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.     

Microbial diversity at Mitchell Peninsula,Eastern Antarctica: a potential biodiversity “hotspot”

Mitchell Peninsula is located towards the East of the Windmill Islands in eastern Antarctica. It is an ice-free polar desert, and knowledge of its soil microbial taxonomic composition is limited. In this study, we investigated the soil microbial taxonomic composition using multiplex 454 pyrosequencing targeting the bacterial 16S rRNA and the fungal ITS genes; and the bacterial and fungal abundances were estimated using quantitative PCR. In total, 40 bacterial and five fungal phyla were identified comprising 111 bacterial and 22 fungal classes, respectively. Mitchell Peninsula soil exhibited a unique bacterial taxonomic profile. In contrast to the usual dominance of Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes in polar and temperate soils, Mitchell Peninsula was rich in the poorly studied Chloroflexi (31.7 %), candidate divisions WPS-2 (8.1 %) and AD3 (5.1 %), while the commonly observed Bacteroidetes and Firmicutes were present in relative abundances below 1 %. The fungal community consisted of Ascomycota (77 %) and Basidiomycota (10 %), and was dominated by the lichenous fungal class Lecanoromycetes (46.4 %). Network analysis revealed the presence of several microbial clusters that each potentially occupied a different environmental niche, and fewer numbers of correlations were identified between bacteria within each cluster compared with the lichen community, where extensive community dynamics may be present. As Mitchell Peninsula exhibits a unique microbial taxonomic composition, not previously observed in any reported polar or temperate ecosystem, we believe it is a potential microbial biodiversity “hotspot”, which warrants further investigation to examine the role of the dominance of these uncharacterised candidate divisions in this extreme ecosystem.     

Bio-Prospecting Laccases in the Bacterial Diversity of Activated Sludge From Pulp and Paper Industry

Activated sludge is an artificial ecosystem known to harbor complex microbial communities. Bacterial diversity in activated sludge from pulp and paper industry was studied to bioprospect for laccase, the multicopper oxidase applicable in a large number of industries due to its ability to utilize a wide range of substrates. Bacterial diversity using 454 pyrosequencing and laccase diversity using degenerate primers specific to conserved copper binding domain of laccase like multicopper oxidase (LMCO) genes were investigated. 1231 OTUs out of 11,425 sequence reads for bacterial diversity and 11 OTUs out of 15 reads for LMCO diversity were formed. Phylum Proteobacteria (64.95 %) with genus Thauera (13.65 %) was most abundant followed by phylum Bacteriodetes (11.46 %) that included the dominant genera Paludibacter (1.93 %) and Lacibacter (1.32 %). In case of LMCOs, 40 % sequences showed affiliation with Proteobacteria and 46.6 % with unculturable bacteria, indicating considerable novelty, and 13.3 % with Bacteroidetes. LMCOs belonged to H and J families.     

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.     

Spatial and successional dynamics of microbial biofilm communities in a grassland stream ecosystem

Biofilms represent a metabolically active and structurally complex component of freshwater ecosystems. Ephemeral prairie streams are hydrologically harsh and prone to frequent perturbation. Elucidating both functional and structural community changes over time within prairie streams provides a general understanding of microbial responses to environmental disturbance. We examined microbial succession of biofilm communities at three sites in a third‐order stream at Konza Prairie over a 2‐ to 64‐day period. Microbial abundance (bacterial abundance, chlorophyll a concentrations) increased and never plateaued during the experiment. Net primary productivity (net balance of oxygen consumption and production) of the developing biofilms did not differ statistically from zero until 64 days suggesting a balance of the use of autochthonous and allochthonous energy sources until late succession. Bacterial communities (MiSeq analyses of the V4 region of 16S rRNA) established quickly. Bacterial richness, diversity and evenness were high after 2 days and increased over time. Several dominant bacterial phyla (Beta‐, Alphaproteobacteria, Bacteroidetes, Gemmatimonadetes, Acidobacteria, Chloroflexi) and genera (Luteolibacter, Flavobacterium, Gemmatimonas, Hydrogenophaga) differed in relative abundance over space and time. Bacterial community composition differed across both space and successional time. Pairwise comparisons of phylogenetic turnover in bacterial community composition indicated that early‐stage succession (≤16 days) was driven by stochastic processes, whereas later stages were driven by deterministic selection regardless of site. Our data suggest that microbial biofilms predictably develop both functionally and structurally indicating distinct successional trajectories of bacterial communities in this ecosystem.     

