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Halema AA, El-Beltagi HS, Al-Dossary O, Alsubaie B, Henawy AR, Rezk AA, Almutairi HH, Mohamed AA, Elarabi NI, Abdelhadi AA. Omics technology draws a comprehensive heavy metal resistance strategy in bacteria. World J Microbiol Biotechnol 2024; 40:193. [PMID: 38709343 DOI: 10.1007/s11274-024-04005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/24/2024] [Indexed: 05/07/2024]
Abstract
The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.
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Affiliation(s)
- Asmaa A Halema
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia.
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt.
| | - Othman Al-Dossary
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Bader Alsubaie
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Ahmed R Henawy
- Microbiology Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Adel A Rezk
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
- Plant Virology Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, 12619, Egypt
| | - Hayfa Habes Almutairi
- Chemistry Department, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia
| | - Amal A Mohamed
- Chemistry Dept, Al-Leith University College, Umm Al-Qura University, P.O. Box 6725- 21955, Makkah, Saudi Arabia
| | - Nagwa I Elarabi
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
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Kaya C, Uğurlar F, Ashraf M, Hou D, Kirkham MB, Bolan N. Microbial consortia-mediated arsenic bioremediation in agricultural soils: Current status, challenges, and solutions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170297. [PMID: 38272079 DOI: 10.1016/j.scitotenv.2024.170297] [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: 11/14/2023] [Revised: 01/01/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024]
Abstract
Arsenic poisoning in agricultural soil is caused by both natural and man-made processes, and it poses a major risk to crop production and human health. Soil quality, agricultural production, runoff, ingestion, leaching, and absorption by plants are all influenced by these processes. Microbial consortia have become a feasible bioremediation technique in response to the urgent need for appropriate remediation solutions. These diverse microbial populations collaborate to combat arsenic poisoning in soil by facilitating mechanisms including oxidation-reduction, methylation-demethylation, volatilization, immobilization, and arsenic mobilization. The current state, problems, and remedies for employing microbial consortia in arsenic bioremediation in agricultural soils are examined in this review. Among the elements affecting their success include diversity, activity, community organization, and environmental conditions. Also, we emphasize the sensitivity and accuracy limits of existing assessment techniques. While earlier reviews have addressed a variety of arsenic remediation options, this study stands out by concentrating on microbial consortia as a viable strategy for arsenic removal and presents performance evaluation and technical problems. This work gives vital insights for tackling the major issue of arsenic pollution in agricultural soils by explaining the potential methods and components involved in microbial consortium-mediated arsenic bioremediation.
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Affiliation(s)
- Cengiz Kaya
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa, Turkey.
| | - Ferhat Uğurlar
- Soil Science and Plant Nutrition Department, Harran University, Sanliurfa, Turkey
| | - Muhammed Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Pakistan
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
| | - Mary Beth Kirkham
- Department of Agronomy, Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS, United States
| | - Nanthi Bolan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia 6009, Australia; The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia 6009, Australia
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Olaya‐Abril A, Biełło K, Rodríguez‐Caballero G, Cabello P, Sáez LP, Moreno‐Vivián C, Luque‐Almagro VM, Roldán MD. Bacterial tolerance and detoxification of cyanide, arsenic and heavy metals: Holistic approaches applied to bioremediation of industrial complex wastes. Microb Biotechnol 2024; 17:e14399. [PMID: 38206076 PMCID: PMC10832572 DOI: 10.1111/1751-7915.14399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Cyanide is a highly toxic compound that is found in wastewaters generated from different industrial activities, such as mining or jewellery. These residues usually contain high concentrations of other toxic pollutants like arsenic and heavy metals that may form different complexes with cyanide. To develop bioremediation strategies, it is necessary to know the metabolic processes involved in the tolerance and detoxification of these pollutants, but most of the current studies are focused on the characterization of the microbial responses to each one of these environmental hazards individually, and the effect of co-contaminated wastes on microbial metabolism has been hardly addressed. This work summarizes the main strategies developed by bacteria to alleviate the effects of cyanide, arsenic and heavy metals, analysing interactions among these toxic chemicals. Additionally, it is discussed the role of systems biology and synthetic biology as tools for the development of bioremediation strategies of complex industrial wastes and co-contaminated sites, emphasizing the importance and progress derived from meta-omic studies.
