Diversity Analysis of Bacterial Community from Permafrost Soil of Mo-he in China

The permafrost soil of Mo-he in Northeast China presents a typical cold environment colonized by psychrophilic microorganisms. This study is aimed at assessing the bacterial communities of permafrost soil of Mo-he in China by sequencing the 16S rRNA genes and Mothur analysis. PCR products with universal 16S rRNA gene primers were cloned and partially sequenced, and bacterial identification at the species was performed by comparative analysis with the GenBank/EMBL/DDBJ database. A total of 266 clones were obtained with the average length of 1,050 bp. Mothur analysis showed that the coverage value of clone library was 53.78 %, Shannon diversity (H) was 4.03, Simpson diversity value was 0.018, and 74 operational taxonomic units were generated. Through phylogenetic assignment using BLASTN by more than 97 % similarity, a total of 87 tentative taxa were identified. The majority of bacterial sequences recovered in this study belonged to the Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi and Chlorobi. Among them, Acidobacteria are dominant community, accounting for 30.1 % of total bacteria, followed by Proteobacteria which accounted for 22.2 %. This result reflected the acidic characteristics of the permafrost soil of which pH value was 6.0. Our study indicated that the permafrost soil of Mo-he in China has a high diversity of bacteria and represents a vast potential resource of novel bacteria. As far as we knew, this is the first report on bacterial diversity of permafrost soil of Mo-he in China.     

Mucosa-Associated Bacterial Diversity in Necrotizing Enterocolitis

Background

Previous studies of infant fecal samples have failed to clarify the role of gut bacteria in the pathogenesis of NEC. We sought to characterize bacterial communities within intestinal tissue resected from infants with and without NEC.

Methods

26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. Analysis allowed for taxonomic identification, and quantitative PCR was used to quantify the bacterial load within samples.

Results

NEC samples generally contained an increased total burden of bacteria. NEC and non-NEC sample sets were both marked by high inter-individual variability and an abundance of opportunistic pathogens. There was no statistically significant distinction between the composition of NEC and non-NEC microbial communities. K-means clustering enabled us to identify several stable clusters, including clusters of NEC and midgut volvulus samples enriched with Clostridium and Bacteroides. Another cluster containing both NEC and non-NEC samples was marked by an abundance of Enterobacteriaceae and decreased diversity among NEC samples.

Conclusions

The results indicate that NEC is a disease without a uniform pattern of microbial colonization, but that NEC is associated with an abundance of strict anaerobes and a decrease in community diversity.     

Interactive Effects of Viral and Bacterial Production on Marine Bacterial Diversity

A general model of species diversity predicts that the latter is maximized when productivity and disturbance are balanced. Based on this model, we hypothesized that the response of bacterial diversity to the ratio of viral to bacterial production (VP/BP) would be dome-shaped. In order to test this hypothesis, we obtained data on changes in bacterial communities (determined by terminal restriction fragment length polymorphism of 16S rRNA gene) along a wide VP/BP gradient (more than two orders of magnitude), using seawater incubations from NW Mediterranean surface waters, i.e., control and treatments with additions of phosphate, viruses, or both. In December, one dominant Operational Taxonomic Unit accounted for the major fraction of total amplified DNA in the phosphate addition treatment (75±20%, ± S.D.), but its contribution was low in the phosphate and virus addition treatment (23±19%), indicating that viruses prevented the prevalence of taxa that were competitively superior in phosphate-replete conditions. In contrast, in February, the single taxon predominance in the community was held in the phosphate addition treatment even with addition of viruses. We observed statistically robust dome-shaped response patterns of bacterial diversity to VP/BP, with significantly high bacterial diversity at intermediate VP/BP. This was consistent with our model-based hypothesis, indicating that bacterial production and viral-induced mortality interactively affect bacterial diversity in seawater.     

