Comparison of the structure and composition of bacterial communities from temperate and tropical freshwater ecosystems

We used a partial 16S rRNA sequencing approach to compare the structure and composition of the bacterial communities in three large, deep subalpine lakes in France with those of communities in six shallow tropical reservoirs in Burkina Faso. Despite the very different characteristics of these ecosystems, we found that their bacterial communities share the same composition in regard to the relative proportions of the different phyla, suggesting that freshwater environmental conditions lead to convergence in this composition. In the same way, we found no significant difference in the richness and diversity of the bacterial communities in France and Burkina Faso. We defined core and satellite operational taxonomic units (OTUs) (sequences sharing at least 98% identity) on the basis of their abundance and their geographical distribution. The core OTUs were found either ubiquitously or only in temperate or tropical and subtropical areas, and they contained more than 70% of all the sequences retrieved in this study. In contrast, satellite OTUs were characterized by having a more restricted geographical distribution and by lower abundance. Finally, the bacterial community composition of these freshwater ecosystems in France and Burkina Faso was markedly different, showing that the history of these ecosystems and regional environmental parameters have a greater impact on the relative abundances of the different OTUs in each bacterial community than the local environmental conditions.     

Analyses of soil bacterial diversity of the Schirmacher Oasis,Antarctica

Schirmacher Oasis, Antarctica, is a region with relatively large exposed area and consisted of many freshwater lakes. Nevertheless, only a few studies were done on the bacterial diversity of this region. Hence, this project was undertaken to determine the bacterial community in soil samples collected from the Schirmacher Oasis using the denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA fragments. A total of 79 partial 16S rDNA sequences were obtained from the excised DGGE bands, which corresponded to 63 different operational taxonomic units (OTUs) representing bacteria from seven different phyla. The most dominant phyla in descending order were Acidobacteria, Proteobacteria, Bacteroidetes, and Actinobacteria, Planctomycetes, Cyanobacteria and BRC1. There were 5.4 % of unclassified bacteria which cannot be grouped into any of the existing phyla. Eighty-seven percent of the OTUs had highest similarity with the uncultured bacteria from the NCBI GenBank database. Thirty-two percent of the OTUs were similar to bacteria reported in other parts of the Antarctica, while the others were related to bacteria found elsewhere outside the Antarctic.     

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. ‘Cerrado stricto sensu’ and ‘Cerradao’ share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while ‘Floresta decidual’ and ‘Campo graminoide’ show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.     

pH Influences the Importance of Niche-Related and Neutral Processes in Lacustrine Bacterioplankton Assembly

pH is an important factor that shapes the structure of bacterial communities. However, we have very limited information about the patterns and processes by which overall bacterioplankton communities assemble across wide pH gradients in natural freshwater lakes. Here, we used pyrosequencing to analyze the bacterioplankton communities in 25 discrete freshwater lakes in Denmark with pH levels ranging from 3.8 to 8.8. We found that pH was the key factor impacting lacustrine bacterioplankton community assembly. More acidic lakes imposed stronger environmental filtering, which decreased the richness and evenness of bacterioplankton operational taxonomic units (OTUs) and largely shifted community composition. Although environmental filtering was determined to be the most important determinant of bacterioplankton community assembly, the importance of neutral assembly processes must also be considered, notably in acidic lakes, where the species (OTU) diversity was low. We observed that the strong effect of environmental filtering in more acidic lakes was weakened by the enhanced relative importance of neutral community assembly, and bacterioplankton communities tended to be less phylogenetically clustered in more acidic lakes. In summary, we propose that pH is a major environmental determinant in freshwater lakes, regulating the relative importance and interplay between niche-related and neutral processes and shaping the patterns of freshwater lake bacterioplankton biodiversity.     

