Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater

Yu, Miao; Liao, Runhua; Zhang, Xuxiang; Wang, Yuan; Zhu, Wancheng; Shi, Peng; Liu, Bo; Li, Aimin

doi:10.1016/j.watres.2015.02.042

Cited by 199 publications

(46 citation statements)

References 47 publications

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“…6, 15 Environmental variables, such as temperature and heavy metals, can affect functional gene distribution by altering bacterial community. 21,32 This study indicated that residual chlorine was the key contributing factor driving the bacterial community shift in the drinking water. The difference in chlorine sensitivity among bacterial populations in drinking water may be the main reason for the succession dynamics and diversification of microbial community.…”

Section: ■ Discussionmentioning

confidence: 89%

“…An online tool kit (Galaxy, https://usegalaxy.org/) was utilized to filter low quality reads to ensure (1) less than three ambiguous nucleotides in one read; (2) more than 90% bases with quality score greater than 30; and (3) no sequencing artifacts. 32 BLAST tool was applied to annotate sequencing reads against an offline database of ARGs previously established, 15 to determine ARGs abundance and their potential hosts following Kristiansson et al 26 MGEs (integrons, plasmids, and insertion sequences (ISs)) were also quantified using metagenomic methods according to our previous study. 15 The metagenomic data have been deposited in NCBI Sequence Read Archive under accession number SRA178672.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

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Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination

Jia

Shi

et al. 2015

Environ. Sci. Technol.

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390

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For comprehensive insights into the effects of chlorination, a widely used disinfection technology, on bacterial community and antibiotic resistome in drinking water, this study applied high-throughput sequencing and metagenomic approaches to investigate the changing patterns of antibiotic resistance genes (ARGs) and bacterial community in a drinking water treatment and distribution system. At genus level, chlorination could effectively remove Methylophilus, Methylotenera, Limnobacter, and Polynucleobacter, while increase the relative abundance of Pseudomonas, Acidovorax, Sphingomonas, Pleomonas, and Undibacterium in the drinking water. A total of 151 ARGs within 15 types were detectable in the drinking water, and chlorination evidently increased their total relative abundance while reduced their diversity in the opportunistic bacteria (p < 0.05). Residual chlorine was identified as the key contributing factor driving the bacterial community shift and resistome alteration. As the dominant persistent ARGs in the treatment and distribution system, multidrug resistance genes (mainly encoding resistance-nodulation-cell division transportation system) and bacitracin resistance gene bacA were mainly carried by chlorine-resistant bacteria Pseudomonas and Acidovorax, which mainly contributed to the ARGs abundance increase. The strong correlation between bacterial community shift and antibiotic resistome alteration observed in this study may shed new light on the mechanism behind the chlorination effects on antibiotic resistance.

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Section: ■ Discussionmentioning

confidence: 89%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination

Jia

Shi

et al. 2015

Environ. Sci. Technol.

Self Cite

390

137

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show abstract

“…The raw Illumina read data of the two samples has been deposited in the European Nucleotide Archive, under the accession PRJEB13054 (http://www.ebi.ac.uk/ena/data/view/PRJEB13054). An online tool kit (Galaxy, https://usegalaxy.org/) was utilized to filter low quality reads to ensure (1) less than three ambiguous nucleotides in one read; (2) more than 90% bases with quality score greater than 30; and (3) no sequencing artifacts (Miao et al, 2015).…”

Section: Illumina High-throughput Sequencingmentioning

confidence: 99%

Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

et al. 2016

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a b s t r a c tThis study aimed to reveal how antibiotic resistance genes (ARGs) and their horizontal and vertical transfer-related items (mobilome and bacterial hosts) respond to the transformation of anaerobic digestion (AD) from mesophilic to thermophilic using one-step temperature increase. The resistomes and mobilomes of mesophilic and thermophilic sludge were investigated using metagenome sequencing, and the changes in 24 representative ARGs belonging to three categories, class 1 integron and bacterial genera during the transition period were further followed using quantitative PCR and 454-pyrosequencing. After the temperature increase, resistome abundance in the digested sludge decreased from 125.97 ppm (day 0, mesophilic) to 50.65 ppm (day 57, thermophilic) with the reduction of most ARG types except for the aminoglycoside resistance genes. Thermophilic sludge also had a smaller mobilome, including plasmids, insertion sequences and integrons, than that of mesophilic sludge, suggesting the lower horizontal transfer potential of ARGs under thermophilic conditions. On the other hand, the total abundance of 18 bacterial genera, which were suggested as the possible hosts for 13 ARGs through network analysis, decreased from 23.27% in mesophilic sludge to 11.92% in thermophilic sludge, indicating fewer hosts for the vertical expansion of ARGs after the increase in temperature. These results indicate that the better reduction of resistome abundance by thermophilic AD might be associated with the decrease of both the horizontal and vertical transferability of ARGs.

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“…For quality control, the raw reads containing three or more unknown nucleotides or contaminated by adapter (415 bp overlap) were removed . FASTX toolkit tools in Galaxy (https:// usegalaxy.org/) were then used to remove low quality sequences to ensure that more than 75% bases of each filtered read having quality scores greater than 30 (indicating 0.1% sequencing error rate) (Miao et al, 2015). The filtered clean reads were normalized to 11,958,534 per sample for further metagenomic analyses at the same sequencing depth.…”

Section: Illumina High-throughput Sequencingmentioning

confidence: 99%

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water

Tang

Zhang

et al. 2016

Ecotoxicology and Environmental Safety

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132

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Metagenomic insights into Cr(VI) effect on microbial communities and functional genes of an expanded granular sludge bed reactor treating high-nitrate wastewater

Cited by 199 publications

References 47 publications

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination

Bacterial Community Shift Drives Antibiotic Resistance Promotion during Drinking Water Chlorination

Changes of resistome, mobilome and potential hosts of antibiotic resistance genes during the transformation of anaerobic digestion from mesophilic to thermophilic

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water

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