Exploration of deep intraterrestrial microbial life: current perspectives

Intraterrestrial life has been found at depths of several thousand metres in deep sub-sea floor sediments and in the basement crust beneath the sediments. It has also been found at up to 2800-m depth in continental sedimentary rocks, 5300-m depth in igneous rock aquifers and in fluid inclusions in ancient salt deposits from salt mines. The biomass of these intraterrestrial organisms may be equal to the total weight of all marine and terrestrial plants. The intraterrestrial microbes generally seem to be active at very low but significant rates and several investigations indicate chemolithoautotrophs to form a chemosynthetic base. Hydrogen, methane and carbon dioxide gases are continuously generated in the interior of our planet and probably constitute sustainable sources of carbon and energy for deep intraterrestrial biosphere ecosystems. Several prospective research areas are foreseen to focus on the importance of microbial communities for metabolic processes such as anaerobic utilisation of hydrocarbons and anaerobic methane oxidation.     

微生物物种多样性、群落构建与功能性状研究进展

微生物主要包括细菌、真菌、古菌、病毒等类群, 是地球上出现时间最早、分布最广泛、个体数量最多, 以及物种和基因多样性十分丰富的生物类群。为了适应各种生境, 微生物衍生出腐生、寄生、共生等多样的生存策略, 在生物地球化学循环、生态系统演替与稳定性、环境修复以及人类健康等方面发挥着重要作用。传统的微生物监测方法限制了我们对微生物多样性的认知; 但是, 近年来高通量测序技术和生物信息学的发展极大推动了微生物多样性的研究进展。本文概述了近年来在微生物多样性分布格局与维持、群落构建以及功能属性多样性的最新进展; 总结分析了细菌、古菌、真菌的多样性纬度分布格局及其驱动因子, 选择、扩散、成种、漂变等过程对细菌、古菌、真菌的群落构建的贡献, 以及细菌和真菌的形态、生理生化、生长繁殖、扩散、基因组等功能性状的多样性; 提出了未来微生物多样性研究的重要领域: 环境宏真菌组研究, 微生物多样性与生态系统多功能性的关系研究, 以及微生物互作网络的生态功能研究。     

海洋沉积物微生物介导有机碳转化研究进展

海洋沉积物是地球上最大的有机碳库,其中生存的微生物总量大、分布范围广、类群多样、代谢方式复杂,并共同构成海洋沉积物微生物组。海洋沉积物微生物组介导的有机碳降解与矿化过程不但能为沉积物中的生命活动提供物质和能量,也能参与调控碳循环过程,并在长时间尺度上对地球气候系统产生重大影响。沉积物中的有机碳在复杂多样的微生物代谢活动下被逐步降解,其最终的矿化过程与不同的电子受体消耗相偶合,并形成对应的地球化学分区。研究海洋沉积物微生物及其介导的有机碳转化过程对我们深入认识沉积物中的元素循环过程,并进一步评估其对整个地球系统的影响具有重要科学意义。本文对海洋沉积物微生物组的体量、包含的微生物多样性、代谢活性以及在不同地球化学分区中主要的微生物类群和代谢机制进行综述,最后基于研究现状展望了海洋沉积物微生物组的未来研究方向。     

土壤动物多样性及其生态功能

土壤无脊椎动物生物量通常小于土壤生物总生物量的10%,但它们种类丰富,取食行为及生活史策略多种多样,且土壤动物之间,土壤动物与微生物之间存在着复杂的相互作用关系。土壤动物的生态功能主要通过取食作用(trophic effect)和非取食作用(non-trophic effect)来实现。原生动物数量大、周转快,故原生动物本身的代谢活动(即取食作用)对碳氮矿化的贡献可以接近甚至超过细菌的贡献;然而大多数中小型土壤动物的本身代谢过程对碳氮矿化的贡献远低于土壤微生物,但它们可以通过取食作用来调节微生物进而影响碳氮的矿化。大型节肢动物中的蜘蛛和地表甲虫等捕食者经常活跃于地表,它们常常会通过级联效应对土壤生态系统产生重要的影响。蚯蚓、白蚁等大型土壤动物除可以通过取食作用以外,还可以通过非取食作用调控土壤微生物,进而显著影响土壤碳氮过程。土壤动物取食行为的多样性和复杂的非营养关系的存在造就了多维度的土壤食物网,给土壤动物的生态功能研究带来了巨大的挑战。介绍了土壤动物的多样性及主要的生态功能,并对研究的热点和前沿问题进行了探讨,以期引起关于土壤动物多样性及其生态功能的深入思考。     

