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印度北喜马拉雅山脉一座中温温泉中硫生物地球化学循环的微生物生态学

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.

作者信息

Nagar Shekhar, Talwar Chandni, Motelica-Heino Mikael, Richnow Hans-Hermann, Shakarad Mallikarjun, Lal Rup, Negi Ram Krishan

机构信息

Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, New Delhi, India.

UMR 7327, Centre National de la Recherche Scientifique, Institut des Sciences de la Terre D'Orleans (ISTO), Université d'Orleans-Brgm, Orleans, France.

出版信息

Front Microbiol. 2022 Apr 13;13:848010. doi: 10.3389/fmicb.2022.848010. eCollection 2022.

Abstract

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as , , , and (). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both genes ( = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r) suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive evolutionary time-scale phylogeny proved that the earliest (but not the first) proteins belong to anaerobic with other () oxidizers, also we confirm that (ii) SRBs belongs to δ- occurring independent lateral gene transfer (LGT) of genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of (TM score = 0.86, 0.98, 0.96) and (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

摘要

栖息在温泉中的硫相关原核生物为探索完整生态系统过程的无限可能性提供了良好机会。宏基因组分析进一步扩展了这些非凡的硫(S)代谢微生物的系统发育广度,以及它们在环境生物系统中的复杂代谢网络和互营相互作用。通过这项研究,我们通过对位于喜马拉雅山脉北部受硫污染温泉的宏基因组分析,探索并扩展了以硫循环基因为重点的微生物遗传库。分析揭示了在硫循环中具有既定作用的微生物群落的丰富多样性,如 、 、 和 ()。从每千碱基读取数(RPKs)分类为翻译和核糖体结构及生物发生反映出,推断在微生物垫、沉积物和水中丰富的主要基因家族被归类为 。序列相似性分析表明,从所有宏基因组中检索到的两个 基因( = 178)具有保守模式,而其他硫歧化蛋白由于不同的结构和化学底物而有所不同。具有保守(r)的硫氧化细菌(SOB)和硫酸盐还原细菌(SRB)的多样性表明,这是该位点微生物适应性的重要适应特征。在这里,(i)氧化和还原 的进化时间尺度系统发育证明,最早(但不是第一个)的 蛋白属于厌氧 与其他()氧化器,我们还证实(ii)SRB属于δ-,发生 基因向不同且少数新谱系的独立横向基因转移(LGT)。此外,未分配的DsrAB蛋白的结构预测证实了它们与 (TM得分 = 0.86、0.98、0.96)和 (TM得分 = 0.97、0.98)物种的相关性。我们提出,该遗传库可能为研究这些基因在生物地球化学硫循环中的时间尺度进化和水平基因转移提供基础。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69d1/9044081/5719cdfb0f05/fmicb-13-848010-g001.jpg

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