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Affiliation(s)
- Alfonso Olaya‐Abril
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Karolina Biełło
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Gema Rodríguez‐Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Purificación Cabello
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Lara P. Sáez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Conrado Moreno‐Vivián
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - Víctor Manuel Luque‐Almagro
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus de RabanalesUniversidad de CórdobaCórdobaSpain
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4
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Xu Y, Teng Y, Wang X, Ren W, Zhao L, Luo Y, Christie P, Greening C. Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil. ENVIRONMENT INTERNATIONAL 2023; 176:107962. [PMID: 37196568 DOI: 10.1016/j.envint.2023.107962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/11/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
Abstract
Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of 13C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Wenjie Ren
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ling Zhao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Yongming Luo
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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5
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Prosenkov A, Cagnon C, Gallego JLR, Pelaez AI. The microbiome of a brownfield highly polluted with mercury and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 323:121305. [PMID: 36804142 DOI: 10.1016/j.envpol.2023.121305] [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: 11/18/2022] [Revised: 02/11/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.
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Affiliation(s)
- Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain
| | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, 33600 Mieres, Asturias, Spain
| | - Ana Isabel Pelaez
- Area of Microbiology, Department of Functional Biology, Environmental Biogeochemistry and Raw Materials Group and IUBA, University of Oviedo, 33006 Oviedo, Asturias, Spain.
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6
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Kumar J, Sharma N, Singh SP. Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:50864-50882. [PMID: 36807860 DOI: 10.1007/s11356-023-25893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/08/2023] [Indexed: 04/16/2023]
Abstract
Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.
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Affiliation(s)
- Jitesh Kumar
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Nitish Sharma
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, Department of Biotechnology (DBT), Govt. of India, S.A.S. Nagar, Sector-81, (Knowledge City) Mohali, 140306, India.
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7
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Li Y, Lin H, Gao P, Yang N, Xu R, Sun X, Li B, Xu F, Wang X, Song B, Sun W. Synergistic Impacts of Arsenic and Antimony Co-contamination on Diazotrophic Communities. MICROBIAL ECOLOGY 2022; 84:44-58. [PMID: 34398256 DOI: 10.1007/s00248-021-01824-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen (N) shortage poses a great challenge to the implementation of in situ bioremediation practices in mining-contaminated sites. Diazotrophs can fix atmospheric N2 into a bioavailable form to plants and microorganisms inhabiting adverse habitats. Increasing numbers of studies mainly focused on the diazotrophic communities in the agroecosystems, while those communities in mining areas are still not well understood. This study compared the variations of diazotrophic communities in composition and interactions in the mining areas with different extents of arsenic (As) and antimony (Sb) contamination. As and Sb co-contamination increased alpha diversities and the abundance of nifH encoding the dinitrogenase reductase, while inhibited the diazotrophic interactions and substantially changed the composition of communities. Based on the multiple lines of evidence (e.g., the enrichment analysis of diazotrophs, microbe-microbe network, and random forest regression), six diazotrophs (e.g., Sinorhizobium, Dechloromonas, Trichormus, Herbaspirillum, Desmonostoc, and Klebsiella) were identified as keystone taxa. Environment-microbe network and random forest prediction demonstrated that these keystone taxa were highly correlated with the As and Sb contamination fractions. All these results imply that the above-mentioned diazotrophs may be resistant to metal(loid)s.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
- College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai, 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-Environmental Pollution Control and Management, Institute of Eco-Environmental and Soil Sciences, Guangdong Academy of Sciences, 808 Tianyuan Road, Guangzhou, 510650, Guangdong, China.
- School of Environment, Henan Normal University, Xinxiang, China.
- Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Xinxiang, China.
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Vidal P, Martínez-Martínez M, Fernandez-Lopez L, Roda S, Méndez-García C, Golyshina OV, Guallar V, Peláez AI, Ferrer M. Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation. Front Microbiol 2022; 13:868839. [PMID: 35663881 PMCID: PMC9162777 DOI: 10.3389/fmicb.2022.868839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/14/2022] [Indexed: 01/17/2023] Open
Abstract
Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33–68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30–65°C, retaining 20–61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.
