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Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments.
The ISME Journal ( IF 10.8 ) Pub Date : 2020-02-17 , DOI: 10.1038/s41396-020-0615-5 Ibrahim F Farag 1 , Jennifer F Biddle 1 , Rui Zhao 1 , Amanda J Martino 2 , Christopher H House 3 , Rosa I León-Zayas 1, 4
The ISME Journal ( IF 10.8 ) Pub Date : 2020-02-17 , DOI: 10.1038/s41396-020-0615-5 Ibrahim F Farag 1 , Jennifer F Biddle 1 , Rui Zhao 1 , Amanda J Martino 2 , Christopher H House 3 , Rosa I León-Zayas 1, 4
Affiliation
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Numerous archaeal lineages are known to inhabit marine subsurface sediments, although their distributions, metabolic capacities, and interspecies interactions are still not well understood. Abundant and diverse archaea were recently reported in Costa Rica (CR) margin subseafloor sediments recovered during IODP Expedition 334. Here, we recover metagenome-assembled genomes (MAGs) of archaea from the CR margin and compare them to their relatives from shallower settings. We describe 31 MAGs of six different archaeal lineages (Lokiarchaeota, Thorarchaeota, Heimdallarchaeota, Bathyarcheota, Thermoplasmatales, and Hadesarchaea) and thoroughly analyze representative MAGs from the phyla Lokiarchaeota and Bathyarchaeota. Our analysis suggests the potential capability of Lokiarchaeota members to anaerobically degrade aliphatic and aromatic hydrocarbons. We show it is genetically possible and energetically feasible for Lokiarchaeota to degrade benzoate if they associate with organisms using nitrate, nitrite, and sulfite as electron acceptors, which suggests a possibility of syntrophic relationships between Lokiarchaeota and nitrite and sulfite reducing bacteria. The novel Bathyarchaeota lineage possesses an incomplete methanogenesis pathway lacking the methyl coenzyme M reductase complex and encodes a noncanonical acetogenic pathway potentially coupling methylotrophy to acetogenesis via the methyl branch of Wood-Ljungdahl pathway. These metabolic characteristics suggest the potential of this Bathyarchaeota lineage to be a transition between methanogenic and acetogenic Bathyarchaeota lineages. This work expands our knowledge about the metabolic functional repertoire of marine benthic archaea.
中文翻译：
从哥斯达黎加深部沉积物的基因组解析古细菌谱系的代谢潜能。
尽管尚不清楚它们的分布，代谢能力和种间相互作用，但仍有许多古细菌世袭栖息于海洋地下沉积物中。最近，在IODP第334次探险中发现了在哥斯达黎加（CR）边缘海底沉积物中发现的古细菌种类繁多。在这里，我们从CR边缘回收古细菌的基因组组装基因组（MAG），并将其与较浅环境中的亲戚进行比较。我们描述了六个不同的古细菌谱系（Lokiarchaeota，Thorarchaeota，Heimdallarchaeota，Bathyarcheota，Thermoplasmatales和Hadesarchaea）的31个MAG，并彻底分析了门类Lokiarchaeota和Bathyarchaeota的代表性MAG。我们的分析表明，Lokiarchaeota成员具有厌氧降解脂肪族和芳香族烃的潜在能力。我们显示如果Lokiarchaeota与使用硝酸盐，亚硝酸盐和亚硫酸盐作为电子受体的生物体缔合，降解其苯甲酸盐在遗传上是可行的，并且在能源上可行，这表明Lokiarchaeota与亚硝酸盐和亚硫酸盐还原菌之间存在营养关系。新的Bathyarchaeota谱系拥有不完整的甲烷生成途径，缺少甲基辅酶M还原酶复合物，并编码非规范的产乙酸途径，可能通过Wood-Ljungdahl途径的甲基分支将甲基营养与产乙酸耦合。这些代谢特征表明，该Bathyarchaeota血统可能是产甲烷和产乙酸的Bytharchaeota血统之间的过渡。这项工作扩大了我们对海洋底栖古细菌的代谢功能库的认识。
更新日期：2020-02-17
中文翻译：
从哥斯达黎加深部沉积物的基因组解析古细菌谱系的代谢潜能。
尽管尚不清楚它们的分布，代谢能力和种间相互作用，但仍有许多古细菌世袭栖息于海洋地下沉积物中。最近，在IODP第334次探险中发现了在哥斯达黎加（CR）边缘海底沉积物中发现的古细菌种类繁多。在这里，我们从CR边缘回收古细菌的基因组组装基因组（MAG），并将其与较浅环境中的亲戚进行比较。我们描述了六个不同的古细菌谱系（Lokiarchaeota，Thorarchaeota，Heimdallarchaeota，Bathyarcheota，Thermoplasmatales和Hadesarchaea）的31个MAG，并彻底分析了门类Lokiarchaeota和Bathyarchaeota的代表性MAG。我们的分析表明，Lokiarchaeota成员具有厌氧降解脂肪族和芳香族烃的潜在能力。我们显示如果Lokiarchaeota与使用硝酸盐，亚硝酸盐和亚硫酸盐作为电子受体的生物体缔合，降解其苯甲酸盐在遗传上是可行的，并且在能源上可行，这表明Lokiarchaeota与亚硝酸盐和亚硫酸盐还原菌之间存在营养关系。新的Bathyarchaeota谱系拥有不完整的甲烷生成途径，缺少甲基辅酶M还原酶复合物，并编码非规范的产乙酸途径，可能通过Wood-Ljungdahl途径的甲基分支将甲基营养与产乙酸耦合。这些代谢特征表明，该Bathyarchaeota血统可能是产甲烷和产乙酸的Bytharchaeota血统之间的过渡。这项工作扩大了我们对海洋底栖古细菌的代谢功能库的认识。
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