicates that increased inflows of terrestrial organic matter-loaded freshwater to coastal areas would promote specialist bacteria, which in turn might enhance the transformation of terrestrial organic matter in estuarine environments.     

Investigation of total bacterial and ammonia-oxidizing bacterial community composition in a full-scale aerated submerged biofilm reactor for drinking water pretreatment in China

The community composition of total bacteria and ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment was characterized by analysis of 16S rRNA gene and the functional gene amoA, respectively. Sampling was performed in February and in July. 16S rRNA gene clone libraries revealed 13 bacterial divisions. At both sampling dates, the majority of clone sequences were related to the Alpha- and Betaproteobacteria. A minor proportion belonged to the following groups: Gammaproteobacteria, Deltaproteobacteria, Nitrospira, Firmicutes, Acidobacteria, Verrucomicrobia, Actinobacteria, Planctomycetes, Chloroflexi, Gemmatimonadetes and the Cytophaga-Flavobacterium-Bacteroides group. Some sequences related to bacteria owning high potential metabolic capacities were detected in both samples, such as Rhodobacter-like rRNA gene sequences. Surveys of cloned amoA genes from the two biofilm samples revealed ammonia-oxidizing bacterial sequences affiliated with the Nitrosomonas oligotropha lineage, Nitrosomonas communis lineage. An unknown Nitrosomonas group of amoA gene sequences was also detected.     

Bacterial community of sediments from the Australian-Antarctic ridge

Benthic bacterial communities in the ocean comprise the vast majority of prokaryotes on Earth and play crucial roles in the biogeochemical cycles and remineralization of organic matter. Despite the importance of the benthic bacterial communities in the ecosystem, no previous investigations of the bacterial community of sediments from the Australian-Antarctic ridge (AAR) have been conducted to date. In this study, the composition of the bacterial community in the surface sediments from AAR was revealed by the 454 pyrosequencing method. Bacterial communities inhabiting the sediments of AAR were highly diverse, covering 39 distinct major lineages of bacteria. Among them, Gammaproteobacteria, Planctomycetes, Actinobacteria, Deltaproteobacteria, Acidobacteria, Alphaproteobacteria, Chloroflexi, Bacteroidetes, Chlorobi, and Gemmatimonadetes were dominant, accounting for 85–88 % of the bacterial community. The 16S rDNA sequences of major OTUs with 1 % or higher relative abundance showed high similarity (96.6–100 %) with uncultured environmental sequences that were primarily recovered from the sediments of various areas of the Arctic, Southern, Atlantic, Indian, and Pacific Oceans. As the first report of the bacterial community of marine sediments in the AAR region, the results presented herein suggest that members of the predominant phyla are well adapted to the environment of marine sediment and that the low variability in the bacterial communities of deep-sea sediments might reflect the similar environmental conditions among various regions of the deep sea.     

藻华爆发期太湖不同区域沉积物细菌多样性

本研究以藻华爆发期的太湖不同区域沉积物为对象, 测定氮、磷和生物量碳等理化性质, 并通过末端限制性酶切片断长度多态性分析(T-RFLP)的分子生态学手段, 鉴定不同富营养化湖区7个标准采样位点沉积物中细菌群落结构差异。结果表明, 总氮、总磷含量以6#、16#样品最高, 且各形态氮和各形态磷的趋势也与总氮、总磷趋势基本一致; 生物量碳为6#和16#明显高于其他位点, 其余各位点相近。T-RFLP结果显示, 各位点细菌多样性间存在差异, 其中16#样品的多样性指数最低, 6#、7#和1#较高; 在种群组成上各个位点无论是组分还是比例均有显著差异。另外, 所取7个沉积物样品中与氮、磷循环相关的α、β和γ-变形菌纲含量非常丰富, 且与硫、铁循环相关的δ-变形菌纲含量也很丰富。     

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany)

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity (H') ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites.     

