An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

Yin, Huaqun; Niu, Jun; Ren, Youhua; Cong, Jing; Zhang, Xiaoxia; Fan, Fenliang; Xiao, Yunhua; Zhang, Xian; Deng, Jie; Xie, Mao; He, Zhili; Zhou, Jizhong; Liang, Yili; Liu, Xueduan

doi:10.1038/srep14266

Cited by 225 publications

(90 citation statements)

References 55 publications

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“…The higher alpha-diversity of the soil microbial community in the more As contaminated soil suggests that many microbial species could cope with the long term As stress. Genus like Steroidobacter had higher relative abundance in the heavy metal contaminated soils [46]. Similarly, in our study, the relative abundance of the genus Steroidobacter in the soil contaminated with more As was also higher than that in the lower As containing soil (Fig 4).…”

Section: Discussionsupporting

confidence: 83%

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

Nostrand

et al. 2017

PLoS ONE

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To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community.

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Section: Discussionsupporting

confidence: 83%

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

Nostrand

et al. 2017

PLoS ONE

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“…The distributions of degree in both constructed MENs were well in accordance with the power law model, with the linear correlation of 0.68 (Supporting Information ). The average path distance was 1.46, suggesting a closer correlation among all nodes, compared to the previous literature (Yin et al., ).…”

Section: Resultssupporting

confidence: 47%

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

Yuan

Zhai

Mao

et al. 2019

Water Environment Research

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This study explores the prevalence, emission, and reduction of five ARGs (sulI, tetA, mphB, qnrD, and mcr‐1) and integron (intI) through a distributed swine wastewater purification facility and the effluent‐receiving environment. Typical metal resistance genes (MRGs), pathogenic bacterial indicators, the bacterial community, and wastewater properties were also explored to determine their effects on the fates of ARGs. Results indicated that the purification process could hardly effectively remove ARGs’ prevalence. 3.1 × 104–7.1 × 108 copies/L were present after purification, and 4%–57% of them persisted in the subsequent creek and adjacent soil. 16S rRNA sequencing suggested that the discharge of wastewater significantly changed the bacterial community in receiving creek and soil. Molecular ecological networks analysis detected the wide co‐occurrence among ARGs, MRGs, and PBGs, which could further facilitate the propagation of antibiotic resistance. ARG incidence and specific bacterial genera were closely correlated, suggesting an extensive hosting relationship. Redundancy analyses showed wastewater organics and nutrients showed positive correlation to most ARGs’ abundance, but negatively correlated to their relative abundance. Practitioner points Fate of five ARGs and intI was studied in a swine wastewater treatment system. The treatment process could not effectively reduce ARGs’ abundance. ARGs and pathogens in wastewater were transferred to the receiving creek and soil. The network analysis found wide co‐occurrence among ARGs, metal resistance genes, and pathogens. Wastewater nutrients positively correlated to ARG's abundance but negatively correlated to their relative abundance.

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“…Microbial response to environmental stresses is always a critical issue in ecological fields (Yin et al, 2015). A long-term experiment with Escherichia coli revealed complex coupling between organismal adaptation and genome evolution, which occurred even in a constant environment (Barrick et al, 2009).…”

Section: Resultsmentioning

confidence: 99%

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

Zhang

Liu

et al. 2016

Front. Microbiol.

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Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.

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An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

Cited by 225 publications

References 55 publications

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

Fates of antibiotic resistance genes in a distributed swine wastewater treatment plant

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

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