Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)
Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea)
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对底栖古菌世界性、Thermoprofundales (MBG-D 古菌)生态和代谢的基因组和转录组见解
DOI：
10.1038/s41396-018-0321-8
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发表时间：
2018-12
期刊：
影响因子：
--
通讯作者：
Li Meng
中科院分区：
文献类型：
--
作者：
Zhou Zhichao;Liu Yang;Lloyd Karen G;Pan Jie;Yang Yuchun;Gu Ji-Dong;Li Meng
几十年前通过 16S rRNA 基因调查发现的海洋底栖 D 类 (MBG-D) 古细菌具有重要的生态意义，但尚未得到充分研究和未培养的沉积古细菌。本研究基于MBG-D古菌16S rRNA基因的综合荟萃分析表明，MBG-D古菌是全球沉积物中最常见的古菌谱系之一，分布广泛、丰度较高，共包括16个亚类。有趣的是，一些亚组表现出对盐度和甲烷渗漏的显着分离。共现分析表明 MBG-D 古菌与 Lokiarchaeota（在咸水和淡水沉积物中）和 Hadesarchaea 存在显着的非随机关联，表明这些古菌群体之间存在潜在的相互作用。同时，基于从红树林和潮间带泥滩沉积物重建的四个近乎完整的宏基因组组装基因组（MAG）和相应的宏转录组，我们提供了关于MBG-D古菌的代谢潜力和生态功能的见解。 MBG-D 古细菌似乎能够运输和同化肽并通过发酵产生乙酸盐和乙醇。宏转录组分析表明，乙酸盐和氨基酸利用以及肽酶基因高表达，尤其是 M09B 型胞外肽酶（胶原酶）在所有四种红树林 MAG 中均表现出高表达水平。除了异养中心碳代谢之外，MBG-D基因组还包括可能编码两种自养途径的基因：使用H4MPT和H4叶酸作为C1载体的Wood-Ljundahl（WL）途径，以及不完整的二羧酸/4-羟基丁酸循环，在过程中从丙酮酸到苹果酸/草酰乙酸的替代旁路 双羧化。这些发现表明MBG-D古菌是一种重要的普遍存在的底栖沉积古菌类群，具有特定的混合营养代谢，因此我们建议将其命名为Thermoprofundales作为热原体纲中的一个新目。在全球范围内，Thermoprofundales和其他底栖古菌可能会协同转化底栖有机物，可能在沉积碳循环中发挥至关重要的作用。
Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood–Ljundahl (WL) pathways using both H4MPT and H4folate as C1carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.
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影响因子：
14.9
作者：
Ludwig, W;Strunk, O;Schleifer, KH
通讯作者：
Schleifer, KH
影响因子：
14.9
作者：
Rawlings ND;Barrett AJ;Finn R
通讯作者：
Finn R
DOI：
10.1073/pnas.0600035103
发表时间：
2006-03-07
影响因子：
11.1
作者：
Biddle, JF;Lipp, JS;Hinrichs, KU
通讯作者：
Hinrichs, KU
DOI：
10.1073/pnas.0601602103
发表时间：
2006-06-06
影响因子：
11.1
作者：
Newman, M. E. J.
通讯作者：
Newman, M. E. J.
影响因子：
14.9
作者：
Trifinopoulos J;Nguyen LT;von Haeseler A;Minh BQ
通讯作者：
Minh BQ