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Salgueiro V, Manageiro V, Rosado T, Bandarra NM, Botelho MJ, Dias E, Caniça M. Snapshot of resistome, virulome and mobilome in aquaculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166351. [PMID: 37604365 DOI: 10.1016/j.scitotenv.2023.166351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/28/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.
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Affiliation(s)
- Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Tânia Rosado
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Narcisa M Bandarra
- Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, Lisbon, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal
| | - Maria João Botelho
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal; Division of Oceanography and Marine Environment, Portuguese Institute for the Sea and Atmosphere, Lisbon, Portugal
| | - Elsa Dias
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal; CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal.
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Guo Y, Wu C, Wang Z, Shi Y, Sun J. Co-occurrence of toxic metals, bacterial communities and metal resistance genes in coastal sediments from Bohai bay. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 338:122666. [PMID: 37788796 DOI: 10.1016/j.envpol.2023.122666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
Sediment heavy metal contamination poses substantial risks to microbial community composition and functional gene distribution. Bohai Bay (BHB), the second-largest bay in the Bohai Sea, is subject to severe anthropogenic pollution. However, to date, there have been no studies conducted to evaluate the distribution of metal resistance genes (MRGs) and bacterial communities in the coastal sediments of BHB. In this study, we employed high-throughput sequencing based on 16S rRNA genes and real-time quantitative PCR (qPCR) to provide a comprehensive view of toxic metals, MRGs, and bacterial communities in BHB's coastal sediment samples across two seasons. We detected high levels of Cd in the summer samples and As in the autumn samples. The metal content in most autumn samples and all summer samples, based on ecological indices, indicated low ecological risk. Proteobacteria dominated all samples, followed by Desulfobacterota, Bacteroidota and Campilobacterota. Bacterial community variability was higher between autumn sampling sites but more stable in summer. We detected 9 MRG subtypes in all samples, with abundances ranging from 4.58 × 10-1 to 2.25 copies/16S rRNA copies. arsB exhibited the highest relative abundance, followed by acr3, czcA and arrA. The efflux mechanism is a common mechanism for sediment resistance to metal stress in Bohai Bay. Procrustes analysis indicated that bacterial community composition may be a determinant of MRGs composition in BHB sediments. Network analysis suggested that eight classes could be potential hosts for six MRGs. However, this type of correlation requires further validation. To summarize, our study offers preliminary insights into bacterial community and MRG distribution patterns in heavy metal-exposed sediments, laying the groundwork for understanding microbial community adaptations in multi-metal polluted environments and supporting ecological restoration efforts.
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Affiliation(s)
- Yiyan Guo
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Chao Wu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong, 266071, China
| | - Zhi Wang
- Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Yifeng Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China
| | - Jun Sun
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences (Wuhan), Wuhan, 430074, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China; Research Centre for Indian Ocean Ecosystem, Tianjin University of Science and Technology, Tianjin, 300457, China; Institute for Advanced Marine Research, China University of Geosciences, Guangzhou, 511462, China.
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Fu L, Yu Y, Yu F, Xiao J, Fang H, Li W, Xie Z, Zhang F, Lin S. Profiles and spatial distributions of heavy metals, microbial communities, and metal resistance genes in sediments from an urban river. Front Microbiol 2023; 14:1188681. [PMID: 37455724 PMCID: PMC10340544 DOI: 10.3389/fmicb.2023.1188681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/29/2023] [Indexed: 07/18/2023] Open
Abstract
The occurrence and propagation of resistance genes due to exposure to heavy metals (HMs) in rivers is an emerging environmental issue. Little is known about resistance genes in microbial communities in river sediments with low HM concentrations. The profiles and spatial distributions of HMs, the microbial community, and metal resistance genes (MRGs) were analyzed in sediment samples from the Zhilong River basin in Yangjiang city, near the Pearl River Delta. Concentrations of copper (Cu), cadmium (Cd), lead (Pb), chromium (Cr), and nickel (Ni) were relatively low compared with those in other urban river sediments in China. HM chemical composition and fractions and the structure of the microbial community varied along the main channel, but the composition and abundance of MRGs were relatively homogeneous. Variations in HMs and microbial communities in mid- to upstream areas were related to the presence of tributaries, whose inputs were one of the major factors affecting HM chemical fractions and genera structure in mainstream sediments. There were no significant correlations (p < 0.05) between HM concentrations, bacterial communities, and the MRG profiles; thus, HM concentrations were not the main factor affecting MRGs in sediments. These results contribute to understanding the propagation of MRGs in urban rivers in developing cities.