Interactions between exotic invasive plants and soil microbes in the rhizosphere suggest that 'everything is not everywhere'

BACKGROUND: The study of soil biota in the context of exotic plant invasions has led to an explosion in our understanding of the ecological roles of many different groups of microbes that function in roots or at the root-soil interface. Part of this progress has been the emergence of two biogeographic patterns involving invasive plants and soil microbes. First, in their non-native ranges invasive plants commonly interact differently with the same soil microbes than native plants. Second, in their native ranges, plants that are invasive elsewhere commonly interact functionally with soil microbes differently in their home ranges than they do in their non-native ranges. These studies pose a challenge to a long-held paradigm about microbial biogeography - the idea that microbes are not limited by dispersal and are thus free from the basic taxonomic, biogeographical and evolutionary framework that characterizes all other life on Earth. As an analogy, the global distribution of animals that function as carnivores does not negate the fascinating evolutionary biogeographic patterns of carnivores. Other challenges to this notion come from new measurements of genetic differences among microbes across geographic boundaries, which also suggest that meaningful biogeographic patterns exist for microorganisms. SCOPE AND CONCLUSIONS: We expand this discussion of whether or not 'everything is everywhere' by using the inherently biogeographic context of plant invasions by reviewing the literature on interactions among invasive plants and the microorganisms in the rhizosphere. We find that these interactions can be delineated at multiple scales: from individual plants to continents. Thus the microbes that regulate major aspects of plant biology do not appear to be exempt from the fundamental evolutionary processes of geographical isolation and natural selection. At the important scales of taxonomy, ecotype and ecosystem functions, the fundamental ecology of invaders and soil microbes indicates that everything might not be everywhere.     

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.     

Enhancing soil carbon storage for carbon remediation: potential contributions and constraints by microbes

Terrestrial carbon sequestration represents an important option for partially mitigating anthropogenic CO(2) emissions. Evidence suggests that terrestrial ecosystems can be managed for carbon sequestration, but it is not certain to what extent the microbes within them can be manipulated. Challenges include identifying which specific microbes and mechanisms contribute to sequestered carbon; understanding how microbial communities respond over large spatial and long temporal scales to crucial environmental variables; and developing management strategies suitable for large spatial and long temporal scales. The growing recognition that microbes produce proteins that limit organic matter degradation suggests targets for basic research. Directly manipulating microbes to sequester CO(2) through other processes such as mineral formation offers intriguing alternatives that merit further attention, but at present the prospects for practical implementation appear remote.     

The maturing of microbial ecology.

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.     

Divergence in plant and microbial allocation strategies explains continental patterns in microbial allocation and biogeochemical fluxes

Allocation trade‐offs shape ecological and biogeochemical phenomena at local to global scale. Plant allocation strategies drive major changes in ecosystem carbon cycling. Microbial allocation to enzymes that decompose carbon vs. organic nutrients may similarly affect ecosystem carbon cycling. Current solutions to this allocation problem prioritise stoichiometric tradeoffs implemented in plant ecology. These solutions may not maximise microbial growth and fitness under all conditions, because organic nutrients are also a significant carbon resource for microbes. I created multiple allocation frameworks and simulated microbial growth using a microbial explicit biogeochemical model. I demonstrate that prioritising stoichiometric trade‐offs does not optimise microbial allocation, while exploiting organic nutrients as carbon resources does. Analysis of continental‐scale enzyme data supports the allocation patterns predicted by this framework, and modelling suggests large deviations in soil C loss based on which strategy is implemented. Therefore, understanding microbial allocation strategies will likely improve our understanding of carbon cycling and climate.     