Bacterial Community Composition in Different Sediments from the Eastern Mediterranean Sea: a Comparison of Four 16S Ribosomal DNA Clone Libraries

The regional variability of sediment bacterial community composition and diversity was studied by comparative analysis of four large 16S ribosomal DNA (rDNA) clone libraries from sediments in different regions of the Eastern Mediterranean Sea (Thermaikos Gulf, Cretan Sea, and South lonian Sea). Amplified rDNA restriction analysis of 664 clones from the libraries indicate that the rDNA richness and evenness was high: for example, a near-1:1 relationship among screened clones and number of unique restriction patterns when up to 190 clones were screened for each library. Phylogenetic analysis of 207 bacterial 16S rDNA sequences from the sediment libraries demonstrated that Gamma-, Delta-, and Alphaproteobacteria, Holophaga/Acidobacteria, Planctomycetales, Actinobacteria, Bacteroidetes, and Verrucomicrobia were represented in all four libraries. A few clones also grouped with the Betaproteobacteria, Nitrospirae, Spirochaetales, Chlamydiae, Firmicutes, and candidate division OPl 1. The abundance of sequences affiliated with Gammaproteobacteria was higher in libraries from shallow sediments in the Thermaikos Gulf (30 m) and the Cretan Sea (100 m) compared to the deeper South Ionian station (2790 m). Most sequences in the four sediment libraries clustered with uncultured 16S rDNA phylotypes from marine habitats, and many of the closest matches were clones from hydrocarbon seeps, benzene-mineralizing consortia, sulfate reducers, sulk oxidizers, and ammonia oxidizers. LIBSHUFF statistics of 16S rDNA gene sequences from the four libraries revealed major differences, indicating either a very high richness in the sediment bacterial communities or considerable variability in bacterial community composition among regions, or both.     

胜利油藏不同时间细菌群落结构的比较

利用聚合酶链式反应-变性梯度凝胶电泳(PCR-DGGE)和构建16S rRNA基因克隆文库2种方法,对孤岛油田两口井(注水井G和采油井L)在相距9个月的2个时间点(A和B)所采集样品的细菌群落结构进行了比较。DGGE图谱聚类分析表明注水井在2个时间点的微生物群落结构相似性为48.1%,而采油井的相似性只有28.7%。16S rRNA基因克隆文库结果表明,A时间点样品G中的优势菌群为Betaproteobacteria、Gammaproteobacteria,还有Deferribacteres、Firmicutes、Bacteroidetes等;而样品L中,Gammaproteobacteria中的Moraxellaceae含量达到97%。B时间点G中除了优势菌Betaproteobacteria之外,Deferribacteres的数量显著增加,成为优势菌;而L在B时间点优势菌除Gammaproteobacteria外,还有Betaproteobacteria和Firmicutes。采油井中的微生物群落结构随时间发生了显著改变,而注水井变化不显著。这一结果部分揭示了微生物采油过程中地层微生物群落的变化规律,有助于进一步阐明微生物驱油的机理。     

Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe,China)

1. Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood.
2. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China.
3. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities.
4. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability.

     

Phylogenetic diversity, composition and distribution of bacterioplankton community in the Dongjiang River, China

Bacterioplankton community compositions in the Dongjiang River were characterized using denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library construction. Water samples in nine different sites were taken along the mainstem and three tributaries. In total, 24 bands from DGGE gels and 406 clones from the libraries were selected and sequenced, subsequently analyzed for the bacterial diversity and composition of those microbial communities. Bacterial 16S rRNA gene sequences from freshwater bacteria exhibited board phylogenetic diversity, including sequences representing the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Bacteriodetes, Verrucomicrobia, and candidate division TM7. Members of Betaproteobacteria group were the most dominant in all sampling sites, followed by Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria. DGGE profiles and the ∫-LIBSHUFF analysis revealed similar patterns of bacterial diversity among most sampling sites, while spatial distribution variances existed in all sites along the river basin. Statistical analysis showed that bacterial species distribution strongly correlated with environmental variables, such as nitrate and ammonia, suggesting that nitrogen nutrients may shape the microbial community structure and composition in the Dongjiang River. This study had important implications for the comparison with other rivers elsewhere and contributed to the growing data set on the factors that structure bacterial communities in freshwater ecosystems.     

