Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes

Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within- and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters. The euphotic zone, deep chlorophyll maximum and 890 m depth each contain two negatively correlated ‘modules'' (groups of many inter-correlated bacteria and environmental conditions) suggesting regular transitions between two contrasting environmental states. Two-thirds of pairwise correlations of bacterial taxa between depths lagged such that changes in the abundance of deeper organisms followed changes in shallower organisms. Taken in conjunction with previous observations of seasonality at 890 m, these trends suggest that planktonic microbial communities throughout the water column are linked to environmental conditions and/or microbial communities in overlying waters. Poorly understood groups including Marine Group A, Nitrospina and AEGEAN-169 clades contained taxa that showed diverse association patterns, suggesting these groups contain multiple ecological species, each shaped by different factors, which we have started to delineate. These observations build upon previous work at this location, lending further credence to the hypothesis that sinking particles and vertically migrating animals transport materials that significantly shape the time-varying patterns of microbial community composition.     

Extracellular enzymes in terrestrial, freshwater, and marine environments: perspectives on system variability and common research needs

Extracellular enzymes produced by heterotrophic microbial communities are major drivers of carbon and nutrient cycling in terrestrial, freshwater, and marine environments. Although carbon and nutrient cycles are coupled on global scales, studies of extracellular enzymes associated with terrestrial, freshwater, and marine microbial communities are not often compared across ecosystems. In part, this disconnect arises because the environmental parameters that control enzyme activities in terrestrial and freshwater systems, such as temperature, pH, and moisture content, have little explanatory power for patterns of enzyme activities in marine systems. Instead, factors such as the functional diversity of microbial communities may explain varying patterns of enzyme activities observed in the ocean to date. In any case, many studies across systems focus on similar issues that highlight the commonalities of microbial community organization. Examples include the effective lifetime of enzymes released into the environment; the extent to which microbial communities coordinate enzyme expression to decompose complex organic substrates; and the influence of microbial community composition on enzyme activities and kinetics. Here we review the often-disparate research foci in terrestrial, freshwater, and marine environments. We consider the extent to which environmental factors may regulate extracellular enzyme activities within each ecosystem, and highlight commonalities and current methodological challenges to identify research questions that may aid in integrating cross-system perspectives in the future.     

土壤微生物多样性海拔格局研究进展

生物多样性的海拔分布格局与维持机制是生物多样性与生态系统功能研究的热点领域。相比动植物多样性海拔分布格局,土壤微生物多样性海拔分布格局的研究还处在起步阶段。近年来,随着以罗氏454、Illumina Mi Seq等为代表的高通量测序平台的发展,土壤微生物海拔梯度分布格局的研究进展较快。对土壤微生物多样性海拔分布格局最新研究综述发现,土壤微生物海拔分布模式并不明确,表现为无趋势、下降、单峰或者下凹型等多种海拔分布模式。这与大型动植物并不相同,暗示其驱动机制可能存在一定的差异。微生物由于其个体微小、扩散能力强以及较高的多样性和个体丰度而在局域尺度上可能更易受到气候环境因素的影响。土壤pH、碳、氮等因子是影响微生物多样性和群落组成在海拔梯度上变异的重要因素。此外,温度和降水也具有重要作用。另外,除微生物自身属性以及取样限制外,测序深度可能是影响土壤微生物物种丰富度海拔分布格局的重要因素。目前,对土壤微生物群落的研究在功能基因、群落构建机制以及生态学理论的验证方面还存在着不足。未来的研究应进一步加大测序深度,增加取样密度,着重关注全球气候变化及生物多样性丧失背景下土壤微生物群落的构建和维持机制及其生态系统功能等方面。     

Spatial scaling of arbuscular mycorrhizal fungal diversity is affected by farming practice

