微生物生态学理论框架

微生物是生态系统的重要组成部分,直接或间接地参与所有的生态过程。微生物生态学是基于微生物群体的科学,利用微生物群体DNA/RNA等标志物,重点研究微生物群落构建、组成演变、多样性及其与环境的关系,在生态学理论的指导和反复模型拟合下由统计分析得出具有普遍意义的结论。其研究范围从基因尺度到全球尺度。分子生物学技术的发展,使人们可以直接从基因水平上考查其多样性,从而使得对微生物空间分布格局及其成因的深入研究成为可能。进而可以从方法学探讨微生物生物多样性、分布格局、影响机制及其对全球变化的响应等。在微生物生态学研究中,群落构建与演化、分布特征(含植物-微生物相互关系)、执行群体功能的机理(生物地球化学循环等)、对环境变化的响应与反馈机理是今后需要关注的重点领域。概述了微生物生态学的概念,并初步提出其理论框架,在对比宏观生态学基础理论和模型的基础上,分析微生物多样性的研究内容、研究方法和群落构建的理论机制,展望了今后研究的重点领域。     

全球变化背景下内蒙古草原土壤微生物多样性维持机制研究进展

全球变化对人类环境的影响是近几十年世界广泛关注的热点之一。内蒙古草原不仅是我国重要的牲畜和饲料生产基地, 而且有着不可替代的生态系统功能。土壤微生物是地球上多样性最高的生物类群, 在驱动碳氮循环等多种生态系统过程中发挥着至关重要的作用。由于研究技术的限制和群落结构复杂等原因, 土壤微生物生态学研究还处于描述性阶段, 理论研究还很缺乏。鉴于此, 利用分子生物学技术尤其是新一代测序技术, 从理论层面上系统地研究全球变化背景下我国北方草地微生物多样性的维持机制具有重要意义。本文在比较各种环境变化对土壤微生物群落的相对影响的基础上, 分析全球变化对微生物多样性影响的物理化学和生态学机制, 并对未来内蒙古草原微生物多样性的重点研究领域进行了展望, 包括: (1)加强全球变化多因素综合研究; (2)加强微生物多样性维持的生态学机制的研究; (3)加强地上与地下多样性关联机制的研究; (4)加强全球大尺度多生态系统的整合研究。     

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。     

河流沉积物氮循环主要微生物的生态特征

微生物驱动的氮循环过程是全球生物地球化学循环的重要组成部分,由于人类活动的影响,氮循环负荷加剧,氮素的生态平衡和微生物的功能特征也相应地受到干扰。河流生态系统是陆地与海洋联系的纽带,因人类活动过量活性氮的输入导致水体富营养化,明显影响着河流的生态功能以及河口沿岸海洋生态系统的平衡。富含微生物的沉积物对氮素的转化和去除起着至关重要的作用。本文主要介绍河流沉积物氮循环主要功能微生物,包括氨氧化细菌、氨氧化古菌、亚硝酸盐氧化菌、反硝化细菌和厌氧氨氧化细菌的群落特征和生态功能,总结氮相关营养盐、溶氧和季节变化等环境因子,以及河道控制管理措施和污水处理厂扰动等条件下氮循环过程主要功能类群的生态特征和响应关系。指出还需深入全面地研究河流沉积物生态系统氮循环过程的驱动机制和微生物的贡献效率,加强城市河流沉积物微生物功能作用的研究及河道生物修复技术的开发。     

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。     

湖泊微生物反硝化过程及速率研究进展

湖泊中微生物介导的反硝化过程对于区域乃至全球的气候环境变化有着深远的影响。因此,研究湖泊微生物反硝化过程及速率有助于我们深刻理解湖泊氮元素生物地球化学循环规律,全面认识湖泊生境对全球氮循环的贡献。本文综述了湖泊生境中反硝化过程(包括典型的反硝化过程及与其他物质循环耦合的反硝化过程,如与有机氮耦合的共反硝化作用、与碳循环耦合的硝酸盐/亚硝酸盐依赖型厌氧甲烷氧化、与铁循环耦合的硝酸盐依赖型铁氧化、与硫循环耦合的硝酸盐还原硫氧化)的速率、驱动微生物及其影响因素。最后对湖泊反硝化过程研究现状和未来发展方向提出总结与展望。     

