Department of Marine Science, University of Texas-Austin, Marine Science Institute, 750 Channel View Dr., Port Aransas, TX 78373 USA ; Department of Earth and Environmental Sciences, University of Michigan, 1100 N. University Ave., Ann Arbor, MI 48109 USA.
Department of Marine Sciences, University of North Carolina, Chapel Hill, NC USA ; Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences, Department of Geosciences, University of Bremen, Bremen, Germany.
Microbiome. 2015 Apr 13;3:14. doi: 10.1186/s40168-015-0077-6. eCollection 2015.
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.
河口是地球上生产力最高的栖息地之一。河口沉积物中的细菌控制着有机碳的转化和氮、硫的循环。这些群落非常复杂，主要由未培养的谱系组成，因此对于生态和代谢过程在沉积物中是如何分配的知之甚少。
从头组装和分类结果从河口沉积物的不同氧化还原区重建了 82 个细菌基因组。这些基因组属于 23 个细菌群，包括未培养的候选门（例如，KSB1、TA06 和 KD3-62）和三个新描述的门（白橡树河（WOR）-1、WOR-2 和 WOR-3）。未培养的门通常在硫酸盐-甲烷过渡带（SMTZ）和富含甲烷的区域中最为丰富，基因组数据预测它们介导着河口环境的重要生物地球化学过程，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具有硫氧化、硝酸盐和亚硝酸盐还原基因的新型γ变形菌。有趣的是，反硝化的最后步骤（NO3 到 N2O，然后 N2O 到 N2）存在于不同的细菌种群中。
该数据集扩展了我们对几个未培养门的代谢潜力的认识。在沉积物中，对于重要的生物地球化学过程，不同谱系（通常是不同的门）在基因组潜力上存在冗余。我们能够绘制出碳和营养物质通过细菌处理的多个地球化学层的流动，并揭示群落内潜在的生态相互作用。
