Improved Bacteriophage Genome Data is Necessary for Integrating Viral and Bacterial Ecology

The recent rise in “omics”-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases—currently, only 0.001 % of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.     

矿区高硫煤覆盖对土壤细菌群落组成和多样性的影响

【背景】土壤微生物生态研究对于矿区污染生态影响调查和矿区生态恢复都具有非常重要的意义,高硫煤覆盖对其下方土壤微生物群落的影响目前尚不清楚。【目的】探究煤矿区长期高硫煤覆盖对其下方土壤细菌群落组成和多样性产生的影响。【方法】从高硫煤矿附近煤场采集3种类型土壤样品(高硫煤覆盖层、高硫煤下方土壤、对照土壤),通过测定土壤理化性质和运用高通量测序技术研究高硫煤覆盖对土壤性质和细菌群落产生的影响。【结果】与对照土壤相比,高硫煤覆盖使其下方土壤pH值降低,硫酸盐、有机质、有效氮、有效磷含量升高。高硫煤覆盖使其下方土壤中细菌的多样性指数降低,细菌群落组成发生了较大改变。在属水平上,与对照土壤相比,高硫煤下方土壤中Bacillus的相对丰度较高;Acidiphilium与Sulfobacillus在3个样本组中的相对丰度呈现为高硫煤覆盖层>高硫煤下方土壤>对照土壤,硫氧化菌在高硫煤中的优势地位及其对下方土壤的影响由此可以得到证实。共现性网络分析表明,Acidiphilium和Sulfobacillus在高硫煤覆盖区域的土壤细菌群落中占有重要地位,对其他细菌类群影响非常大。【结论】高硫煤覆盖及硫氧化菌的优势存在,对高硫煤下方土壤的理化性质及细菌群落产生明显影响。研究结果有助于增进对矿区土壤微生物生态的认识,为高硫煤矿区生态恢复治理提供微生物学理论基础。     

From molecules to dynamic biological communities

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.     

土壤微生物群落构建理论与时空演变特征

土壤微生物作为陆地生态系统的重要组成部分,直接或间接地参与几乎所有的土壤生态过程,在物质循环、能量转换以及污染物降解等过程中都发挥着重要作用。对土壤微生物时空演变规律及其形成机制的研究,不仅是微生物演变和进化的基础科学问题,也是预测微生物及其所介导的生态功能对环境条件变化响应、适应和反馈的理论依据。讨论了土壤微生物群落的定义、测度方法和指标,认为群落是联系动植物宏观生态学与微生物生态学的基础,群落构建机制是宏观和微观生态学都需要研究的核心科学问题;从生态学的群落构建理论出发,阐述了包括生态位理论/中性理论、过程理论和多样性-稳定性理论在土壤微生物时空演变研究中的应用,以及微生物群落在时间和空间上的分布特征及其尺度效应;确立了以微生物群落构建理论为基础、不同时空尺度下土壤微生物群落演变特征为主要内容的微生物演变研究的基本框架。     

生物炭对农田土壤微生物生态的影响研究进展

生物炭作为新型土壤改良剂在国内外环境科学等领域受到广泛的关注.关于生物炭对土壤理化性质的改良研究较早,目前虽然已深入到土壤微生物生态的领域,但是大多数将土壤理化性质与土壤微生物生态分开考虑,缺乏对二者相互作用的系统评述.本文总结了施用生物炭后土壤理化性质的改变与土壤微生物群落变化之间的相互关系:生物炭不仅能够提高土壤pH值、增强土壤的持水能力、增加土壤有机质等,而且会影响土壤微生物的群落结构、改变细菌和真菌的丰度;施用生物炭后,土壤环境和土壤微生物之间互相影响互相制约,共同促进了土壤微生物生态系统的改良.本文旨在为生物炭改良农田土壤微生态的深入研究提供新的思路,从生态系统的角度促进生物炭环境效应影响的研究,使生物炭的应用更具有科学性和有效性,并对生物炭在相关领域的应用进行了展望.     

Diagnostic microbial microarrays in soil ecology

Soil microbial communities are responsible for important physiological and metabolic processes. In the last decade soil microorganisms have been frequently analysed by cultivation-independent techniques because only a minority of the natural microbial communities are accessible by cultivation. Cultivation-independent community analyses have revolutionized our understanding of soil microbial diversity and population dynamics. Nevertheless, many methods are still laborious and time-consuming, and high-throughput methods have to be applied in order to understand population shifts at a finer level and to be better able to link microbial diversity with ecosystems functioning. Microbial diagnostic microarrays (MDMs) represent a powerful tool for the parallel, high-throughput identification of many microorganisms. Three categories of MDMs have been defined based on the nature of the probe and target molecules used: phylogenetic oligonucleotide microarrays with short oligonucleotides against a phylogenetic marker gene; functional gene arrays containing probes targeting genes encoding specific functions; and community genome arrays employing whole genomes as probes. In this review, important methodological developments relevant to the application of the different types of diagnostic microarrays in soil ecology will be addressed and new approaches, needs and future directions will be identified, which might lead to a better insight into the functional activities of soil microbial communities.     