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Xie X, Yuan K, Chen X, Zhao Z, Huang Y, Hu L, Liu H, Luan T, Chen B. Characterization of metal resistance genes carried by waterborne free-living and particle-attached bacteria in the Pearl River Estuary. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121547. [PMID: 37028791 DOI: 10.1016/j.envpol.2023.121547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
Toxic metals can substantially change the bacterial community and functions thereof in aquatic environments. Herein, metal resistance genes (MRGs) are the core genetic foundation for microbial responses to the threats of toxic metals. In this study, waterborne bacteria collected from the Pearl River Estuary (PRE) were separated into the free-living bacteria (FLB) and particle-attached bacteria (PAB), and analyzed using metagenomic approaches. MRGs were ubiquitous in the PRE water and mainly related to Cu, Cr, Zn, Cd and Hg. The levels of PAB MRGs in the PRE water ranged from 8.11 × 109 to 9.93 × 1012 copies/kg, which were significantly higher than those of the FLB (p < 0.01). It could be attributed to a large bacterial population attached on the suspended particulate matters (SPMs), which was evidenced by a significant correlation between the PAB MRGs and 16S rRNA gene levels in the PRE water (p < 0.05). Moreover, the total levels of PAB MRGs were also significantly correlated with those of FLB MRGs in the PRE water. The spatial pattern of MRGs of both FLB and PAB exhibited a declining trend from the low reaches of the PR to the PRE and on to the coastal areas, which was closely related to metal pollution degree. MRGs likely carried by plasmids were also enriched on the SPMs with a range from to 3.85 × 108 to 3.08 × 1012 copies/kg. MRG profiles and taxonomic composition of the predicted MRG hosts were significantly different between the FLB and PAB in the PRE water. Our results suggested that FLB and PAB could behave differential response to heavy metals in the aquatic environments from the perspective of MRGs.
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Affiliation(s)
- Xiuqin Xie
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519082, China
| | - Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519082, China
| | - Xin Chen
- South China Sea Environmental Monitoring Center, South China Sea Bureau, Ministry of Natural Resources, Guangzhou, 510300, China
| | - Zongshan Zhao
- School of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Yongshun Huang
- Guangdong Provincial Hospital for Occupational Diseases Prevention and Treatment, Guangzhou, 510300, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hongtao Liu
- Instrumental Analysis and Research Center, Sun Yat-sen University, Guangzhou, 510300, China
| | - Tiangang Luan
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519082, China.
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Samson R, Rajput V, Yadav R, Shah M, Dastager S, Khairnar K, Dharne M. Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162125. [PMID: 36773904 DOI: 10.1016/j.scitotenv.2023.162125] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.
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Affiliation(s)
- Rachel Samson
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Vinay Rajput
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Rakeshkumar Yadav
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Manan Shah
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India
| | - Syed Dastager
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Krishna Khairnar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India; Environmental Virology Cell (EVC), CSIR, National Environmental Engineering Research Institute (NEERI), Nehru Marg, Nagpur 440020, India.
| | - Mahesh Dharne
- National Collection of Industrial Microorganisms (NCIM), Biochemical Sciences Division, CSIR-National Chemical Laboratory (NCL), Pune 411008, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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Yang Q, Jie S, Lei P, Gan M, He P, Zhu J, Zhou Q. Effect of Anthropogenic Disturbances on the Microbial Relationship during Bioremediation of Heavy Metal-Contaminated Sediment. Microorganisms 2023; 11:1185. [PMID: 37317159 DOI: 10.3390/microorganisms11051185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Soil, sediment, and waters contaminated with heavy metals pose a serious threat to ecosystem function and human health, and microorganisms are an effective way to address this problem. In this work, sediments containing heavy metals (Cu, Pb, Zn, Mn, Cd, As) were treated differently (sterilized and unsterilized) and bio-enhanced leaching experiments were carried out with the addition of exogenous iron-oxidizing bacteria A. ferrooxidans and sulfur-oxidizing bacteria A. thiooxidans. The leaching of As, Cd, Cu, and Zn was higher in the unsterilized sediment at the beginning 10 days, while heavy metals leached more optimally in the later sterilized sediment. The leaching of Cd from sterilized sediments was favored by A. ferrooxidans compared to A. thiooxidans. Meanwhile, the microbial community structure was analyzed using 16S rRNA gene sequencing, which revealed that 53.4% of the bacteria were Proteobacteria, 26.22% were Bacteroidetes, 5.04% were Firmicutes, 4.67% were Chlamydomonas, and 4.08% were Acidobacteria. DCA analysis indicated that microorganisms abundance (diversity and Chao values) increased with time. Furthermore, network analysis showed that complex networks of interactions existed in the sediments. After adapting to the acidic environmental conditions, the growth of some locally dominant bacteria increased the microbial interactions, allowing more bacteria to participate in the network, making their connections stronger. This evidence points to a disruption in the microbial community structure and its diversity following artificial disturbance, which then develops again over time. These results could contribute to the understanding of the evolution of microbial communities in the ecosystem during the remediation of anthropogenically disturbed heavy metals.
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Affiliation(s)
- Quanliu Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shiqi Jie
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Pan Lei
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Min Gan
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Peng He
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Jianyu Zhu
- School of Minerals Processing and Bioengineering, Key Laboratory of Biohydrometallurgy of Ministry of Education, Central South University, Changsha 410083, China
| | - Qingming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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Bai X, Li Y, Jing X, Zhao X, Zhao P. Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress. Front Microbiol 2023; 14:1116535. [PMID: 36910173 PMCID: PMC9992798 DOI: 10.3389/fmicb.2023.1116535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/27/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats. Methods In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH). Results The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes. Discussion As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.