Evaluation of microbial population dynamics in the co-composting of cow manure and rice straw using high throughput sequencing analysis

Microbial population dynamics in co-composting of cow manure and rice straw were evaluated using 16S high throughput sequencing technology. Physicochemical factors, including temperature, pH, nitrogen contents, the ratio of carbon and nitrogen, and germination index, were also determined in this study. 16S high throughput sequencing results showed that bacterial community structure and composition significantly varied in each phase of composting. The major phyla included Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria and Planctomycetes, respectively. Bacteroidetes and Proteobacteria were the most abundant phyla in all phases, and Actinobacteria was just dominant in the mesophilic phase, while Firmicutes and Planctomycetes were ubiquitous. At the genus level, Simiduia, Flavobacterium, unclassified Chitinophagaceae and Flexibacter notably changed in each phase of composting. Bacterial community diversity in the mesophilic phase was higher than that in others based on the Shannon–Wiener index and Simpson diversity index. The ratio of carbon and nitrogen and germination index indicated that the co-composting of cow manure and rice straw reached maturation. The result of nitrogen contents showed that nitrogen loss mainly occurred in the thermophilic phase. In addition, the differences in the distributions of key OTUs between in the late thermophilic phase and the cooling and maturation phase were unobvious compared with other phase’s base on the principal component analysis. Redundancy analysis revealed that the changes of nitrogen played a predominant role in the distributions of OTUs during the composting process.     

Bacterial diversity within five unexplored freshwater lakes interconnected by surface channels in East Antarctic Dronning Maud Land (Schirmacher Oasis) using amplicon pyrosequencing

The Schimacher Oasis, an ice-free plateau in East Antarctic Dronning Maud Land, consists of over 120 freshwater lakes. These lakes are connected largely through four major surface channels. The bacterial diversity in these lake ecosystems remains largely unexplored. In this study, we compared the bacterial diversity in five freshwater lakes (L42, L46, L47, L50, and L51) interconnected by two surface channels using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) method. We further compared the resultant bacterial composition from these five lakes with another freshwater lake in the Schirmacher Oasis, Lake Tawani(P), which is not connected through the same surface channels. Using bTEFAP, we differentiated nine different phyla with the phyla Proteobacteria (especially the class Alphaproteobacteria) and Bacteroidetes (the class Sphingobacteria) dominating in lakes interconnected by surface channel 1, while the phyla Chloroflexi and Firmicutes were highly abundant in lakes interconnected by surface channel 2. The operational taxonomic unit (OTU) network and Principle Coordinate Analysis (PCoA) plot based on unweighted UNIFRAC determined that the bacterial assemblages found in these five lakes are different than the bacterial composition residing in Lake Tawani(P). The distribution and the diversity of the bacterial communities in Schirmacher Oasis freshwater lakes that are connected through surface channels may provide an insight into the role of the extreme physico-chemical parameters that help shape microbially driven functional ecosystems in other oases on this icy continent.     

鄱阳湖湖泊细菌群落组成及结构——以松门山为例

于2011年5月在鄱阳湖——松门山湖区采集底泥与表层水样,分别提取了表层水体浮游和底泥微生物基因组DNA,利用454高通量测序技术对细菌的16S rRNA基因进行了序列测定,分析了湖泊底泥细菌、水体浮游细菌群落结构特征。结果显示:底泥细菌OTUs(Operational Taxonomic Units)为1454,表层水体浮游细菌OTUs为269;底泥细菌群落比表层水体更加多样化,底泥细菌的物种数大大多于表层水体。同时,底泥细菌群落与表层浮游细菌群落结构存在显著差异。物种分类显示鄱阳湖底泥细菌种类隶属于20门,228属,其中优势种群为δ-变形菌纲(Deltaproteobacteria)、β-变形菌纲(Betaproteobacteria)和疣微菌门(Verrucomicrobia);表层水体浮游细菌隶属于13门116属,优势种群为β-变形菌纲、拟杆菌门(Bacteroidetes)和放线菌门(Actinobacteria)。结果进一步揭示,无论是浮游细菌群落还是沉积物细菌群落,优势细菌种群的基因型多样性更高。     

