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宏基因组组装基因组为了解津巴布韦布赫拉盐碱湖的微生物分类和生态提供了见解。

Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.

作者信息

Mangoma Ngonidzashe, Zhou Nerve, Ncube Thembekile

机构信息

Faculty of Applied Science, Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe.

Faculty of Sciences, Biological Sciences and Biotechnology Department, Botswana International University of Science and Technology, Palapye, Botswana.

出版信息

PLoS One. 2024 Dec 2;19(12):e0299620. doi: 10.1371/journal.pone.0299620. eCollection 2024.


DOI:10.1371/journal.pone.0299620
PMID:39621710
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11611182/
Abstract

The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.

摘要

宏基因组学的应用极大地增进了我们对极端环境微生物群落的分类学、系统发育和生态学的理解。如今,生物信息学的进展使得从宏基因组序列数据中重建几乎完整的微生物基因组(即宏基因组组装基因组,MAGs)成为可能,从而能够对未培养的嗜极微生物进行更精确的细胞水平分类学、系统发育和功能分析。在此,我们报告了从位于津巴布韦东部的布埃拉盐碱地中回收和鉴定宏基因组组装基因组的情况。尽管该生态系统具有独特的地球化学性质以及作为独特微生物栖息地的潜力,但此前尚未得到研究。使用DNA纳米球测序(DNBSEQR)技术对盐碱地的宏基因组DNA进行了测序。在知识库(KBase)平台上进行的序列分析包括质量评估、读段组装、重叠群分箱和MAG提取。为了确定这些MAGs在盐碱地生态系统中可能的生态作用,对其进行了分类定位、系统发育分析和功能注释。总共回收了16个中高质量的细菌MAGs,它们均分布在以假单胞菌门和芽孢杆菌门为主的五个门中。在分类到属水平的10个MAGs中,有5个属于嗜盐/嗜盐碱菌属,即嗜碱杆菌属、弧菌属、硫碱弧菌属、塞氏菌属和硝化球菌属,这突出了嗜盐碱菌在布埃拉盐碱地中的重要性。功能分析表明,MAGs拥有多种碳水化合物代谢途径,其中糖酵解和磷酸戊糖途径似乎是该生态系统中的关键途径。几个MAGs拥有与氮和硫循环某些关键方面相关的途径。一些MAGs同时具有硫酸盐还原途径和呼吸途径,这表明通过硫酸盐呼吸进行ATP生物合成的一种可能机制。这项研究证明了从极端环境中回收高质量微生物基因组并进行分类和功能注释的可行性,从而能够确定未培养微生物的生态作用和生物技术潜力。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/811c/11611182/0f52540859cf/pone.0299620.g008.jpg
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本文引用的文献

[1]
Characterization of metagenome-assembled genomes from the International Space Station.

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[2]
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Front Microbiol. 2022-12-1

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Metagenome-assembled genome extraction and analysis from microbiomes using KBase.

Nat Protoc. 2023-1

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Nucleic Acids Res. 2023-1-6

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