The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem''s food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu²⁺, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.     

3 次连续重复提取DNA 能较好反映土壤微生物丰度

【目的】研究同一个土壤需要反复提取几次才能在最大程度上反映土壤微生物的丰度,探讨风干土壤代替新鲜土壤用于微生物丰度研究的可行性。【方法】针对两种理化性质具有较大差异的旱地和稻田新鲜土壤及其风干土壤,分别对土壤微生物进行5次连续裂解提取DNA。通过实时荧光定量PCR技术分析连续反复提取对土壤古菌和细菌16S rRNA gene数量、氨氧化古菌和细菌功能基因amoA数量的影响。【结果】3次连续提取DNA占5次提取DNA总量的76%以上,氨氧化古菌、氨氧化细菌、古菌和细菌4类微生物的3次连续提取最低回收率为77.5%;与新鲜土壤相比,风干处理导致氨氧化古菌、氨氧化细菌、古菌、细菌的数量分别降低84.3%、81.2%、12.5%和90.3%,然而,2种土壤风干过程中主要微生物类群的数量变化规律基本一致,表明土壤微生物对风干处理的响应可能受土壤类型的影响较小。【结论】土壤微生物连续3次裂解能较好反映微生物丰度。与新鲜土壤相比,风干过程显著降低了土壤微生物丰度,然而,通过风干土壤中微生物丰度的变化趋势反映新鲜土壤中微生物数量变化规律具有一定的可行性。     

基因芯片技术在微生物学研究中的应用

近年来,基因芯片技术的诞生使得在一个实验中就可以同时对成千上万个基因进行转录水平的表达和DNA同源性分析成为可能。该项技术已被应用于揭示许多微生物体的转录表达和基因组的差异,随着越来越多的微生物基因组全序列测定的完成,基因芯片正逐渐成为许多微生物学研究领域中的一项常规技术。归纳了该技术在微生物生理,致病性,流行病学,生态,进化,代谢工程及发酵优化等研究中的应用。     

Engineering issues of microbial ecology in space agriculture]

Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define how to conduct preventive maintenance for keeping cultivating soil healthy and productive. 3) Does microbial ecology contribute to building sustainable and expandable human habitation by utilizing the on site extraterrestrial resources? We are assessing technical feasibility of converting regolith to farming soil and structural materials for space agriculture. In the case of Mars habitation, carbon dioxide and a trace amount of nitrogen in atmosphere, and potassium and phosphor in minerals are the sources we consider. Excess oxygen can be accumulated by woods cultivation and their use for lumber. 4) Is the operation of space agriculture robust and safe, if it adopts hyper-thermophilic aerobic microbial ecology? Any ecological system is complex and non-linear, and shows latency and memory effects in its response. It is highly important to understand those features to design and operate space agriculture without falling into the fatal failure. Assessment should be made on the microbial safety and preparation of the preventive measures to eliminate negative elements that would either retard agricultural production or harm the healthy environment. It is worth to mention that such space agriculture would be an effective engineering testbed to solve the global problem on energy and environment. Mars and Moon exploration itself is a good advocate of healthy curiosity expressed by the sustainable civilization of our humankind. We propose to work together towards Mars and Moon with microbial ecology to assure pleasant habitation there.     

Applying population and community ecology theory to advance understanding of belowground biogeochemistry

Approaches to quantifying and predicting soil biogeochemical cycles mostly consider microbial biomass and community composition as products of the abiotic environment. Current numerical approaches then primarily emphasise the importance of microbe–environment interactions and physiology as controls on biogeochemical cycles. Decidedly less attention has been paid to understanding control exerted by community dynamics and biotic interactions. Yet a rich literature of theoretical and empirical contributions highlights the importance of considering how variation in microbial population ecology, especially biotic interactions, is related to variation in key biogeochemical processes like soil carbon formation. We demonstrate how a population and community ecology perspective can be used to (1) understand the impact of microbial communities on biogeochemical cycles and (2) reframe current theory and models to include more detailed microbial ecology. Through a series of simulations we illustrate how density dependence and key biotic interactions, such as competition and predation, can determine the degree to which microbes regulate soil biogeochemical cycles. The ecological perspective and model simulations we present lay the foundation for developing empirical research and complementary models that explore the diversity of ecological mechanisms that operate in microbial communities to regulate biogeochemical processes.     

