New Estimation of Antibiotic Resistance Genes in Sediment Along the Haihe River and Bohai Bay in China: A Comparison Between Single and Successive DNA Extraction Methods
Abstract:Sediment is thought to be a vital reservoir for antibiotic resistance genes (ARGs). Often, studies describing and comparing ARGs and their potential hosts in sediment are based on single DNA extractions. To date, however, no study has been conducted to assess the influence of DNA extraction efficiency on ARGs in sediment. To determine whether the abundance of ARGs is underestimated, we performed five successive extraction cycles with a widely used commercial kit in 10 sediment samples collected from the Haihe … Show more
“…Marine sediments are considered reservoirs of genes bearing resistance to antibiotics and toxic compounds (e.g . , heavy metals), representing a pool that can contribute to their spreading, transfer, and evolution (Vignaroli et al 2018 ; Wu et al 2021 ; Yang et al 2013 ). Furthermore, resistance genes from contaminated sediment can be mobilized and resuspended in the overlaying water, posing a health risk particularly in coastal areas (Heß et al 2018 ).…”
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from ‘omics’ approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.
“…Marine sediments are considered reservoirs of genes bearing resistance to antibiotics and toxic compounds (e.g . , heavy metals), representing a pool that can contribute to their spreading, transfer, and evolution (Vignaroli et al 2018 ; Wu et al 2021 ; Yang et al 2013 ). Furthermore, resistance genes from contaminated sediment can be mobilized and resuspended in the overlaying water, posing a health risk particularly in coastal areas (Heß et al 2018 ).…”
Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from ‘omics’ approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.
“…This order belonged to Lactic acid bacteria (LAB), the group is known for their ability to synthesize antimicrobial substances (Alakomi et al, 2000;De Vuyst & Leroy, 2007). The isolation of Lactobacillus strains from sediments has received increasing attention in recent years, due to their potential applications as natural preservatives in the food industry (Issazadeh et al, 2012;Wu et al, 2021).…”
Section: Composition Of Bacterial Communitiesmentioning
The prokaryotic community in sediment plays an important role in the nutrient cycles of lagoon ecosystems. However, the diversity of microbiota in sediments of Vietnamese lagoons has not been discovered. In this study, sediment samples from three lagoons in Central Vietnam were collected. The microbial community structure in the sediments was determined using Illumina sequencing of 16S rRNA at V3V4 regions. Mother software was used to analyze the data and identify the Operational Taxonomic Units (OTUs). Proteobacteria, Firmicutes, Campilobacterota, and Bacteroidetes were the major phyla in three lagoons, while Fusobacteria, Verrucomicrobia, Acidobacteria, Actinobacteria, and Chloroflexi were the minor. These groups of bacteria have been reported to be involved in organic metabolism cycles in sediments. Tam Giang lagoon showed more diversity in species composition when compared with Nai and Thi Nai lagoons. Class Clostridia were predominant in Tam Giang sediment (46%), which may indicate the presence of organic sewage in the environment. Thi Nai and Nai lagoons witnessed the significant presence of Lactobacilales and Vibrionales. While Vibrionales is an indicator of urban pollution, Lactobacilales and other groups of phylum Actinobacteria were potential materials for the screening of natural antibiotics.
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