地中海长读数元基因组中海洋浮游氨氧化古细菌种群的微观多样性。

IF 4.3 2区 生物学 Q2 MICROBIOLOGY Environmental microbiology Pub Date : 2024-07-30 DOI:10.1111/1462-2920.16684
Pablo Suárez-Moo, Jose M. Haro-Moreno, Francisco Rodriguez-Valera
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引用次数: 0

摘要

要了解微生物种群的适应性,关键是要了解一个物种内不同种群水平的运作过程以及单个原核生物基因组的遗传变异性。在这里,我们利用元基因组招募方法和长读数(PacBio HiFi)元基因组测序,确定了氨氧化古细菌(AOA)种群灵活基因组的特征。在地中海西部的低光照区(75 米深),Nitrosopelagicus brevis CN25 和 Nitrosopumilus catalinensis SPOT1 基因组在现有的完整 AOA 基因组中具有最高的招募值。我们利用这两个基因组分析了柔性基因(因菌株而异)的多样性,方法是研究位于柔性基因组岛(fGIs)内的长读数,而柔性基因组岛是由它们的低招募值确定的。两个 AOA 基因组都有一个大的 fGI,参与暴露结构的糖基化,高度可变,富含糖基转移酶。N. brevis有两个fGI,分别与磷和铵的运输有关。N. catalinensis 的 fGIs 参与磷的运输和金属的吸收。之前在 N. brevis 中被报告为 "未指定功能 "的 fGI5 可能与防御有关。这些研究结果表明,利用第三代测序元基因组学方法,可以有效地描述包括 AOA 在内的海洋微生物种群的微观多样性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome

The knowledge of the different population-level processes operating within a species, and the genetic variability of the individual prokaryotic genomes, is key to understanding the adaptability of microbial populations. Here, we characterized the flexible genome of ammonia-oxidizing archaeal (AOA) populations using a metagenomic recruitment approach and long-read (PacBio HiFi) metagenomic sequencing. In the lower photic zone of the western Mediterranean Sea (75 m deep), the genomes Nitrosopelagicus brevis CN25 and Nitrosopumilus catalinensis SPOT1 had the highest recruitment values among available complete AOA genomes. They were used to analyse the diversity of flexible genes (variable from strain to strain) by examining the long-reads located within the flexible genomic islands (fGIs) identified by their under-recruitment. Both AOA genomes had a large fGI involved in the glycosylation of exposed structures, highly variable, and rich in glycosyltransferases. N. brevis had two fGIs related to the transport of phosphorus and ammonium respectively. N. catalinensis had fGIs involved in phosphorus transportation and metal uptake. A fGI5 previously reported as ‘unassigned function’ in N. brevis could be associated with defense. These findings demonstrate that the microdiversity of marine microbe populations, including AOA, can be effectively characterized using an approach that incorporates third-generation sequencing metagenomics.

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来源期刊
Environmental microbiology
Environmental microbiology 环境科学-微生物学
CiteScore
9.90
自引率
3.90%
发文量
427
审稿时长
2.3 months
期刊介绍: Environmental Microbiology provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens
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