厌氧甲烷氧化微生物物质代谢与能量代谢研究进展

甲烷既是一种温室气体,也是一种潜在的能源物质,其源与汇的平衡对地球化学循环及工程应用均有重要意义。厌氧甲烷氧化(anaerobic oxidation of methane,AOM)过程是深海、湿地和农田等自然生境中重要的甲烷汇,在缓解温室气体排放方面发挥了巨大作用。AOM微生物的中枢代谢机制及其能量转化途径则是介导厌氧甲烷氧化耦合其他物质还原的关键所在。因此,本文从电子受体多样性的视角,主要分析了硫酸盐型,硝酸盐/亚硝酸盐型,金属还原型厌氧甲烷氧化微生物的生理生化过程及环境分布,并对近些年发现的新型厌氧甲烷氧化进行了梳理;重点总结了厌氧甲烷氧化微生物细胞内电子传递路径以及胞外电子传递方式;根据厌氧甲烷氧化微生物环境分布及反应特征,就其生态学意义及在污染治理与能源回收方面的潜在应用价值进行了展望。本综述以期深化对厌氧甲烷氧化过程的微生物学认知,并为其潜在的工程应用方向提供新的思路。     

厌氧氨氧化菌驱动脱氮途径的研究进展

厌氧氨氧化菌(anaerobic ammonia-oxidizing bacteria, AnAOB)的代谢多样性,使得该菌群能够在海洋、湿地和陆地等不同的自然生态系统中广泛分布,甚至在一些极热和极寒环境中也检测到了该菌群的存在。本文回顾并总结了厌氧氨氧化菌在不同生态系统中的发现、分布及脱氮贡献等方面的研究,分析了厌氧氨氧化菌分布的主要环境影响因素。该综述将帮助我们更好地理解全球氮循环中厌氧氨氧化菌的实际角色和功能,并基于厌氧氨氧化(anaerobicammoniaoxidation,anammox)过程,探究能与其进行协作的新型生物脱氮工艺,以期为这些工艺的研发和推广提供生态学基础和新的思考,从而实现脱氮工艺的技术变革。     

油藏微生物多样性的分子生态学研究进展

油藏微生物是一类宝贵的资源, 在油层生态系统的物质循环和能量流动中发挥着主导作用。传统上, 主要依赖纯培养技术, 使得大部分油藏微生物都没能得到充分认识。分子方法克服了纯培养方法中遇到的问题, 能更好地了解环境微生物群落多样性。近年来, 在油藏微生物群落多样性研究中的应用进展迅速, 对油藏微生物学和生态学的发展产生了重要影响。文中评述了近年来国内外在油藏微生物分子生态方面的研究进展, 并对进一步的研究提出了展望。     

污水脱氮功能微生物的组学研究进展

生物脱氮是污水处理厂的核心,掌握生物脱氮过程相关微生物代谢特性,对于探索微生物资源和提高污水处理厂脱氮性能具有重要意义。近年来,分子生物学方法不断发展和改进,已被广泛应用于揭示脱氮微生物群落多样性、组成结构和潜在功能等方面,大幅提升了研究者们对污水生物脱氮系统中微生物,尤其是不可培养微生物的代谢机理、抑制调控原理及新型生物脱氮工艺途径的认识。本文对流行的分子生物学方法（16S rRNA基因测序、实时荧光定量PCR技术、宏基因组学、宏转录组学、宏蛋白质组学和代谢组学）进行了介绍,综述了其在硝化细菌、反硝化细菌、完全氨氧化细菌、厌氧氨氧化细菌、厌氧铁氨氧化细菌、硫酸盐型厌氧氨氧化细菌及亚硝酸盐/硝酸盐型厌氧甲烷氧化微生物等方面的研究进展,阐明了这些氮素转化微生物在氮循环过程的代谢途径和酶促反应,并从标准测定方法构建、不同方法的联用及跨学科结合和检测方法的简易化这3个方面展望了分子生物学方法的技术突破及其在污水生物处理系统中的应用前景。本综述从系统角度全面认识脱氮微生物群落及其结构,为未来污水处理生物脱氮微生物的研究提供了新方向。     

