Antibiotic Resistome Biomarkers associated to the Pelagic Sediments of the Gulfs of Kathiawar Peninsula and Arabian Sea

Abstract

Antibiotic resistance has been one of the most persistent global issue. Specifically, marine microbiomes have served as complex reservoirs of antibiotic resistant genes. Molecular advancements have enabled exploration of the uncultured microbial portion from hitherto difficult to sample niches such as deeper oceans. The Gulfs of Kathiawar Peninsula have been known for their unique properties like extreme tidal variations, different sediment textures and physicochemical variations. Pelagic sediment cores across four coordinates each of the Gulf of Kutch, Gulf of Khambhat and an open Arabian Sea were collected, processed for metagenomic sequencing and assessed for antibiotic and metal resistome. The dominant genes were mostly resistant to macrolides, glycopeptides and tetracycline drugs. Studied samples divided into three clusters based on their resistome with carA, macB, bcrA, taeA, srmB, tetA, oleC and sav1866 among the abundant genes. Samples from creek of Gulf of Kutch and mouth of Gulf of Khambhat were most diverse in resistance gene profile. Biomarkers observed include gyrA mutation conferring resistance gene in the Arabian Sea; Proteobacteria species in Gulf of Kutch and Arabian sea; while Aquificae, Acidobacteria and Firmicutes species in the Gulf of Khambhat. Region-wise differentially abundant 23 genes and 3 taxonomic biomarkers were proposed for antibiotic resistance monitoring.

Antibiotic Resistance Genes Associated with Marine Surface Sediments: A Baseline from the Shores of Kuwait

“…This is almost comparable to 17 gene families discovered at Tolo Harbour in the South China Sea [30]. The RA of all the genes varied according to the sampling location [50,60,61]. In the present study, the presence of ARGs was also recorded in sediments from sites S4 and S12 that were not in proximity to outfalls.…”

Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome

“…We believe their prevalence is due to the selective force imposed by the pharmaceuticals and antibiotics discharged into the ocean through wastewater streams [ 32 , 33 , 36 , 58 ]. Analogous findings were reported in polluted marine environments of the South China Sea [ 2 ], the Gulf of Kathiawar, and the Arabian Sea [ 18 , 19 , 58 ]. ARG abundances associated with mangrove sediments were predicted to be higher in Asian countries [ 19 ].…”

“…Next-generation sequencing has gained immense popularity since 2010 for comprehensively profiling microbial populations in polluted environments [ 57 ]. The high throughput sequencing approach employed in the present investigation successfully captured microbes from bacterial, archaeal, fungal, and viral domains [ 18 , 58 , 59 ]. This is the first study reporting the taxonomic profiles of all four microbial communities in the coastal sediments, suggesting the validity of shotgun sequencing in comprehensive biomonitoring.…”

“…Advances in high-throughput sequencing have revolutionized the detection of genes in complex environmental communities, offering a more promising avenue for comprehensive genetic profiling. The taxonomic and functional profiles of microbes have been reported from estuaries, rivers, lakes, coral reefs, mangroves, sediments in coastal areas, and deep marine sediments using a high-throughput sequencing approach [ 4 , 12 , 14 , 15 , 16 , 17 , 18 , 19 ]. Recently, more research has been focused on the environmental DNA whole genome sequencing of sediments receiving pollutants, such as metals, oil discharges, and industrial and domestic waste [ 12 , 20 , 21 , 22 , 23 , 24 , 25 ].…”

309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula

“…Study of microbial diversity and functions in the mentioned Gulfs have largely been focused on cultivation based approaches and very few molecular studies have been conducted on the shore sediments. Additionally, the presence of several on-shore industries like fertilizer, chemicals, oil refineries, power plants and ASSBRY (Alang Ship Breaking Yard) may have also influenced the deeper sediment microbiome leading to their variable gene profile 7 . Our previous insights into the pelagic sediment resistome profile by metagenomics approach have shown that the deeper sediments, earlier thought to be primeval are actually hosting microbes with a concerning number of resistance genes 7,8 .…”