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Affiliation(s)
- Xue Bai
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Yvjing Li
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Xiuqing Jing
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Xiaodong Zhao
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Pengyu Zhao
- Department of Biology, Taiyuan Normal University, Taiyuan, China
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George SE, Devereux R, James J, Wan Y, Diamond GL, Bradham KD, Thomas DJ. Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114430. [PMID: 37192935 PMCID: PMC10181873 DOI: 10.1016/j.ecoenv.2022.114430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The effect of dietary lead on the intestinal microbiome has not been fully elucidated. To determine if there was an association between microflora modulation, predicted functional genes, and Pb exposure, mice were provided diets amended with increasing concentrations of a single lead compound, lead acetate, or a well characterized complex reference soil containing lead, i.e. 6.25-25 mg/kg Pb acetate (PbOAc) or 7.5-30 mg/kg Pb in reference soil SRM 2710a having 0.552 % Pb among other heavy metals such as Cd. Feces and ceca were collected following 9 days of treatment and the microbiome analyzed by 16 S rRNA gene sequencing. Treatment effects on the microbiome were observed in both feces and ceca of mice. Changes in the cecal microbiomes of mice fed Pb as Pb acetate or as a constituent in SRM 2710a were statistically different except for a few exceptions regardless of dietary source. This was accompanied by increased average abundance of functional genes associated with metal resistance, including those related to siderophore synthesis and arsenic and/or mercury detoxification. Akkermansia, a common gut bacterium, was the highest ranked species in control microbiomes whereas Lactobacillus ranked highest in treated mice. Firmicutes/Bacteroidetes ratios in the ceca of SRM 2710a treated mice increased more than with PbOAc, suggestive of changes in gut microbiome metabolism that promotes obesity. Predicted functional gene average abundance related to carbohydrate, lipid, and/or fatty acid biosynthesis and degradation were greater in the cecal microbiome of SRM 2710a treated mice. Bacilli/Clostridia increased in the ceca of PbOAc treated mice and may be indicative of increased risk of host sepsis. Family Deferribacteraceae also was modulated by PbOAc or SRM 2710a possibly impacting inflammatory response. Understanding the relationship between microbiome composition, predicted functional genes, and Pb concentration, especially in soil, may provide new insights into the utility of various remediation methodologies that minimize dysbiosis and modulate health effects, thus assisting in the selection of an optimal treatment for contaminated sites.
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Affiliation(s)
- S. Elizabeth George
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Richard Devereux
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Joseph James
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | - Yongshan Wan
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, Gulf Breeze, FL 32561, United States
| | | | - Karen D. Bradham
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Environmental Measurement & Modeling, Research Triangle Park, NC 27711, United States
| | - David J. Thomas
- U. S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure, Chemical Characterization & Exposure Division, Research Triangle Park, NC 27711, United States
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Zhang M, Zhang T, Zhou L, Lou W, Zeng W, Liu T, Yin H, Liu H, Liu X, Mathivanan K, Praburaman L, Meng D. Soil microbial community assembly model in response to heavy metal pollution. ENVIRONMENTAL RESEARCH 2022; 213:113576. [PMID: 35710022 DOI: 10.1016/j.envres.2022.113576] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Heavy metal pollution affected the stability and function of soil ecosystem. The impact of heavy metals on soil microbial community and the interaction of microbial community has been widely studied, but little was known about the response of community assembly to the heavy metal pollution. In this study, we collected 30 soil samples from non (CON), moderately (CL) and severely (CH) contaminated fields. The prokaryotic community was studied using high-throughput Illumina sequencing of 16s rRNA gene amplicons, and community assembly were quantified using phylogenetic-bin-based null approach (iCAMP). Results showed that diversity and composition of both bacterial and archaeal community changed significantly in response to heavy metal pollution. The microbial community assembly tended to be more deterministic with the increase of heavy metal concentration. Among the assembly processes, the relative importance of homogeneous selection (deterministic process) increased significantly (increased by 16.2%), and the relative importance of drift and dispersal limitation (stochastic process) decreased significantly (decreased by 11.4% and 5.4%, respectively). The determinacy of bacterial and archaeal community assembly also increased with heavy metal stress, but the assembly models were different. The deterministic proportion of microorganisms tolerant to heavy metals, such as Thiobacillus, Euryarchaeota and Crenarchaeota (clustered in bin 32, bin59 and bin60, respectively) increased, while the stochastic proportion of microorganisms sensitive to heavy metals, such as Koribacteraceae (clustered in bin23) increased. Therefore, the heavy metal stress made the prokaryotic community be deterministic, however, the effects on the assembly process of different microbial groups differed obviously.
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Affiliation(s)
- Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Hunan Urban and Rural Environmental Construction Co., Ltd, Changsha, 410118, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, 101148, China
| | - Wei Lou
- Hunan Heqing Environmental Technology Co., Ltd, 410221, China
| | - Weiai Zeng
- Changsha Tobacco Company of Hunan Province, Changsha, 410011, China
| | - Tianbo Liu
- Tobacco Research Institute of Hunan Province, Changsha, 410004, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Hongwei Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China
| | - Krishnamurthy Mathivanan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Loganathan Praburaman
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China; Key Laboratory of Biometallurgy, Ministry of Education, Changsha, 410083, China.
