Zhang Wei, Li Yingdong, Chu Yunmeng, Liu Hao, Jing Hongmei, Xia Qianfeng
NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou 571199, China.
Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China.
Mar Drugs. 2024 Dec 31;23(1):17. doi: 10.3390/md23010017.
The deep-sea ecosystem, a less-contaminated reservoir of antibiotic resistance genes (ARGs), has evolved antibiotic resistance for microbes to survive and utilize scarce resources. Research on the diversity and distribution of these genes in deep-sea environments is limited. Our metagenomics study employed short-read-based (SRB) and assembled-contig-based (ACB) methods to identify ARGs in deep-sea waters and sediments and assess their potential pathogenicity. SRB prediction was found to be more effective for studying the abundance and diversity of these genes, while combining both methods better illustrated the relationship of ARGs with the hosts. Deep-sea waters (DSW) and trenches had the highest diversity of ARGs, including β-lactams, multidrug resistance genes, and rifamycins. Mobile genetic elements, such as IncQ and RP4 plasmids, were also identified. The ratio of nonsynonymous to synonymous substitutions (pN/pS) values of these genes suggest different evolutionary strategies in response to deep-sea conditions and possible human impacts. These resistome profiles provide valuable insights into their natural origins as well as the ecological and evolutionary implications of antibiotic resistance in deep-sea ecosystems. The exploration of the global distribution of ARGs in diverse deep-sea environments is a novel approach that will assist in understanding their potential reservoirs and evolutionary mechanisms. Therefore, employing a comprehensive approach to studying ARGs is particularly necessary. Unique microbial life in deep-sea ecosystems, especially in deep-sea cold seeps sediments (DSCSS), deep-sea waters (DSW), and trench waters (TW), could be a valuable source of new antibiotics and resistance discovery.
深海生态系统是抗生素抗性基因（ARGs）受污染较少的储存库，为微生物进化出了抗生素抗性，以便其在稀缺资源条件下生存和利用资源。关于这些基因在深海环境中的多样性和分布的研究有限。我们的宏基因组学研究采用基于短读长（SRB）和基于拼接重叠群（ACB）的方法，来鉴定深海水体和沉积物中的ARGs，并评估其潜在致病性。研究发现，SRB预测在研究这些基因的丰度和多样性方面更有效，而将两种方法结合起来能更好地阐明ARGs与宿主的关系。深海水体（DSW）和海沟中的ARGs多样性最高，包括β-内酰胺类、多药耐药基因和利福霉素。还鉴定出了移动遗传元件，如IncQ和RP4质粒。这些基因的非同义替换与同义替换比率（pN/pS）值表明，它们针对深海条件和可能的人类影响采取了不同的进化策略。这些抗性组图谱为它们的天然起源以及深海生态系统中抗生素抗性的生态和进化意义提供了有价值的见解。探索ARGs在不同深海环境中的全球分布是一种新方法，将有助于了解它们的潜在储存库和进化机制。因此，采用综合方法研究ARGs尤为必要。深海生态系统中独特的微生物生命，特别是在深海冷泉沉积物（DSCSS）、深海水体（DSW）和海沟水体（TW）中，可能是发现新抗生素和抗性的宝贵来源。
