Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf

Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge

Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.

Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India

Introduction

The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.

Methods

The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment.

Results and discussion

Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, β-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.

Spatiotemporal distribution and potential risks of antibiotics in coastal water of Beibu Gulf, South China Sea: Livestock and poultry emissions play essential effect

Antibiotics have been the subject of much attention in recent years due to their widespread use and the potential ecological risks and resistance risks. In this study, we conducted an extensive survey of 19 antibiotics in a wide range of waters of the Beibu Gulf during summer and winter (154 samples). The total concentrations of the 19 antibiotics (Σ19ABs, ng/L) were significantly higher in winter (n.d.-364) than in summer (n.d.-70.1) and were mainly concentrated in areas of seagoing rivers (1.50-364). The primary route for antibiotics entering Beibu Gulf was through riverine input. Precisely, florfenicol (FF) (n.d.-278 ng/L) discharged from livestock and poultry farms upstream of Nanliu River, predominantly in swine farming, constitutes the main pollutant in Beibu Gulf throughout the year. The Nanliu River (988 kg/a) accounts for 85% of the gulf's total annual antibiotic emission flux. Source analysis identified livestock and poultry farming, particularly swine farming, as the primary pollution source, contributing 58% in summer. Risk assessment reveals that algae (0.51 ± 0.56) exhibited relatively high sensitivity to antibiotics, presenting a medium-high risk at specific sites in Nanliu River during winter. Additionally, FF discharged from swine farming demonstrates a certain level of antibiotic resistance risk. Therefore, reinforcing control measures for antibiotic discharges from livestock and poultry farming, especially upstream of Nanliu River, can effectively mitigate antibiotic-related risks in the water bodies of Beibu Gulf.