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10
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George SE, James J, Devereux R, Wan Y, Diamond GL, Bradham KD, Scheckel KG, Thomas DJ. Ingestion of remediated lead-contaminated soils affects the fecal microbiome of mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155797. [PMID: 35561906 PMCID: PMC9830667 DOI: 10.1016/j.scitotenv.2022.155797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/12/2022] [Accepted: 05/05/2022] [Indexed: 05/08/2023]
Abstract
The relationship between ingestion of diets amended with a Pb-contaminated soil and the composition of the fecal microbiome was examined in a mouse model. Mice consumed diets amended with a Pb-contaminated soil in its native (untreated) state or after treatment for remediation with phosphoric acid or triple superphosphate alone or in combination with iron-waste material or biosolids compost. Subacute dietary exposure of mice receiving treated soil resulted in modulation of the fecal intestinal flora, which coincided with reduced relative Pb bioavailability in the bone, blood and kidney and differences in Pb speciation compared to untreated soil. Shifts in the relative abundance of several phyla including Verrucomicrobia, Tenericutes, Firmicutes, Proteobacteria, and TM7 (Candidatus Saccharibacteria) were observed. Because the phyla persist in the presence of Pb, it is probable that they are resistant to Pb. This may enable members of the phyla to bind and limit Pb uptake in the intestine. Families Ruminococcaceae, Lachnospiraceae, Erysipelotrichaceae, Verrucomicrobiaceae, Prevotellaceae, Lactobacilaceae, and Bacteroidaceae, which have been linked to health or disease, also were modulated. This study is the first to explore the relationship between the murine fecal microbiome and ingested Pb contaminated soils treated with different remediation options designed to reduce bioavailability. Identifying commonalities in the microbiome that are correlated with more positive health outcomes may serve as biomarkers to assist in the selection of remediation approaches that are more effective and pose less risk.
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Affiliation(s)
- S Elizabeth George
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States.
| | - Joseph James
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Richard Devereux
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Yongshan Wan
- Center for Environmental Measurement & Modeling, Gulf Ecosystem Measurement & Modeling Division, U.S. Environmental Protection Agency, Office of Research & Development, Gulf Breeze, FL 32561, United States
| | - Gary L Diamond
- SRC, Inc., North Syracuse, New York 13212, United States
| | - Karen D Bradham
- Center for Environmental Measurement & Modeling, Watershed & Ecosystem Characterization Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
| | - Kirk G Scheckel
- Center for Environmental Solutions and Emergency Response, Land Remediation & Technology Division, U.S. Environmental Protection Agency, Office of Research & Development, Cincinnati, OH 45224, United States
| | - David J Thomas
- Center for Computational Toxicology & Exposure, Chemical Characterization & Exposure Division, U.S. Environmental Protection Agency, Office of Research & Development, Research Triangle Park, NC 27711, United States
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11
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Zhang K, Li K, Tong M, Xia Y, Cui Y, Liu Z, Chen Q, Li Q, Hu F, Yang F. Distribution Pattern and Influencing Factors of Heavy Metal Resistance Genes in the Yellow River Sediments of Henan Section. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191710724. [PMID: 36078440 PMCID: PMC9517883 DOI: 10.3390/ijerph191710724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 05/11/2023]
Abstract
The transformation of heavy metal resistance genes (MRGs) in the environment has attracted increasing attention in recent years. However, few studies have reported the MRG content in the Yellow River, one of the main irrigation water sources in the North China Plain. In this study, we quantified MRG abundance by a metagenomic approach, and assessed the influence on MRGs of both bioavailable and total heavy metal (HM) content. The results indicate that Cu-resistant genes are the most common genes, and the prevalence of arsM needs more attention. Comamonadaceae is the dominant family in the Yellow River, and the presence of organic pollutants may contribute to the prevalence of Vicinamibacteraceae, Nocardioidaceae, and Flavobacteriacea. The results of the Mantel test and Spearman analysis indicate that both the bioavailable fractions and total content of HMs could have little influence on MRGs. Network analysis results indicate that some dominant bacteria could be the potential hosts of some prevalent MRGs, which may exert an adverse impact on human health.
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Affiliation(s)
- Kai Zhang
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
- Correspondence: (K.Z.); (F.Y.)
| | - Kuangjia Li
- Development Research Center, Ministry of Water Resources of People’s Republic of China, Beijing 100032, China
| | - Minghui Tong
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Yangchun Xia
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Yongxin Cui
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Ziyi Liu
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Qi Chen
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Qidi Li
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Feiyue Hu
- School of Geographic Sciences, Xinyang Normal University, Xinyang 464000, China
- Henan Key Laboratory for Synergistic Prevention of Water and Soil Environmental Pollution, Xinyang Normal University, Xinyang 464000, China
| | - Fengxia Yang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, China
- Correspondence: (K.Z.); (F.Y.)
