Seasonality of biogeochemically relevant microbial genes in a coastal ocean microbiome

Microbes drive the biogeochemical cycles of marine ecosystems through their vast metabolic diversity. While we have a fairly good understanding of the spatial distribution of these metabolic processes in various ecosystems, less is known about their seasonal dynamics. We investigated the annual patterns of 21 biogeochemical relevant functions in an oligotrophic coastal ocean site by analysing the presence of key genes, analysing high-rank gene taxonomy and the dynamics of nucleotide variants. Most genes presented seasonality: photoheterotrophic processes were enriched during spring, phosphorous-related genes were dominant during summer, coinciding with potential phosphate limitation, and assimilatory nitrate reductases appeared mostly during summer and autumn, correlating negatively with nitrate availability. Additionally, we identified the main taxa driving each function at each season and described the role of underrecognized taxa such as Litoricolaceae in carbon fixation (rbcL), urea degradation (ureC), and CO oxidation (coxL). Finally, the seasonality of single variants of some families presented a decoupling between the taxonomic abundance patterns and the functional gene patterns, implying functional specialization of the different genera. Our study unveils the seasonality of key biogeochemical functions and the main taxonomic groups that harbour these relevant functions in a coastal ocean ecosystem.     

The use of stable isotope probing techniques in bioreactor and field studies on bioremediation

Stable isotope probing (SIP) is a molecular technique that allows investigators to follow the flow of atoms in isotopically enriched molecules through complex microbial communities into metabolically active microorganisms. Thus, SIP has immense promise for discovering microorganisms responsible for ecologically important biogeochemical reactions in nature. Applications of SIP to biodegradation and bioremediation processes are still in their infancy. In the past few years, approximately a dozen biodegradation studies using SIP based on the analysis of labeled DNA, RNA or phospholipid fatty acids have been completed. Results have begun to link biomarkers (especially sequences of 16S ribosomal RNA and functional genes) to biodegradation reactions in naturally occurring microbial communities. As extensive compilations of ecologically important genotypes and phenotypes accrue, predictive abilities for contaminant metabolism in particular habitats may be achieved.     

稳定性同位素探测技术在微生物生态学研究中的应用

稳定性同位素标记技术同分子生物学技术相结合而发展起来的稳定性同位素探测技术（stableisotope probing,SIP）,在对各种环境中微生物群落组成进行遗传分类学鉴定的同时,可确定其在环境过程中的功能,提供复杂群落中微生物相互作用及其代谢功能的大量信息,具有广阔的应用前景.其基本原理是：将原位或微宇宙（microcosm）的环境样品暴露于稳定性同位素富集的基质中,这些样品中存在的某些微生物能够以基质中的稳定（性同位素为碳源或氮源进行物质代谢并满足其自身生长需要,基质中的稳定性同位素被吸收同化进入微生物体内,参与各类物质如核酸（DNA和RNA）及磷脂脂肪酸（PLFA）等的生物合成,通过提取、分离、纯化、分析这些微生物体内稳定性同位素标记的生物标志物,从而将微生物的组成与其功能联系起来.在介绍稳定性同位素培养基质的选择及标记方法、合适的生物标志物的选择及提取分离方法的基础上,举例阐述了此项技术在甲基营养菌、有机污染物降解菌、根际微生物生态、互营微生物、宏基因组学等方面的应用.     

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.Subject terms: Microbial ecology, Metagenomics     

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.     

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。     

溶磷微生物在土壤磷循环中的作用研究进展

磷是生物分子中的重要元素,是陆地生态系统初级生产的主要限制因子之一。全球粮食需求的增加和现代农业对磷肥的消耗导致集约农田中磷的过量输入,进而引起土壤磷流失的增加和地表水的持续富营养化。溶磷微生物(phosphate solubilizing microorganisms, PSMs)被认为是可以提高农业生产力的生态友好型肥料,在改善土壤肥力方面有重要意义。全面和深入理解PSMs功能及其在磷的土壤生物化学转化过程中的作用,对提高土壤磷有效性有至关重要的作用。本文系统综述了PSMs的种类和分布多样性,主要参与微生物磷循环的功能基因,以及PSMs如何参与土壤磷循环和这些过程背后的反应机制,以便更好地认识PSMs能力及其在土壤磷循环中的作用,以便于在未来的应用中发挥更大的潜力。     