Bacterial diversity at different depths in lead-zinc mine tailings as revealed by 16S rRNA gene libraries

Bacterial communities at 10 cm, 100 cm, and 200 cm depths in a 100-year-old lead-zinc tailing heap were evaluated by constructing 16S rRNA gene libraries. In total, 98 operational taxonomic units (OTUs) were identified from 193 clones at a 3% sequence difference level. The OTU number and species richness decreased with the depth. Species composition was significantly different between the three libraries. Fifty-seven percent of the examined clones were Acidobacteria and 27% belonged to Proteobacteria. Other sequences included Chloroflexi, Firmicutes, Chlamydiae, Actinobacteria, Gemmatimonadetes, Nitrospira, and three unclassified OTUs. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were mainly distributed in the rhizosphere of naturally colonizing plants; however, Deltaproteobacteria, Acidobacteria, and Chloroflexi tended to inhabit the deeper tailings (below the 100 cm-depth).     

Identification and isolation of a Castellaniella species important during biostimulation of an acidic nitrate- and uranium-contaminated aquifer

Immobilization of uranium in groundwater can be achieved through microbial reduction of U(VI) to U(IV) upon electron donor addition. Microbial community structure was analyzed in ethanol-biostimulated and control sediments from a high-nitrate (>130 mM), low-pH, uranium-contaminated site in Oak Ridge, TN. Analysis of small subunit (SSU) rRNA gene clone libraries and polar lipid fatty acids from sediments revealed that biostimulation resulted in a general decrease in bacterial diversity. Specifically, biostimulation resulted in an increase in the proportion of Betaproteobacteria (10% of total clones in the control sediment versus 50 and 79% in biostimulated sediments) and a decrease in the proportion of Gammaproteobacteria and Acidobacteria. Clone libraries derived from dissimilatory nitrite reductase genes (nirK and nirS) were also dominated by clones related to Betaproteobacteria (98% and 85% of total nirK and nirS clones, respectively). Within the nirK libraries, one clone sequence made up 59 and 76% of sequences from biostimulated sediments but only made up 10% of the control nirK library. Phylogenetic analysis of SSU rRNA and nirK gene sequences from denitrifying pure cultures isolated from the site indicate that all belong to a Castellaniella species; nearly identical sequences also constituted the majority of biostimulated SSU rRNA and nirK clone libraries. Thus, by combining culture-independent with culture-dependent techniques, we were able to link SSU rRNA clone library information with nirK sequence data and conclude that a potentially novel Castellaniella species is important for in situ nitrate removal at this site.     

Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge <Emphasis Type="Italic">Swartschewskia papyracea</Emphasis>

The diversity of the symbiotic community of the endemic Baikal sponge Swartschewskia papyracea was studied, and an analysis of the polyketide synthases genes spectrum in sponge-associated microorganisms was carried out. Six bacterial phyla were detected in the S. papyracea microbiome: Verrucomicrobia, Cyanobacteria, Actinobacteria, Bacteroidetes, Proteobacteria, and Planctomycetes. Unlike the microbial associations of other freshwater sponges, the community under study was dominated by the phylaVerrucomicrobia (42.1%) and Cyanobacteria (17.5%), while the proportion of the Proteobacteria was unusually low (9.7%). In the S. papyracea community metagenome, there were identified 18 polyketide synthases genes fragments, the closest homologues of which included the polyketide synthases of the microorganisms belonging to the bacterial phyla Cyanobacteria, Proteobacteria (classes Betaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), and Acidobacteria as well as the eukaryotic algae of the phylum Heterokonta (class Eustigmatophyceae). Polyketide synthase sequences from S. papyracea formed three groups on the phylogenetic tree: a group of hybrid NRPS/PKS complexes, a group of cyanobacterial polyketide synthases, and a group of homologues of the eukaryotic alga Nannochloropsis gaditana. Notably, the identified polyketide synthase genes fragments showed only a 57–88% similarity to the sequences from the databases, which implies the presence of genes controlling the synthesis of the novel, still unstudied, polyketide compounds in the S. papyracea community. It was proposed that the habitat conditions of S. papyracea affect the taxonomic composition of the microorganisms associated with the sponge, including the diversity of the producers of secondary metabolites.     