Effect of oxygen minimum zone formation on communities of marine protists

Changes in ocean temperature and circulation patterns compounded by human activities are leading to oxygen minimum zone (OMZ) expansion with concomitant alteration in nutrient and climate active trace gas cycling. Here, we report the response of microbial eukaryote populations to seasonal changes in water column oxygen-deficiency using Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island British Columbia, as a model ecosystem. We combine small subunit ribosomal RNA gene sequencing approaches with multivariate statistical methods to reveal shifts in operational taxonomic units during successive stages of seasonal stratification and renewal. A meta-analysis is used to identify common and unique patterns of community composition between Saanich Inlet and the anoxic/sulfidic Cariaco Basin (Venezuela) and Framvaren Fjord (Norway) to show shared and unique responses of microbial eukaryotes to oxygen and sulfide in these three environments. Our analyses also reveal temporal fluctuations in rare populations of microbial eukaryotes, particularly anaerobic ciliates, that may be of significant importance to the biogeochemical cycling of methane in OMZs.     

Biogeochemistry and hydrography shape microbial community assembly and activity in the eastern tropical North Pacific Ocean oxygen minimum zone

Oceanic oxygen minimum zones (OMZs) play a pivotal role in biogeochemical cycles due to extensive microbial activity. How OMZ microbial communities assemble and respond to environmental variation is therefore essential to understanding OMZ functioning and ocean biogeochemistry. Sampling along depth profiles at five stations in the eastern tropical North Pacific Ocean (ETNP), we captured systematic variations in dissolved oxygen (DO) and associated variables (nitrite, chlorophyll, and ammonium) with depth and between stations. We quantitatively analysed relationships between oceanographic gradients and microbial community assembly and activity based on paired 16S rDNA and 16S rRNA sequencing. Overall microbial community composition and diversity were strongly related to regional variations in density, DO, and other variables (regression and redundancy analysis r² = 0.68–0.82), displaying predictable patterns with depth and between stations. Although similar factors influenced the active community, diversity was substantially lower within the OMZ. We also identified multiple active microbiological networks that tracked specific gradients or features – particularly subsurface ammonium and nitrite maxima. Our findings indicate that overall microbial community assembly is consistently shaped by hydrography and biogeochemistry, while active segments of the community form discrete networks inhabiting distinct portions of the water column, and that both are tightly tuned to environmental conditions in the ETNP.     

Genome-resolved viral ecology in a marine oxygen minimum zone

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O₂) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.     

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high‐throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate‐ and iron‐reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane‐cycling microbes and their partners being observed in the iron/sulfate‐rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane‐rich environments.     

木质素在海洋中的生物转化及其对海洋碳循环的影响

微型生物参与的海洋碳汇是海洋重要的储碳途径,可调节全球气候变化。木质素是地球上第二大光合而成的碳库,其在海洋中的生物地球化学过程与海洋碳循环密切相关。异养微生物所主导的代谢活动是木质素生物转化的主要途径。近年来,迅速发展的高通量测序技术与传统微生物技术相结合,在探索自然生境中木质素代谢菌群,发现木质素代谢新物种,挖掘相关功能基因等方面已取得一系列成果。然而绝大多数的研究主要集中于陆地生态系统,对于海洋生态系统的研究仍较少。陆源有机碳在海洋中的转化过程仍是一个"谜",故解析海洋木质素碳转化是海洋碳循环研究的重要任务。本文综述了参与海洋木质素转化的功能微生物、木质素代谢机理以及微生物碳代谢活动与海洋碳汇过程的内在联系,为今后的研究提供参考。     

