Abstract
Background Antibiotics have been spread widely in environments, asserting profound effects on environmental microbes as well as antibiotic resistance genes (ARGs) within these microbes. Therefore, investigating the associations between ARGs and bacterial communities become an important issue for environment protection. Ocean microbiomes are potentially large ARG reservoirs, but the marine ARG distribution and its associations with bacterial communities remain unclear.
Methods we have utilized the big-data mining techniques on ocean microbiome data to analysis the marine ARGs and bacterial distribution on a global scale, and applied comprehensive statistical analysis to unveil the associations between ARG contents, ocean microbial community structures, and environmental factors by reanalyzing 132 metagenomic samples from the Tara Oceans project.
Results We identified in total 1,926 unique ARGs and found that: firstly, ARGs are more abundant and diverse in the mesopelagic zone than other water layers. Additionally, ARG-enriched genera are closely connected in co-occurrence network. We also found that ARG-enriched genera are often more abundant than their ARG-less neighbors. Furthermore, we found that samples from the Mediterranean that is surrounded by human activities often contain more ARGs.
Conclusion Our research for investigating the marine ARG distribution and revealing the association between ARG and bacterial communities provide a deeper insight into the marine bacterial communities. We found that ARG-enriched genera were often more abundant than their ARG-less neighbors in the same environment, indicating that genera enriched with ARGs might possess an advantage over others in the competition for survival in the oceanic microbial communities.
Abbreviation
- ARG
- antibiotic resistance genes
- WGS
- whole genome sequence
- bacA
- Bacitracin Transport ATP-binding Gene
- KEGG
- Kyoto Encyclopedia of Genes and Genomes
- OTU
- Operational Taxonomic Unit
- ARDB
- Antibiotic Resistance Genes Database
- SRF
- Surface Water Layer
- DCM/MIX
- Subsurface Epipelagic Mixed Layer
- MES
- Mesopelagic Zone
- mexF, mexB, ceoB
- Multidrug Resistance Efflux Pump
- acrB
- Acriflavin Resistance
- ksgA
- Kasugamycin Resistance
- EBI
- The European Bioinformatics Institute
- SPO
- South Pacific Ocean
- NPO
- North Pacific Ocean
- RS
- Red Sea
- MS
- Mediterranean
- SIO
- South Indian Ocean
- NIO
- North Indian Ocean
- NAO
- North Atlantic Ocean
- SAO
- South Atlantic Ocean
- PCC
- Pearson Correlation Coefficient