Effect of electrode potentials on the microbial community of photo bioelectrochemical systems

Increasing attention is being paid to the adoption of photoautotrophic microbes in bioelectrochemical systems (BESs) because of the advantages of self-sustainability. Biased potential on the anode was capable of adjusting the performance of non-photo BESs, and the microbial community structure was also changed; however, few studies have been conducted to investigate the effects of potential on microbial community structure in photo-BESs. In this work, the response of microbial community structure to different potentials (i.e., 0, 0.2, 0.4 and 0.6 V vs. Ag/AgCl) was characterized with 454 pyrosequencing. Four samples were collected and they generated 42865 16S rDNA sequencing reads with an average length of 429 bp. The potential at 0.2 V resulted in the highest current density (378.8 mA m^?2) and showed a strong selection for γ-proteobacteria (30.8% of the sequences). α-Diversity analysis showed that microbial diversity increased with increased potential. Rhodopseudomonas palustris was dominant among known exoelectrogens in the biofilm biased at 0.4 V. The results provided an insight into the mechanism of potential regulation on the performance of photo-BESs and changes in microbial community structure.     

CVTree在454高通量测序分析菌群结构中的应用

目的探究将基于短串频度的CVTree方法用于反映菌群结构的16S rRNA基因的454高通量测序数据分析的可行性,为快速分析高通量菌群结构数据提供新的方法。方法对一个四世同堂的中国家庭7名成员肠道菌群和不同基因型及饮食类型的小鼠肠道菌群用454高通量方法获得16S rRNA基因的V3区的测序数据,用CVTree的方法进行菌群结构的比较分析。结果通过选取合适的短串长度,CVTree的方法能准确检测到各样本间的聚类关系,其结果与之前文献报道的基于Unifrac算法的结果相一致。结论CVTree能快速、有效地处理16S rRNA基因的454高通量测序数据,实现对不同菌群结构相似性的比较分析。     

Discovery and evaluation of candidate sex-determining genes and xenobiotics in the gonads of lake sturgeon (Acipenser fulvescens)

Modern pyrosequencing has the potential to uncover many interesting aspects of genome evolution, even in lineages where genomic resources are scarce. In particular, 454 pyrosequencing of nonmodel species has been used to characterize expressed sequence tags, xenobiotics, gene ontologies, and relative levels of gene expression. Herein, we use pyrosequencing to study the evolution of genes expressed in the gonads of a polyploid fish, the lake sturgeon (Acipenser fulvescens). Using 454 pyrosequencing of transcribed genes, we produced more than 125 MB of sequence data from 473,577 high-quality sequencing reads. Sequences that passed stringent quality control thresholds were assembled into 12,791 male contigs and 32,629 female contigs. Average depth of coverage was 4.2 × for the male assembly and 5.5× for the female assembly. Analytical rarefaction indicates that our assemblies include most of the genes expressed in lake sturgeon gonads. Over 86,700 sequencing reads were assigned gene ontologies, many to general housekeeping genes like protein, RNA, and ion binding genes. We searched specifically for sex determining genes and documented significant sex differences in the expression of two genes involved in animal sex determination, DMRT1 and TRA-1. DMRT1 is the master sex determining gene in birds and in medaka (Oryzias latipes) whereas TRA-1 helps direct sexual differentiation in nematodes. We also searched the lake sturgeon assembly for evidence of xenobiotic organisms that may exist as endosymbionts. Our results suggest that exogenous parasites (trematodes) and pathogens (protozoans) apparently have infected lake sturgeon gonads, and the trematodes have horizontally transferred some genes to the lake sturgeon genome.     

