湖泊硫循环微生物研究进展

湖泊是响应气候和环境变化的关键生态系统,是研究元素(如碳、氮和硫等)生物地球化学循环的热点环境。湖泊(尤其咸盐湖)具有硫酸盐含量高且含硫化合物种类丰富的特点,因而湖泊中硫元素生物地球化学循环过程非常活跃。微生物是驱动湖泊硫循环的重要推手。因此,研究湖泊中微生物参与的硫元素生物地球化学循环过程以及相关微生物类群构成,对于深入探索微生物在湖泊生态系统中的作用具有重要意义。本文综述了湖泊中驱动硫循环的微生物(硫氧化菌和硫酸盐还原菌)种群多样性、功能基因、代谢途径、硫氧化/硫酸盐还原速率及其对环境条件变化响应等方面的研究现状,并对未来湖泊微生物驱动的硫循环研究方向进行了展望。     

极地陆域微生物多样性研究进展

极地是指高纬度、高海拔地区,包括南极(60°S以南)、北极(60°N以北)和被称为“第三极”的青藏高原地区(平均海拔4,500 m).这些地区气温极低、养分极度贫乏,生态系统非常脆弱,对全球气候变化极为敏感,该地区生态系统一旦破坏将很难恢复.尽管极地地区自然条件恶劣,但在这些极端环境中栖息着大量微生物,是元素生物地球化学循环的主要驱动者,对极地生态系统的构建和维持具有非常重要的作用.本文综述了极地土壤、湖泊和冰川等陆域环境微生物研究进展.在这些极地环境中,目前已发现了Acidobacteria,Actinobacteria,Bacteroidetes,Cyanobacteria和Firmicutes等类群,这些微生物具有嗜盐/耐盐及耐低温等特征.我国在极地微生物生态学研究方面落后于发达国家,建议优先发展较易到达的青藏高原地区微生物生态学长期定位观测,这将有助于较快提升我国极地微生物多样性研究水平,深入了解极端生命过程及其生态学效应.     

三极冰川冰尘微生物及其介导的碳氮生物地球化学循环研究进展

冰尘是散落在冰川表面由矿物质、有机质和微生物组成的聚合体,其主要来源包括远源输送来的细粉尘和气溶胶组分、局地源的粗冰碛物及来自周围生态系统的土壤和植物碎屑等。冰尘对太阳辐射具有较强的吸收作用,可降低冰面反照率、促进冰川融化。冰尘也是迄今为止生物多样性最高的冰川表面微生物栖息地,生活着细菌、真菌、藻类等。冰尘微生物是冰川表面地球化学循环的主要驱动者,微生物分解转化冰尘内有机质,降低冰川表面反照率影响冰川物质平衡。基于冰尘的重要性,本文综述了南极、北极、青藏高原第三极冰川冰尘的物理和化学特征及其影响因素,冰尘微生物群落组成及其介导的碳氮生物地球化学循环过程,并展望了冰尘微生物研究的前景。     

生物地球化学锰循环中的微生物胞外电子传递机制

微生物是生物地球化学元素循环的重要驱动者,在锰等变价金属元素的氧化还原过程中起着至关重要的作用。近年来,Mn(Ⅲ)的发现以及在一些环境中的广泛存在,丰富了人们对Mn(Ⅲ)以及自然界锰循环过程的认识。研究发现,锰的生物地球化学循环,尤其是锰还原过程,与微生物胞外电子传递紧密相关,且目前已知的5种胞外电子传递机制均与锰还原有关联。因此,本文综述了锰的生物地球化学循环及其意义,并从微生物胞外电子传递的机制、微生物介导锰氧化、微生物介导锰还原等3个方面来介绍参与锰循环的微生物多样性;以及微生物地球化学锰循环的环境意义。对微生物参与锰循环过程的研究不仅可以进一步丰富相关理论,同时也能推动生物除锰、污染物原位修复及生物冶金等应用领域的发展。     

南极海-陆界面营养物质流动和磷循环

南极大陆气候严寒、营养贫瘠,企鹅、海豹等生物能传递海洋中的营养物质到陆地,这些营养物质是维系南极无冰区生态系统的基础.本文首先阐述了海洋向南极无冰区输入营养物质的方式,重点介绍了生物方式输入的营养物质对无冰区生态系统组成、结构和功能的影响,以及无冰区向近海输入营养物质的方式及其影响.然后,以西南极法尔兹半岛为例,对企鹅、海豹传输的营养物质磷在陆地、淡水生态系统中的记录进行了分析,讨论了南极近海磷的生物地球化学循环及其机理,估算了磷循环通量.结果表明,南极阿德雷岛磷的外来营养源包括物理输入、生物输入和大气沉降输入3种,其中,生物输入(企鹅粪)占94.34％ ～ 99.74％,在近海磷循环中起着关键作用.     