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Affiliation(s)
- Paula Vidal
- Institute of Catalysis, Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mónica Martínez-Martínez
- Institute of Catalysis, Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Laura Fernandez-Lopez
- Institute of Catalysis, Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
| | - Celia Méndez-García
- Área de Microbiología, Departamento Biología Funcional e Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Olga V. Golyshina
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Ana I. Peláez
- Área de Microbiología, Departamento Biología Funcional e Instituto de Biotecnología de Asturias, Universidad de Oviedo, Oviedo, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Department of Applied Biocatalysis, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- *Correspondence: Manuel Ferrer,
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9
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Santos JLA, Busato JG, Pittarello M, da Silva J, Horák-Terra I, Evaristo AB, Dobbss LB. Alkaline extract from vermicompost reduced the stress promoted by As on maize plants and increase their phytoextraction capacity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:20864-20877. [PMID: 34741736 DOI: 10.1007/s11356-021-17255-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Arsenic (As) represents an environmental risk and phytoremediation has been identified as a good technique to recover contaminated soils. Plants defense mechanisms needed to be enhanced against As stress-promoting action by biostimulants such as humic materials. This work sought to determine the effectiveness of an alkaline vermicompost extract (AEV) and in mitigating stresses promoted by As in maize plants, increasing their potential use for phytoextraction. The AEV were extracted from vermicompost and two preliminary assays in Leonard pots were carried out: the first one to define the best AEV concentration-response dose and the second to point out the toxic As concentration. The second step was to set up a 28-day long experiment with the following four treatments: control, AEV, As, As + AEV. AEV attenuated As-induced stress in maize plants. Maize dry biomass was reduced in the As treatment and rebalanced to values similar to the control in the As + HS treatment while the plants treated only with HS showed the highest biomass among the treatments. The concentrations of P, Fe, Cu, Mn and Ni, and catalase (CAT), ascorbate peroxidase (APX) and superoxide dismutase (SOD) antioxidant activity increased in the As treatment and decreased in the As + AEV treatment. The rate of photosynthesis decreased, and the internal CO2 concentration increased with stress induced by As, where both effects were attenuated by AEV. Our results show the positive effect of the AEV in alleviating As abiotic stress on maize growth, offering new options of employment of humic substances in phytoremediation process.
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Affiliation(s)
- Jefferson Luiz Antunes Santos
- Institute of Agricultural Sciences (ICA), Federal University of the Jequitinhonha and Mucuri (UFVJM), Unaí, MG, 38610-000, Brazil.
| | - Jader Galba Busato
- Faculty of Agronomy and Veterinary Medicine, University of Brasilia (UnB), Brasília, DF, 70910-900, Brazil
| | - Marco Pittarello
- Department of Agronomy, Animals and the Environment (DAFNAE), Natural Resources, University of Padova, 35020, FoodLegnaro, Italy
| | - Juscimar da Silva
- Brazilian Agricultural Research Corporation (Embrapa), Fazenda Tamanduá, Embrapa HortaliçasParque Estação Biológica, Brasília, DF, 70770-901, Brazil
| | - Ingrid Horák-Terra
- Institute of Agricultural Sciences (ICA), Federal University of the Jequitinhonha and Mucuri (UFVJM), Unaí, MG, 38610-000, Brazil
| | - Anderson Barbosa Evaristo
- Institute of Agricultural Sciences (ICA), Federal University of the Jequitinhonha and Mucuri (UFVJM), Unaí, MG, 38610-000, Brazil
| | - Leonardo Barros Dobbss
- Institute of Agricultural Sciences (ICA), Federal University of the Jequitinhonha and Mucuri (UFVJM), Unaí, MG, 38610-000, Brazil
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10
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Bertin PN, Crognale S, Plewniak F, Battaglia-Brunet F, Rossetti S, Mench M. Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:9462-9489. [PMID: 34859349 PMCID: PMC8783877 DOI: 10.1007/s11356-021-17817-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 11/23/2021] [Indexed: 04/16/2023]
Abstract
Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.
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Affiliation(s)
- Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France.
| | - Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS - Université de Strasbourg, Strasbourg, France
| | | | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Rome, Italy
| | - Michel Mench
- Univ. Bordeaux, INRAE, BIOGECO, F-33615, Pessac, France
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11
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Li Y, Lin H, Gao P, Yang N, Xu R, Sun X, Li B, Xu F, Wang X, Song B, Sun W. Variation in the diazotrophic community in a vertical soil profile contaminated with antimony and arsenic. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 291:118248. [PMID: 34592324 DOI: 10.1016/j.envpol.2021.118248] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
A nitrogen (N) deficiency will usually hinder bioremediation efforts in mining-derived habitats such as occurring in mining regions. Diazotrophs can provide N to support the growth of plants and microorganisms in these environments. However, diazotrophic communities in mining areas have been not studied frequently and are more poorly understood than those in other environments, such as in agricultural soils or in the presence of legumes. The current study compares the differences in depth-resolved diazotrophic community compositions and interactions in two contrasting sites (to depths of 2 m), including a highly contaminated and a moderately contaminated site. Antimony (Sb) and arsenic (As) co-contamination induced a loosely connected biotic interaction, and a selection of deep soils by diazotrophic communities. Multiple lines of evidence, including the enrichment of diazotrophic taxa in the highly contaminated sites, microbe-microbe interactions, environment-microbe interactions, and a machine learning approach (random forests regression), demonstrated that Rhizobium was the keystone taxon within the vertical profile of contaminated soil and was resistant to the Sb and As contaminant fractions. All of these observations suggest that one diazotroph, Rhizobium, may play an important role in N fixation in the examined contaminated sites.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai, 201620, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Xiaoyu Wang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Benru Song
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510650, China; School of Environment, Henan Normal University, China; Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, China.