Diversity of Bacterial Endosymbionts of Environmental Acanthamoeba Isolates

Free-living amoebae are frequent hosts for bacterial endosymbionts. In this study, the symbionts of eight novel environmental Acanthamoeba strains isolated from different locations worldwide were characterized. Phylogenetic analysis revealed that they were related to one of four evolutionary lineages of amoeba symbionts recognized previously. This study provides evidence for the existence of only a small number of phylogenetically well-separated groups of obligate intracellular endosymbionts of acanthamoebae with global distribution.     

五氯酚厌氧生物降解体系中细菌的多样性分析

为了解五氯酚(PCP)降解过程中参与PCP降解的微生物多样性,本文应用16S rRNA基因克隆文库方法对PCP厌氧生物降解体系中细菌群落的组成和相对丰度进行了研究.结果表明,TM7类群的微生物在整个细菌群落中占有最大丰度(48.6%),检测到的序列与在三氯乙烯污染的地下水中检测的克隆子有一定的序列相似性(93.6%).丰度位居第二的微生物类群为β-变形菌纲(Betaproteobacteria)细菌,其中的一些克隆子(10.8%)与脱氯微生物Dechlorosoma suillum具有极高的序列同缘性(99.7%).此外,也检测到少数Clostridium属[厚壁菌门(Firmicutes)类群]的微生物.克隆文库中发现许多序列(占整个克隆文库的51.3%)与GenBank中已报道的序列具有较远的同源性(小于93.4%),它们可能代表新的微生物.本研究进一步拓宽了对PCP降解微生物多样性的认识.     

A Modular View of the Diversity of Cell-Density-Encoding Schemes in Bacterial Quorum-Sensing Systems

Certain environmental parameters are accessible to cells only indirectly and require an encoding step for cells to retrieve the relevant information. A prominent example is the phenomenon of quorum sensing by microorganisms, where information about cell density is encoded by means of secreted signaling molecules. The mapping of cell density to signal molecule concentration and the corresponding network modules involved have been at least partially characterized in many bacteria, and vary markedly between different systems. In this study, we investigate theoretically how differences in signal transport, signal modification, and site of signal detection shape the encoding function and affect the sensitivity and the noise characteristics of the cell-density-encoding process. We find that different modules are capable of implementing both fairly basic as well as more complex encoding schemes, whose qualitative characteristics vary with cell density and are linked to network architecture, providing the basis for a hierarchical classification scheme. We exploit the tight relationship between encoding behavior and network architecture to constrain the network topology of partially characterized natural systems, and verify one such prediction by showing experimentally that Vibrio harveyi is capable of importing Autoinducer 2. The framework developed in this research can serve not only to guide reverse engineering of natural systems but also to stimulate the design of synthetic systems and generally facilitate a better understanding of the complexities arising in the quorum-sensing process because of variations in the physical organization of the encoder network module.     

Bacterial Diversity of Lonar Soda Lake of India

Total seventy four bacteria were isolated from Lonar soda lake of Maharashtra state, India. Eleven isolates were identified using morphological, biochemical and molecular analysis. The bacteria isolated belonged to phylum firmicutes and proteobacteria. Majorities (eight) were firmicutes and three were proteobacteria. For the first time we are reporting Alcanivorax spp. which is a genus well known for its oil degradation capacity, indicate the probable existence of oil reservoir in vicinity of Lonar lake. In addition all the eleven bacteria are potential producers of industrially important enzymes, pigments, antibiotics as well.     

Ultraviolet Radiation Alters Maize Phyllosphere Bacterial Diversity

Epiphytic bacteria are subjected to very stressful environments, including UV radiation. Bacterial assemblages on Zea mays (maize) leaves exposure were examined with and without UV-B radiation. Culture-independent molecular techniques were utilized for bacterial identification, diversity analysis and selection of putative UV exposure marker sequences. Few sequences corresponded to previously characterized phyllosphere bacteria. There was a strong tendency toward increased 16S rDNA sequence diversity in UV samples. Overall community structure was assessed using denaturing gel gradient electrophoresis; significant alterations in community structure were found in comparisons of phyllosphere bacterial samples from control and solar UV-B exposed plants.     