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt

Soil microbial communities regulate global biogeochemical cycles and respond rapidly to changing environmental conditions. However, understanding how soil microbial communities respond to climate change, and how this influences biogeochemical cycles, remains a major challenge. This is especially pertinent in alpine regions where climate change is taking place at double the rate of the global average, with large reductions in snow cover and earlier spring snowmelt expected as a consequence. Here, we show that spring snowmelt triggers an abrupt transition in the composition of soil microbial communities of alpine grassland that is closely linked to shifts in soil microbial functioning and biogeochemical pools and fluxes. Further, by experimentally manipulating snow cover we show that this abrupt seasonal transition in wide-ranging microbial and biogeochemical soil properties is advanced by earlier snowmelt. Preceding winter conditions did not change the processes that take place during snowmelt. Our findings emphasise the importance of seasonal dynamics for soil microbial communities and the biogeochemical cycles that they regulate. Moreover, our findings suggest that earlier spring snowmelt due to climate change will have far reaching consequences for microbial communities and nutrient cycling in these globally widespread alpine ecosystems.Subject terms: Metagenomics, Climate-change ecology, Microbial ecology, Biogeochemistry, Soil microbiology     

Linking soil process and microbial ecology in freshwater wetland ecosystems

Soil microorganisms mediate many processes such as nitrification, denitrification, and methanogenesis that regulate ecosystem functioning and also feed back to influence atmospheric chemistry. These processes are of particular interest in freshwater wetland ecosystems where nutrient cycling is highly responsive to fluctuating hydrology and nutrients and soil gas releases may be sensitive to climate warming. In this review we briefly summarize research from process and taxonomic approaches to the study of wetland biogeochemistry and microbial ecology, and highlight areas where further research is needed to increase our mechanistic understanding of wetland system functioning. Research in wetland biogeochemistry has most often been focused on processes (e.g., methanogenesis), and less often on microbial communities or on populations of specific microorganisms of interest. Research on process has focused on controls over, and rates of, denitrification, methanogenesis, and methanotrophy. There has been some work on sulfate and iron transformations and wetland enzyme activities. Work to date indicates an important process level role for hydrology and soil nutrient status. The impact of plant species composition on processes is potentially critical, but is as yet poorly understood. Research on microbial communities in wetland soils has primarily focused on bacteria responsible for methanogenesis, denitrification, and sulfate reduction. There has been less work on taxonomic groups such as those responsible for nitrogen fixation, or aerobic processes such as nitrification. Work on general community composition and on wetland mycorrhizal fungi is particularly sparse. The general goal of microbial research has been to understand how microbial groups respond to the environment. There has been relatively little work done on the interactions among environmental controls over process rates, environmental constraints on microbial activities and community composition, and changes in processes at the ecosystem level. Finding ways to link process-based and biochemical or gene-based assays is becoming increasingly important as we seek a mechanistic understanding of the response of wetland ecosystems to current and future anthropogenic perturbations. We discuss the potential of new approaches, and highlight areas for further research.     

土壤微生物的分离、提取与纯化研究进展

综合评述了土壤微生物提取与纯化研究的最新进展及存在的主要问题。土壤微生物的分离提取过程一般分为土壤分散、提取与纯化3个步骤。采用过滤、离心和淘选3种方法可以成功地分离提取大部分土壤细菌;但土壤真菌的提取则相对较为困难,目前可采用的方法有旋转框技术、液相提取与滤膜检测、以及低速离心技术,这些方法可提取出部分真菌菌丝。两相分离技术可用以提取的土壤微生物进行纯化。     

蚯蚓对土壤微生物残留物的影响研究评述与展望

蚯蚓如何影响土壤有机碳的固持是土壤生态学的关键科学问题之一。蚯蚓能同时促进土壤有机碳分解和稳定,这种两面作用带来的不确定性被研究者称为"蚯蚓困境"。研究证据和新兴的"土壤微生物碳泵"概念模型表明土壤微生物残留物是土壤有机质的主要贡献者。为系统了解蚯蚓对土壤微生物残留物的影响与可能的机制,研究分析和总结了已有的国内外蚯蚓与微生物残留物（氨基糖）的相关研究成果,表明：（1）过往的研究忽略了蚯蚓对微生物残留物的影响,导致这一方向的研究严重滞后;（2）蚯蚓对土壤微生物残留物影响的方向和大小仍有很大的不确定性,可供量化分析其驱动机制的研究还很缺乏。研究尝试将蚯蚓整合到"土壤微生物碳泵"概念框架中,分析蚯蚓影响土壤微生物残留物3个方面的可能机制,即：（1）改变土壤微生物量、群落结构,（2）改变微生物生理特性,（3）改变土壤团聚体结构等,影响土壤有机碳的积累。同时,本文提出了未来相关研究的6个重点方向,包括：（1）蚯蚓对微生物的选择性取食,（2）肠道介导的微生物"涨落"现象,（3）蚯蚓对矿质结合有机物的"破坏"与"重组",（4）蚯蚓引起的"激发"和"续埋"效应,（5）多生态型相互作用,（6）全球变化背景下的蚯蚓生态学等,以期为进一步揭示蚯蚓-微生物相互作用影响土壤有机碳累积与稳定性的机制提供参考。     