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12
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Wei Y, Yi K, Shen C, Chen X, Iqbal T, Cao M, Chen T, Luo Y, Li J, Zhou X, Li C, Chen L. Whole Transcriptome Profiling of the Effects of Cadmium on the Liver of the Xiangxi Yellow Heifer. Front Vet Sci 2022; 9:846662. [PMID: 35498726 PMCID: PMC9047687 DOI: 10.3389/fvets.2022.846662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/07/2022] [Indexed: 11/21/2022] Open
Abstract
Cadmium (Cd) is a major heavy metal toxicant found in industrial zones. Humans and animals are exposed to it through their diet, which results in various physiological problems. In the current study, the toxic effects of Cd on the liver were investigated by whole-transcriptome sequencing (RNA-seq) of the livers of Xiangxi heifers fed a diet with excess Cd. We randomly divided six healthy heifers into two groups. The first group received a control diet, whereas the second group received Cd-exceeding diets for 100 days. After 100 days, the livers were collected. A total of 551 differentially expressed mRNAs, 24 differentially expressed miRNAs, and 169 differentially expressed lncRNAs were identified (p < 0.05, |log2FC| >1). Differentially expressed genes (DEGs) were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. We found that under Cd exposure, DEGs were enriched in the adenosine 5'-monophosphate-activated protein kinase pathway, which is involved in autophagy regulation, and the peroxisome proliferator-activated receptor pathway, which is involved in lipid metabolism. In addition, the apolipoprotein A4 gene, which has anti-inflammatory and antioxidant effects, the anti-apoptotic gene ATPase H+/K+ transporting the nongastric alpha2 subunit, and the cholesterol metabolism-associated gene endothelial lipase gene were significantly downregulated. C-X-C motif chemokine ligand 3, cholesterol 7α-hydroxylase, and stearoyl-CoA desaturase, which are involved in the development of fatty liver, were significantly upregulated. These genes revealed the main effects of Cd on the liver of Xiangxi yellow heifers. The current study provides insightful information regarding the DEGs involved in autophagy regulation, apoptosis, lipid metabolism, anti-inflammation, and antioxidant enzyme activity. These may serve as useful biomarkers for predicting and treating Cd-related diseases in the future.
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Affiliation(s)
- Yameng Wei
- College of Animal Sciences, Jilin University, Changchun, China
| | - Kangle Yi
- Grassland and Herbivore Research Laboratory, Hunan Animal Husbandry and Veterinary Research Institute, Changsha, China
| | - Caomeihui Shen
- College of Animal Sciences, Jilin University, Changchun, China
| | - Xue Chen
- College of Animal Sciences, Jilin University, Changchun, China
| | - Tariq Iqbal
- College of Animal Sciences, Jilin University, Changchun, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, China
| | - Tong Chen
- College of Animal Sciences, Jilin University, Changchun, China
| | - Yang Luo
- Grassland and Herbivore Research Laboratory, Hunan Animal Husbandry and Veterinary Research Institute, Changsha, China
| | - Jianbo Li
- Grassland and Herbivore Research Laboratory, Hunan Animal Husbandry and Veterinary Research Institute, Changsha, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, China
| | - Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, China
| | - Lu Chen
- College of Animal Sciences, Jilin University, Changchun, China
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13
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Shen Z, Wang F, Liang Y, Li Y, Liu Q, Liu F. Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake. Lett Appl Microbiol 2021; 75:1093-1102. [PMID: 34890483 DOI: 10.1111/lam.13627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/26/2021] [Accepted: 12/06/2021] [Indexed: 11/28/2022]
Abstract
Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism of how microbes adapted to heavy metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12 989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22·84 and 70·69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.
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Affiliation(s)
- Z Shen
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - F Wang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Y Liang
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Y Li
- School of life Sciences, Huaibei Normal University, Huaibei, China
| | - Q Liu
- HeFei University of Technology, Hefei, China
| | - F Liu
- School of life Sciences, Huaibei Normal University, Huaibei, China
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14
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Lu Z, Su H. Employing gene chip technology for monitoring and assessing soil heavy metal pollution. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 194:2. [PMID: 34862584 DOI: 10.1007/s10661-021-09650-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
Soil heavy metals pollution can cause many serious environment problems because of involving a very complex pollution process for soil health. Therefore, it is very important to explore methods that can effectively evaluate heavy metal pollution. Researchers were actively looking for new ideas and new methods for evaluating and predicting levels of soil heavy metal pollution. The study on microbial communities is one of the effective methods using gene chip technology. Gene chip technology, as a high-throughput metagenomics analysis technique, has been widely used for studying the structure and function of complex microbial communities in different polluted environments from different pollutants, including the soil polluted by heavy metals. However, there is still a lack of a systematic summarization for the polluted soil by heavy metals. This paper systematically analyzed soil heavy metals pollution via reviewing previous studies on applying gene chip technology, including single species, tolerance mechanisms, enrichment mechanisms, anticipation and evaluation of soil remediation, and multi-directional analysis. The latest gene chip technologies and corresponding application cases for discovering critical species and functional genes via analyzing microbial communities and evaluating heavy metal pollution of soil were also introduced in this paper. This article can provide scientific guidance for researchers actively investigating the soil polluted by heavy metals.
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Affiliation(s)
- ZiChun Lu
- College of Hehai, Chongqing University of Technology, Chongqing, 400717, China
| | - HaiFeng Su
- Key Laboratory of Degraded and Unused Land Consolidation Engineering, the Ministry of Natural and Resources, Xi'an, Shanxi, 710075, China.
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Science, Chongqing, 400714, China.