病毒辅助代谢基因的研究进展

病毒通过影响微生物的营养循环、生物多样性和遗传信息传递等,在全球海洋的生物地球化学循环中发挥关键作用。病毒还可以控制微生物的群落组成、关键代谢过程等,这些依赖于病毒基因组上的辅助代谢基因(auxiliary metabolic genes,AMGs)。AMGs在病毒感染宿主的过程中表达并参与调控宿主的代谢过程。病毒基因组中的AMGs包括中央碳代谢、氮代谢、磷和硫循环、核苷酸代谢以及与氧化应激反应相关的基因。AMGs有利于子代病毒更高效地组装和释放,对于病毒种群的繁衍具有重要意义,同时对病毒-宿主相互作用机制的研究产生重要影响。本文针对病毒辅助代谢基因的起源、类别及其重要的生态作用进行简要综述,以期为进一步阐明病毒在不同生态系统中的功能提供依据。     

Functional diversity of terrestrial microbial decomposers and their substrates

The relationship between biodiversity and biogeochemical processes gained much interest in light of the rapidly decreasing biodiversity worldwide. In this article, we discuss the current status, challenges and prospects of functional concepts to plant litter diversity and microbial decomposer diversity. We also evaluate whether these concepts permit a better understanding of how biodiversity is linked to litter decomposition as a key ecosystem process influencing carbon and nutrient cycles. Based on a literature survey, we show that plant litter and microbial diversity matters for decomposition, but that considering numbers of taxonomic units appears overall as little relevant and less useful than functional diversity. However, despite easily available functional litter traits and the well-established theoretical framework for functional litter diversity, the impact of functional litter diversity on decomposition is not yet well enough explored. Defining functional diversity of microorganisms remains one of the biggest challenges for functional approaches to microbial diversity. Recent developments in microarray and metagenomics technology offer promising possibilities in the assessment of the functional structure of microbial communities. This might allow significant progress in measuring functional microbial diversity and ultimately in our ability to predict consequences of biodiversity loss in the decomposer system for biogeochemical processes.     

Coupled C,H, N,S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt

Microbial activity is a major contributor to the biogeochemical cycles that make up the life support system of planet Earth. A 613 m deep geomicrobiological perforation and a systematic multi-analytical characterization revealed an unexpected diversity associated with the rock matrix microbiome that operates in the subsurface of the Iberian Pyrite Belt (IPB). Members of 1 class and 16 genera were deemed the most representative microorganisms of the IPB deep subsurface and selected for a deeper analysis. The use of fluorescence in situ hybridization allowed not only the identification of microorganisms but also the detection of novel activities in the subsurface such as anaerobic ammonium oxidation (ANAMMOX) and anaerobic methane oxidation, the co-occurrence of microorganisms able to maintain complementary metabolic activities and the existence of biofilms. The use of enrichment cultures sensed the presence of five different complementary metabolic activities along the length of the borehole and isolated 29 bacterial species. Genomic analysis of nine isolates identified the genes involved in the complete operation of the light-independent coupled C, H, N, S and Fe biogeochemical cycles. This study revealed the importance of nitrate reduction microorganisms in the oxidation of iron in the anoxic conditions existing in the subsurface of the IPB.     

