Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments
Metagenomics coupled with biogeochemical rates measurements provide evidence that nitrate addition stimulates respiration in salt marsh sediments
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DOI：
10.1002/lno.11326
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发表时间：
2019-10-11
影响因子：
4.5
通讯作者：
Bowen, Jennifer L.
中科院分区：
文献类型：
--
作者：
Bulseco, Ashley N.;Vineis, Joseph H.;Bowen, Jennifer L.
高通量测序使强大的鸟枪宏基因组测序，告知我们的重要地球化学过程的遗传基础的理解。然而，这些工具在受控实验框架中的应用发展较慢，这将该领域从探索性分析推向假设驱动的研究。我们进行了流通反应器实验，以研究如何盐沼沉积物从不同的深度响应硝酸盐的添加和链接到这个潜在的遗传基础的地球化学过程。了解盐沼沉积物中碳和氮循环的机制基础对于预测沼泽提供的重要生态系统服务（包括碳储存和营养物去除）将如何应对全球变化至关重要。在添加硝酸盐之前，我们使用宏基因组学来研究沉积物微生物群落的功能潜力，所述沉积物微生物群落发生沿着深度梯度，其中有机物反应性由于分解而改变。宏基因组数据表明，编码呼吸作用（包括反硝化作用）的酶的基因在浅层沉积物中含量较高，而指示资源限制的基因在深层最高。硝酸盐富集92天后，我们测量了溶解无机碳生产，反硝化和异化硝酸盐还原为铵的累积增加;这些速率与编码这些重要途径中必需酶的基因密切相关。我们的研究结果强调了控制实验在将地球化学速率与潜在遗传途径联系起来方面的重要性。此外，它们表明硝酸盐作为电子受体在促进微生物呼吸中的重要性，这对沿海海洋系统中的碳和氮循环和命运产生了影响。
High-throughput sequencing has enabled robust shotgun metagenomic sequencing that informs our understanding of the genetic basis of important biogeochemical processes. Slower to develop, however, are the application of these tools in a controlled experimental framework that pushes the field beyond exploratory analysis toward hypothesis-driven research. We performed flow-through reactor experiments to examine how salt marsh sediments from varying depths respond to nitrate addition and linked biogeochemical processes to this underlying genetic foundation. Understanding the mechanistic basis of carbon and nitrogen cycling in salt marsh sediments is critical for predicting how important ecosystem services provided by marshes, including carbon storage and nutrient removal, will respond to global change. Prior to the addition of nitrate, we used metagenomics to examine the functional potential of the sediment microbial community that occurred along a depth gradient, where organic matter reactivity changes due to decomposition. Metagenomic data indicated that genes encoding enzymes involved in respiration, including denitrification, were higher in shallow sediments, and genes indicative of resource limitation were greatest at depth. After 92 d of nitrate enrichment, we measured cumulative increases in dissolved inorganic carbon production, denitrification, and dissimilatory nitrate reduction to ammonium; these rates correlated strongly with genes that encode essential enzymes in these important pathways. Our results highlight the importance of controlled experiments in linking biogeochemical rates to underlying genetic pathways. Furthermore, they indicate the importance of nitrate as an electron acceptor in fueling microbial respiration, which has consequences for carbon and nitrogen cycling and fate in coastal marine systems.