微生物在地球化学铁循环过程中的作用

铁元素虽然只在地壳含量中位列第4,但却是地球上分布最广的变价金属元素之一,微生物介导的铁循环及其与生源要素碳、氮、氧和硫等耦合的氧化还原反应是微生物地球化学循环的重要驱动力.由于铁循环过程中氧化态三价铁Fe(Ⅲ)在环境p H条件下大多以不溶状态存在,因而由其参与的地球化学循环进程通常较为缓慢.研究表明,微生物在铁元素的地球化学循环过程中起着举足轻重的作用,并在该过程中参与矿物的生成与转化.近年来的最新研究发现,参与地球化学铁循环的微生物之间,微生物与矿物之间,以及矿物介导的微生物之间存在着多样的相互作用,而含铁矿物介导的微生物胞外电子传递机制是其中最受瞩目的研究热点.本文综述了微生物介导的地球化学铁循环过程的类型及其过程中的主导微生物,并针对铁还原过程中已知的微生物胞外电子传递机制做了介绍.文中涉及的微生物地球化学铁循环过程中的各种相互作用,已经成为相关研究领域的热点问题,最新研究结果将为进一步阐明微生物地球化学铁循环过程、机制及其环境效应提供重要的理论依据和研究基础.     

稻田土壤关键元素的生物地球化学耦合过程及其微生物调控机制

水稻土是在长期植稻下人为培育的特殊耕作土壤,是我国土壤学的特色,其研究也反映我国土壤学的国际地位。水稻土是研究土壤生物地球化学过程的理想模型。稻田土壤关键元素(碳氮磷硫铁等)的生物地球化学循环过程、耦合机理及其驱动机制研究是土壤生物学研究的核心之一。因此,以国际土壤年为契机,结合中国科学院院士工作局资助的"土壤生物学发展战略研究"项目的部分成果,以稻田关键元素(碳氮磷硫铁等)生物地球化学循环过程及其耦合的微生物驱动机制为核心,重点讨论了稻田土壤基本生物化学特征、稻田土壤碳-氮、碳-氮-磷、碳-氮-铁等多元素耦合过程及其与微生物之间的反馈机制,并由此提出了稻田土壤关键元素生物地球化学循环微生物驱动机制研究的未来重点发展方向为:1)土壤关键元素生物地球化学过程的异质性及其微生物过程的互作机制研究;2)微生物参与机制对土壤关键元素循环过程的响应、反馈机制与调控机制研究;3)土壤关键生物地球化学过程的计量学研究。     

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。     

红树林沉积物中微生物驱动硫循环研究进展北大核心CSCD

红树林滨海湿地是在周期性咸水、淡水作用下形成的特殊生态系统,其沉积物中有机质含量丰富,微生物驱动的营养物质循环活跃。由于红树林沉积物中硫酸盐含量高、硫化物种类多,因此红树林是研究硫元素生物地球化学循环过程和机制的理想系统。本文综述了红树林生态系统中主要的硫元素循环过程,重点总结了硫氧化和硫酸盐还原过程及其功能微生物,分析了影响硫氧化和硫酸盐还原的主要环境因素,并对红树林沉积物中微生物驱动硫循环的重点研究方向进行了展望。鉴于微生物驱动的硫循环过程耦合碳、氮和金属元素循环,本文可为深入探究微生物驱动的生物地球化学元素循环耦合机制提供参考。     

红树林沉积物中微生物驱动硫循环研究进展

红树林滨海湿地是在周期性咸水、淡水作用下形成的特殊生态系统,其沉积物中有机质含量丰富,微生物驱动的营养物质循环活跃。由于红树林沉积物中硫酸盐含量高、硫化物种类多,因此红树林是研究硫元素生物地球化学循环过程和机制的理想系统。本文综述了红树林生态系统中主要的硫元素循环过程,重点总结了硫氧化和硫酸盐还原过程及其功能微生物,分析了影响硫氧化和硫酸盐还原的主要环境因素,并对红树林沉积物中微生物驱动硫循环的重点研究方向进行了展望。鉴于微生物驱动的硫循环过程耦合碳、氮和金属元素循环,本文可为深入探究微生物驱动的生物地球化学元素循环耦合机制提供参考。     

Bacteriophage in polar inland waters

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.     

Bacteria beneath the West Antarctic Ice Sheet

Subglacial environments, particularly those that lie beneath polar ice sheets, are beginning to be recognized as an important part of Earth's biosphere. However, except for indirect indications of microbial assemblages in subglacial Lake Vostok, Antarctica, no sub-ice sheet environments have been shown to support microbial ecosystems. Here we report 16S rRNA gene and isolate diversity in sediments collected from beneath the Kamb Ice Stream, West Antarctic Ice Sheet and stored for 15 months at 4°C. This is the first report of microbes in samples from the sediment environment beneath the Antarctic Ice Sheet. The cells were abundant (∼10⁷ cells g⁻¹) but displayed low diversity (only five phylotypes), likely as a result of enrichment during storage. Isolates were cold tolerant and the 16S rRNA gene diversity was a simplified version of that found in subglacial alpine and Arctic sediments and water. Although in situ cell abundance and the extent of wet sediments beneath the Antarctic ice sheet can only be roughly extrapolated on the basis of this sample, it is clear that the subglacial ecosystem contains a significant and previously unrecognized pool of microbial cells and associated organic carbon that could potentially have significant implications for global geochemical processes.     

Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert

Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.     

土壤微生物生物量碳氮磷与土壤酶化学计量对气候变化的响应机制

微生物和土壤酶是陆地生态系统中生物地球化学循环的重要驱动力,深入理解微生物在生态系统中的调节作用以及气候变化过程中微生物量和土壤酶的响应机制是生态学领域关注的重要科学问题.本研究从气候因素角度出发,基于生态化学计量学理论,综述了微生物和土壤酶在陆地生态系统碳氮磷循环中的作用,以及土壤微生物生物量碳氮磷和土壤酶化学计量对气候变化的响应机制,即: 改变微生物代谢速率和酶活性;调整微生物群落结构;调整微生物生物量碳氮磷与土壤酶化学计量特征;改变碳氮磷养分元素利用效率.最后分析当前研究的不足,并提出了该领域亟待解决的科学问题: 综合阐明土壤微生物和土壤酶对气候变化的响应机制;探究土壤微生物和胞外酶养分耦合机理;深入探究土壤微生物量和土壤酶化学计量特征对气候变化的适应对策.     

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

In-depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo-genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human-induced global changes.     

Dissolved gases in frozen basal water from the NGRIP borehole: implications for biogeochemical processes beneath the Greenland Ice Sheet

Little information exists on biogeochemical transformations in aquatic ecosystems beneath polar ice sheets (i.e., water-saturated sediments, streams, rivers, and lakes) and their role in global elemental cycles. Subglacial environments may represent important sources of atmospheric CO₂ and/or CH₄ during deglaciation, thus acting as amplifiers in the climate system. However, the role of subglacial environments in global climate processes has been difficult to assess given the absence of biogeochemical data from the basal zones of inland polar ice sheets. Here, we report on the concentrations of CO₂, CH₄, and H₂ in samples of refrozen basal water recovered at a depth of ~3,042 meters below the surface during the North Greenland Ice Core Project (NGRIP). CH₄ and H₂ concentrations in the NGRIP samples were approximately 60- and 700-fold higher, respectively, relative to air-equilibrated water, whereas CO₂ was ~fivefold lower. Metabolic pathways such as (1) methanogenesis, (2) organic matter fermentation, carboxydotrophic, and/or methylotrophic activity, and (3) CO₂ fixation provide plausible biotic explanations for the observed CH₄, H_2, and CO₂ concentrations, respectively.     

Responses of freshwater ecosystems to global change: research progress and outlook

全球变化已经通过提高水温、改变降水格局和水流状况、促进物种入侵、增加极端事件, 对不同的淡水生态系统造成严重的威胁。该文将全球变化背景下淡水生态学的主要研究内容归纳为: (1)全球变化各要素对个体、种群、群落及至生态系统水平的影响; (2)全球变化过程中生态系统生物地球化学循环的改变; (3)淡水生态系统对全球变化的适应对策。最近10-15年淡水生态系统与全球变化研究快速发展, 取得的重要突破有: (1)阐明淡水生态系统结构与功能对全球气候变化尤其是水温升高的响应过程与机制; (2)揭示淡水生态系统(湿地、湖泊、河流等)是全球碳循环的重要组成部分, 在全球变化因素的影响下呈现有机碳埋藏减少和矿化速率提高。今后的研究中, 需要进一步加强对淡水生态系统全要素的系统观测与整合; 开展以“河流”为介质耦合多系统的碳输运和转化过程研究; 强化基础理论研究揭示淡水生态系统对全球变化的适应机制。     

Thermodynamic constraints on the utility of ecological stoichiometry for explaining global biogeochemical patterns

Carbon and nitrogen cycles are coupled through both stoichiometric requirements for microbial biomass and dissimilatory metabolic processes in which microbes catalyse reduction‐oxidation reactions. Here, we integrate stoichiometric theory and thermodynamic principles to explain the commonly observed trade‐off between high nitrate and high organic carbon concentrations, and the even stronger trade‐off between high nitrate and high ammonium concentrations, across a wide range of aquatic ecosystems. Our results suggest these relationships are the emergent properties of both microbial biomass stoichiometry and the availability of terminal electron acceptors. Because elements with multiple oxidation states (i.e. nitrogen, manganese, iron and sulphur) serve as both nutrients and sources of chemical energy in reduced environments, both assimilative demand and dissimilatory uses determine their concentrations across broad spatial gradients. Conceptual and quantitative models that integrate rather than independently examine thermodynamic, stoichiometric and evolutionary controls on biogeochemical cycling are essential for understanding local to global biogeochemical patterns.     

水环境低温噬菌体多样性研究进展

低温环境分布最广,生物圈约80%以上的部分为常年低于5℃的低温地区,而在水环境（包括深海、极地海洋、海冰和高纬度湖泊等）中病毒的分布和含量是非常丰富的。在这些低温环境中,噬菌体在生态系统调控、全球生物地球化学循环（尤其是碳循环）、深海代谢和生物基因多样性保存等方面扮演着重要角色。该文主要对海洋和淡水湖泊中低温噬菌体的多样性进行简要综述。