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Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome
bioRxiv - Microbiology Pub Date : 2020-07-02 , DOI: 10.1101/2020.07.02.184564
Esmaeil Forouzan , Ali Asghar Karkhane , Bagher Yakhchali

Heavy metal pollution is a major global health challenge. In order to develop bioremediation solution for decontamination of environment from heavy metals one appropriate step is to investigate heavy metal resistance strategies used by microbial communities in the metal contaminated environments. The aim of the present study was to understand detailed mechanisms by which long time heavy metal (HM) exposed microbial community use to cope with excess of HMs. We exploited the Illumina high throughput metagenomic approach to examine taxonomical and functional diversity of copper enriched soil metagenome. Three enriched metagenomes were compared against 94 metagenomes derived from non-contaminated soils. Taxonomic composition analysis showed that phylogenetic profile of metal contaminated soils were enriched with γ-Proteobacteria. Comparison of functional profile of the two group reveled significant difference with potential role in HM resistance (HMR). Enriched SEED categories were "Membrane Transport", "Cell Wall and Capsule", "Stress Response", "Iron acquisition and metabolism" and "virulence and defense mechanisms". Raw metagenomic reads were assembled into scaffolds and predicted Open Reading Frames (ORFs) were searched against metal resistance gene database (BacMet). Based on enriched genes and gene categories and search of known HMR genes we concluded the microbial community cope with HM using at least 10 different mechanisms. Copper resistance genes were more abundant in the metagenome relative to other metals and pumping metals out of the cell were more abundant relative to other HMR mechanism. Results of the present study could be very helpful in understanding of HMR mechanism used by microbial communities.

中文翻译:

探索富铜金属矿基因组中的金属抗性基因及其机制

重金属污染是全球健康的重大挑战。为了开发用于从重金属去除环境污染的生物修复解决方案,一个适当的步骤是研究微生物群落在金属污染的环境中使用的对重金属的抗性策略。本研究的目的是了解长期暴露于重金属(HM)的微生物群落用于应对过量HM的详细机制。我们利用Illumina高通量宏基因组学方法来研究富铜土壤基因组的分类学和功能多样性。比较了三个富集的基因组与来自非污染土壤的94个基因组。分类学组成分析表明,金属污染土壤的系统发育谱富含γ-变形杆菌。两组功能概况的比较显示,其在HM抵抗(HMR)中的潜在作用存在显着差异。SEED丰富的类别包括“膜运输”,“细胞壁和胶囊”,“压力反应”,“铁的获取和代谢”以及“毒力和防御机制”。将原始的宏基因组读段组装到支架中,并针对金属抗性基因数据库(BacMet)搜索预测的开放阅读框(ORF)。基于丰富的基因和基因类别以及已知HMR基因的搜索,我们得出结论,微生物群落至少使用10种不同的机制应对了HM。相对于其他金属,铜抗性基因在元基因组中更为丰富,相对于其他HMR机制,将铜的抗性基因从细胞中抽出更为丰富。
更新日期:2020-07-03
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