Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes
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 e...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-12-01
|
| Series: | Marine Drugs |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1660-3397/23/1/17 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832588066061025280 |
|---|---|
| author | Wei Zhang Yingdong Li Yunmeng Chu Hao Liu Hongmei Jing Qianfeng Xia |
| author_facet | Wei Zhang Yingdong Li Yunmeng Chu Hao Liu Hongmei Jing Qianfeng Xia |
| author_sort | Wei Zhang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-705da406650047929ce95861964acc98 |
| institution | Kabale University |
| issn | 1660-3397 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Marine Drugs |
| spelling | doaj-art-705da406650047929ce95861964acc982025-01-24T13:39:29ZengMDPI AGMarine Drugs1660-33972024-12-012311710.3390/md23010017Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance GenesWei Zhang0Yingdong Li1Yunmeng Chu2Hao Liu3Hongmei Jing4Qianfeng Xia5NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou 571199, ChinaInstitute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaInstitute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, ChinaNHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou 571199, ChinaThe 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.https://www.mdpi.com/1660-3397/23/1/17antibiotic resistance genesshort-read sequencingassembled contig sequencingevolutionary strategiesdeep-sea ecosystems |
| spellingShingle | Wei Zhang Yingdong Li Yunmeng Chu Hao Liu Hongmei Jing Qianfeng Xia Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes Marine Drugs antibiotic resistance genes short-read sequencing assembled contig sequencing evolutionary strategies deep-sea ecosystems |
| title | Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes |
| title_full | Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes |
| title_fullStr | Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes |
| title_full_unstemmed | Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes |
| title_short | Deep-Sea Ecosystems as an Unexpected Source of Antibiotic Resistance Genes |
| title_sort | deep sea ecosystems as an unexpected source of antibiotic resistance genes |
| topic | antibiotic resistance genes short-read sequencing assembled contig sequencing evolutionary strategies deep-sea ecosystems |
| url | https://www.mdpi.com/1660-3397/23/1/17 |
| work_keys_str_mv | AT weizhang deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes AT yingdongli deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes AT yunmengchu deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes AT haoliu deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes AT hongmeijing deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes AT qianfengxia deepseaecosystemsasanunexpectedsourceofantibioticresistancegenes |