虾-贝-红树林耦合循环水养殖系统中微生物群落分析

海水循环水养殖系统是重要的生态养殖模式发展趋势之一, 为了深入了解循环水养殖生态系统, 通过对系统各功能区水体中细菌16S rRNA基因V4V5区进行高通量测序和生物信息学分析, 从微生物生态学角度分析了循环水养殖系统不同功能区的细菌群落结构动态。测序分析结果显示, 海水循环水养殖系统中优势细菌种群分别属于变形菌门(Proteobacteria)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)和浮霉菌门(Planctomycetes)。红树林湿地水体中变形菌门和厚壁菌门丰度较高, 而对虾养殖池的拟杆菌门和浮霉菌门丰度较高。在不同优势类群中, 变形菌门多样性指数平均值最高, 其次是拟杆菌门, 厚壁菌门最低。在各功能区中, 红树林细菌多样性最高, 虾池最低。MDS分析结果显示虾池、贝池和红树林湿地水体中细菌群落结构有明显差异, 虾池与其他功能区差异最大。研究表明, 高密度对虾养殖对虾池水体中细菌群落有显著影响, 但其影响在循环水养殖系统后续功能区中逐渐减弱。     

Bacterial community of very wet and acidic subalpine forest and fire-induced grassland soils

The subalpine forest and grassland ecosystems at Tatajia in Yushan National Park, Taiwan, at an elevation of 2,700 m, mean annual precipitation of 4,100 mm, mean annual temperature of 9.5°C, and soil pH near 3.5, represent land types whose bacterial communities have not been previously characterized. To this end, small subunit (SSU) rRNA libraries were prepared from environmental DNA, and 319 clones were sequenced and characterized. Despite differences in vegetation, Acidobacteria, Proteobacteria and Firmicutes were the most abundant phyla in soil communities from the forest and grassland. Although not significantly different, on the basis of Chao1, Shannon and other indices and rarefaction analyses, the diversity of the bacterial community of grassland appeared higher than that of the forest. The composition of the most abundant operational taxonomic units (OTUs) also differed between the grassland and forest communities. Because the grassland was formed by fire 30 years ago from forest, these results indicated a different bacterial community could form within that time. Moreover, most of the OTUs abundant in Tatajia soils had been previously detected in other studies, but in lower numbers. Therefore, the bacterial communities in Tatajia differed in relative abundance but not in types of bacteria present. However, one acidobacterial OTU abundant in Tatajia had previously been found to be abundant in soils from around the world. Thus, this OTU may represent a particularly abundant and cosmopolitan bacterial phylotype.     

云南松林次生演替阶段土壤细菌群落的变化

土壤细菌多样性是维持森林生态系统功能的关键因子,森林演替是影响其动态变化的重要因素。研究云南松林不同演替阶段土壤细菌群落结构及其多样性的变化规律,有助于深入理解森林生态系统恢复过程的驱动机制。本研究以云南省永仁县皆伐后形成的针叶林、针阔混交林和常绿阔叶林为对象,基于Illumina Hiseq高通量测序技术,分析森林演替过程中土壤细菌群落组成、结构、多样性及其影响因子的变化。结果表明: 土壤细菌的种群分类单元、Ace指数、Chao1指数和Shannon指数均随着演替进行呈减少趋势,演替早期阶段土壤的细菌总数、菌群丰富度及复杂程度最高。不同演替阶段细菌群落结构存在显著差异,其中,针阔混交林的差异最大,变形菌门和酸杆菌门为各演替序列共有的优势类群,放线菌门、绿弯菌门和Patescibacteria是演替早期的优势类群,且随着演替进行呈现减少趋势;变形菌门和WPS-2相对多度随演替进行呈增加趋势。土壤pH和乔木层物种丰富度是驱动次生演替过程中土壤细菌群落组成变化的关键因子。随着演替的进行,土壤细菌多样性减少,群落组成差异加大。     

Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia

Karstic cave systems in Slovenia receive substantial amounts of organic input from adjacent forest and freshwater systems. These caves host microbial communities that consist of distinct small colonies differing in colour and shape. Visible to the naked eye, the colonies cover cave walls and are strewn with light-reflecting water droplets. In this study, the diversity of prokaryotes constituting these unusual microbial communities in Pajsarjeva jama cave was examined. A molecular survey based on small subunit rRNA diversity showed a high diversity within the Bacteria , while members of Archaea were not recovered. A total of eight bacterial phyla were detected. The application of various species richness estimators confirmed the diverse nature of the microbial community sample. Members of Gammaproteobacteria were most abundant in the clone libraries constructed and were followed in abundance by members of Actinobacteria and Nitrospira . In addition, members of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria as well as Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi and Gemmatimonadetes were identified in clone libraries. The high number of clones most closely related to environmental 16S rRNA gene clones showed the broad spectrum of unknown and yet to be cultivated microorganisms inhabiting these cave systems.     

