若尔盖高原泥炭沼泽湿地土壤细菌群落空间分布及其驱动机制

了解高原泥炭沼泽湿地生态系统土壤微生物群落结构组成、多样性及空间分布特征对认识高原湿地生态特征及演化过程至关重要。利用高通量测序技术，在局域尺度上研究了四川若尔盖高原泥炭沼泽湿地土壤细菌群落结构与多样性特征。通过进一步测定土壤及植物基本理化指标，量化采样点之间的地理距离，比较了细菌群落不同成员（稀有种和丰富种）的空间周转差异，分析了土壤环境变量和空间因子对细菌群落结构的相对贡献。结果表明：若尔盖泥炭土壤细菌群落主要由绿弯菌门（Chloroflexi）（26.25%）、变形菌门（Proteobacteria）（23.21%）、厚壁菌门（Firmicutes）（10.56%）等优势物种门类组成；土壤细菌群落结构表现出较强的空间依赖关系，群落结构相似性随采样点地理距离增加而逐渐降低，细菌群落的周转速率表现为总细菌群落 > 丰富种 > 稀有种；Mantel检验结果显示，地上生物量与细菌群落呈极显著相关性（P<0.01），其中，影响稀有种空间分布特征的环境因子还包括土壤硫含量、活性磷、Mn和土壤pH值；方差分解分析表明，局域尺度上的土壤因子对若尔盖高原泥炭沼泽土壤细菌群落构建的相对贡献大于空间因子，土壤异质性是影响微生物空间分布特征的关键因素。研究为开展高原湿地泥炭土壤微生物多样性调查及揭示微生物群落构建机制提供了重要参考。     

Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

Purpose

To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil.

Method

A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions.

Result

The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

     

Characterization of the prokaryotic diversity through a stratigraphic permafrost core profile from the Qinghai-Tibet Plateau

Permafrost on the Qinghai-Tibet Plateau is one of the most sensitive regions to climate warming, thus characterizing its microbial diversity and community composition may be important for understanding their potential responses to climate changes. Here, we investigated the prokaryotic diversity in a 10-m-long permafrost core from the Qinghai-Tibet Plateau by restriction fragment length polymorphism analysis targeting the 16S rRNA gene. We detected 191 and 17 bacterial and archaeal phylotypes representing 14 and 2 distinct phyla, respectively. Proteobacteria was the dominant bacterial phylum, while archaeal communities were characterized by a preponderance of Thaumarchaeota. Some of prokaryotic phylotypes were closely related to characterized species involved in carbon and nitrogen cycles, including nitrogen fixation, methane oxidation and nitrification. However, the majority of the phylotypes were only distantly related to known taxa at order or species level, suggesting the potential of novel diversity. Additionally, both bacterial α diversity and community composition changed significantly with sampling depth, where these communities mainly distributed according to core horizons. Arthrobacter-related phylotypes presented at high relative abundance in two active layer soils, while the deeper permafrost soils were dominated by Psychrobacter-related clones. Changes in bacterial community composition were correlated with most measured soil variables, such as carbon and nitrogen contents, pH, and conductivity.     

环境选择和扩散限制驱动温带森林土壤细菌群落的构建

环境选择和扩散限制是生态系统中生物群落构建的两个基本过程,而两者相对作用的大小因研究尺度、群落属性和类型等有所不同.目前对温带亚高山森林土壤微生物群落构建的驱动因子和机制尚缺乏了解.本文利用PCR-DGGE技术研究庞泉沟自然保护区内5种典型森林包括华北落叶松林、青杄林、白杄林、油松林以及桦树林的6个森林土壤细菌群落(Lp MC1、Lp MC2、Pw MC、Pm MC、Pt MC、BMC)的结构特征及其影响因素,分析细菌群落结构与环境因子的相关性,以及土壤因子、植被和空间因素对细菌群落结构的影响.结果表明:研究区各样地土壤细菌群落的结构和生物多样性具有显著差异,低海拔落叶松和油松土壤细菌群落多样性较高(20条带),白杄林土壤细菌群落(13条带)多样性最低,高海拔落叶松土壤细菌群落多样性最高;土壤环境因子,如pH、土壤含水量、总碳、总氮、土壤有机质、速效磷以及土壤酶活性与土壤细菌群落多样性和结构显著相关;样地土壤细菌群落的beta多样性与群落的空间距离呈显著相关,表明扩散限制对群落结构具有一定的影响;方差分解分析结果显示,6个样地细菌群落结构的驱动因素大小依次为土壤因子(0.27)、空间因素(0.19)和植被(0.15);将区域土壤微生物作为"源群落",微宇宙试验结果显示,土壤因子是细菌群落结构形成的主要驱动力(0.35),同时源群落丰富的物种多样性对微宇宙土壤细菌群落结构具有显著影响.总之,在局域尺度下,环境选择对温带森林土壤细菌群落结构动态和多样性发挥主导作用,地理距离对群落结构具有显著影响,即确定性过程和随机过程共同决定局域森林土壤细菌群落结构,前者占主导地位.对于土壤细菌群落而言,扩散群落的组成和结构受到源群落的多样性特征和环境因子的双重影响.     