象山港网箱养殖区与非养殖区的细菌群落分布

近海集约化养殖是导致我国近海污染的主要来源之一。浮游细菌在近海生态系统的物质循环过程中发挥重要作用,研究海洋浮游细菌群落对养殖活动的响应,对于指示和评价海水养殖生态系统健康具有重要意义。采集了象山港网箱养殖区与非养殖区3个深度,包括表层(0.5 m)、中层(2.5 m)、底层(8.0 m)的水样,利用焦磷酸测序技术测定16S rRNA基因,研究浮游细菌的群落结构和多样性。结果表明:网箱养殖活动不仅使得附近区域水体理化性质发生改变,如化学需氧量浓度显著高于非养殖区域,而且显著地(P0.05)改变了浮游细菌的群落结构,但不同深度间群落结构和多样性的差异不显著。网箱养殖区和非养殖区中主要浮游细菌类群为α-变形菌(Alphaproteobacteria)、γ-变形菌(Gammaproteobacteria)、拟杆菌(Bacteroidetes)、放线菌(Actinobacteria)、β-变形菌(Betaproteobacteria)、ε-变形菌(Epsilonproteobacteria)和其它变形菌(Unclassified Proteobacteria),占细菌总序列数的98.64%。有些细菌类群的平均相对丰度从网箱区到非养殖区差异显著,如拟杆菌(P0.01)和放线菌(P0.05)显著降低,而γ-变形菌(P0.05)显著增加。相似度分析表明γ-变形菌、α-变形菌和拟杆菌是造成网箱区和非养殖区群落差异的主要类群,对群落差异总贡献率达到45.02%。偏冗余分析表明,影响细菌群落分布的主要环境因子有化学需氧量、磷酸盐、铵盐和总有机碳,共解释38.18%的群落变异,空间距离单独解释10.66%的群落变异。实验结果表明,养殖活动导致浮游细菌群落的改变,其中拟杆菌、放线菌和γ-变形菌的丰度显著变化,可能用于评价养殖水体的水质状况。     

Effects of rhizoma peanut cultivars (Arachis glabrata Benth.) on the soil bacterial diversity and predicted function in nitrogen fixation

There is a growing awareness of the importance of soil microorganisms in agricultural management practices. Currently, much less is known about whether different crop cultivar has an effect on the taxonomic structure and diversity, and specific functions of soil bacterial communities. Here, we examined the changes of the diversity and composition and enzyme‐encoding nitrogenase genes in a long‐term field experiment with seven different rhizoma peanut cultivars in southeastern USA, coupling high‐throughput 16S rRNA gene sequencing and the sequence‐based function prediction with Tax4Fun. Of the 32 phyla detected (Proteobacteria class), 13 were dominant: Acidobacteria, Alphaproteobacteria, Actinobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Deltaproteobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi, and Planctomycetes (relative abundance >1%). We found no evidence that the diversity and composition of bacterial communities were significantly different among different cultivars, but the abundance of some dominant bacterial groups that have N‐fixation potentials (at broad or fine taxonomic level) and predicted abundances of some enzyme‐encoding nitrogenase genes showed significant across‐cultivar differences. The nitrogenase genes were notably abundant in Florigraze and Latitude soils while remarkably lower in Arbook and UF_TITO soils when compared with other cultivars, indicating different nitrogen fixation potentials among different cultivars. The findings also suggest that the abundance of certain bacterial taxa and the specific function bacteria perform in ecosystems can have an inherent association. Our study is helpful to understand how microbiological responses and feedback to different plant genotypes through the variation in structure and function of their communities in the rhizosphere.     