Assessment of Bacterial Community Assembly Patterns and Processes in Pig Manure Slurry

The bacterial community assembly patterns and processes are poorly understood in pig manure slurry. We collected pig manure slurry samples during the winter and summer seasons from eight commercial pig farms in South Korea. The V3 region of 16S rRNA genes was PCR amplified and sequenced using paired-end Illumina technology for in-depth characterization of bacterial community. Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Tenericutes were the predominant bacterial phyla present in slurry samples. Bacterial taxonomic community composition was not influenced by the season; however, phylogenetic community composition was affected by seasonal variations. The community composition and diversity patterns were strongly influenced by pH. The bacterial diversity indices showed a unimodal relationship with pH. Phylogenetic signals were detected over only short phylogenetic distances, revealing that closely related bacterial operational taxonomic units (OTUs) tend to co-occur in the same environment; hence, they are ecologically similar. Across all samples, a niche-based process, through strong environmental filtering imposed by pH, primarily governed bacterial community assembly; however, in samples close to the neutral pH range, the role of environmental filtering was decreased due to neutral community assembly. In summary, pH emerged as the major physico-chemical variable in pig manure slurry that regulates the relative importance of niche-based and neutral processes in shaping the community assembly of bacteria.     

Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.     

Phylogenetic diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis

In this study, for the first time the diversity of bacteria associated with the endemic freshwater sponge Lubomirskia baicalensis collected from the Sousern Basin of Lake Baikal was investigated employing cultivation-independent approaches. In total, 102 bacterial 16S rRNA clones were screened using restriction fragment length polymorphism (RFLP) and 30 were selected for sequencing. BLASTN and phylogenetic analysis based on near full length 16S rDNA sequences showed that 22 operational taxonomic units (OTUs) were clustered in six known phyla: Actinobacteria (8 OTUs), alpha-Proteobacteria (4 OTUs), beta-Proteobacteria (4 OTUs), Verrucomicrobia (4 OTUs), Nitrospiracea (1 OTU) and Bacteroidetes (1 OTU). Remarkably all phylotypes were affiliated to uncultured microorganisms, however, all alpha-Proteobacteria sequences were closely related to bacteria derived from the freshwater sponge Spongilla lacustris. Our results reveal a high diversity in the L. baicalensis bacterial community and provide an insight into microbial ecology and diversity within freshwater sponges inhabiting the ancient Lake Baikal ecosystem.     

Changes and drivers of zooplankton diversity patterns in the middle reach of Yangtze River floodplain lakes,China

Anthropogenic habitat alteration interferes the natural aquatic habitats and the system''s hydrodynamics in the Yangtze River floodplain lakes, resulting in a serious decline in freshwater biodiversity. Zooplankton communities possess major position in freshwater ecosystems, which play essential parts in maintaining biological balance of freshwater habitats. Knowledge of processes and mechanisms for affecting variations in abundance, biomass, and diversity of zooplankton is important for maintaining biological balance of freshwater ecosystems. Here, we analyzed that the temporal and spatial changes in the structure of zooplankton community and their temporal and spatial variations respond to changes in environmental factors in the middle reach of Yangtze River floodplain lakes. The results showed that zooplankton samples were classified into 128 species, and Rotifera was the most common taxa. Significant seasonal differences were found among the abundance and diversity of zooplankton. Similarly, we also found significant seasonal differences among the biomass of zooplankton functional groups. The spatial turnover component was the main contributor to the β diversity pattern, which indicated that study areas should establish habitat restoration areas to restore regional biodiversity. The NMDS plot showed that the structure of zooplankton community exhibited significant seasonal changes, where the community structure was correlated with pH, water temperature, water depth, salinity, total nitrogen, chlorophyll‐a, and total phosphorus based on RDA. This study highlights that it is very important to ensure the floodplain ecosystem''s original state of functionality for maintaining the regional diversity of the ecosystem as a whole.     

