基于宏基因组技术解析南极不同纬度地区土壤抗生素抗性基因的分布与迁移

Deciphering distribution and migration of soil antibiotic resistance genes in different latitude regions of Antarctica by metagenomics

摘要:

[目的] 南极洲不同地区环境极端多样，且受人类活动影响不一。本研究旨在探究南极不同纬度地区土壤抗生素抗性基因（ARGs）的分布特征与迁移机制。[方法] 下载南极不同纬度地区及加拿大阿尔伯特地区养殖场附近土壤宏基因组数据集，利用MetaWRAP进行组装，使用CARD、PlasFlow和ICEberg数据库对ARGs与可移动遗传元件（MGEs）进行注释。[结果] 在南极不同纬度地区土壤中，优势菌门为变形菌门、放线菌门、拟杆菌门和厚壁菌门。共注释出25类406种ARGs，以多重耐药类、四环素类及氨基糖苷类抗生素抗性基因为主。NMDS分析结果表明，南极不同纬度地区与养殖场附近土壤中ARGs的分布特征显著不同（ANISOM，P=0.001）。南极高纬度地区ARGs占总基因数的比例为0.28%，显著低于低纬度地区（1.93%，P<0.01）。不同抗生素类型的ARGs呈现不同的区域分布模式，其中硝基咪唑类、氨基糖苷类、糖肽类与大环内酯类ARGs主要分布在南极高纬度地区，四环素类与磺胺类ARGs主要分布在南极低纬度地区（P<0.05）。南极土壤中ARGs的迁移研究表明，质粒携带的ARGs占检测到的ARGs的17%。同时，共发现163个整合与接合元件（ICEs）可携带多抗耐药类、肽类和四环素类等14类ARGs。这些携带ARGs的ICEs主要分布于α-、β-与γ-变形菌纲中。[结论] 南极高纬度与南极低纬度地区土壤中ARGs的分布存在差异性，质粒与ICEs共同介导ARGs的迁移。本研究为进一步了解抗生素时代之前的原始抗性组提供数据基础。

Abstract:

[Objective] Antarctic environments are extremely diverse and affected by human activities in varying degrees. The aim of this study is to explore distribution and migration of soil antibiotic resistant genes (ARGs) in different latitude regions of Antarctica.[Methods] We selected soil metagenomic data from Antarctic high (HLG) and low latitude regions (LLG) and surrounding regions of feedlot. Metagenomic reads was assembled using software MetaWRAP. ARGs, plasmids and integrative and conjugative elements (ICEs) were annotated using CARD (The Comprehensive Antibiotic Resistance Database), PlasFlow and ICEberg, respectively. [Results] In the Antarctic soils, Proteobacteria, Actinomycetes, Bacteroidetes and Firmicutes were the dominant phyla. Belonging to 25 ARG types, 406 ARGs were found, among which multidrug, tetracycline and aminoglycoside resistance genes dominated. The NMDS analysis showed that the characteristics of ARGs in Antarctic soils were significantly different from those in agricultural soils nearby feedlot (ANOSIM, P=0.001). The proportion of ARGs in all ORFs in the Antarctic HLG was 0.28%, lower than that in the LLG (1.93%, P<0.01). Different ARGs present different latitude-region resistance patterns. Therein, nitroimidazole, aminoglycoside, glycopeptide and macrolide resistance genes were mainly distributed in the HLG, while tetracycline and sulfonamide resistance genes were mainly distributed in the LLG (P<0.05). The migration analysis of ARGs in Antarctic soils showed that 17% of the detected ARGs were carried by plasmids. In addition, 163 ICEs carrying ARGs, belonging to 14 ARG types (e.g., multidrug, peptide and tetracycline resistance genes), were found. These ICEs carrying ARGs were extensively distributed among α-, β- and γ-proteobacteria. [Conclusion] The differences in microbial communities and ARGs between the Antarctic high and low latitude areas occurred, plasmids and ICEs facilitated migration of nature ARGs. This study provided a certain data basis for understanding the natural antibiotic resistance from the pre-antibiotic era.