Phylogenetic diversity of microorganisms associated with the deep-water sponge Baikalospongia intermedia

The diversity of bacteria associated with deep-water sponge Baikalospongia intermedia was evaluated by sequence analysis of 16S rRNA genes from two sponge samples collected in Lake Baikal from depths of 550 and 1204 m. A total of 64 operational taxonomic units, belonging to nine bacterial phyla, Proteobacteria (classes Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria), Actinobacteria, Planctomycetes, Cloroflexi, Verrucomicrobia, Acidobacteria, Chlorobi, and Nitrospirae, including candidate phylum WS5, were identified. Phylogenetic analysis showed that the examined communities contained phylotypes exhibiting homology to uncultured bacteria from different lake ecosystems, freshwater sediments, soil and geological formations. Moreover, a number of phylotypes were relative to psychrophilic, methane-oxidizing, sulfate-reducing bacteria, and to microorganisms resistant to the influence of heavy metals. It is noted that the unusual habitation conditions of deep-water sponges contribute to the taxonomic diversity of associated bacteria and have an influence on the presence of functionally important microorganisms in bacterial communities.     

Benthic bacterial diversity from freshwater tufas of the Iberian Range (Spain)

Aiming to characterize the bacterial diversity of modern tufa systems of the Iberian Range (Spain), we surveyed the 16S rRNA gene sequence diversity from 24 sites within three rivers (A?amaza, Mesa and Piedra). These tufas record substantial calcareous growth under different physicochemical conditions and are part of an important, regional landscape-building system. The bacterial community structure and composition, richness and diversity were quantified from denaturing gradient gel electrophoresis fingerprints. Retrieved DNA sequences could be assigned to 10 bacterial phyla and included a variety of phototrophic and heterotrophic groups. Cyanobacteria, mainly filamentous taxa, constituted 43% of all the retrieved sequences, followed by Firmicutes (11%), Gammaproteobacteria (10%), Alphaproteobacteria (7%), Acidobacteria (6%), Bacteroidetes (5%), Betaproteobacteria (4%), Planctomycetes (4%), Actinobacteria (3%) and Deltaproteobacteria (2%). Diatom and Xanthophyceae chloroplast sequences were also detected. Physicochemical variables measured at each site were modelled with multivariate statistics. Principal component analyses yielded the highest variance for salinity-related variables (conductivity; Na(+) , Cl(-) and SO4(2-) concentrations), which correlated negatively and significantly with diversity indices. However, the highest variance explained by individual principal components was relatively low (< 34%). Overall, we show that these young fluvial tufas are inhabited by a large variety of bacteria in diverse and widespread communities.     

Spatial heterogeneity of bacterial community structure in the sediments of the Pearl River estuary

Denaturing gradient gel electrophoresis (DGGE) and multivariate statistical analytical methods were applied to investigate the spatial variation of bacterial community structure in the Pearl River estuary sediment and to address the relationship between microbial community composition and bottom water chemistry in ten different stations. Preliminary results of sequencing analysis of the excised DGGE bands suggested that α-Proteobacteria, γ-Proteobacteria, Acidobacteria and Actinobacteria were the dominant bacterial groups in the Pearl River estuary sediment. Results of multidimensional scaling analysis of these field data suggested that the composition of bacterial communities varied with sampling sites. Finally, canonical correspondence analysis of the data of environmental variables and bacterial community suggested that bacterial community structure was significantly influenced by the change of environmental variables (total phosphorus, nitrite, ammonium, dissolved oxygen, pH and salinity).