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15
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Trace Element Contamination in One of the Yangtze Tributaries (Hunan, China)—Source Review and Potential Release from Sediments. WATER 2021. [DOI: 10.3390/w13030271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Spatio-temporal distribution and leachability of some trace elements (TE) were investigated in sediments of the Xiangjiang River, tributary of the Yangtze River. Based on data collected during 2015–2017, a literature review and geoaccumulation indexes, the pollution level was the highest for Cd, Sb and Hg (Igeo > 3). Over the period reviewed, the TE contamination level displayed almost no temporal variation but an obvious spatial distribution. The most upstream contamination hotspot (Cd > Cr > As, Cu, Pb, Zn > Hg, Sb) was the Songbai section. This hotspot did not spread further downstream. The second hotspot identified was the Zhuzhou–Xiangtan section, impacted by Cd > Hg, Pb, Zn > Cu, with the Zhuzhou area being particularly highly impacted by Pb and Zn. A 30-day leaching experimental protocol under aerobic and anaerobic conditions was carried out to access TE mobility. Low percentages of TE released were calculated, showing that the TE fate mostly depends on the stability of bearing phases under specific physicochemical and microbial conditions. In this case, the studied sediments can be an important sink for these TE. However, some environmental issues have to be considered as some leachate concentrations of contaminants (As, Cr, Cu and U) released into water exceed freshwater aquatic life criteria.
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16
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Abstract
The aquatic ecosystem is continuously threatened by the infiltration and discharge of anthropogenic wastewaters. This issue requires the unending improvement of monitoring systems to become more comprehensive and specific to targeted pollutants. This review intended to elucidate the overall aspects explored by researchers in developing better water pollution monitoring tools in recent years. The discussion is encircled around three main elements that have been extensively used as the basis for the development of monitoring methods, namely the dissolved compounds, bacterial indicator, and nucleic acids. The latest technologies applied in wastewater and surface water mapped from these key players were reviewed and categorized into physicochemical and compound characterizations, biomonitoring, and molecular approaches in taxonomical and functional analyses. Overall, researchers are continuously rallying to enhance the detection of causal source for water pollution through either conventional or mostly advanced approaches focusing on spectrometry, high-throughput sequencing, and flow cytometry technology among others. From this review’s perspective, each pollution evaluation technology has its own advantages and it would be beneficial for several aspects of pollutants assessments to be combined and established as a complementary package for better aquatic environmental management in the long run.
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17
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Elizabeth George S, Wan Y. Advances in characterizing microbial community change and resistance upon exposure to lead contamination: Implications for ecological risk assessment. CRITICAL REVIEWS IN ENVIRONMENTAL SCIENCE AND TECHNOLOGY 2019; 50:2223-2270. [PMID: 34326626 PMCID: PMC8318135 DOI: 10.1080/10643389.2019.1698260] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent advancement in molecular techniques has spurred waves of studies on responses of microorganisms to lead contamination exposure, leveraging detailed phylogenetic analyses and functional gene identification to discern the effects of lead toxicity on microbial communities. This work provides a comprehensive review of recent research on (1) microbial community changes in contaminated aquatic sediments and terrestrial soils; (2) lead resistance mechanisms; and (3) using lead resistance genes for lead biosensor development. Sufficient evidence in the literature, including both in vitro and in situ studies, indicates that exposure to lead contamination inhibits microbial activity resulting in reduced respiration, suppressed metabolism, and reduced biomass as well as altered microbial community structure. Even at sites where microbial communities do not vary compositionally with contamination levels due to extremely long periods of exposure, functional differences between microbial communities are evident, indicating that some microorganisms are susceptible to lead toxicity as others develop resistance mechanisms to survive in lead contaminated environments. The main mechanisms of lead resistance involve extracellular and intracellular biosorption, precipitation, complexation, and/or efflux pumps. These lead resistance mechanisms are associated with suites of genes responsible for specific lead resistance mechanisms and may serving as indicators of lead contamination in association with dominance of certain phyla. This allows for development of several lead biosensors in environmental biotechnology. To promote applications of these advanced understandings, molecular techniques, and lead biosensor technology, perspectives of future work on using microbial indicators for site ecological assessment is presented.
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Affiliation(s)
- S. Elizabeth George
- US EPA Office of Research and Development, National Health and Environmental Effects Laboratory, Gulf Ecology Division, Sabine Island Drive, Gulf Breeze, FL 32561
| | - Yongshan Wan
- US EPA Office of Research and Development, National Health and Environmental Effects Laboratory, Gulf Ecology Division, Sabine Island Drive, Gulf Breeze, FL 32561
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18
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Song W, Qi R, Zhao L, Xue N, Wang L, Yang Y. Bacterial community rather than metals shaping metal resistance genes in water, sediment and biofilm in lakes from arid northwestern China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113041. [PMID: 31421577 DOI: 10.1016/j.envpol.2019.113041] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/26/2019] [Accepted: 08/09/2019] [Indexed: 05/25/2023]
Abstract
Lakes in arid northwestern China are valuable freshwater resources that drive socioeconomic development. Environmental pollution can significantly influence the composition of microbial communities and the distribution of functional genes in lakes. This study investigated heavy metal pollution to identify possible correlations with metal resistance genes (MRGs) and bacterial community composition in water, sediment and biofilm samples from Bosten Lake and Ebi Lake in northwestern China. High levels of zinc were detected in all samples. However, the metals detected in the sediment samples of both lakes were determined to be at low risk levels according to an ecological index. The mercury resistance gene subtype merP had the greatest average abundance (4.61 × 10-3 copies per 16S rRNA) among all the samples, followed by merA and merC. The high abundance of merA in the pelagic zone rather than in benthic sediment suggests that the pelagic microbial community was important in mercury reduction. Proteobacteria were the main phylum found in the microbial communities in all samples. However, microbial communities in most of the water, sediment and biofilm samples had different compositions, indicating that the habitat niche plays an important role in shaping the bacterial communities in lakes. The microbial community, rather than the heavy metals, was the main driver of MRG distribution. The abundances of some bacterial genera involved in the decomposition of organic matter and the terrestrial nitrogen cycle were negatively correlated with heavy metals. This result suggests that metal pollution can adversely affect the biogeochemical processes that occur in lakes.