Evidence suggests that microbial communities show patterns of spatial scaling which can be driven by geographical distance and environmental heterogeneity. Here we demonstrate that human management can have a major impact on microbial distribution patterns at both the local and landscape scale. Mycorrhizal fungi are vital components of terrestrial ecosystems, forming a mutualistic symbiosis with plant roots which has a major impact on above ground ecology and productivity. We used contrasting agricultural systems to investigate the spatial scaling of the most widespread mycorrhizal fungus group, the arbuscular mycorrhizal fungi (AMF). Using multiple sampling sites with a maximum separation of 250 km we describe for the first time the roles which land management, environmental heterogeneity and geographical distance play in determining spatial patterns of microbial distribution. Analysis of AMF taxa–area relationships at each sampling site revealed that AMF diversity and spatial turnover was greater under organic relative to conventional farm management. At the regional scale (250 km) distance–decay analyses showed that there was significant change in AMF community composition with distance, and that this was greater under organic relative to conventional management. Environmental heterogeneity was found to be the major factor determining turnover of AMF taxa at the landscape scale. Overall we demonstrate that human management can play a key role in determining the turnover of microbial communities at both the local and regional scales.     

Significance of microbial interactions in control of microbial ecosystems

A microbial ecosystem represents a delicately balanced population of microorganisms each interacting with and influencing the other members of the population. An understanding of the nature and effects of these interactions is essential to improving the performance of these ecologies, which are important, in such diverse processes as biological waste treatment procedures, water pollution abatement, industrial fermentations, human or animal digestives processes and in soil. There are several types of mocrobial interactions, such as commensalism, inhibition, food competition, predation, parasitism, and synergism, which either singly or in combination may influence the functioning of the microbial ecology. To understand interactions, it is necessary to perform a detailed study of the physiology of the individual predominating microorganisms to establish their requirements with respect to such environmental factors as nutrients, temperature, pH, oxidation-reduction potential, removal of waste products, or toxic materials which may be involved in control processes and to determine how these factors affect their capabilities. The sum total of this information will indicate the possible interactions between the microorganisms and will form the basis for conducting experiments either in the laboratory or with mathematical models. Such experiments will lead to an understanding of microbial activities and to the formulation of control measures, often using an alteration of the environmental factors for regulation of the microbial ecologies. Extensive research remains to be done on the microbial interact inns in obtain the desired, precise control of these ecological processes.     

中国东海微型鞭毛虫群落的分布特征及其环境影响因子

海洋微型鞭毛虫是海洋原生生物中一类高度异质化的类群,物种多样性高,具有多种营养方式,在全球海洋生态系统中占据广阔的生态位,在生物地球化学循环中发挥着关键作用。然而关于其生物多样性和群落结构的认识十分有限,特别是有关环境因子与其生物地理分布关系的研究更为罕见。为了探究微型鞭毛虫群落多样性、群落结构以及影响其生物地理分布格局的环境因素,将高通量测序技术与传统的显微镜观测方法相结合,全面调查了中国东海春季和秋季微型鞭毛虫的群落特征,并深入探讨了与环境因子之间的关系。结果表明：东海微型鞭毛虫的丰度平均为2.27×10~3个/mL,表现为近岸处较高、随离岸距离的增加而下降的趋势;Shannon多样性指数呈现表层低于底层、近岸区低于陆架区的特征,反映了生物群落的稳定程度以及对环境条件的适应程度;不同类群的鞭毛虫具有各自独特的营养模式和相对固定的粒级,表现出对温度、盐度、溶解氧等环境因素的不同响应,从而使群落的物种组成和分布模式呈现明显的季节变化和生境差异。研究结果可为深入认识东海海洋微型鞭毛虫的群落结构、分布格局以及环境影响因素提供理论依据。     

It’s the song,not the singer: an exploration of holobiosis and evolutionary theory