Do microbial numbers count? Quantifying the regulation of biogeochemical fluxes by population size and cellular activity

In order to enhance understanding of the interrelationships among community members and between them and their environment, the concept of regulation analysis is extended from biochemistry into microbial ecology. Ecological regulation analysis quantifies how biogeochemical fluxes are regulated by the microorganisms performing the process; the degree to which changes in fluxes are due to changes in population size and to changes in activity cell(-1) (cellular activity). Regulation analysis requires data on biogeochemical fluxes and the numbers of cells through which these fluxes run. Its application to five biogeochemical processes (aerobic methane oxidation, aerobic nitrite oxidation, methanogenesis, sulfate reduction and reductive dehalogenation) revealed that in general, but not always, flux was primarily regulated by cellular activity, i.e. by changes in the size and properties of the enzyme pool and in the concentrations of substrates and metabolites. Thus, it is often not sufficient to count the numbers of cells performing a particular step in a biogeochemical process in order to estimate its flux. Ecological regulation analysis can be extended to address which aspects of cellular activity require quantification in order to describe biogeochemical fluxes better. Its application is discussed in the context of the complexity of microbial communities (e.g. functional redundancy) and their functioning.     

Characteristics and adaptability of iron- and sulfur-oxidizing microorganisms used for the recovery of metals from minerals and their concentrates

Microorganisms are used in large-scale heap or tank aeration processes for the commercial extraction of a variety of metals from their ores or concentrates. These include copper, cobalt, gold and, in the past, uranium. The metal solubilization processes are considered to be largely chemical with the microorganisms providing the chemicals and the space (exopolysaccharide layer) where the mineral dissolution reactions occur. Temperatures at which these processes are carried out can vary from ambient to 80°C and the types of organisms present depends to a large extent on the process temperature used. Irrespective of the operation temperature, biomining microbes have several characteristics in common. One shared characteristic is their ability to produce the ferric iron and sulfuric acid required to degrade the mineral and facilitate metal recovery. Other characteristics are their ability to grow autotrophically, their acid-tolerance and their inherent metal resistance or ability to acquire metal resistance. Although the microorganisms that drive the process have the above properties in common, biomining microbes usually occur in consortia in which cross-feeding may occur such that a combination of microbes including some with heterotrophic tendencies may contribute to the efficiency of the process. The remarkable adaptability of these organisms is assisted by several of the processes being continuous-flow systems that enable the continual selection of microorganisms that are more efficient at mineral degradation. Adaptability is also assisted by the processes being open and non-sterile thereby permitting new organisms to enter. This openness allows for the possibility of new genes that improve cell fitness to be selected from the horizontal gene pool. Characteristics that biomining microorganisms have in common and examples of their remarkable adaptability are described.     

极端酸性矿山环境微生物基于CRISPR系统的适应性免疫机制

【目的】通过对酸性矿山环境中嗜酸硫杆菌属(Acidithiobacillus)、脱硫弧菌属(Desulfovibrio)、钩端螺旋菌属(Leptospirillum)、硫化杆菌属(Sulfobacillus)、酸原体属(Acidiplasma)和铁质菌属(Ferroplasma)的100株冶金微生物基因组中CRISPR-Cas系统的结构特征和同源关系进行生物信息学分析,在基因组水平上解析冶金微生物基于CRISPR系统对极端环境的适应性免疫机制。【方法】从NCBI网站下载基因组序列,采用CRISPR Finder定位基因组中潜在的CRISPR簇。分析CRISPR系统的组成结构与功能:利用Clustal Omega对重复序列(repeat)分类;将间隔序列(spacer)分别与nr数据库、质粒数据库和病毒数据库比对,获得注释信息;根据Cas蛋白的种类和同源性对酸性矿山环境微生物的CRISPR-Cas系统分型。【结果】在100株冶金微生物基因组中共鉴定出415个CRISPR簇,在176个c CRISPR簇中共有80种不同的重复序列和4147条间隔序列。对重复序列分类,发现12类重复序列均能形成典型的RNA二级结构,Cluster10中的重复序列在冶金微生物中最具有代表性。间隔序列注释结果表明,这些微生物曾遭受来自细菌质粒与病毒的攻击,并通过不同的防御机制抵抗外源核酸序列的入侵。冶金微生物细菌的大部分CRISPR-Cas系统属于I-C和I-E亚类型,而古菌的CRISPR-Cas系统多为I-D亚类型,两者基于CRISPR-Cas系统的进化过程中存在显著差异。【结论】酸性矿山环境微生物的CRISPR结构可能采用不同免疫机制介导外源核酸序列与Cas蛋白的相互作用,为进一步揭示极端环境微生物的适应性进化机理奠定了基础。     