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Affiliation(s)
- Wenjuan Song
- State Key Laboratory of Desert & Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China.
| | - Ran Qi
- Chinese People's Armed Police Golden Headquarters, Beijing, 100055, China
| | - Li Zhao
- State Key Laboratory of Desert & Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
| | - Nana Xue
- State Key Laboratory of Desert & Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Liyi Wang
- State Key Laboratory of Desert & Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Science, Beijing, 100049, China
| | - Yuyi Yang
- University of Chinese Academy of Science, Beijing, 100049, China; Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; School of Life Sciences, University of Dundee, Dundee, DD1 5EH, Scotland, UK.
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19
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Jordaan K, Comeau AM, Khasa DP, Bezuidenhout CC. An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa. PLoS One 2019; 14:e0216758. [PMID: 31112559 PMCID: PMC6528982 DOI: 10.1371/journal.pone.0216758] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/26/2019] [Indexed: 01/03/2023] Open
Abstract
Bacterial communities in human-impacted rivers and streams are exposed to multiple anthropogenic contaminants, which can eventually lead to biodiversity loss and function. The Wonderfonteinspruit catchment area is impacted by operational and abandoned gold mines, farms, and formal and informal settlements. In this study, we used 16S rRNA gene high-throughput sequencing to characterize bacterial communities in the lower Wonderfonteinspruit and their response to various contaminant sources. The results showed that composition and structure of bacterial communities differed significantly (P<0.05) between less (downstream) and more (upstream) polluted sites. The taxonomic and functional gene dissimilarities significantly correlated with each other, while downstream sites had more distinct functional genes. The relative abundance of Proteobacteria, Bacteroidetes and Actinobacteria was higher at upstream sites, while Acidobacteria, Cyanobacteria, Firmicutes and Verrucomicrobia were prominent at downstream sites. In addition, upstream sites were rich in genera pathogenic and/or potentially pathogenic to humans. Multivariate and correlation analyses suggest that bacterial diversity was significantly (P<0.05) impacted by pH and heavy metals (cobalt, arsenic, chromium, nickel and uranium). A significant fraction (~14%) of the compositional variation was explained by a combination of anthropogenic inputs, of which mining (~6%) was the main contributor to bacterial community variation. Network analysis indicated that bacterial communities had non-random inter- and intra-phyla associations and that the main taxa showed both positive and negative linkages to environmental parameters. Our results suggest that species sorting, due to environmental parameters, was the main process that structured bacterial communities. Furthermore, upstream sites had higher relative abundances of genes involved in xenobiotic degradation, suggesting stronger removal of polycyclic aromatic hydrocarbons and other organic compounds. This study provides insights into the influences of anthropogenic land use on bacterial community structure and functions in the lower Wonderfonteinspruit.
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Affiliation(s)
- K. Jordaan
- Unit for Environmental Sciences and Management, Microbiology, North-West University, South Africa, Potchefstroom, South Africa
- * E-mail:
| | - A. M. Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - D. P. Khasa
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - C. C. Bezuidenhout
- Unit for Environmental Sciences and Management, Microbiology, North-West University, South Africa, Potchefstroom, South Africa
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20
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Mahamoud Ahmed A, Lyautey E, Bonnineau C, Dabrin A, Pesce S. Environmental Concentrations of Copper, Alone or in Mixture With Arsenic, Can Impact River Sediment Microbial Community Structure and Functions. Front Microbiol 2018; 9:1852. [PMID: 30158909 PMCID: PMC6104476 DOI: 10.3389/fmicb.2018.01852] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/24/2018] [Indexed: 12/03/2022] Open
Abstract
In many aquatic ecosystems, sediments are an essential compartment, which supports high levels of specific and functional biodiversity thus contributing to ecological functioning. Sediments are exposed to inputs from ground or surface waters and from surrounding watershed that can lead to the accumulation of toxic and persistent contaminants potentially harmful for benthic sediment-living communities, including microbial assemblages. As benthic microbial communities play crucial roles in ecological processes such as organic matter recycling and biomass production, we performed a 21-day laboratory channel experiment to assess the structural and functional impact of metals on natural microbial communities chronically exposed to sediments spiked with copper (Cu) and/or arsenic (As) alone or mixed at environmentally relevant concentrations (40 mg kg-1 for each metal). Heterotrophic microbial community responses to metals were evaluated both in terms of genetic structure (using ARISA analysis) and functional potential (using exoenzymatic, metabolic and functional genes analyses). Exposure to Cu had rapid marked effects on the structure and most of the functions of the exposed communities. Exposure to As had almost undetectable effects, possibly due to both lack of As bioavailability or toxicity toward the exposed communities. However, when the two metals were combined, certain functional responses suggested a possible interaction between Cu and As toxicity on heterotrophic communities. We also observed temporal dynamics in the functional response of sediment communities to chronic Cu exposure, alone or in mixture, with some functions being resilient and others being impacted throughout the experiment or only after several weeks of exposure. Taken together, these findings reveal that metal contamination of sediment could impact both the genetic structure and the functional potential of chronically exposed microbial communities. Given their functional role in aquatic ecosystems, it poses an ecological risk as it may impact ecosystem functioning.