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12
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Plewniak F, Crognale S, Bruneel O, Sismeiro O, Coppée JY, Rossetti S, Bertin P. Metatranscriptomic outlook on green and brown food webs in acid mine drainage. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:606-615. [PMID: 33973709 DOI: 10.1111/1758-2229.12958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 04/15/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
Acid mine drainages (AMDs), metal-rich acidic effluents generated by mining activities, are colonized by prokaryotic and eukaryotic microorganisms widely distributed among different phyla. We compared metatranscriptomic data from two sampling stations in the Carnoulès AMD and from a third station in the nearby Amous River, focussing on processes involved in primary production and litter decomposition. A synergistic relationship between the green and brown food webs was favoured in the AMD sediments by the low carbon content and the availability of mineral nutrients: primary production of organic matter would benefit C-limited decomposers whose activity of organic matter mineralization would in turn profit primary producers. This balance could be locally disturbed by heterogeneous factors such as an input of plant debris from the riparian vegetation, strongly boosting the growth of Tremellales which would then outcompete primary producers. In the unpolluted Amous River on the contrary, the competition for limited mineral nutrients was dominated by the green food web, fish and bacterivorous protists having a positive effect on phytoplankton. These results suggest that in addition to direct effects of low pH and metal contamination, trophic conditions like carbon or mineral nutrient limitations also have a strong impact on assembly and activities of AMDs' microbial communities.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Odile Bruneel
- HydroSciences Montpellier, University of Montpellier - CNRS - IRD, Montpellier, France
| | - Odile Sismeiro
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Institut Pasteur, Transcriptome and Epigenome Platform, Biomics Pole, Paris, France
- Biologie des ARN des Pathogènes Fongiques, Institut Pasteur, Paris, France
| | - Simona Rossetti
- Istituto di Ricerca Sulle Acque, Consiglio Nazionale Delle Ricerche, Rome, Italy
| | - Philippe Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS - University of Strasbourg, Strasbourg, France
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13
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Li M, Wen J. Recent progress in the application of omics technologies in the study of bio-mining microorganisms from extreme environments. Microb Cell Fact 2021; 20:178. [PMID: 34496835 PMCID: PMC8425152 DOI: 10.1186/s12934-021-01671-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/11/2022] Open
Abstract
Bio-mining microorganisms are a key factor affecting the metal recovery rate of bio-leaching, which inevitably produces an extremely acidic environment. As a powerful tool for exploring the adaptive mechanisms of microorganisms in extreme environments, omics technologies can greatly aid our understanding of bio-mining microorganisms and their communities on the gene, mRNA, and protein levels. These omics technologies have their own advantages in exploring microbial diversity, adaptive evolution, changes in metabolic characteristics, and resistance mechanisms of single strains or their communities to extreme environments. These technologies can also be used to discover potential new genes, enzymes, metabolites, metabolic pathways, and species. In addition, integrated multi-omics analysis can link information at different biomolecular levels, thereby obtaining more accurate and complete global adaptation mechanisms of bio-mining microorganisms. This review introduces the current status and future trends in the application of omics technologies in the study of bio-mining microorganisms and their communities in extreme environments.
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Affiliation(s)
- Min Li
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China.,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering, Tianjin University, Tianjin, China. .,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin, China. .,Frontier Science Center of Ministry of Education, Tianjin University, Tianjin, China.