微生物胞外呼吸电子传递机制研究进展

胞外呼吸是近年来发现的新型微生物厌氧能量代谢方式,主要包括铁呼吸、腐殖质呼吸与产电呼吸3种形式。微生物胞外呼吸与传统的有氧呼吸、胞内厌氧呼吸存在显著差异。其电子受体多以固态形式存在于胞外;氧化产生的电子必须通过电子传递链从胞内转移到细胞周质和外膜,并通过外膜上的细胞色素c、纳米导线或自身产生的电子穿梭体等方式,最终将电子传递至胞外的末端受体。胞外呼吸的本质问题是微生物与胞外电子受体(铁/锰氧化物、固态电极或腐殖质等)的相互作用,即微生物如何将胞内电子传递至胞外受体。胞外呼吸的研究丰富了人们对微生物呼吸多样性的认识,同时在污染物原位修复及清洁生物能源提取方面具有重要应用前景,是当前研究的热点问题。总结了胞外呼吸类型和胞外呼吸菌的多样性,重点阐述了胞外呼吸的电子传递过程,并提出了其应用前景及今后的研究方向。     

微生物介导的碳氮循环过程对全球气候变化的响应

土壤是地球表层最为重要的碳库也是温室气体的源或汇。自工业革命以来,对土壤温室气体的容量、收支平衡和通量等已有较多研究和估算,但对关键过程及其源/汇的研究却十分有限。微生物是土壤碳氮转化的主要驱动者, 在生态系统碳氮循环过程中扮演重要的角色,对全球气候变化有着响应的响应、适应及反馈,然而其个体数量,群落结构和多样性如何与气候扰动相互关联、进而怎样影响生态系统过程的问题仍有待进一步探索。从微生物介导的碳氮循环过程入手,重点讨论微生物对气候变化包括温室气体(CO₂,CH₄,N₂O)增加、全球变暖、大气氮沉降等的响应和反馈,并由此提出削减温室气体排放的可能途径和今后发展的方向。     

Environmental diversity of bacteria and archaea

The microbial way of life spans at least 3.8 billion years of evolution. Microbial organisms are pervasive, ubiquitous, and essential components of all ecosystems. The geochemical composition of Earth's biosphere has been molded largely by microbial activities. Yet, despite the predominance of microbes during the course of life's history, general principles and theory of microbial evolution and ecology are not well developed. Until recently, investigators had no idea how accurately cultivated microorganisms represented overall microbial diversity. The development of molecular phylogenetics has recently enabled characterization of naturally occurring microbial biota without cultivation. Free from the biases of culture-based studies, molecular phylogenetic surveys have revealed a vast array of new microbial groups. Many of these new microbes are widespread and abundant among contemporary microbiota and fall within novel divisions that branch deep within the tree of life. The breadth and extent of extant microbial diversity has become much clearer. A remaining challenge for microbial biologists is to better characterize the biological properties of these newly described microbial taxa. This more comprehensive picture will provide much better perspective on the natural history, ecology, and evolution of extant microbial life.     

The Microbial Efficiency‐Matrix Stabilization (MEMS) framework integrates plant litter decomposition with soil organic matter stabilization: do labile plant inputs form stable soil organic matter?

The decomposition and transformation of above‐ and below‐ground plant detritus (litter) is the main process by which soil organic matter (SOM) is formed. Yet, research on litter decay and SOM formation has been largely uncoupled, failing to provide an effective nexus between these two fundamental processes for carbon (C) and nitrogen (N) cycling and storage. We present the current understanding of the importance of microbial substrate use efficiency and C and N allocation in controlling the proportion of plant‐derived C and N that is incorporated into SOM, and of soil matrix interactions in controlling SOM stabilization. We synthesize this understanding into the Microbial Efficiency‐Matrix Stabilization (MEMS) framework. This framework leads to the hypothesis that labile plant constituents are the dominant source of microbial products, relative to input rates, because they are utilized more efficiently by microbes. These microbial products of decomposition would thus become the main precursors of stable SOM by promoting aggregation and through strong chemical bonding to the mineral soil matrix.     

