A global survey of arsenic-related genes in soil microbiomes
A global survey of arsenic-related genes in soil microbiomes
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DOI：
10.1186/s12915-019-0661-5
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发表时间：
2019-05-30
期刊：
影响因子：
5.4
通讯作者：
Shade, Ashley
中科院分区：
文献类型：
--
作者：
Dunivin, Taylor K.;Yeh, Susanna Y.;Shade, Ashley
背景：环境抗性组包括可转移的微生物基因。一个重要的抗性组成分是对砷的抗性，砷是一种普遍存在的有毒非金属，可能对人类和动物健康产生负面和长期的影响。砷抗性和代谢基因在环境中的分布尚不清楚。然而，微生物群落及其抗性组介导砷的关键转化，预计会影响生物地球化学和局部毒性。结果：我们检查了 922 个土壤基因组和 38 个宏基因组中砷抗性和代谢基因的系统发育多样性、基因组位置（染色体或质粒）以及生物地理学。为此，我们开发了一个生物信息学工具包，其中包括 BLAST 数据库、隐马尔可夫模型和用于基因靶向组装九个砷抗性和代谢基因的资源：acr3、aioA、arsB、arsC (grx)、arsC (trx)、arsD、arsM、arrA 和 arxA。尽管与砷相关的基因很常见，但并未普遍检测到，这与所有生物体都具有这些基因的普遍猜想相矛盾。从砷相关基因的主要进化枝，我们推断出它们水平和垂直转移的潜力。在土壤中检测到不同类型和比例的基因，表明微生物群落组成将部分决定当地的砷毒性和生物地球化学。虽然砷相关基因在全球范围内分布，但特定序列变异是高度流行的（例如 acr3），表明传播受到限制。编码砷甲基化酶 arsM 的基因在土壤宏基因组中出人意料地丰富（中位数为 48%），表明它在全球砷生物地球化学中发挥着重要作用。结论：我们的分析增进了对砷抗性、代谢和生物地球化学的理解，我们的方法为环境抗性组的生态研究提供了路线图。
Background: Environmental resistomes include transferable microbial genes. One important resistome component is resistance to arsenic, a ubiquitous and toxic metalloid that can have negative and chronic consequences for human and animal health. The distribution of arsenic resistance and metabolism genes in the environment is not well understood. However, microbial communities and their resistomes mediate key transformations of arsenic that are expected to impact both biogeochemistry and local toxicity.Results: We examined the phylogenetic diversity, genomic location (chromosome or plasmid), and biogeography of arsenic resistance and metabolism genes in 922 soil genomes and 38 metagenomes. To do so, we developed a bioinformatic toolkit that includes BLAST databases, hidden Markov models and resources for gene-targeted assembly of nine arsenic resistance and metabolism genes: acr3, aioA, arsB, arsC (grx), arsC (trx), arsD, arsM, arrA, and arxA. Though arsenic-related genes were common, they were not universally detected, contradicting the common conjecture that all organisms have them. From major clades of arsenic-related genes, we inferred their potential for horizontal and vertical transfer. Different types and proportions of genes were detected across soils, suggesting microbial community composition will, in part, determine local arsenic toxicity and biogeochemistry. While arsenic-related genes were globally distributed, particular sequence variants were highly endemic (e.g., acr3), suggesting dispersal limitation. The gene encoding arsenic methylase arsM was unexpectedly abundant in soil metagenomes (median 48%), suggesting that it plays a prominent role in global arsenic biogeochemistry.Conclusions: Our analysis advances understanding of arsenic resistance, metabolism, and biogeochemistry, and our approach provides a roadmap for the ecological investigation of environmental resistomes.