Bacterial Diversity of Weathered Terrestrial Icelandic Volcanic Glasses

The diversity of microbial communities inhabiting two terrestrial volcanic glasses of contrasting mineralogy and age was characterised. Basaltic glass from a <0.8 Ma hyaloclastite deposit (Valafell) harboured a more diverse Bacteria community than the younger rhyolitic glass from ～150-300 AD (D?madalshraun lava flow). Actinobacteria dominated 16S rRNA gene clone libraries from both sites, however, Proteobacteria, Acidobacteria and Cyanobacteria were also numerically abundant in each. A significant proportion (15-34%) of the sequenced clones displayed <85% sequence similarities with current database sequences, thus suggesting the presence of novel microbial diversity in each volcanic glass. The majority of clone sequences shared the greatest similarity to uncultured organisms, mainly from soil environments, among these clones from Antarctic environments and Hawaiian and Andean volcanic deposits. Additionally, a large number of clones within the Cyanobacteria and Proteobacteria were more similar to sequences from other lithic environments, included among these Icelandic clones from crystalline basalt and rhyolite, however, no similarities to sequences reported from marine volcanic glasses were observed. PhyloChip analysis detected substantially greater numbers of phylotypes at both sites than the corresponding clone libraries, but nonetheless also identified the basaltic glass community as the richer, containing approximately 29% unique phylotypes compared to rhyolitic glass.     

A New Framework to Accurately Quantify Soil Bacterial Community Diversity from DGGE

Denaturing gradient gel electrophoresis (DGGE) has been and remains extensively used to assess and monitor the effects of various treatments on soil bacterial communities. Considering only abundant phylotypes, the diversity estimates produced by this technique have been proven to be uncorrelated to true community diversity. The aim of this paper was to develop a framework to estimate a community’s true diversity from DGGE. Developed using in silico DGGE profiles generated from published pyrosequencing datasets, this framework elongates the rank-abundance distributions (RADs) drawn by band quantification using the peak-to-signal ratio (PSR) parameter, which was proven to be related to bacterial richness. The ability to compare DGGE-based diversity estimates to the true diversity of communities led to a unique opportunity to identify potential pitfalls when analyzing DGGE gels with commercial analysis software programs and gain insight into the process of DNA band clustering in the profiles. Bacterial diversity was compared through richness, Shannon, and Simpson’s 1/D indices. Intermediate results demonstrated that, even though commercial gel analysis software programs were unable to produce consistent results throughout all samples, a newly developed Matlab-based framework unraveled the dominance profiles of communities from band quantification. Elongating these partial RADs using the PSRs extracted from the DGGE profiles chiefly made it possible to accurately estimate the true diversity of communities. For all the samples analyzed, the estimated Shannon and Simpson’s 1/D were accurate at ±10 %. Richness estimations were less accurate, ranging from ?11 to 31 % of the expected values. The framework showed great potential to study the structure and diversity of soil bacterial communities.     

宜春温泉水体与泉底沉积物细菌多样性分析

研究宜春富硒温泉水体与泉底沉积物的细菌群落多样性。利用高通量测序技术分析泉水与沉积物中细菌群落结构与多样性。温泉水中主要的细菌类群为变形菌门和拟杆菌门,而在沉积物样品中的主要优势菌群为OP1、蓝细菌、浮霉菌门和绿弯菌门。细菌在属分类水平上,温泉水中优势菌群为不动杆菌属、假单胞菌属、水栖菌属、Thermosynechococcus、鞘脂杆菌属和金黄杆菌属等。沉积物样品细菌中优势菌群属于未知物种,在数据库中并没有相关的注释信息;其中已知的优势菌属为Candidatus acetothermum、Thermosynechococcus、亚热栖菌属、不动杆菌属。宜春温汤富硒温泉水体与沉积物中存在着丰富的微生物群落且组成差异性很大,该研究为了解与发掘温泉微生物菌种资源具有重要价值。     

