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。     

南海环境微生物对聚球藻有机物质的响应

【背景】海洋浮游植物产生的有机物质与异养细菌之间的相互作用是上层海洋物质和能量循环过程中的重要组成部分。【目的】探究寡营养海域微生物群落对聚球藻有机物(Synechococcus-derived organic matter,SOM)的响应和代谢利用过程,加深对海洋微生物介导的生物地球化学循环过程的认识。【方法】利用南海海域微生物群落,添加聚球藻有机物质后黑暗培养,对培养过程中有机碳、营养盐和活性微生物群落结构的变化进行追踪。【结果】在短期的培养过程中,有60%-73%的SOM被微生物所利用。γ-变形菌(Gammaproteobacteria)在培养过程中响应最快,也是最优势微生物类群。SOM的加入改变了原位微生物群落结构,并且随着活性有机物质逐步被消耗,微生物群落结构也发生了演替。【结论】SOM中的大部分物质都属于活性有机物质,可以快速地被微生物所降解利用。不同微生物类群响应不同生物可利用性有机物质,推动了海洋物质和能量的循环。     

海洋碳迁移转化与主要化学驱动因子的相互关系

分析了化学驱动因子对海洋碳迁移转化过程的影响.海洋碳迁移转化与各种化学驱动因子参与的生物地球化学过程密切相关.营养盐水平、pH、溶解氧浓度（DO）、氧化还原电位（Eh）、SO₄^2-及硫电位（Es）等主要化学驱动因子的消长导致了海洋化学环境的变化,进而对海洋碳的迁移转化产生影响.在营养盐的供给和生物吸收情况良好的海域,CO₂由于光合作用,并通过沉降有机物的氧化,不断被转移到海水深层,使得海水中的CO₂分压（P_CO2）降低,CO₂的海-气交换量和有机碳输出通量增大,从使该海域表现为CO₂的汇.由于CO₂的溶解与吸收以及有机物的降解造成了海洋环境的日益酸化,引起了海水中碳酸盐溶解度增大;沉积物中酸碱环境的变化也与有机物的矿化以及碳酸盐的溶解、沉淀过程密切相关.此外,DO、Eh、SO₄^2-及Es的变化与水体中有机碳的矿化分解过程和碳在沉积层中沉积埋葬过程相耦合.在水体中,高DO、高Eh利于有机碳向无机碳转化;而在DO和Eh较低的沉积环境中,高SO₄^2-不利于有机碳的埋葬与保存.     

地下水微生物功能群及生物地球化学循环

地下水系统是地球关键带的重要组成部分,为微生物提供了特殊的栖息环境和复杂的生存条件,进而演化出复杂的生物地球化学过程。随着多技术、多学科的交叉融合及发展,近几十年地下水微生物功能群及生物地球化学循环研究取得了引人瞩目的重要进展。本文从地下水中的微生物群功能分区、微生物介导的地球化学元素循环、污染与修复中的生物地球化学过程,以及生物地球化学过程数值模拟等方面对国内外相关研究进展进行了综述,并对地下水系统中微生物"暗物质、暗过程"、微生物修复、地下水医学地质学,以及地下水多学科交叉融合等研究方向和前景进行了展望。     

海洋颗粒物/沉积物中的氨基酸及其对有机质降解的指示作用

氨基酸是海洋有机质尤其是有机氮的重要组分,其地球化学行为活跃,在海洋有机质生物地球化学循环过程中起着重要作用.氨基酸的含量、组成和分布等信息可有效指示有机质的降解状态.本研究系统总结了海洋颗粒物/沉积物中氨基酸的分布特征及影响因素,以及氨基酸对有机质降解程度的指示作用.海洋颗粒物/沉积物氨基酸的主要成分为甘氨酸(Gly)、谷氨酸(Glu)、丙氨酸(Ala)和天冬氨酸(Asp),其含量从近岸到大洋逐渐降低,并随深度增加呈下降趋势组.氨基酸的碳、氮归一化产率()越低,表明有机质%AA-C/TOC,%AA-N/TN)以及基于氨基酸成的降解因子(DI的降解程度越高.基于非蛋白质氨基酸以及)D型氨基酸含量与组成的活性因子(RI)和D型氨基酸与L型氨基酸比值(D/L等指标可以根据细菌对氨基酸的转化作用来指示有机质的降解程度,其中RI值越接近于0,D/L值越高,蛋白质与非蛋白质氨基酸的比值的高Asp/β-Ala和Glu/γ-Aba(氨基丁酸)越小,均表明有机质受到微生物降解和转化程度越.颗粒物/沉积物中氨基酸的迁移转化过程主要受到溶解氧、营养盐水平、有机质来源、沉积环境以及微生物转化等因素的影响.今后应加强颗粒物和沉积物之间的协同效应以及微生物对氨基酸的影响与具体调控机理研究.     

