Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.
Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.
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DOI：
10.1038/ismej.2015.257
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发表时间：
2016-08
期刊：
影响因子：
--
通讯作者：
Mußmann M
中科院分区：
文献类型：
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作者：
Dyksma S;Bischof K;Fuchs BM;Hoffmann K;Meier D;Meyerdierks A;Pjevac P;Probandt D;Richter M;Stepanauskas R;Mußmann M
海洋沉积物是地球上最大的碳汇。海洋中近一半的暗碳固定发生在沿海沉积物中，但负责的微生物在很大程度上是未知的。通过将16S rRNA方法、单细胞基因组学、宏基因组学和转录组学与14c -碳同化实验相结合，我们发现未培养的γ变形菌占沿海沉积物中暗碳固定的70%至86%。首先，我们对欧洲和澳大利亚的13个潮汐和沿海沉积物中的细菌16S rRNA基因多样性进行了调查，以确定普遍存在的主要与硫氧化细菌相关的γ变形菌属核心群。它们也占了缺氧、490厘米深的地下沉积物中微生物群落的很大一部分。然后，我们通过闪烁法对从沉积物中提取和流动分类的特定微生物种群进行量化，这些微生物种群与14c -碳酸氢盐短期孵卵。我们确定了三个不同的伽马变形菌分支，涵盖了从科到目的多样性范围（酸化铁杆菌-，JTB255-和ssr -分支），它们构成了潮汐沉积物中50%以上的暗碳固定。与这些活性测量结果一致，硫氧化和碳固定基因的环境转录本主要与硫氧化γ变形菌相关。硫和氢氧化途径关键基因的共定位及其在未培养的γ变形菌基因组中的表达说明了海洋沉积物中硫氧化剂的未知代谢可塑性。鉴于其全球分布和高丰度，我们提出一个稳定的代谢灵活的γ变形菌群驱动海洋碳和硫循环的重要部分。
Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single cell genomics, metagenomics and -transcriptomics with 14C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70 to 86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490 cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with 14C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter-, JTB255- and SSr-clades) that made up more than 50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drive important parts of marine carbon and sulfur cycles.