Bacterial Diversity in Agricultural Soils during Litter Decomposition

Denaturing gradient gel electrophoresis (DGGE) of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of crop residues in agricultural soils. Ten strains were tested, and eight of these strains produced a single band. Furthermore, a mixture of strains yielded distinguishable bands. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. A field experiment performed with litter in nylon bags was used to evaluate the bacterial diversity during the decomposition of readily degradable rye and more refractory wheat material in comparable luvisols and cambisols in northern, central, and southern Germany. The amount of bacterial DNA in the fresh litter was small. The DNA content increased rapidly after the litter was added to the soil, particularly in the rapidly decomposing rye material. Concurrently, diversity indices, such as the Shannon-Weaver index, evenness, and equitability, which were calculated from the number and relative abundance (intensity) of the bacterial DNA bands amplified from genes coding for 16S rRNA, increased during the course of decomposition. This general trend was not significant for evenness and equitability at any time. The indices were higher for the more degradation-resistant wheat straw than for the more easily decomposed rye grass. Thus, the DNA band patterns indicated that there was increasing bacterial diversity as decomposition proceeded and substrate quality decreased. The bacterial diversity differed for the sites in northern, central, and southern Germany, where the same litter material was buried in the soil. This shows that in addition to litter type climate, vegetation, and indigenous microbes in the surrounding soil affected the development of the bacterial communities in the litter.     

Bacterial Diversity in Linglong Gold Mine,China

Bacteria have been actively regulating cycles of various elements in the environment. To explore the potential bacterial role in gold biogeochemical cycling, this study analyzed the bacterial diversity of mine rock (MR) and surface soil (SS) samples from Linglong gold mine using 16S rRNA gene clone library analysis and cultivation method. From MR, 24 operational taxonomic units (OTUs) were identified from MR, covering 3 phyla and 18 genera. Meanwhile, 24 OTUs were identified from SS, including 4 phyla and 18 genera. Compared with 16S rRNA gene clone library analysis, 28 aerobic and 34 anaerobic isolates were obtained, whereas 26 aerobic and 71 anaerobic strains were isolated from SS. The cultivable bacteria were affiliated with Firmicutes, Proteobacteria and Actinobacteria phyla, and dominated by Firmicutes. These results underscore the high level of bacterial diversity in the gold mine. Our study provides information on the microbial diversity in Linglong gold mine and sheds light on the existence and potential function of bacteria in the gold biogeochemical cycling.     

Diversity of Bacterial Communities in Container Habitats of Mosquitoes

We investigated the bacterial diversity of microbial communities in water-filled, human-made and natural container habitats of the mosquitoes Aedes aegypti and Aedes albopictus in suburban landscapes of New Orleans, Louisiana in 2003. We collected water samples from three classes of containers, including tires (n = 12), cemetery urns (n = 23), and miscellaneous containers that included two tree holes (n = 19). Total genomic DNA was extracted from water samples, and 16S ribosomal DNA fragments (operational taxonomic units, OTUs) were amplified by PCR and separated by denaturing gradient gel electrophoresis (DGGE). The bacterial communities in containers represented diverse DGGE-DNA banding patterns that were not related to the class of container or to the local spatial distribution of containers. Mean richness and evenness of OTUs were highest in water samples from tires. Bacterial phylotypes were identified by comparative sequence analysis of 90 16S rDNA DGGE band amplicons. The majority of sequences were placed in five major taxa: Alpha-, Beta- and Gammaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and an unclassified group; Proteobacteria and Bacteroidetes were the predominant heterotrophic bacteria in containers. The bacterial communities in human-made containers consisted mainly of undescribed species, and a phylogenetic analysis based on 16S rRNA sequences suggested that species composition was independent of both container type and the spatial distribution of containers. Comparative PCR-based, cultivation-independent rRNA surveys of microbial communities associated with mosquito habitats can provide significant insight into community organization and dynamics of bacterial species. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.