氮沉降对森林土壤有机质和凋落物分解的影响及其微生物学机制

氮沉降持续增加背景下土壤C∶N∶P化学计量比和pH环境等的改变及其可能的土壤微生物学机制已经成为陆地生态系统与全球变化研究的新生长点和科学研究前沿.以生态化学计量学和土壤微生物生态学为理论基础,综述了氮沉降对森林土壤有机质和凋落物分解的影响及其微生物学机制的基本理论、最新进展、研究热点与难点,旨在促进全球变化背景下陆地生态系统地下生态学的研究.氮沉降持续增加会导致森林生态系统磷循环加速,导致磷限制.氮沉降不但改变森林土壤有机质和凋落物的C∶N∶P化学计量比和降低土壤pH值,而且改变土壤微生物生物量碳氮磷、细菌、真菌和放线菌的组成以及影响碳氮磷分解的关键酶活性.氮沉降对森林土壤有机质和凋落物分解的影响表现为促进、抑制和无影响,其影响的差异可能来源于微生物效应的不同.叶片在凋落前有显著的氮磷养分回收,但是根无明显的养分回收,造成土壤有机质和凋落物的C∶N∶P化学计量比存在明显差异.基于DNA/RNA等分子生物学方法为土壤微生物生态学研究提供了强有力的手段,将促进氮沉降对森林土壤有机质和凋落物化学计量比改变的微生物学机制研究.     

Vertebrate Decomposition Is Accelerated by Soil Microbes

Carrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.     

A Coexisting Fungal-Bacterial Community Stabilizes Soil Decomposition Activity in a Microcosm Experiment

How diversity influences the stability of a community function is a major question in ecology. However, only limited empirical investigations of the diversity–stability relationship in soil microbial communities have been undertaken, despite the fundamental role of microbial communities in driving carbon and nutrient cycling in terrestrial ecosystems. In this study, we conducted a microcosm experiment to investigate the relationship between microbial diversity and stability of soil decomposition activities against changes in decomposition substrate quality by manipulating microbial community using selective biocides. We found that soil respiration rates and degradation enzyme activities by a coexisting fungal and bacterial community (a taxonomically diverse community) are more stable against changes in substrate quality (plant leaf materials) than those of a fungi-dominated or a bacteria-dominated community (less diverse community). Flexible changes in the microbial community composition and/or physiological state in the coexisting community against changes in substrate quality, as inferred by the soil lipid profile, may be the mechanism underlying this positive diversity–stability relationship. Our experiment demonstrated that the previously found positive diversity–stability relationship could also be valid in the soil microbial community. Our results also imply that the functional/taxonomic diversity and community ecology of soil microbes should be incorporated into the context of climate–ecosystem feedbacks. Changes in substrate quality, which could be induced by climate change, have impacts on decomposition process and carbon dioxide emission from soils, but such impacts may be attenuated by the functional diversity of soil microbial communities.     

Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes

The rhizosphere differs from the bulk soil in a range of biochemical, chemical and physical processes that occur as a consequence of root growth, water and nutrient uptake, respiration and rhizodeposition. These processes also affect microbial ecology and plant physiology to a considerable extent. This review concentrates on two features of this unique environment: rhizosphere geometry and heterogeneity in both space and time. Although it is often depicted as a soil cylinder of a given radius around the root, drawing a boundary between the rhizosphere and bulk soil is an impossible task because rhizosphere processes result in gradients of different sizes. For instance, because of diffusional constraints, root uptake can result in a depletion zone extending <1 mm for phosphate to several centimetres for nitrate, while respiration may affect the bulk of the soil. Rhizosphere processes are responsible for spatial and temporal heterogeneities in the soil, although these are sometimes difficult to distinguish from intrinsic soil heterogeneity. A further complexity is that these processes are regulated by plants, microbial communities and soil constituents, and their many interactions. Novel in situ techniques and modelling will help in providing a holistic view of rhizosphere functioning, which is a prerequisite for its management and manipulation.