五大连池火山土壤细菌多样性及其群落结构

火山熔岩生境孕育了独特的土壤微生物群落。为了解火山生态系统土壤细菌群落多样性和群落结构及其关键影响因子,选择五大连池新、老期火山为研究样点,非火山为对照,基于高通量测序方法,分析不同采样点土壤细菌群落结构和多样性,结合土壤理化指标,进一步分析影响火山生态系统土壤细菌群落多样性的环境因子。结果表明：细菌操作分类单元（OTUs）、Ace指数、Chao1指数和Simpson指数变化趋势一致,表现为非火山 > 新期火山 > 老期火山。三个样点土壤的共有OUTs数量为713个,各自特有的OTUs数量不尽相同。三个样点土壤中检测到共有细菌16个类群,其中变形菌门、酸杆菌门、放线菌门和绿弯菌门为优势菌群,老期火山土壤中酸杆菌门、疣微菌门、Rokubacteria相对丰度最大,而Patescibacteria相对丰度最小。三个样点的土壤细菌群落具有明显的空间关系,相似性差异较大,但不符合随地理距离的增加而降低的模型。土壤理化性质测定结果标明：老期火山土壤pH、有机质、全氮、全磷、铵态氮和硝态氮显著高于新期火山和非火山,新期火山土壤含水量和速效磷显著低于老期火山和非火山。喷发时间和火成岩基质等特性会导致不同火山土壤理化性质的差异,进而影响土壤细菌多样性和群落结构。Pearson相关性分析表明：土壤pH显著影响细菌的多样性指数。冗余分析（RDA）结果表明：土壤氮含量、pH和有机质是影响火山森林生态系统土壤细菌群落结构的主要因子。     

Patterns of functional and taxonomic organization of stream fishes: inferences based on α, β, and γ diversities

The primary objective of this study was to determine whether total biodiversity (γ) is partitioned into within‐community (α) and among‐community (β) components differently for taxonomic and functional organization. I hypothesized that α diversity will contribute more to the functional organization of γ diversity and that β diversity will contribute more to the taxonomic organization of γ diversity. A secondary objective was to determine whether the relationship between taxonomic and functional diversity is scale dependent. Species abundance data was obtained from fisheries surveys conducted by the Texas Parks and Wildlife Dept that focused on least disturbed streams from 11 different ecoregions of Texas, including 62 localities from 18 drainages. Functional and taxonomic organization of assemblages was quantified with two different measures of biodiversity, including richness and the numbers equivalent of Shannon diversity. Scale‐dependent effects on these indices were assessed by multiplicatively partitioning γ into α and β components. The contribution of α and β components to γ diversity differed between functional and taxonomic organization and among different measures of biodiversity. Among‐community components were more influential in structuring the taxonomic organization of stream‐fish assemblages, whereas within‐community components were more important in structuring the functional organization of assemblages. The relationship between taxonomic and functional diversity differed between α and β components and between spatial scales. Indeed, ecological patterns not only change with spatial scale, but how they change is dependent on which aspect of biodiversity is considered.     

Response of fungal, bacterial and ureolytic communities to synthetic sheep urine deposition in a grassland soil

In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.     

Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales

The extent to which the distribution of soil bacteria is controlled by local environment vs. spatial factors (e.g. dispersal, colonization limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here, we constrained environmental factors (soil chemistry, climate, above‐ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 10² km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilization) was also shown to be highly correlated with community structure, but not to abiotic factors, suggesting nonstochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio‐temporal patterns of microbial diversity, as well as life history of the groups being investigated, much as is the case for macro‐organisms.     

Terrestrial origin of bacterial communities in complex boreal freshwater networks

Bacteria inhabiting boreal freshwaters are part of metacommunities where local assemblages are often linked by the flow of water in the landscape, yet the resulting spatial structure and the boundaries of the network metacommunity have never been explored. Here, we reconstruct the spatial structure of the bacterial metacommunity in a complex boreal aquatic network by determining the taxonomic composition of bacterial communities along the entire terrestrial/aquatic continuum, including soil and soilwaters, headwater streams, large rivers and lakes. We show that the network metacommunity has a directional spatial structure driven by a common terrestrial origin of aquatic communities, which are numerically dominated by taxa recruited from soils. Local community assembly is driven by variations along the hydrological continuum in the balance between mass effects and species sorting of terrestrial taxa, and seems further influenced by priority effects related to the spatial sequence of entry of soil bacteria into the network.     

