Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae

IF 3.3 2区 生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Emily St. John, Anna-Louise Reysenbach
{"title":"Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae","authors":"Emily St. John,&nbsp;Anna-Louise Reysenbach","doi":"10.1016/j.syapm.2024.126507","DOIUrl":null,"url":null,"abstract":"<div><p>Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse <em>Thermoproteota.</em> Despite their prevalence in high-temperature submarine communities, <em>Thermoproteota</em> are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the <em>Aeropyrum–Thermodiscus–Caldisphaera</em>. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the <em>Aeropyrum–Thermodiscus–Caldisphaera.</em> At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. <em>Tiamatella incendiivivens, Hestiella acidicharens</em> and <em>Calypsonella navitae.</em> A fourth genus was also identified related to <em>Thermodiscus maritimus,</em> for which no available sequenced genome exists. We propose the novel species <em>Thermodiscus eudorianus</em> to describe our high-quality <em>Thermodiscus</em> MAG<em>,</em> which represents the type genome for the genus. All three novel genera and <em>T. eudorianus</em> are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some <em>Tiamatella, Calypsonella</em> and <em>T. eudorianus</em> may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, <em>Hestiella,</em> may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family <em>Acidilobaceae</em> be amended to include <em>Caldisphaera, Aeropyrum, Thermodiscus</em> and <em>Stetteria</em> and the novel genera described here.</p></div>","PeriodicalId":22124,"journal":{"name":"Systematic and applied microbiology","volume":"47 2","pages":"Article 126507"},"PeriodicalIF":3.3000,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Systematic and applied microbiology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0723202024000213","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum–Thermodiscus–Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum–Thermodiscus–Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.

与 Aeropyrum、Thermodiscus 和 Caldisphaera 相关的深海热液属的基因组比较,以及拟议的 Acidilobaceae 科的修订描述
深海热液喷口拥有嗜热古生物和细菌群落,包括在分类和功能上多种多样的热保护层。尽管它们在高温海底群落中普遍存在,但热保护层在基因组数据库中的代表性长期不足,而且在它们的命名方面也出现了问题,特别是在Aeropyrum-Thermodiscus-Caldisphaera中。为了解决其中的一些问题,我们从以前发表的 20 个深海热液喷口和海底火山元基因组以及公共数据库中的 24 个元基因组中确定了该支系中的 47 个元基因组(MAGs)。利用系统发生组分析、基因组分类数据库工具包(GTDB-Tk)分类评估、16S rRNA 基因系统发生、平均氨基酸同一性(AAI)和功能基因模式,我们重新评估了Aeropyrum-Thermodiscus-Caldisphaera 的分类。我们发现至少有九个属级支系具有两个或两个以上的 MAGs。根据 SeqCode 的要求和建议,我们提出了三个新属的名称,即 Tiamatella incendiivivens、Hestiella acidicharens 和 Calypsonella navitae。我们还发现了与 Thermodiscus maritimus 相关的第四个属,但该属的基因组尚未测序。我们提出了新物种 Thermodiscus eudorianus 来描述我们高质量的 Thermodiscus MAG,它代表了该属的模式基因组。所有三个新属和 T. eudorianus 都可能是厌氧异养动物,能够发酵富含蛋白质的碳源,而一些 Tiamatella、Calypsonella 和 T. eudorianus 还可能还原多硫化物、硫代硫酸盐、硫和/或亚硒酸盐,而可能嗜酸的 Hestiella 可能还原硝酸盐和/或高氯酸盐。根据系统发生组学证据,我们还建议对嗜酸菌科(Acidilobaceae)进行修正,以包括Caldisphaera、Aeropyrum、Thermodiscus和Stetteria以及本文描述的新属。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Systematic and applied microbiology
Systematic and applied microbiology 生物-生物工程与应用微生物
CiteScore
7.50
自引率
5.90%
发文量
57
审稿时长
22 days
期刊介绍: Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology:
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信