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14
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Li Y, Zhang M, Xu R, Lin H, Sun X, Xu F, Gao P, Kong T, Xiao E, Yang N, Sun W. Arsenic and antimony co-contamination influences on soil microbial community composition and functions: Relevance to arsenic resistance and carbon, nitrogen, and sulfur cycling. ENVIRONMENT INTERNATIONAL 2021; 153:106522. [PMID: 33812041 DOI: 10.1016/j.envint.2021.106522] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/02/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Microorganisms can mediate arsenic (As) and antimony (Sb) transformation and thus change the As and Sb toxicity and mobility. The influence of As and Sb on the innate microbiome has been extensively characterized. However, how microbial metabolic potentials are influenced by the As and Sb co-contamination is still ambiguous. In this study, we selected two contrasting sites located in the Shimen realgar mine, the largest realgar mine in Asia, to explore the adaptability and response of the soil microbiome to As and Sb co-contamination and the impact of co-contamination on microbial metabolic potentials. It is observed that the geochemical parameters, including the As and Sb fractions, were the driving forces that reshaped the community composition and metabolic potentials. Bacteria associated with Bradyrhizobium, Nocardioides, Sphingomonas, Burkholderia, and Streptomyces were predicted to be tolerant to high concentrations of As and Sb. Co-occurrence network analysis revealed that the genes related to C fixation, nitrate/nitrite reduction, N fixation, and sulfate reduction were positively correlated with the As and Sb fractions, suggesting that As and Sb biogeochemical cycling may interact with and benefit from C, N, and S cycling. The results suggest that As and Sb co-contamination not only influences As-related genes, but also influences other genes correlated with microbial C, N, and S cycling.
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Affiliation(s)
- Yongbin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Miaomiao Zhang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Rui Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Hanzhi Lin
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Fuqing Xu
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Pin Gao
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China; College of Environmental Science and Engineering, Textile Pollution Controlling Engineering Center of Ministry of Environmental Protection, Donghua University, Shanghai 201620, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Enzong Xiao
- Innovation Center and Key Laboratory of Waters Safety & Protection in the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Nie Yang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China.
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15
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Zhang B, Liu J, Sheng Y, Shi J, Dong H. Disentangling Microbial Syntrophic Mechanisms for Hexavalent Chromium Reduction in Autotrophic Biosystems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:6340-6351. [PMID: 33866784 DOI: 10.1021/acs.est.1c00383] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Hexavalent chromium [Cr(VI)] is one of the common heavy-metal contaminants in groundwater, and the availability of electron donors is considered to be a key parameter for Cr(VI) biotransformation. During the autotrophic remediation process, however, much remains to be illuminated about how complex syntrophic microbial communities couple Cr(VI) reduction with other elemental cycles. Two series of Cr(VI)-reducing groundwater bioreactors were independently amended by elemental sulfur and iron and inoculated with the same inoculum. After 160 days of incubation, both bioreactors showed similar archaea-dominating microbiota compositions, whereas a higher Cr(VI)-reducing rate and more methane production were detected in the Fe0-driven one. Metabolic reconstruction of 23 retrieved genomes revealed complex symbiotic relationships driving distinct elemental cycles coupled with Cr(VI) reduction in bioreactors. In both bioreactors, these Cr(VI) reducers were assumed to live in syntrophy with oxidizers of sulfur, iron, hydrogen, and volatile fatty acids and methane produced by carbon fixers and multitrophic methanogens, respectively. The significant difference in methane production was mainly due to the fact that the yielded sulfate greatly retarded acetoclastic methanogenesis in the S-bioreactor. These findings provide insights into mutualistic symbioses of carbon, sulfur, iron, and chromium metabolisms in groundwater systems and have implications for bioremediation of Cr(VI)-contaminated groundwater.