稻田土壤亚硝酸盐型甲烷厌氧氧化菌群落结构的时空特征

稻田是温室气体甲烷的重要排放源之一,对全球气候变化具有重要影响.由隶属于NC10门的Candidatus Methylomirabilis oxyfera(M.oxyfera)-like细菌介导的亚硝酸盐型甲烷厌氧氧化是控制稻田甲烷排放的新途径.目前,有关此类微生物群落在稻田土壤中的时空分布特征及其环境影响因素尚不明确...     

Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing

Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [(13)C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the (13)C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or (12)C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the (13)C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.     

Land use and climatic factors structure regional patterns in soil microbial communities

Aim  Although patterns are emerging for macroorganisms, we have limited understanding of the factors determining soil microbial community composition and productivity at large spatial extents. The overall objective of this study was to discern the drivers of microbial community composition at the extent of biogeographical provinces and regions. We hypothesized that factors associated with land use and climate would drive soil microbial community composition and biomass.
Location  Great Basin Province, Desert Province and California Floristic Province, California, USA.
Methods  Using phospholipid fatty acid analysis, we compared microbial communities across eight land-use types sampled throughout the State of California, USA ( n = 1117).
Results  The main factor driving composition and microbial biomass was land-use type, especially as related to water availability and disturbance. Dry soils were more enriched in Gram-negative bacteria and fungi, and wetter soils were more enriched in Gram-positive, anaerobic and sulphate-reducing bacteria. Microbial biomass was lowest in ecosystems with the wettest and driest soils. Disturbed soils had less fungal and more Gram-positive bacterial biomass than wildland soils. However, some factors known to influence microbial communities, such as soil pH and specific plant taxa, were not important here.
Main conclusions  Distinct microbial communities were associated with land-use types and disturbance at the regional extent. Overall, soil water availability was an important determinant of soil microbial community composition. However, because of the inclusion of managed and irrigated agricultural ecosystems, the effect of precipitation was not significant. Effects of environmental and management factors, such as flooding, tillage and irrigation, suggest that agricultural management can have larger effects on soil microbial communities than elevation and precipitation gradients.     

Architectural design influences the diversity and structure of the built environment microbiome

Buildings are complex ecosystems that house trillions of microorganisms interacting with each other, with humans and with their environment. Understanding the ecological and evolutionary processes that determine the diversity and composition of the built environment microbiome—the community of microorganisms that live indoors—is important for understanding the relationship between building design, biodiversity and human health. In this study, we used high-throughput sequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes and airborne bacterial communities at a health-care facility. We quantified airborne bacterial community structure and environmental conditions in patient rooms exposed to mechanical or window ventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities was lower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbial communities than did window-ventilated rooms. Bacterial communities in indoor environments contained many taxa that are absent or rare outdoors, including taxa closely related to potential human pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relative humidity and temperature, were correlated with the diversity and composition of indoor bacterial communities. The relative abundance of bacteria closely related to human pathogens was higher indoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity. The observed relationship between building design and airborne bacterial diversity suggests that we can manage indoor environments, altering through building design and operation the community of microbial species that potentially colonize the human microbiome during our time indoors.     

Predicting spatial patterns of soil bacteria under current and future environmental conditions

Soil bacteria are largely missing from future biodiversity assessments hindering comprehensive forecasts of ecosystem changes. Soil bacterial communities are expected to be more strongly driven by pH and less by other edaphic and climatic factors. Thus, alkalinisation or acidification along with climate change may influence soil bacteria, with subsequent influences for example on nutrient cycling and vegetation. Future forecasts of soil bacteria are therefore needed. We applied species distribution modelling (SDM) to quantify the roles of environmental factors in governing spatial abundance distribution of soil bacterial OTUs and to predict how future changes in these factors may change bacterial communities in a temperate mountain area. Models indicated that factors related to soil (especially pH), climate and/or topography explain and predict part of the abundance distribution of most OTUs. This supports the expectations that microorganisms have specific environmental requirements (i.e., niches/envelopes) and that they should accordingly respond to environmental changes. Our predictions indicate a stronger role of pH over other predictors (e.g. climate) in governing distributions of bacteria, yet the predicted future changes in bacteria communities are smaller than their current variation across space. The extent of bacterial community change predictions varies as a function of elevation, but in general, deviations from neutral soil pH are expected to decrease abundances and diversity of bacteria. Our findings highlight the need to account for edaphic changes, along with climate changes, in future forecasts of soil bacteria.Subject terms: Microbial ecology, Metagenomics, Climate-change ecology     