Composition and dynamics of microbial community in a zeolite biofilter-membrane bioreactor treating coking wastewater

In this study, a lab-scale anaerobic/anoxic/zeolite biofilter-membrane bioreactor (A₁/A₂/ZB-MBR) was designed to treat coking wastewater. The 454 pyrosequencing was used to obtain the composition and dynamics of microbial community about the treatment system. The results showed that the system yielded stable effluent chemical oxidation demand (158.5?±?21.8 mg/L) and ammonia (8.56?±?7.30 mg/L), but fluctuant total nitrogen (31.4–165.1 mg/L) concentrations. In addition, 66,256 16S rRNA gene sequences were obtained from A₂ and ZB-MBR, and the microbial diversity and richness for five samples were determined. Although community compositions in the five samples were quite different, bacteria assigned to phylum Proteobacteria and class Flavobacteria commonly existed and dominated the microbial populations. The pyrosequencing analysis revealed that the microbial community shifted in the ZB-MBR with the presence of zeolite. Some taxa began to appear in ZB-MBR and contributed to the system performance. Additionally, Nitrosomonas and Nitrobacter gradually became the dominant ammonia-oxidizing bacteria and nitrite-oxidizing bacteria during the operation, respectively, which are favorable for the stabilized ammonia removal. Our results proved that the ZB-MBR is an alternative technique for treating coking wastewater.     

Eukaryotic microbial communities in hypersaline soils and sediments from the alkaline hypersaline Huama Lake as revealed by 454 pyrosequencing

In hypersaline ecosystems, microbial assemblages are structurally distinctive and play important roles in many microbiological and ecological processes. Here, eukaryotic microorganisms in hypersaline samples were investigated by 454 pyrosequencing of internal transcribed spacer (ITS) gene libraries. In total, 4,645, 1,677, and 5,912 reads were obtained from ITS libraries of waterlogged samples, salt crusts, and saline loess from the alkaline Huama Lake in Shaanxi, China. Analyses of pyrosequencing data revealed that the dominant genera were Dunaliella, Alternaria and Chlamydomonas, which dominated the microbial assemblages in the waterlogged sediments, the salt crusts and the saline loess from the lake banks, respectively. The various infrequent species were not commonly shared by the three types of samples, demonstrating that the eukaryotic microbial compositions of the different environments were distinct. However, the micro-eukaryotic assemblages associated with similar environmental conditions shared some components and were phylogenetically related. The eukaryotic microbial community composition was correlated with the pH value of the site (p = 0.001; r² = 0.99), but not with the concentration of total nitrogen or the inorganic ions investigated in this study. The results of this study demonstrated that the hypersaline ecosystems hosted surprisingly diverse eukaryotic microbial community.     

Functional rigidity of a methane biofilter during the temporal microbial succession

Temporal microbial succession was investigated in relation to the performance of a methane biofilter. A laboratory-scale biofilter packed with perlite was operated for 108 days, without a deliberate biomass control. The system performance was stable over the period with a mean elimination capacity of 1,563 g m^?3 day^?1, despite a temporal deterioration (45–56 days). Ribosomal-tag pyrosequencing showed that bacterial communities at days 14–28 were distinct from those of days 68–108. The accumulation of nonviable substances strongly coincided with the community change (R ²?>?0.97). Rhodobacter, Hydrogenophaga, and Methylomonas were dominated in the earlier period, while Methylocaldum and Methylococcus were abundant in the later period. The methanotrophic proportion gradually increased to 41 %, and type I methanotrophs became predominant over time. However, community structure and methanotrophic population density stably retained over time, allowing the system to keep the similar performance. Therefore, the perlite biofilter system was functionally rigid against the temporal microbial succession.     

Unraveling assembly of stream biofilm communities

Microbial biofilms assemble from cells that attach to a surface, where they develop into matrix-enclosed communities. Mechanistic insights into community assembly are crucial to better understand the functioning of natural biofilms, which drive key ecosystem processes in numerous aquatic habitats. We studied the role of the suspended microbial community as the source of the biofilm community in three streams using terminal-restriction fragment length polymorphism and 454 pyrosequencing of the 16S ribosomal RNA (rRNA) and the 16S rRNA gene (as a measure for the active and the bulk community, respectively). Diversity was consistently lower in the biofilm communities than in the suspended stream water communities. We propose that the higher diversity in the suspended communities is supported by continuous inflow from various sources within the catchment. Community composition clearly differed between biofilms and suspended communities, whereas biofilm communities were similar in all three streams. This suggests that biofilm assembly did not simply reflect differences in the source communities, but that certain microbial groups from the source community proliferate in the biofilm. We compared the biofilm communities with random samples of the respective community suspended in the stream water. This analysis confirmed that stochastic dispersal from the source community was unlikely to shape the observed community composition of the biofilms, in support of species sorting as a major biofilm assembly mechanism. Bulk and active populations generated comparable patterns of community composition in the biofilms and the suspended communities, which suggests similar assembly controls on these populations.     