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.     

微生物厌氧呼吸与有机污染水体沉积物修复

水体沉积物有机污染是当前全球关注的重要环境问题。微生物具有呼吸和代谢多样性,能以多种污染物作为厌氧呼吸的电子供体或受体,与周围环境中的生物和非生物因素组成代谢网络耦合有机污染物降解转化,是有机污染水体沉积物修复的重要驱动者。本文重点综述了微生物厌氧呼吸、电子传递网络及其对有机污染水体沉积物的修复机制研究进展,并对有机污染水体沉积物微生物修复理论和技术研究的问题和挑战进行了探讨。     

土壤有机碳矿化激发效应的微生物机制研究进展

激发效应是外源易分解有机质输入在短时期内改变原有土壤有机碳矿化过程的自然现象,是联系土壤有机碳收支过程之间的关键环节,对于土壤有机碳库的积累和稳定具有重要意义。土壤微生物对外源有机质输入的响应是形成激发效应的内在驱动力。外源有机质促进或抑制土壤有机碳矿化的微生物机制主要包括:外源有机质促进多种类群微生物及其分泌胞外酶的协同作用,外源有机质驱使特定类群微生物加强对受限资源的利用,外源有机质的化学计量特征导致微生物对适宜分解底物的选择性利用。对于激发效应现象更符合哪一种理论的解释,以及何种类群微生物主导了激发效应过程,目前尚未形成普遍共识。外源有机质总量、化学组成和碳氮比以及温度、水分等环境因子,都可通过影响微生物对外源有机质和土壤有机质的利用从而作用于激发效应。针对现有研究存在的争议与不足,今后需利用新兴技术手段进一步明确不同微生物类群在激发效应过程中的作用,并从外源有机质化学计量特征与微生物需求之间均衡关系的角度展开研究,以期促成激发效应研究与生态化学计量学相关理论的融合与发展。     

海洋奇古菌门认知的拓展：从新类群到新功能

奇古菌门是全球海洋中的重要微生物类群,在海洋原核浮游生物中的比例可达20%–40%。作为一类化能无机自养微生物,奇古菌门成员可通过氧化氨获得能量,实现不依赖光照的无机碳固定,在碳、氮等元素的地球化学循环中起关键作用。奇古菌门是海洋中氨氧化反应的主要执行者,其化能合成的有机质是海洋特别是深海环境中微生物的重要能量来源。随着研究的逐步深入,有关该类群生理代谢特性的认知不断被拓展,包括奇古菌门异养代谢的揭示、不具氨氧化能力类群在深海中的发现,以及最新报道的奇古菌门在厌氧条件下介导氧气、氧化亚氮和氮气的产生等。这些研究揭示了奇古菌门参与海洋生物地球化学循环和气候变化调节的新机制,为围绕该类群的深入探究和培养提供了新的思路和方向。本文从群落组成、环境适应、生态功能、进化历史和培养现状等方面综述了近年来有关海洋奇古菌门的新发现和新认识,以期增进对该类群的了解。     

古菌在红树林沉积物中的多样性及其碳代谢机制

红树林湿地生态系统具有维持生物多样性、净化环境及维持海岸带生态平衡等多种功能。古菌普遍存在于红树林沉积物中,在元素的生物地球化学循环中发挥着重要作用。古菌具有丰富的碳代谢多样性,能固定CO_2,参与甲烷循环,产乙酸,降解蛋白质、多聚碳水化合物等有机质,但目前对于红树林沉积物中古菌碳代谢的研究才刚刚起步。高通量测序技术的快速发展促进了大量新的古菌门类的发现,这些新的古菌门类具备多样的碳代谢潜力。本文简要概述古菌的主要类群与分布,综述国内外有关古菌碳代谢多样性的最新研究进展,并阐明这些古菌在红树林生态系统中的生态分布和功能特征,为进一步探究古菌代谢机制提供知识基础。     

