Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment

Fang, Hao; Huang, Kailong; Yu, Junnan; Ding, Chengcheng; Wang, Zhifeng; Cheng, Zhao; Yuan, Hezhong; Wang, Se; Hu, Jianlin; Cui, Yibin

doi:10.1016/j.chemosphere.2019.02.068

Cited by 77 publications

(16 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Contendobacterodensis is the second most abundant bacteria at the species level in the biofloc system and it is known to actively involved in nitrogen fixation, nitrate reduction to nitrite to ammonia and in polyhydroxyalkanoate (PHA) synthesis (McIlroy et al, 2014). Previous studies have also proved the presence of Proteobacteria , Actinobacteria , Bacteroidetes , Chloroflexi , Verrucomicrobia , Planctomycetes and Cyanobacteria in the freshwater crab aquaculture (Fang et al,2019). The presence of the above bacterial community in the biofloc system might involve in various functions including maintenance of water quality, bioremediation, nitrogen assimilation and pathogenic reduction.…”

Section: Discussionmentioning

confidence: 89%

Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT)

Meenakshisundaram¹,

Felix

Muthukumar³

et al. 2021

Aquaculture Research

View full text Add to dashboard Cite

The bacterial community characterization of biofloc in grow‐out system of GIFT (Genetically Improved Farmed Tilapia) was carried out to ascertain the dynamics and community structure of the microbiome. GIFT (5.1 ± 0.05 g) were stocked for 180 days at the stocking density of 15/m3 in triplicates. Distillery spent wash as carbon source was used for maintaining the C:N ratio at 10:1. Recorded water quality parameters revealed no significant difference among the replicates. The microscopic characterisation of the floc observed to be of uniform size (5–30 µm) but varied in shape throughout the culture period. Metagenomic profile of the floc was done through shotgun sequencing using Illumina NextSeq500 platform. High‐quality data of 9.36 GB were obtained consisting 911,255 genes. The kingdom‐level abundance was found in the order of 70.80% of Bacteria, 23.35% of Unclassified, 5.08% Eukarya, 0.62% of Archaea and 0.16% of Viruses. At the generic level composition, Proteobacteria and Caldilinea aerophila were the most abundant genus identified. Gene ontology using KEGG and SEED classification revealed predominantly carbohydrate metabolism associated genes. The present study is the first of its kind to study the microbial composition in biofloc of outdoor GIFT Tilapia grow‐out culture and to identify the functional attributes of the microbiome in the biofloc system.

show abstract

Section: Discussionmentioning

confidence: 89%

Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT)

Meenakshisundaram¹,

Felix

Muthukumar³

et al. 2021

Aquaculture Research

View full text Add to dashboard Cite

show abstract

“…The antibiotics fluoroquinolone, ciprofloxacin, amoxicillin, azithromycin, clarithromycin, and erythromycin are included in the aforementioned Watch List [ 13 ]. Antibiotics are usually administered to aquaculture in the addition to feed or by immersion through closed containers [ 19 ]. After the addition of antibiotics, their concentrations increase in the water column, in sediments under the cages, and in fish.…”

Section: Antibiotic Residues As Emerging Pollutantsmentioning

confidence: 99%

Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area

Pepi

Focardi

2021

IJERPH

103

View full text Add to dashboard Cite

Aquaculture is the productive activity that will play a crucial role in the challenges of the millennium, such as the need for proteins that support humans and the respect for the environment. Aquaculture is an important economic activity in the Mediterranean basin. A great impact is presented, however, by aquaculture practices as they involve the use of antibiotics for treatment and prophylaxis. As a consequence of the use of antibiotics in aquaculture, antibiotic resistance is induced in the surrounding bacteria in the column water, sediment, and fish-associated bacterial strains. Through horizontal gene transfer, bacteria can diffuse antibiotic-resistance genes and mobile resistance genes further spreading genetic determinants. Once triggered, antibiotic resistance easily spreads among aquatic microbial communities and, from there, can reach human pathogenic bacteria, making vain the use of antibiotics for human health. Climate change claims a significant role in this context, as rising temperatures can affect cell physiology in bacteria in the same way as antibiotics, causing antibiotic resistance to begin with. The Mediterranean Sea represents a ‘hot spot’ in terms of climate change and aspects of antibiotic resistance in aquaculture in this area can be significantly amplified, thus increasing threats to human health. Practices must be adopted to counteract negative impacts on human health, with a reduction in the use of antibiotics as a pivotal point. In the meantime, it is necessary to act against climate change by reducing anthropogenic impacts, for example by reducing CO2 emissions into the atmosphere. The One Health type approach, which involves the intervention of different skills, such as veterinary, ecology, and medicine in compliance with the principles of sustainability, is necessary and strongly recommended to face these important challenges for human and animal health, and for environmental safety in the Mediterranean area.

show abstract

“…A read was annotated as an integron if the nucleotide sequence identity of the best BLASTn was greater than 90% with an alignment length of at least 50 bp. The plasmid-like tags in all data sets were determined by alignments with a nucleotide sequence identity above 95% over a length of at least 90 bp [30,31].…”

Section: Bioinformatics Analysismentioning

confidence: 99%

Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols

Han

Yoo

2020

Water

View full text Add to dashboard Cite

Wastewater treatment plants (WWTPs) have been considered hotspots for the development and dissemination of antibiotic resistance in the environment. Although researchers have reported a significant increase in bioaerosols in WWTPs, the associated bacterial taxa, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) remain relatively unknown. In this study, we have investigated the abundance and occurrences of ARGs and MGEs, as well as the bacterial community compositions in activated sludge (AS), dewatered sludge (DS) and bioaerosols (BA) in a WWTP. In total, 153 ARG subtypes belonging to 19 ARG types were identified by the broad scanning of metagenomic profiles obtained using Illumina HiSeq. The results indicated that the total occurrences and abundances of ARGs in AS and DS samples were significantly higher than those in BA samples (p < 0.05). However, some specific ARG types related to sulfonamide, tetracycline, macrolide resistance were present in relatively high abundance in BA samples. Similar to many other full-scale WWTPs, the Proteobacteria (58%) and Bacteroidetes (18%) phyla were dominant in the AS and DS samples, while the Firmicutes (25%) and Actinobacteria (20%) phyla were the most dominant in the BA samples. Although the abundance of genes related to plasmids and integrons in bioaerosols were two to five times less than those in AS and DS samples, different types of MGEs were observed in BA samples. These results suggest that comprehensive analyses of resistomes in BA are required to better understand the emergence of both ARGs and MGEs in the wastewater treatment process due to the significant increase of scientific attention toward bioaerosols effects.

show abstract

Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment

Cited by 77 publications

References 81 publications

Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT)

Metagenomic characterization of biofloc in the grow‐out culture of Genetically Improved Farmed Tilapia (GIFT)

Antibiotic-Resistant Bacteria in Aquaculture and Climate Change: A Challenge for Health in the Mediterranean Area

Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols

Contact Info

Product

Resources

About