陆地和淡水生态系统新型微生物氮循环研究进展

氮生物地球化学循环是地球物质循环的重要枢纽,是决定陆地生态系统生产力水平、水资源安全、温室气体生成排放的关键过程。氮循环是由微生物介导的一系列复杂过程,不同形态、价态氮化合物的转化分别由相应的功能微生物驱动完成。随着厌氧氨氧化、完全氨氧化等新型氮转化过程的相继报道和发现更新了人们对氮循环的认识。本文综述了陆地和淡水生态系统中厌氧氨氧化(anammox)、硝酸盐异化还原为铵(DNRA)、完全氨氧化(comammox)等新型氮循环过程的发生机制、热区分布及环境效应,并总结了这三种氮循环的相互关系。     

Anaerobic ammonium oxidation in marine environments: contribution to biogeochemical cycles and biotechnological developments for wastewater treatment

Microbial processes are responsible for most reactions involved in the nitrogen cycle in the oceans, which determine the fluxes of this crucial nutrient in these environments. The present review provides an overview of the contribution of anaerobic ammonium oxidation (Anammox) to marine biogeochemical processes. Besides the conventional Anammox process, anaerobic ammonium oxidation coupled to the microbial reduction of alternative electron acceptors, such as sulfate (Sulfammox), ferric iron (Feammox), and natural organic matter (NOM-dependent Anammox) is also described in the context of global marine biogeochemical cycles. Also, the complex interactions among the oceanic biogeochemical cycles of N, S and Fe are discussed at the light of the new findings available in the literature. The review also underlines the important role of the microbial processes performing the Anammox reaction in the development of wastewater treatment systems for the removal of nitrogen from saline effluents. Strategies to enrich and immobilize Anammox bacteria in different reactor configurations for the treatment of saline wastewaters are also described as well as future directions for novel biotechnological developments based on Anammox.

     

The microbial nitrogen cycle

This special issue highlights several recent discoveries in the microbial nitrogen cycle including the diversity of nitrogen-fixing bacteria in special habitats, distribution and contribution of aerobic ammonium oxidation by bacteria and crenarchaea in various aquatic and terrestrial ecosystems, regulation of metabolism in nitrifying bacteria, the molecular diversity of denitrifying microorganisms and their enzymes, the functional diversity of freshwater and marine anammox bacteria, the physiology of nitrite-dependent anaerobic methane oxidation and the degradation of recalcitrant organic nitrogen compounds. Simultaneously the articles in this issue show that many questions still need to be addressed, and that the microbes involved in catalyzing the nitrogen conversions still harbour many secrets that need to be disclosed to fully understand the biogeochemical nitrogen cycle, and make future predictions and global modelling possible.     

Dissimilatory sulfur cycling in oxygen minimum zones: an emerging metagenomics perspective

Biological diversity in marine OMZs (oxygen minimum zones) is dominated by a complex community of bacteria and archaea whose anaerobic metabolisms mediate key steps in global nitrogen and carbon cycles. Molecular and physiological studies now confirm that OMZs also support diverse micro-organisms capable of utilizing inorganic sulfur compounds for energy metabolism. The present review focuses specifically on recent metagenomic data that have helped to identify the molecular basis for autotrophic sulfur oxidation with nitrate in the OMZ water column, as well as a cryptic role for heterotrophic sulfate reduction. Interpreted alongside marker gene surveys and process rate measurements, these data suggest an active sulfur cycle with potentially substantial roles in organic carbon input and mineralization and critical links to the OMZ nitrogen cycle. Furthermore, these studies have created a framework for comparing the genomic diversity and ecology of pelagic sulfur-metabolizing communities from diverse low-oxygen regions.