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

Nitrate is an important nutrient and electron acceptor for microorganisms, having a key role in nitrogen (N) cycling and electron transfer in anoxic sediments. High-nitrate inputs into sediments could have a significant effect on N cycling and its associated microbial processes. However, few studies have been focused on the effect of nitrate addition on the functional diversity, composition, structure and dynamics of sediment microbial communities in contaminated aquatic ecosystems with persistent organic pollutants (POPs). Here we analyzed sediment microbial communities from a field-scale in situ bioremediation site, a creek in Pearl River Delta containing a variety of contaminants including polybrominated diphenyl ethers (PBDEs) and polycyclic aromatic hydrocarbons (PAHs), before and after nitrate injection using a comprehensive functional gene array (GeoChip 4.0). Our results showed that the sediment microbial community functional composition and structure were markedly altered, and that functional genes involved in N-, carbon (C)-, sulfur (S)-and phosphorus (P)- cycling processes were highly enriched after nitrate injection, especially those microorganisms with diverse metabolic capabilities, leading to potential in situ bioremediation of the contaminated sediment, such as PBDE and PAH reduction/degradation. This study provides new insights into our understanding of sediment microbial community responses to nitrate addition, suggesting that indigenous microorganisms could be successfully stimulated for in situ bioremediation of POPs in contaminated sediments with nitrate addition.     

Thermophilic anaerobes in Arctic marine sediments induced to mineralize complex organic matter at high temperature

Marine sediments harbour diverse populations of dormant thermophilic bacterial spores that become active in sediment incubation experiments at much higher than in situ temperature. This response was investigated in the presence of natural complex organic matter in sediments of two Arctic fjords, as well as with the addition of freeze‐dried Spirulina or individual high‐molecular‐weight polysaccharides. During 50°C incubation experiments, Arctic thermophiles catalysed extensive mineralization of the organic matter via extracellular enzymatic hydrolysis, fermentation and sulfate reduction. This high temperature‐induced food chain mirrors sediment microbial processes occurring at cold in situ temperatures (near 0°C), yet it is catalysed by a completely different set of microorganisms. Using sulfate reduction rates (SRR) as a proxy for organic matter mineralization showed that differences in organic matter reactivity determined the extent of the thermophilic response. Fjord sediments with higher in situ SRR also supported higher SRR at 50°C. Amendment with Spirulina significantly increased volatile fatty acids production and SRR relative to unamended sediment in 50°C incubations. Spirulina amendment also revealed temporally distinct sulfate reduction phases, consistent with 16S rRNA clone library detection of multiple thermophilic Desulfotomaculum spp. enriched at 50°C. Incubations with four different fluorescently labelled polysaccharides at 4°C and 50°C showed that the thermophilic population in Arctic sediments produce a different suite of polymer‐hydrolysing enzymes than those used in situ by the cold‐adapted microbial community. Over time, dormant marine microorganisms like these are buried in marine sediments and might eventually encounter warmer conditions that favour their activation. Distinct enzymatic capacities for organic polymer degradation could allow specific heterotrophic populations like these to play a role in sustaining microbial metabolism in the deep, warm, marine biosphere.     

Microarray-based characterization of microbial community functional structure and heterogeneity in marine sediments from the Gulf of Mexico

Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing approximately 2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO(4)(3-), NH(4)(+), Mn(II), porosity, and Si(OH)(4) might play major roles in shaping the microbial community structure in the marine sediments.     

Harnessing microbially generated power on the seafloor

In many marine environments, a voltage gradient exists across the water sediment interface resulting from sedimentary microbial activity. Here we show that a fuel cell consisting of an anode embedded in marine sediment and a cathode in overlying seawater can use this voltage gradient to generate electrical power in situ. Fuel cells of this design generated sustained power in a boat basin carved into a salt marsh near Tuckerton, New Jersey, and in the Yaquina Bay Estuary near Newport, Oregon. Retrieval and analysis of the Tuckerton fuel cell indicates that power generation results from at least two anode reactions: oxidation of sediment sulfide (a by-product of microbial oxidation of sedimentary organic carbon) and oxidation of sedimentary organic carbon catalyzed by microorganisms colonizing the anode. These results demonstrate in real marine environments a new form of power generation that uses an immense, renewable energy reservoir (sedimentary organic carbon) and has near-immediate application.     

Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin,Guaymas Basin

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.     

Activity and community structures of sulfate-reducing microorganisms in polar,temperate and tropical marine sediments

Temperature has a fundamental impact on the metabolic rates of microorganisms and strongly influences microbial ecology and biogeochemical cycling in the environment. In this study, we examined the catabolic temperature response of natural communities of sulfate-reducing microorganisms (SRM) in polar, temperate and tropical marine sediments. In short-term sediment incubation experiments with ³⁵S-sulfate, we demonstrated how the cardinal temperatures for sulfate reduction correlate with mean annual sediment temperatures, indicating specific thermal adaptations of the dominant SRM in each of the investigated ecosystems. The community structure of putative SRM in the sediments, as revealed by pyrosequencing of bacterial 16S rRNA gene amplicons and phylogenetic assignment to known SRM taxa, consistently correlated with in situ temperatures, but not with sediment organic carbon concentrations or C:N ratios of organic matter. Additionally, several species-level SRM phylotypes of the class Deltaproteobacteria tended to co-occur at sites with similar mean annual temperatures, regardless of geographic distance. The observed temperature adaptations of SRM imply that environmental temperature is a major controlling variable for physiological selection and ecological and evolutionary differentiation of microbial communities.     

