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新型土壤α-变形菌 Novosphingobium terrae 的基因组和生理特征研究,该菌从含有巨型质体的赛拉多土壤中分离得到。

Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid.

机构信息

Laboratório de Microbiologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.

Laboratório de Biologia Molecular, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil.

出版信息

Braz J Microbiol. 2023 Mar;54(1):239-258. doi: 10.1007/s42770-022-00900-4. Epub 2023 Jan 26.


DOI:10.1007/s42770-022-00900-4
PMID:36701110
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9944591/
Abstract

A novel bacterial strain, designated GeG2, was isolated from soils of the native Cerrado, a highly biodiverse savanna-like Brazilian biome. 16S rRNA gene analysis of GeG2 revealed high sequence identity (100%) to the alphaproteobacterium Novosphingobium rosa; however, comparisons with N. rosa DSM 7285 showed several distinctive features, prompting a full characterization of the new strain in terms of physiology, morphology, and, ultimately, its genome. GeG2 cells were Gram-stain-negative bacilli, facultatively anaerobic, motile, positive for catalase and oxidase activities, and starch hydrolysis. Strain GeG2 presented planktonic-sessile dimorphism and cell aggregates surrounded by extracellular matrix and nanometric spherical structures were observed, suggesting the production of exopolysaccharides (EPS) and outer membrane vesicles (OMVs). Despite high 16S rDNA identity, strain GeG2 showed 90.38% average nucleotide identity and 42.60% digital DNA-DNA hybridization identity with N. rosa, below species threshold. Whole-genome assembly revealed four circular replicons: a 4.1 Mb chromosome, a 2.7 Mb extrachromosomal megareplicon, and two plasmids (212.7 and 68.6 kb). The megareplicon contains a few core genes and plasmid-type replication/maintenance systems, consistent with its classification as a chromid. Genome annotation shows a vast repertoire of carbohydrate-active enzymes and genes involved in the degradation of aromatic compounds, highlighting the biotechnological potential of the new isolate. Chemotaxonomic features, including polar lipid and fatty acid profiles, as well as physiological, molecular, and whole-genome comparisons showed significant differences between strain GeG2 and N. rosa, indicating that it represents a novel species, for which the name Novosphingobium terrae is proposed. The type strain is GeG2 (= CBMAI 2313 = CBAS 753).

摘要

一株新型细菌菌株 GeG2 从巴西高度多样化的热带稀树草原生物群落的原生塞拉多土壤中分离得到。通过 GeG2 的 16S rRNA 基因分析发现,它与α变形菌新鞘氨醇单胞菌属的 Novosphingobium rosa 具有高度的序列同一性(100%);然而,与 N. rosa DSM 7285 的比较显示出几个独特的特征,促使对新菌株进行全面的生理、形态和最终的基因组特征描述。GeG2 细胞为革兰氏阴性杆菌,兼性厌氧,运动,过氧化氢酶和氧化酶活性呈阳性,淀粉水解。菌株 GeG2 表现出浮游生物固着的二态性,并且观察到细胞聚集体被细胞外基质和纳米级球形结构包围,表明其产生了胞外多糖(EPS)和外膜囊泡(OMVs)。尽管 16S rDNA 高度一致,但 GeG2 菌株与 N. rosa 的平均核苷酸同一性为 90.38%,数字 DNA-DNA 杂交同一性为 42.60%,低于种的阈值。全基因组组装揭示了四个圆形复制子:一个 4.1 Mb 染色体、一个 2.7 Mb 染色体外巨型复制子和两个质粒(212.7 和 68.6 kb)。巨型复制子包含一些核心基因和质粒型复制/维持系统,这与其作为 chromid 的分类一致。基因组注释显示了大量的碳水化合物活性酶和参与芳香族化合物降解的基因,突出了新分离株的生物技术潜力。化学分类学特征,包括极性脂质和脂肪酸谱,以及生理、分子和全基因组比较,表明 GeG2 菌株与 N. rosa 之间存在显著差异,表明它代表了一个新的物种,提议将其命名为 Novosphingobium terrae。模式菌株是 GeG2(= CBMAI 2313 = CBAS 753)。

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本文引用的文献

[1]
Bacterial extracellular polymeric substances: Impact on soil microbial community composition and their potential role in heavy metal-contaminated soil.

Ecotoxicol Environ Saf. 2022-7-15

[2]
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Front Microbiol. 2020-7-10

[3]
Acidocalcisomes and Polyphosphate Granules Are Different Subcellular Structures in Agrobacterium tumefaciens.

Appl Environ Microbiol. 2020-4-1

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Int J Syst Evol Microbiol. 2020-2

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Bioinformatics. 2020-4-1

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Microbiome. 2019-8-27

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Nat Commun. 2019-5-16

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