Disturbances due to increased salinity and the resilience of zooplankton communities: the potential role of the resting egg bank

When faced with disturbances such as increased salinity, aquatic communities inhabiting inland coastal systems change and may or may not be resilient after salinity decreases. The purpose of this study was to assess the potential role of the resting egg bank for zooplankton community resilience. We predicted that (1) hatching of resting eggs is inhibited by increased salinities and (2) resting eggs remain viable when exposed to salinity and hatch when returned to freshwater. At the community level, we evaluated the hatching responses and the short-term viability of resting eggs exposed to a salinity gradient. The hatching of resting eggs was inhibited at higher salinities (16.0 and 32.0 g l^?1). However, some resting eggs remained viable and hatched when returned to freshwater. Additionally, combining our experimental results to previously published field data, we observed that the pattern of hatching during exposure to salinity matches the temporal succession observed in the zooplankton community at our model system, after increased salinity. The recovery of zooplankton communities after disturbances involving increased salinity is likely facilitated by the presence of an egg bank. This finding has important implications for the recovery of zooplankton communities and the management of aquatic systems vulnerable to salinization worldwide.     

Biogeochemical Stoichiometry Reveals P and N Limitation Across the Post-glacial Landscape of Denali National Park,Alaska

Global warming has accelerated glacial retreat in high-elevation and high-latitude ecosystems, exposing new terrain that can undergo predictable patterns of ecosystem succession, especially in coastal areas with relatively mild climates. However, little work has been done in harsher high-elevation and inland areas where the rate of plant and microbial succession may be greatly slowed by dryness and low temperatures. The present study is the first to address microbial succession at a major glacial foreland (the Middle Fork Toklat Glacier) in the interior of Alaska. We used a spatially nested sampling regime to reveal the landscape patterns in microbial activity and biogeochemical pools during the pre-plant stage of primary succession along this high-elevation and high-latitude chronosequence. Recently deglaciated soils (0–10 years) were colonized by a diverse microbial community that included many chemoautotrophs that likely subsist on high levels of un-weathered minerals (for example, pyrite) found at this site. Rates of N-fixation and extracellular enzyme activities were very low in the youngest soils sampled, but increased during the first 20 years of succession coinciding with a decrease in TOC and C:N levels. In older soils (20–54 years), TOC and TON increased and IN became undetectable perhaps indicating N limitation. Indicators of microbial activity stopped increasing 20 years post de-glaciation and remained at levels well below those seen at lower elevation and lower latitude sites, perhaps indicating severe nutrient limitations. Stoichiometric analyses also indicated phosphorus and nitrogen limitation across the entire chronosequence, with no indication of carbon limitation of microbial activity. These results indicate that nutrient limitation, rather than the constraints of a severe climate, may be the dominant factor slowing the rate of succession at high-latitude and high-altitude glacial forelands.     

Diversity of bacterioplankton in coastal seawaters of Fildes Peninsula,King George Island,Antarctica

The bacterioplankton not only serves critical functions in marine nutrient cycles, but can also serve as indicators of the marine environment. The compositions of bacterial communities in the surface seawater of Ardley Cove and Great Wall Cove were analyzed using a 16S rRNA multiplex 454 pyrosequencing approach. Similar patterns of bacterial composition were found between the two coves, in which Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria were the dominant members of the bacterioplankton communities. In addition, a large fraction of the bacterial sequence reads (on average 5.3 % per station) could not be assigned below the domain level. Compared with Ardley Cove, Great Wall Cove showed higher chlorophyll and particulate organic carbon concentrations and exhibited relatively lower bacterial richness and diversity. Inferred metabolisms of summer bacterioplankton in the two coves were characterized by chemoheterotrophy and photoheterotrophy. Results suggest that some cosmopolitan species (e.g., Polaribacter and Sulfitobacter) belonging to a few bacterial groups that usually dominate in marine bacterioplankton communities may have similar ecological functions in similar marine environments but at different geographic locations.     