Composition of freshwater bacterial communities associated with cyanobacterial blooms in four Swedish lakes

The diversity of freshwater bacterioplankton communities has not been extensively studied despite their key role in foodwebs and the cycling of carbon and associated major elements. In order to explore and characterize the composition of bacterioplankton associated with cyanobacterial blooms, large 16S rRNA clone libraries from four lakes experiencing such blooms were analysed. The four libraries contained 1461 clones, of which 559 were prokaryotic sequences of non-cyanobacterial origin. These clones were classified into 158 operational taxonomic units affiliated mainly with bacterial divisions commonly found in freshwater systems, e.g. Proteobacteria, Bacteriodetes, Actinobacteria, Verrucomicrobia and Planctomycetes. Richness and evenness of non-cyanobacterial clones were similar to other clone libraries obtained for freshwater bacterioplankton, suggesting that bacterial communities accompanying cyanobacterial blooms are as diverse as non-bloom communities. Many of the identified operational taxonomic units grouped with known freshwater clusters but the libraries also contained novel clusters of bacterial sequences that may be characteristic for cyanobacterial blooms. About 25% of the operational taxonomic units were detected in more than one lake. Even so, 16S rRNA heterogeneity analysis demonstrated large differences in community composition between lakes regardless of their similar characteristics and close proximity. Hence even the similar environmental conditions created by different cyanobacterial blooms may foster very dissimilar bacterial communities, which could indicate that the genetic diversity in lake bacteria have been underestimated in the past.     

The biogeography of abundant and rare bacterioplankton in the lakes and reservoirs of China

Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.     

贫营养湖泊花神湖和紫霞湖浮游细菌群落结构分析

以南京市花神湖和紫霞湖两个贫营养型湖泊为研究对象,通过构建花神湖和紫霞湖16S rRNA基因克隆文库探讨了浮游细菌群落结构组成的变化。结果表明,花神湖和紫霞湖两湖泊水体中浮游细菌群落结构相似,主要隶属于放线菌门(Actinobacteria)、蓝藻门(Cyanobacteria)、α-变形菌门(Alphaproteobacteria)、β-变形菌门(Betaproteobacteria)、杆菌门(Bacteroidetes)、浮霉菌门(Planctomycetes)、疣微菌门(Verrucomicrobia)和芽单胞菌门(Gemmatimonadetes),其中放线菌门(Actinobacteria)、蓝藻门(Cyanobacteria)、β-变形菌门(Betaproteobacteria)是优势细菌类群。两个湖泊水体中75%的细菌与GenBank中已有的未培养细菌同源性高于97%,同时在两个克隆文库中还发现了6个淡水细菌新类群。通过对低纬度区域贫营养型湖泊浮游细菌群落结构的分析,加深了我们对浮游细菌多样性的了解,表明湖泊浮游细菌多样性有待进一步认识。     

Bacterial Community Composition of South China Sea Sediments through Pyrosequencing-Based Analysis of 16S rRNA Genes

Background

Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea.

Methodology/Principal Findings

Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea.

Conclusions

This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.     

新疆沙湾冷泉沉积物的细菌系统发育多样性

为了解新疆沙湾冷泉沉积物的细菌群落组成与类群多样性,利用免培养方法直接从沙湾冷泉沉积物中提取环境总DNA,构建细菌16S rRNA基因文库。对随机挑选的241个细菌阳性克隆子进行HaeIII酶切分型得到86个可操作分类单元(OTUs),系统发育分析将其归为11个门:放线菌门(Actinobacteria),酸杆菌门(Acidobacteria),拟杆菌门(Bacteroidetes),绿菌门(Chlorobi),蓝细菌门(Cyanobacteria),厚壁菌门(Firmicutes),芽单胞菌门(Gemmatimonadetes),硝化螺旋菌门(Nitrospirae),变形菌门(Proteobacteria),浮霉菌门(Planctomycetes),疣微菌门(Verrucomicrobia)。其中酸杆菌门和变型菌门为优势类群,分别占细菌克隆文库的48%和25%。超过1/3的OTUs序列与GenBank中已存序列具有较低相似性(相似性小于95%)。此外20%左右的克隆子与固氮细菌和硝酸盐氧化细菌相关。研究结果表明,新疆沙湾冷泉沉积物中细菌种类丰富,代谢类型多样而且存在大量未知类群。