Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria.
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DOI：
10.1186/s40168-015-0077-6
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发表时间：
2015
期刊：
影响因子：
15.5
通讯作者：
Dick GJ
中科院分区：
文献类型：
--
作者：
Baker BJ;Lazar CS;Teske AP;Dick GJ
河口是地球上最具生产力的栖息地之一。河口沉积物中的细菌控制着有机碳的周转和氮、硫的循环。这些社区是复杂的，主要由未培养的谱系，因此很少有人知道生态和代谢过程是如何在沉积物中分配。从头组装和binning导致重建82个细菌基因组从不同的氧化还原制度的河口沉积物。这些基因组属于23个细菌群，包括未培养的候选门（例如，KSB 1，TA 06和KD 3 -62）和三个新描述的门（白色橡树河（WOR）-1，WOR-2和WOR-3）。未培养的门通常是最丰富的硫酸盐-甲烷过渡（SMTZ）和甲烷丰富的区域，基因组数据预测，他们调解河口环境的基本生物地球化学过程，包括有机碳降解和发酵。在富含硫酸盐的层中最丰富的生物是新的γ-变形菌，它们具有氧化硫和还原硝酸盐和亚硝酸盐的基因。有趣的是，反硝化的最终步骤（NO3到N2 O，然后N2 O到N2）存在于不同的细菌种群中。这个数据集扩展了我们对几个未培养的门的代谢潜力的了解。在沉积物中，在不同的谱系，往往是不同的门，基本的地球化学过程的基因组潜力冗余。我们能够通过细菌加工的多个地球化学层绘制碳和营养物质的流动图，并揭示群落内潜在的生态相互作用。本文的在线版本（doi：10.1186/s40168-015-0077-6）包含补充材料，可供授权用户使用。
Estuaries are among the most productive habitats on the planet. Bacteria in estuary sediments control the turnover of organic carbon and the cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments. De novo assembly and binning resulted in the reconstruction of 82 bacterial genomes from different redox regimes of estuary sediments. These genomes belong to 23 bacterial groups, including uncultured candidate phyla (for example, KSB1, TA06, and KD3-62) and three newly described phyla (White Oak River (WOR)-1, WOR-2, and WOR-3). The uncultured phyla are generally most abundant in the sulfate-methane transition (SMTZ) and methane-rich zones, and genomic data predict that they mediate essential biogeochemical processes of the estuarine environment, including organic carbon degradation and fermentation. Among the most abundant organisms in the sulfate-rich layer are novel Gammaproteobacteria that have genes for the oxidation of sulfur and the reduction of nitrate and nitrite. Interestingly, the terminal steps of denitrification (NO3 to N2O and then N2O to N2) are present in distinct bacterial populations. This dataset extends our knowledge of the metabolic potential of several uncultured phyla. Within the sediments, there is redundancy in the genomic potential in different lineages, often distinct phyla, for essential biogeochemical processes. We were able to chart the flow of carbon and nutrients through the multiple geochemical layers of bacterial processing and reveal potential ecological interactions within the communities. The online version of this article (doi:10.1186/s40168-015-0077-6) contains supplementary material, which is available to authorized users.
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影响因子：
5.2
作者：
Comte J;Fauteux L;Del Giorgio PA
通讯作者：
Del Giorgio PA
影响因子：
11
作者：
Bowen, Jennifer L.;Morrison, Hilary G.;Sogin, Mitchell L.
通讯作者：
Sogin, Mitchell L.
DOI：
10.1073/pnas.1112905109
发表时间：
2012-01-31
影响因子：
11.1
作者：
Carlson, Hans K.;Iavarone, Anthony T.;Coates, John D.
通讯作者：
Coates, John D.
影响因子：
4.4
作者：
Berlemont, Renaud;Martiny, Adam C.
通讯作者：
Martiny, Adam C.
DOI：
10.1073/pnas.0709942105
发表时间：
2008-07-29
影响因子：
11.1
作者：
Biddle, Jennifer F.;Fitz-Gibbon, Sorel;House, Christopher H.
通讯作者：
House, Christopher H.