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全球丰度较高的“Udaeobacter”得益于土壤中抗生素的释放,并可能具有痕量气体清除功能。

Globally Abundant " Udaeobacter" Benefits from Release of Antibiotics in Soil and Potentially Performs Trace Gas Scavenging.

机构信息

Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Göttingen, Germany.

Institute of Plant Sciences, University of Bern, Bern, Switzerland.

出版信息

mSphere. 2020 Jul 8;5(4):e00186-20. doi: 10.1128/mSphere.00186-20.

Abstract

affiliated with " Udaeobacter" belong to the most abundant soil bacteria worldwide. Although the synthesis of antibiotics presumably evolved in soil, and environmental pollution with antimicrobials increases, the impact of these complex molecules on " Udaeobacter" remains to be elucidated. In this study, we demonstrate that " Udaeobacter" representatives residing in grassland as well as forest soil ecosystems show multidrug resistance and even take advantage of antibiotics release. Soils treated with up to six different antibiotics exhibited a higher " Udaeobacter" abundance than corresponding controls after 3, 8, and 20 days of incubation. In this context, we provide evidence that " Udaeobacter" representatives may utilize nutrients which are released due to antibiotic-driven lysis of other soil microbes and thereby reduce energetically expensive synthesis of required biomolecules. Moreover, genomic analysis revealed the presence of genes conferring resistance to multiple classes of antibiotics and indicated that " Udaeobacter" representatives most likely oxidize the trace gas H to generate energy. This energy might be required for long-term persistence in terrestrial habitats, as already suggested for other dominant soil bacteria. Our study illustrates, for the first time, that globally abundant " Udaeobacter" benefits from release of antibiotics, which confers advantages over other soil bacteria and represents a so-far overlooked fundamental lifestyle feature of this poorly characterized verrucomicrobial genus. Furthermore, our study suggests that " Udaeobacter" representatives can utilize H as an alternative electron donor. Soil bacteria have been investigated for more than a century, but one of the most dominant terrestrial groups on Earth, " Udaeobacter," remains elusive and largely unexplored. Its natural habitat is considered a major reservoir of antibiotics, which directly or indirectly impact phylogenetically diverse microorganisms. Here, we found that " Udaeobacter" representatives exhibit multidrug resistance and not only evade harmful effects of antimicrobials but even benefit from antibiotic pressure in soil. Therefore, " Udaeobacter" evidently affects the composition of soil resistomes worldwide and might represent a winner of rising environmental pollution with antimicrobials. In addition, our study indicates that " Udaeobacter" representatives utilize H and thereby contribute to global hydrogen cycling. The here-reported findings provide insights into elementary lifestyle features of " Udaeobacter," potentially contributing to its successful global dissemination.

摘要

与“Udaeobacter”相关的细菌属于全球最丰富的土壤细菌。尽管抗生素的合成可能在土壤中进化,并且环境中抗微生物药物的污染增加,但这些复杂分子对“Udaeobacter”的影响仍有待阐明。在这项研究中,我们证明了居住在草原和森林土壤生态系统中的“Udaeobacter”代表具有多药耐药性,甚至利用抗生素的释放。用多达六种不同的抗生素处理的土壤在培养 3、8 和 20 天后,其“Udaeobacter”丰度高于相应的对照。在这种情况下,我们提供了证据表明,“Udaeobacter”代表可能利用由于抗生素驱动的其他土壤微生物裂解而释放的营养物质,从而减少对所需生物分子进行高能量合成的需求。此外,基因组分析显示了赋予对多种抗生素类别的抗性的基因的存在,并表明“Udaeobacter”代表最有可能氧化痕量气体 H 来产生能量。这种能量可能是在陆地栖息地长期生存所必需的,正如其他优势土壤细菌所表明的那样。我们的研究首次表明,全球丰富的“Udaeobacter”受益于抗生素的释放,这使其相对于其他土壤细菌具有优势,并且代表了这种研究不足的疣微菌属的一个迄今为止被忽视的基本生活方式特征。此外,我们的研究表明,“Udaeobacter”代表可以利用 H 作为替代电子供体。土壤细菌已经被研究了一个多世纪,但地球上最主要的陆地群体之一“Udaeobacter”仍然难以捉摸,而且很大程度上尚未被探索。它的自然栖息地被认为是抗生素的主要储存库,这些抗生素直接或间接地影响具有不同系统发育的微生物。在这里,我们发现“Udaeobacter”代表表现出多药耐药性,不仅逃避了抗生素的有害影响,甚至还受益于土壤中的抗生素压力。因此,“Udaeobacter”显然会影响全球土壤抗药性的组成,并且可能代表对抗生素污染不断增加的赢家。此外,我们的研究表明,“Udaeobacter”代表利用 H,从而促进了全球氢气循环。这里报道的发现为“Udaeobacter”的基本生活方式特征提供了见解,可能有助于其在全球范围内的成功传播。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b1f5/7343977/9e296243990f/mSphere.00186-20-f0001.jpg

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本文引用的文献

1
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
Bioinformatics. 2019 Nov 15;36(6):1925-7. doi: 10.1093/bioinformatics/btz848.
2
The MetaCyc database of metabolic pathways and enzymes - a 2019 update.
Nucleic Acids Res. 2020 Jan 8;48(D1):D445-D453. doi: 10.1093/nar/gkz862.
4
antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline.
Nucleic Acids Res. 2019 Jul 2;47(W1):W81-W87. doi: 10.1093/nar/gkz310.
5
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Nat Commun. 2018 Nov 30;9(1):5114. doi: 10.1038/s41467-018-07641-9.
6
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life.
Nat Biotechnol. 2018 Nov;36(10):996-1004. doi: 10.1038/nbt.4229. Epub 2018 Aug 27.
7
Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis.
Nature. 2018 Jun;558(7710):440-444. doi: 10.1038/s41586-018-0207-y. Epub 2018 Jun 13.
8
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Mol Biol Evol. 2018 Jun 1;35(6):1547-1549. doi: 10.1093/molbev/msy096.
9
Shared strategies for β-lactam catabolism in the soil microbiome.
Nat Chem Biol. 2018 Jun;14(6):556-564. doi: 10.1038/s41589-018-0052-1. Epub 2018 Apr 30.

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