Processes of organic carbon in mangrove ecosystems

In addition to carbon accumulation in plants, processes of organic carbon in mangrove ecosystems include origins of sediment organic carbon, carbon fluxes between mangroves and their adjacent systems (coastal waters and atmosphere), and cycling processes. Sediment organic carbon originates from suspending solids in coastal waters, mangrove plants and benthic algae. In mangroves with low organic carbon content in sediments, tidal seawater is the main origin of sediment organic carbon, while in mangroves with high sediment organic carbon contents, sediment organic carbon mainly originates from mangrove plants. Due to tidal flush, there is large material exchange between mangrove ecosystems and their adjacent coastal waters. In China, exports of organic carbon in litter falls and dissolved organic carbon from mangroves to their adjacent coastal waters have not been documented. Processes of mangrove litter falls, including production, decomposition, export and animal consumption, determine linkages among organic carbon among mangrove plants, secondary production and coastal ocean. Consumers especially benthic animals may influence organic carbon in mangrove ecosystems, because (1) their consumption rates are high, and their selective feeding on some food sources will change the relative quantities of export, bury and mineralization of organic carbon from different origins; (2) their consumption is much more than assimilation, resulting in the changes in sizes, forms and qualities of non-assimilated organic matters, and then the changes in availability of export, consumption or mineralization of organic carbon. Respiration and sulfate reduction are important mineralization processes of organic carbon in mangrove sediments. Mineralization rates of organic carbon in mangrove sediments are influenced by quantities, activities and particle sizes of organic matters, and other factors such as forest ages, root activities and animal burrowing activities. Researches on processes of mangrove organic carbon should be based on open systems, and ecological processes of organic carbon should be coupled with vegetation restoration.     

Processes of organic carbon in mangrove ecosystems

In addition to carbon accumulation in plants, processes of organic carbon in mangrove ecosystems include origins of sediment organic carbon, carbon fluxes between mangroves and their adjacent systems (coastal waters and atmosphere), and cycling processes. Sediment organic carbon originates from suspending solids in coastal waters, mangrove plants and benthic algae. In mangroves with low organic carbon content in sediments, tidal seawater is the main origin of sediment organic carbon, while in mangroves with high sediment organic carbon contents, sediment organic carbon mainly originates from mangrove plants. Due to tidal flush, there is large material exchange between mangrove ecosystems and their adjacent coastal waters. In China, exports of organic carbon in litter falls and dissolved organic carbon from mangroves to their adjacent coastal waters have not been documented. Processes of mangrove litter falls, including production, decomposition, export and animal consumption, determine linkages among organic carbon among mangrove plants, secondary production and coastal ocean. Consumers especially benthic animals may influence organic carbon in mangrove ecosystems, because (1) their consumption rates are high, and their selective feeding on some food sources will change the relative quantities of export, bury and mineralization of organic carbon from different origins; (2) their consumption is much more than assimilation, resulting in the changes in sizes, forms and qualities of non-assimilated organic matters, and then the changes in availability of export, consumption or mineralization of organic carbon. Respiration and sulfate reduction are important mineralization processes of organic carbon in mangrove sediments. Mineralization rates of organic carbon in mangrove sediments are influenced by quantities, activities and particle sizes of organic matters, and other factors such as forest ages, root activities and animal burrowing activities. Researches on processes of mangrove organic carbon should be based on open systems, and ecological processes of organic carbon should be coupled with vegetation restoration.     

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.     

Anaerobes into heavy metal: Dissimilatory metal reduction in anoxic environments

Within the last decade, a novel form of microbial metabolism of major environmental significance has been elucidated. In this process, known as dissimilatory metal reduction, specialized microorganisms, living in anoxic aquatic sediments and ground water, oxidize organic compounds to carbon dioxide with metals serving as the oxidant. Recent studies have demonstrated that this metabolism explains a number of important geochemical phenomena in ancient and modern sedimentary environments, affecting not only the cycling of metals but also the fate of organic matter. Furthermore, this metabolism may have practical application in remediation of environments contaminated with toxic metals and/or organics.