That holobionts (microbial communities and their animal or plant hosts) are units of selection squares poorly with the observation that microbes are often recruited (horizontally acquired) from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what is of interest in holobiont thinking, we propose casting metabolic and developmental interaction patterns, rather than the taxa responsible for them, as units of selection. Such units need not directly reproduce or form parent-offspring lineages: their prior existence has created the conditions under which taxa with the genes necessary to carry out their steps have evolved in large numbers. These taxa or genes will reconstruct the original interaction patterns when favorable conditions occur. Interaction patterns will vary (for instance by the alteration or addition of intermediates) in ways that affect the likelihood of and circumstances under which such reconstruction occurs. Thus, they vary in fitness, and evolution by natural selection will occur at this level. It is on the persistence, reconstruction, and spread of such interaction patterns that students of holobiosis should concentrate, we suggest. This model also addresses other multi-species collectively beneficial interactions, such as biofilms or biogeochemical cycles maintaining all life.     

基因芯片技术在环境微生物群落研究中的应用

基因芯片技术作为一种快速、敏感、高通量的检测技术,近几年来在环境微生物群落研究中的应用越来越广泛并且得到充分的发展.它不仅可以研究环境微生物群落的微生物分布、种类、功能、动力学变化,还能分析环境污染等环境因素改变对其微生物生态的影响.本文按照基因芯片探针的设计方法,将环境样品群落研究基因芯片分为系统寡核苷酸芯片、功能基因芯片、群落基因组芯片、宏基因组芯片,并简要综述了该技术在活性污泥、土壤、水等环境样品微生物群落研究上的应用,最后,本文展望了该技术的研究方向和在寻找不同环境微生物群落之间差异微生物、差异基因或差异表达基因研究中的应用前景.     

空间组织模式：微生物群落组装的“游戏”规则

在生物膜形成过程中,微生物种群之间通过主动或者被动的生物过程所形成的独特空间结构被称为空间组织模式。微生物空间组织模式广泛存在于自然和人工环境中,比如医疗、工业和生态系统等,是微生物形成和维持特定群落结构并发挥功能的主要方式,也是形成和维持微生物群落多样性的关键机制。然而,由于微生物群落的复杂性及相关研究方法的局限性,微生物空间组织模式方面的研究目前仍然处于起始阶段。本文梳理了微生物空间组织模式领域的研究进展,系统总结了空间组织模式初始阶段（微生物界面附着）和成熟阶段（空间自组织）的形成过程与协同机制,以及其对微生物养分利用和元素循环、微生物多样性维持和种群进化及功能的影响和调控机制,并分析了影响微生物空间组织模式的关键环境因素。     

Mesocosms of Aquatic Bacterial Communities from the Cuatro Cienegas Basin (Mexico): A Tool to Test Bacterial Community Response to Environmental Stress

Microbial communities are responsible for important ecosystem processes, and their activities are regulated by environmental factors such as temperature and solar ultraviolet radiation. Here we investigate changes in aquatic microbial community structure, diversity, and evenness in response to changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with both microbial mat communities and plankton from natural pools within the Cuatro Cienegas Basin (Mexico). Clone libraries (16S rRNA) were obtained from water samples at the beginning and at the end of the experiment (40 days). Phylogenetic analysis indicated substantial changes in aquatic community composition and structure in response to temperature and UV radiation. Extreme treatments with elevation in temperature or UV radiation reduced diversity in relation to the Control treatments, causing a reduction in richness and increase in dominance, with a proliferation of a few resistant operational taxonomic units. Each phylum was affected differentially by the new conditions, which translates in a differential modification of ecosystem functioning. This suggests that the impact of environmental stress, at least at short term, will reshape the aquatic bacterial communities of this unique ecosystem. This work also demonstrates the possibility of designing manageable synthetic microbial community ecosystems where controlled environmental variables can be manipulated. Therefore, microbial model systems offer a complementary approach to field and laboratory studies of global research problems associated with the environment.     

Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature

Recent studies have focused on linking marine microbial communities with environmental factors, yet, relatively little is known about the drivers of microbial community patterns across the complex gradients from the nearshore to open ocean. Here, we examine microbial dynamics in 15 five-station transects beginning at the estuarine Piver's Island Coastal Observatory (PICO) time-series site and continuing 87 km across the continental shelf to the oligotrophic waters of the Sargasso Sea. 16S rRNA gene libraries reveal strong clustering by sampling site with distinct nearshore, continental shelf and offshore oceanic communities. Water temperature and distance from shore (which serves as a proxy for gradients in factors such as productivity, terrestrial input and nutrients) both most influence community composition. However, at the phylotype level, modelling shows the distribution of some taxa is linked to temperature, others to distance from shore and some by both factors, highlighting that taxa with distinct environmental preferences underlie apparent clustering by station. Thus, continental margins contain microbial communities that are distinct from those of either the nearshore or the offshore environments and contain mixtures of phylotypes with nearshore or offshore preferences rather than those unique to the shelf environment.     

微生物性状揭示物种分布格局、群落构建机制和生态系统功能

微生物性状是指与其存活、生长和繁殖紧密相关的一系列核心属性,这些属性能够反映微生物对环境变化的响应,进而影响微生物的物种分布格局、群落构建机制以及相应的生态系统功能。越来越多的研究表明,相比于微生物分类学信息,微生物性状可以在种群、群落和生态系统尺度等视角扩展我们对微生物生态过程的理解,并提供生态模式的机理性解释。本文回顾微生物性状研究的发展历程,总结近年来基于微生物性状研究的前沿科学问题,比如微生物性状的分类和测定方法、基于性状的功能多样性定义及应用、性状与物种分布格局和群落构建机制的关系、性状对生物多样性和生态系统功能的影响以及对环境变化的响应等。尽管微生物性状研究已经延伸到生态学领域的各个方面,有力推动着各个前沿科学问题的研究发展,但是仍然面临很多机遇与挑战。因此,本文也从研究方法和研究方向等方面对未来基于微生物性状的研究提出了展望。     

绿弯菌的研究现状及展望

绿弯菌是一个深度分支的门级别细菌类群,广泛分布于生物圈各种生境。现已生效发表的绿弯菌构成9个纲,但仅包含56个种;基于分子生态学的研究结果表明尚有大量绿弯菌类群仍是未培养状态。绿弯菌形态多样,营养方式和代谢途径十分丰富,参与了C、N、S等一系列重要生源元素的生物地球化学循环过程。研究该类群不仅有助于认识环境中微生物的多样性及其代谢特征,从而更好的理解微生物参与的生态学过程,还有助于揭示微生物对环境的适应及其进化。本文主要综述了绿弯菌的发现历史、营养、代谢及其在元素循环中的作用,并总结了其分离培养和潜在应用价值,最后展望了未来的研究方向,旨在为深入探究绿弯菌的进化、培养和驱动地球化学元素循环等研究提供参考。     

Contrasting Microbial Community Assembly Hypotheses: A Reconciling Tale from the Río Tinto

Background

The Río Tinto (RT) is distinguished from other acid mine drainage systems by its natural and ancient origins. Microbial life from all three domains flourishes in this ecosystem, but bacteria dominate metabolic processes that perpetuate environmental extremes. While the patchy geochemistry of the RT likely influences the dynamics of bacterial populations, demonstrating which environmental variables shape microbial diversity and unveiling the mechanisms underlying observed patterns, remain major challenges in microbial ecology whose answers rely upon detailed assessments of community structures coupled with fine-scale measurements of physico-chemical parameters.

Methodology/Principal Findings

By using high-throughput environmental tag sequencing we achieved saturation of richness estimators for the first time in the RT. We found that environmental factors dictate the distribution of the most abundant taxa in this system, but stochastic niche differentiation processes, such as mutation and dispersal, also contribute to observed diversity patterns.

Conclusions/Significance

We predict that studies providing clues to the evolutionary and ecological processes underlying microbial distributions will reconcile the ongoing debate between the Baas Becking vs. Hubbell community assembly hypotheses.     