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Affiliation(s)
- Ayanleh Mahamoud Ahmed
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
- CARRTEL, Univ. Savoie Mont Blanc, INRA, Chambéry, France
- Centre de Recherche, Université de Djibouti, Djibouti, Djibouti
| | - Emilie Lyautey
- CARRTEL, Univ. Savoie Mont Blanc, INRA, Chambéry, France
| | - Chloé Bonnineau
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Aymeric Dabrin
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Stéphane Pesce
- Irstea, UR RiverLy, Centre de Lyon-Villeurbanne, Villeurbanne, France
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21
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Cheaib B, Le Boulch M, Mercier PL, Derome N. Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient. Front Microbiol 2018; 9:869. [PMID: 29774016 PMCID: PMC5943556 DOI: 10.3389/fmicb.2018.00869] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 04/16/2018] [Indexed: 11/29/2022] Open
Abstract
Adaptation of microbial communities to anthropogenic stressors can lead to reductions in microbial diversity and disequilibrium of ecosystem services. Such adaptation can change the molecular signatures of communities with differences in taxonomic and functional composition. Understanding the relationship between taxonomic and functional variation remains a critical issue in microbial ecology. Here, we assessed the taxonomic and functional diversity of a lake metacommunity system along a polymetallic pollution gradient caused by 60 years of chronic exposure to acid mine drainage (AMD). Our results highlight three adaptive signatures. First, a signature of taxon—function decoupling was detected in the microbial communities of moderately and highly polluted lakes. Second, parallel shifts in taxonomic composition occurred between polluted and unpolluted lakes. Third, variation in the abundance of functional modules suggested a gradual deterioration of ecosystem services (i.e., photosynthesis) and secondary metabolism in highly polluted lakes. Overall, changes in the abundance of taxa, function, and more importantly the polymetallic resistance genes such as copA, copB, czcA, cadR, cCusA, were correlated with trace metal content (mainly Cadmium) and acidity. Our findings highlight the impact of polymetallic pollution gradient at the lowest trophic levels.
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Affiliation(s)
- Bachar Cheaib
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Malo Le Boulch
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada.,GenPhySE, Institut National de la Recherche Agronomique, Université de Toulouse, INPT, ENVT, Castanet-Tolosan, France
| | - Pierre-Luc Mercier
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec, QC, Canada
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22
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Jacquiod S, Cyriaque V, Riber L, Al-Soud WA, Gillan DC, Wattiez R, Sørensen SJ. Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome. JOURNAL OF HAZARDOUS MATERIALS 2018; 344:299-307. [PMID: 29055834 DOI: 10.1016/j.jhazmat.2017.09.046] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/11/2017] [Accepted: 09/25/2017] [Indexed: 05/19/2023]
Abstract
Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.
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Affiliation(s)
- Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - Valentine Cyriaque
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Leise Riber
- Section of Functional Genomics, Department of Biology, University of Copenhagen, Ole Maaløesvej 5, 2200 Copenhagen N, Denmark.
| | - Waleed Abu Al-Soud
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
| | - David C Gillan
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Ruddy Wattiez
- Proteomics and Microbiology Lab, Research Institute for Biosciences, UMONS, avenue du Champs de Mars 6, 7000 Mons, Belgium.
| | - Søren J Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen Ø, 1, Bygning, 1-1-215, Denmark.
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23
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Escalas A, Troussellier M, Yuan T, Bouvier T, Bouvier C, Mouchet MA, Flores Hernandez D, Ramos Miranda J, Zhou J, Mouillot D. Functional diversity and redundancy across fish gut, sediment and water bacterial communities. Environ Microbiol 2017; 19:3268-3282. [PMID: 28618142 DOI: 10.1111/1462-2920.13822] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 06/07/2017] [Indexed: 11/26/2022]
Abstract
This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.
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Affiliation(s)
- Arthur Escalas
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Marc Troussellier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Tong Yuan
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Thierry Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Corinne Bouvier
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France
| | - Maud A Mouchet
- UMR 7204 CESCO, Muséum d'Histoire Naturelle, 55 rue Buffon, Paris, 75005, France
| | - Domingo Flores Hernandez
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Julia Ramos Miranda
- Centro de Ecología, Pesquerias y Oceanographia de Golfo de México, Universidad Autonoma de Campeche, Campeche, Mexico
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA.,Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - David Mouillot
- UMR 9190 MARBEC, IRD-CNRS-UM-IFREMER, Université Montpellier, 34095 Montpellier Cedex, France.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
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