Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing.
Linking Uncultivated Microbial Populations and Benthic Carbon Turnover by Using Quantitative Stable Isotope Probing.
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DOI：
10.1128/aem.01083-18
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发表时间：
2018-09-15
影响因子：
4.4
通讯作者：
Orsi WD
中科院分区：
文献类型：
--
作者：
Coskun ÖK;Pichler M;Vargas S;Gilder S;Orsi WD
关于未培养的微生物种群在底栖环境碳周转中的生态作用知之甚少。为了更好地理解这一点，我们使用定量稳定同位素探测（qSIP），以量化丰富的多样性，特定群体的未培养的细菌和古菌参与自养和异养在底栖湖泊栖息地。我们的研究结果提供了定量的证据，积极异养和自养代谢的几个知之甚少的微生物组，从而证明了它们的相关性，在底栖环境中的碳周转。微生物氨氧化剂是支持异养细菌生长的原位“暗”初级生产的重要驱动因素。这些发现扩展了我们对底栖食物网中微生物种群的理解，以及未培养微生物在底栖碳周转中的作用。底栖环境具有高度多样性和复杂的微生物群落，控制碳通量，但特定的未培养的微生物群体在有机物周转中的作用知之甚少。在这项研究中，定量DNA稳定同位素探针（DNA-qSIP）首次用于连接未培养的细菌和古菌种群的湖泊表层沉积物中的碳周转。在黑暗中与[13 C]碳酸氢盐孵育1周后，DNA-qSIP显示氨氧化古菌（AOA）是参与新有机物生产的主要活性化能无机自养生物。然后，通过在黑暗中将沉积物与[13 C]碳酸氢盐孵育2.5个月，然后提取和浓缩高分子量（HMW）（>50 kDa）有机物，获得天然13 C标记的有机物。qSIP表明，标记的有机物在1周内被823个微生物种群（操作分类单位[OTU]）转化，这些微生物种群主要属于异养变形菌、绿黄杆菌、疣微菌和拟杆菌。然而，与候选微生物分类群Latescibacteria、Omnitrophica、Aminicenthalf、Cloacimonates、AC 1、Bathyarchaeota和Woesearchaeota（仅从基因组特征已知的组）相关的几个OTU也有助于生物量周转。在这823个标记的OTU中，52%（主要隶属于变形菌门）在与[13 C]碳酸氢盐孵育1周后也被标记，表明它们比仅在与13 C标记的HMW有机物孵育中标记的OTU更快地转化碳。这些分类群主要由厚壁菌门、拟杆菌门、疣微菌门和绿球藻门内的未栽培种群组成，突出了它们的生态重要性。我们的研究有助于确定几个知之甚少，未培养的微生物群体在来自“黑暗”初级生产的底栖碳的周转中的作用。重要性很少有人知道的生态作用，未培养的微生物种群在底栖环境中的碳周转。为了更好地理解这一点，我们使用定量稳定同位素探测（qSIP），以量化丰富的多样性，特定群体的未培养的细菌和古菌参与自养和异养在底栖湖泊栖息地。我们的研究结果提供了定量的证据，积极异养和自养代谢的几个知之甚少的微生物组，从而证明了它们的相关性，在底栖环境中的碳周转。微生物氨氧化剂是支持异养细菌生长的原位“暗”初级生产的重要驱动因素。这些发现扩展了我们对底栖食物网中微生物种群的理解，以及未培养微生物在底栖碳周转中的作用。
Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover. Benthic environments harbor highly diverse and complex microbial communities that control carbon fluxes, but the role of specific uncultivated microbial groups in organic matter turnover is poorly understood. In this study, quantitative DNA stable isotope probing (DNA-qSIP) was used for the first time to link uncultivated populations of bacteria and archaea to carbon turnover in lacustrine surface sediments. After 1-week incubations in the dark with [13C]bicarbonate, DNA-qSIP showed that ammonia-oxidizing archaea (AOA) were the dominant active chemolithoautotrophs involved in the production of new organic matter. Natural 13C-labeled organic matter was then obtained by incubating sediments in the dark for 2.5 months with [13C]bicarbonate, followed by extraction and concentration of high-molecular-weight (HMW) (>50-kDa) organic matter. qSIP showed that the labeled organic matter was turned over within 1 week by 823 microbial populations (operational taxonomic units [OTUs]) affiliated primarily with heterotrophic Proteobacteria, Chloroflexi, Verrucomicrobia, and Bacteroidetes. However, several OTUs affiliated with the candidate microbial taxa Latescibacteria, Omnitrophica, Aminicentantes, Cloacimonates, AC1, Bathyarchaeota, and Woesearchaeota, groups known only from genomic signatures, also contributed to biomass turnover. Of these 823 labeled OTUs, 52% (primarily affiliated with Proteobacteria) also became labeled in 1-week incubations with [13C]bicarbonate, indicating that they turned over carbon faster than OTUs that were labeled only in incubations with 13C-labeled HMW organic matter. These taxa consisted primarily of uncultivated populations within the Firmicutes, Bacteroidetes, Verrucomicrobia, and Chloroflexi, highlighting their ecological importance. Our study helps define the role of several poorly understood, uncultivated microbial groups in the turnover of benthic carbon derived from “dark” primary production. IMPORTANCE Little is known about the ecological role of uncultivated microbial populations in carbon turnover in benthic environments. To better understand this, we used quantitative stable isotope probing (qSIP) to quantify the abundance of diverse, specific groups of uncultivated bacteria and archaea involved in autotrophy and heterotrophy in a benthic lacustrine habitat. Our results provide quantitative evidence for active heterotrophic and autotrophic metabolism of several poorly understood microbial groups, thus demonstrating their relevance for carbon turnover in benthic settings. Archaeal ammonia oxidizers were significant drivers of in situ “dark” primary production supporting the growth of heterotrophic bacteria. These findings expand our understanding of the microbial populations within benthic food webs and the role of uncultivated microbes in benthic carbon turnover.