Do bacterial and fungal communities assemble differently during primary succession?

High‐throughput sequencing technologies are now allowing us to study patterns of community assembly for diverse microbial assemblages across environmental gradients and during succession. Here we discuss potential explanations for similarities and differences in bacterial and fungal community assembly patterns along a soil chronosequence in the foreland of a receding glacier. Although the data are not entirely conclusive, they do indicate that successional trajectories for bacteria and fungi may be quite different. Recent empirical and theoretical studies indicate that smaller microbes (like most bacteria) are less likely to be dispersal limited than are larger microbes – which could result in a more deterministic community assembly pattern for bacteria during primary succession. Many bacteria are also better adapted (than are fungi) to life in barren, early‐successional sediments in that some can fix nitrogen and carbon from the atmosphere – traits not possessed by any fungi. Other differences between bacteria and fungi are discussed, but it is apparent from this and other recent studies of microbial succession that we are a long way from understanding the mechanistic underpinnings of microbial community assembly during ecosystem succession. We especially need a better understanding of global and regional patterns of microbial dispersal and what environmental factors control the development of microbial communities in complex natural systems.     

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.     

Metaproteomics: studying functional gene expression in microbial ecosystems

The recent availability of extensive metagenomic sequences from various environmental microbial communities has extended the postgenomic era to the field of environmental microbiology. Although still restricted to a small number of studies, metaproteomic investigations have revealed interesting aspects of functional gene expression within microbial habitats that contain limited microbial diversity. These studies highlight the potential of proteomics for the study of microbial consortia. However, the application of proteomic investigations to complex microbial assemblages such as seawater and soil still presents considerable challenges. Nonetheless, metaproteomics will enhance the understanding of the microbial world and link microbial community composition to function.     

Phylogenetic distance–decay patterns are not explained by local community assembly processes in freshwater lake microbial communities

While water and sediment microbial communities exhibit pronounced spatio-temporal patterns in freshwater lakes, the underlying drivers are yet poorly understood. Here, we evaluated the importance of spatial and temporal variation in abiotic environmental factors for bacterial and microeukaryotic community assembly and distance–decay relationships in water and sediment niches in Hongze Lake. By sampling across the whole lake during both Autumn and Spring sampling time points, we show that only bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers. Nevertheless, consistent distance–decay relationships were found with both bacterial and microeukaryotic communities, which were relatively stable with both sampling time points. Our results suggest that spatio-temporal variation in environmental factors was important in explaining mainly bacterial community assembly in the sediment, possibly due lesser disturbance. However, clear distance–decay patterns emerged also when the community assembly was stochastic. Together, these results suggest that abiotic environmental factors do not clearly drive the spatial structuring of lake microbial communities, highlighting the need to understand the role of other potential drivers, such as spatial heterogeneity and biotic species interactions.     

Seasonal marine microorganisms change neighbours under contrasting environmental conditions

Marine picoplankton contribute to global carbon sequestration and nutrient recycling. These processes are directly related to the composition of communities, which in turn depends on microbial interactions and environmental forcing. Under regular seasonal cycles, marine communities show strong predictable patterns of annual re-occurrences, but little is known about the effect of environmental perturbation on their organization. The aim of our study was to investigate the co-occurrence patterns of planktonic picoeukaryote, bacteria and archaea under contrasting environmental conditions. The study was designed to have high sampling frequency that could match both the biological rhythm of marine microbes and the short time scale of extreme weather events. Our results show that microbial networks changed from year to year depending on conditions. In addition, individual taxa became less interconnected and changed neighbours, which revealed an unfaithful relationship between marine microorganisms. This unexpected pattern suggests possible switches between organisms that have similar specific functions, or hints at the presence of organisms that share similar environmental niches without interacting. Despite the observed annual changes, the time series showed re-occurring communities that appear to recover from perturbations. Changing co-occurrence patterns between marine microorganisms may allow the long-term stability of ecosystems exposed to contrasting meteorological events.