福建省稻田土壤细菌群落的16S rDNA-PCR-DGGE分析

用不依赖细菌培养的16S rDNA-PCR-DGGE方法对福建省6个不同地区12个取样点的稻田土壤进行细菌群落结构分析.对12份样品直接提取其总DNA,用F341GC/R534引物扩增16SrDNA基因的V3可变区,结合DGGE(denaturing gradient gel electrophoresis)技术分析样品细菌群落组成.结果表明,福建省不同地区的稻田土壤之间细菌群落结构存在较大差异.犬体上可分为闽东、闽南、闽北、闽西4个大类.同一地区的根际土和表土样品之间也存在差异,但差异相对较低,其中龙岩根际土和表土细菌群落结构相似性最大,永泰差异性最大.回收了DGGE图谱中11个条带,测序结果经过Blast比对表明其中10个条带代表的细菌是不可培养的,显示了DGGE技术的优越性.     

Bacterial Community Structure in a Semi-Arid Haloalkaline Soil Using Culture Independent Method

Bacterial community structures in two physicochemically different soils from the coastal region of Gujarat, India were investigated using PCR, 16S rRNA gene clone libraries and sequencing methods. The aim of the study was to determine the diversity of bacterial communities inhabiting haloalkaline soil from a semi-arid coastal region. The phylogenetic diversity of bacteria in a haloalkaline soil (EC 20 dS/m; pH 9.5) was compared with a normal soil (EC 0.93 dS/m; pH 7.2). Clones representing phyla Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Actinobacteria, Acidobacteria and Planctomycetes were found in both soils. Cyanobacteria, Verrucomicrobia, OP10 and Bacteria incertae sedis were detected in normal soil whereas Nitrospira was found only in haloalkaline soil. The dominant phylum in the haloalkaline soil was Bacteroidetes followed by Proteobacteria whereas normal soil was dominated by Proteobacteria and Actinobacteria. About 82% of the sequences from the haloalkaline library were related to those previously retrieved from various saline, alkaline and oil-natural gas field ecosystems whereas 50% of the sequences from normal soil resembled sequences of bacteria retrieved from agriculture-related habitats viz. agriculture fields, rhizosphere and grasslands. One third of the total sequences from both soil samples showed low BLAST identities (<95%) suggesting that these soils may harbor unique, novel taxa. Further, the correlation analysis revealed negative correlations of Shannon diversity indices and species evenness with salinity (EC) and pH but positive correlations with total carbon and total nitrogen contents of the soil samples. The haloalkaline soil exhibited less bacterial diversity and communities were significantly different from those of normal soil. In this study, the haloalkaline soil from a semi-arid region supports oligotrophic microbes.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

How Does Conversion of Natural Tropical Rainforest Ecosystems Affect Soil Bacterial and Fungal Communities in the Nile River Watershed of Uganda?

Uganda''s forests are globally important for their conservation values but are under pressure from increasing human population and consumption. In this study, we examine how conversion of natural forest affects soil bacterial and fungal communities. Comparisons in paired natural forest and human-converted sites among four locations indicated that natural forest soils consistently had higher pH, organic carbon, nitrogen, and calcium, although variation among sites was large. Despite these differences, no effect on the diversity of dominant taxa for either bacterial or fungal communities was detected, using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Composition of fungal communities did generally appear different in converted sites, but surprisingly, we did not observe a consistent pattern among sites. The spatial distribution of some taxa and community composition was associated with soil pH, organic carbon, phosphorus and sodium, suggesting that changes in soil communities were nuanced and require more robust metagenomic methods to understand the various components of the community. Given the close geographic proximity of the paired sampling sites, the similarity between natural and converted sites might be due to continued dispersal between treatments. Fungal communities showed greater environmental differentiation than bacterial communities, particularly according to soil pH. We detected biotic homogenization in converted ecosystems and substantial contribution of β-diversity to total diversity, indicating considerable geographic structure in soil biota in these forest communities. Overall, our results suggest that soil microbial communities are relatively resilient to forest conversion and despite a substantial and consistent change in the soil environment, the effects of conversion differed widely among sites. The substantial difference in soil chemistry, with generally lower nutrient quantity in converted sites, does bring into question, how long this resilience will last.     

Pyrosequencing Reveals Contrasting Soil Bacterial Diversity and Community Structure of Two Main Winter Wheat Cropping Systems in China

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat–rice (WR) and winter wheat–maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.