Metagenomics,biotechnology with non-culturable microbes

Metagenomics as a new field of research has been developed over the past decade to elucidate the genomes of the non-cultured microbes with the goal to better understand global microbial ecology on the one side, and on the other side it has been driven by the increasing biotechnological demands for novel enzymes and biomolecules. Since it is well accepted that the majority of all microbes has not yet been cultured, the not-yet-cultivated microbes represent a shear unlimited and intriguing resource for the development of novel genes, enzymes and chemical compounds for use in biotechnology. However, with respect to biotechnology, metagenomics faces now two major challenges. Firstly, it has to identify truly novel biocatalysts to fulfil the needs of industrial processes and green chemistry. Secondly, the already available genes and enzymes need to be implemented in production processes to further prove the value of metagenome-derived sequences.     

Fate of heterotrophic microbes in pelagic habitats: focus on populations.

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a"Gleasonian" perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.     

Fate of Heterotrophic Microbes in Pelagic Habitats: Focus on Populations

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a “Gleasonian” perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.     

基于BIOLOG技术分析氮沉降和降水对土壤微生物功能多样性的影响

土壤微生物是有机物分解和养分循环的主要介质,因此在维持土壤的功能多样性和持续性方面发挥着关键作用。气候变化驱动因素会影响土壤微生物的生理活动,引起其群落结构和功能多样性的改变,并对生物地球化学循环和气候―生态系统反馈产生连锁效应,其中氮沉降和降水是全球气候变化的研究热点。土壤氮(N)的有效性有可能通过改变微生物的群落组成以调节微生物对降水变化的响应,但目前关于N沉降和降水及其交互作用对土壤微生物群落功能多样性的影响机制仍不清楚。为了准确预测未来气候条件下生态系统的功能状况,需要更好地了解土壤微生物对环境变化的响应。基于BIOLOG技术综述了氮沉降和降水变化及其交互作用对土壤微生物功能多样性影响的相关研究进展,可以为进一步研究全球气候变化背景下地下生态学的发展提供参考。另外,分析阐述了当前工作中存在的一些主要瓶颈,并对未来的研究热点进行了探讨和展望。     

Microbial Activity in Caves−A Geological Perspective

Caves are commonly the home of diverse microbial biotas, the sites of active mineral precipitation, and/or receptacles for the deposition of sediment. Mineral precipitation is commonly considered to be abiogenic despite the fact that microbes are present in caves, especially in the twilight zone. Detailed analysis of cave substrates from a geological perspective shows that microbes can mediate constructive (microbe calcification, trapping and binding, mediation of crystal growth) and destructive (substrate etching and breakdown) processes. Potentially these processes can significantly influence the formation and preservation of any cave deposit. Preservation of microbes is possible if mineralization takes place while the microbe is alive or shortly after its demise. If not, all record of the microbe will be lost to decay. Even if the microbes are preserved, it may be difficult to determine if they played an active or passive role in the formation of the deposits in which they are entombed. For old cave deposits, such an assessment must rely on spatial relationships and comparison of textures with those known to form as a result of microbial activity. Nevertheless, available evidence indicates that microbes can play a major role in the formation and modification of cave deposits. Equally, however, it is apparent that the full scope and impact of microbial activity on cave deposits has yet to be realized. Recognition of microbial activity in old CaCO 3 cave deposits relies on (1) documentation and recognition of mineralized microbes, (2) recognition of stromatolitic structures that formed through microbial activity, and/or (3) the identification of fabrics/textures that are known to be indicative of microbial activity. All of these criteria fundamentally rely on the interpretation of fabrics preserved in the cave deposits. Virtually all of these interpretations are open to debate.