Establishing a core microbiome in acetate-fed microbial fuel cells

Establishing a core microbiome is the first step in understanding and subsequently optimizing microbial interactions in anodic biofilms of microbial fuel cells (MFCs) for increased power, efficiency, and decreased start-up times. In the present study, we used 454 pyrosequencing to demonstrate that a core anodic community would consistently emerge over a period of 4 years given similar conditions. The development and variation across reactor designs of these communities was also explored. The core members present in all high-power generating biofilms were Geobacter, Aminiphilus, Sedimentibacter, Acetoanaerobium, and Spirochaeta, accounting for 72?±?9 % of all genera. Aminiphilus spp., member of the Synergistetes phylum was present at higher abundances than previously reported in any other ecological studies. Results suggest a stable core microbiome in acetate-fed MFCs on both phylogenetic and functional levels.     

Geomicrobiological Changes in Two Ephemeral Desert Playa Lakes in the Western United States

The geochemistry and microbiology of two ephemeral playa lakes in the Western United States, Surprise Valley Alkali Lake (SVAL) and Eldorado Playa (EP), were examined over one wetting cycle, revealing dramatic temporal changes in suspended mineralogy, aqueous chemistry, and bacterial populations. In SVAL the predominant suspended mineral changed from smectite to vermiculite and clinoptilolite, which led to a depletion of soluble Mg²⁺. Nitrate became depleted in both playas as a result of biological nitrogen demand imparted by unusually dense microbial communities reaching ～1 × 10⁸ cultivable heterotrophs per ml of water. One hundred eighty eight bacterial isolates were obtained, representing sixty phylotypes and four phyla: Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes. Phylogenetic analyses suggested that the microbial communities reflected different phases of succession, with SVAL changing from a diverse community with abundant Yonghaparkia to a less diverse late summer community with abundant Bacteroidetes and Proteobacteria such as Loktanella, Rhodobaca, Saccharospirillum, Flexibacter, and phylogenetically novel members of the Flexibacteriaceae. In EP, a diverse assemblage of bacteria often associated with soils was replaced very quickly by a much less even community dominated by Yonghaparkia, Sandarakinorhabdus, and relatives of Belliella baltica. Strikingly, the early summer microbial community from SVAL was not significantly different from the EP community that developed within one week of flooding, even though these playas are almost 1000 km apart, whereas sympatric communities in different phases of succession were different. To our knowledge, this is one of the first geomicrobiological studies of a recharge playa, the dominant playa type worldwide.     

贝壳砂改良土壤中反硝化细菌的分析

【目的】通过对一处经过长期使用贝壳砂进行改良的土壤中的反硝化细菌的多样性和细菌分离分析,研究该土壤中反硝化细菌的组成特征。【方法】采用454焦磷酸测序的方法分析了土壤样品中微生物群落的组成,选用Giltay培养基培养、鉴定从土壤中挑选的分离物的反硝化能力,并对具有反硝化能力的微生物进行了16S rRNA基因鉴定。【结果】该土壤样品中占据优势地位的为Proteobacteria、Acidobacteria、Bacteroidetes、Chloroflexi等门的微生物,属的水平上则有近70%尚未确立分类地位。所分离的细菌中,共得到12株厌氧条件下具有较高硝酸盐去除效率的微生物,分属Pseudomonas、Aeromonas、Serratia和Acinetobacter,均为γ变形菌纲的微生物。【结论】该土壤中具有较高的微生物多样性,包括很多未知类型的微生物和众多类型的反硝化细菌;分离到了11株具有反硝化能力的菌株,可用于该土壤的反硝化过程的进一步研究。     

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.     

松嫩平原碱化草甸恢复演替系列的群落种子流分析

对松嫩平原碱化草甸恢复演替系列4个群落优势种种子源库、土壤种子库及幼苗库进行了比较,建立了种子流模型.结果表明:演替初期虎尾草群落优势种种子源库密度最大,为(446182±180455)粒.m-2,分别是演替中期星星草群落的7.2倍、演替后期星星草 羊草群落的11.4倍、演替顶极羊草群落的164.8倍.土壤种子库和幼苗库密度均以虎尾草群落最大,分别为(63650±14541)粒.m-2和(39160±15192)株.m-2,羊草群落最小,分别为(14310±7686)粒.m-2和(790±745)株.m-2,大体呈随着恢复演替进程而递减的趋势.全体演替系列群落输出的实生苗均以虎尾草为主,占79.8%～100%.在种子流中,优势种的种子源库向土壤种子库输入率在10%～35%之间,输出率差异则较大,虎尾草群落高达62.3%,但星星草群落和羊草群落均没有优势种的幼苗输出.