New genes in alkaloid metabolism and transport

The biosynthetic pathway of plant alkaloids is composed of several distinct enzymes of varying substrate specificities. Homology-based cloning of candidate genes and their subsequent functional testing in heterologous expression systems are accelerating the pace at which the gene catalogues of alkaloid biosynthesis are expanding. Availability of diverse genes involved in the biosynthesis, catabolism, transport, and regulation of pharmaceutically important alkaloids should steadily advance our molecular understanding of alkaloid biology and will enable us to devise more rational strategies for metabolic engineering.     

微生物基因数据库在氮循环功能基因注释中的应用

氮循环是微生物和化学过程介导的生物地球化学循环。利用基因测序技术研究环境中参与氮循环的微生物群落、微生物及功能基因,是环境基因组学和微生物生态学的重要研究热点。近年来,各种类型的数据库被开发并应用到功能分析中。本文结合时下最新研究成果,聚焦由微生物引起的同化硝酸盐还原作用、异化硝酸盐还原作用、反硝化作用、固氮作用、硝化作用(包括完全氨氧化作用)和厌氧氨氧化作用等6种无机氮循环途径的功能基因,对比了National Center for Biotechnology Information (NCBI)、Integrated Microbial Genomes (IMG)、Universal Protein (UniProt)、Kyoto Encyclopedia of Genes and Genomes (KEGG)、Protein Families (Pfam)、Functional Gene (FunGene)、Clusters of Orthologous Groups (COG)和NCycDB等数据库的设计理念和功能特点,并结合环境介质、表征基因、分析方法和比对方法等影响因素,分析了以上数据库在氮循环功能基因注释中的选择及应用方式,展望了未来氮循环基因数据库的发展方向,以期为研究人员了解氮循环基因家族和选择合适的数据分析平台提供参考。     

Rock geochemistry induces stress and starvation responses in the bacterial proteome

Interactions between microorganisms and rocks play an important role in Earth system processes. However, little is known about the molecular capabilities microorganisms require to live in rocky environments. Using a quantitative label‐free proteomics approach, we show that a model bacterium (Cupriavidus metallidurans CH34) can use volcanic rock to satisfy some elemental requirements, resulting in increased rates of cell division in both magnesium‐ and iron‐limited media. However, the rocks also introduced multiple new stresses via chemical changes associated with pH, elemental leaching and surface adsorption of nutrients that were reflected in the proteome. For example, the loss of bioavailable phosphorus was observed and resulted in the upregulation of diverse phosphate limitation proteins, which facilitate increase phosphate uptake and scavenging within the cell. Our results revealed that despite the provision of essential elements, rock chemistry drives complex metabolic reorganization within rock‐dwelling organisms, requiring tight regulation of cellular processes at the protein level. This study advances our ability to identify key microbial responses that enable life to persist in rock environments.     

基于功能基因的微生物碳循环分子生态学研究进展

碳循环是生态系统中重要的生物地球化学元素循环之一。微生物参与碳固定、甲烷代谢、碳降解等多个重要的碳循环过程,深入了解微生物群落在碳循环过程中的功能和作用,有助于获悉微生物对全球气候变化的响应、适应和反馈机制,这也是微生物生态学研究的关键问题之一。传统的研究多集中于微生物分离培养技术,无法覆盖绝大部分未培养微生物,并且无法深入解析碳循环过程中微生物群落的结构和功能,宏基因组学技术的出现克服了这些缺陷,成为研究微生物群落结构和功能的有效手段。本文对目前宏基因组学的主要技术——定量PCR、DNA分子指纹图谱、基因芯片、克隆文库和高通量测序等技术进行了简要介绍,着重介绍了参与碳固定、甲烷生成和氧化、碳降解等主要碳循环过程的关键功能基因的研究现状,最后对碳循环过程中微生物宏基因组学研究的未来发展进行了总结与展望。