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Affiliation(s)
- Baogang Zhang
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Jun Liu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Yizhi Sheng
- Department of Geology and Environmental Earth Science, Miami University, Oxford, Ohio 45056, United States
| | - Jiaxin Shi
- School of Water Resources and Environment, Key Laboratory of Groundwater Circulation and Environmental Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Hailiang Dong
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Beijing 100083, China
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16
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Castaño A, Prosenkov A, Baragaño D, Otaegui N, Sastre H, Rodríguez-Valdés E, Gallego JLR, Peláez AI. Effects of in situ Remediation With Nanoscale Zero Valence Iron on the Physicochemical Conditions and Bacterial Communities of Groundwater Contaminated With Arsenic. Front Microbiol 2021; 12:643589. [PMID: 33815330 PMCID: PMC8010140 DOI: 10.3389/fmicb.2021.643589] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/25/2021] [Indexed: 12/31/2022] Open
Abstract
Nanoscale Zero-Valent Iron (nZVI) is a cost-effective nanomaterial that is widely used to remove a broad range of metal(loid)s and organic contaminants from soil and groundwater. In some cases, this material alters the taxonomic and functional composition of the bacterial communities present in these matrices; however, there is no conclusive data that can be generalized to all scenarios. Here we studied the effect of nZVI application in situ on groundwater from the site of an abandoned fertilizer factory in Asturias, Spain, mainly polluted with arsenic (As). The geochemical characteristics of the water correspond to a microaerophilic and oligotrophic environment. Physico-chemical and microbiological (cultured and total bacterial diversity) parameters were monitored before and after nZVI application over six months. nZVI treatment led to a marked increase in Fe(II) concentration and a notable fall in the oxidation-reduction potential during the first month of treatment. A substantial decrease in the concentration of As during the first days of treatment was observed, although strong fluctuations were subsequently detected in most of the wells throughout the six-month experiment. The possible toxic effects of nZVI on groundwater bacteria could not be clearly determined from direct observation of those bacteria after staining with viability dyes. The number of cultured bacteria increased during the first two weeks of the treatment, although this was followed by a continuous decrease for the following two weeks, reaching levels moderately below the initial number at the end of sampling, and by changes in their taxonomic composition. Most bacteria were tolerant to high As(V) concentrations and showed the presence of diverse As resistance genes. A more complete study of the structure and diversity of the bacterial community in the groundwater using automated ribosomal intergenic spacer analysis (ARISA) and sequencing of the 16S rRNA amplicons by Illumina confirmed significant alterations in its composition, with a reduction in richness and diversity (the latter evidenced by Illumina data) after treatment with nZVI. The anaerobic conditions stimulated by treatment favored the development of sulfate-reducing bacteria, thereby opening up the possibility to achieve more efficient removal of As.
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Affiliation(s)
- Ana Castaño
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain
| | - Alexander Prosenkov
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain
| | - Diego Baragaño
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, Mieres, Spain
| | - Nerea Otaegui
- TECNALIA, Basque Research and Technology Alliance (BRTA), Parque Tecnológico de Bizkaia, Derio, Spain
| | - Herminio Sastre
- Department of Chemical and Environmental Engineering and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain
| | - Eduardo Rodríguez-Valdés
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, Mieres, Spain
| | - José Luis R Gallego
- INDUROT and Environmental Biogeochemistry and Raw Materials Group, Campus of Mieres, University of Oviedo, Mieres, Spain
| | - Ana Isabel Peláez
- Area of Microbiology, Department of Functional Biology and Environmental Biogeochemistry and Raw Materials Group, University of Oviedo, Oviedo, Spain.,University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, Oviedo, Spain
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17
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Taleski V, Dimkić I, Boev B, Boev I, Živković S, Stanković S. Bacterial and fungal diversity in the lorandite (TlAsS2) mine 'Allchar' in the Republic of North Macedonia. FEMS Microbiol Ecol 2021; 96:5891424. [PMID: 32785579 DOI: 10.1093/femsec/fiaa155] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/10/2020] [Indexed: 01/04/2023] Open
Abstract
The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.
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Affiliation(s)
- Vaso Taleski
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Ivica Dimkić
- University of Belgrade, Faculty of Biology, Studentski trg 16, P.O. box 11 000 Belgrade, Serbia
| | - Blazo Boev
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Ivan Boev
- Goce Delčev University of Štip, "Krste Misirkov" 10-A, P.O. box 201, Stip, North Macedonia
| | - Sanja Živković
- University of Belgrade, Institute of Nuclear Sciences Vinca, Mike Petrovica Alasa 12-14, P.O. box 11 351, Vinca, Belgrade, Serbia
| | - Slaviša Stanković
- University of Belgrade, Faculty of Biology, Studentski trg 16, P.O. box 11 000 Belgrade, Serbia
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18
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Coclet C, Garnier C, D’Onofrio S, Durrieu G, Pasero E, Le Poupon C, Omanović D, Mullot JU, Misson B, Briand JF. Trace Metal Contamination Impacts Predicted Functions More Than Structure of Marine Prokaryotic Biofilm Communities in an Anthropized Coastal Area. Front Microbiol 2021; 12:589948. [PMID: 33679628 PMCID: PMC7933014 DOI: 10.3389/fmicb.2021.589948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/29/2021] [Indexed: 12/25/2022] Open
Abstract
Trace metal (TM) contamination in marine coastal areas is a worldwide threat for aquatic communities. However, little is known about the influence of a multi-chemical contamination on both marine biofilm communities' structure and functioning. To determine how TM contamination potentially impacted microbial biofilms' structure and their functions, polycarbonate (PC) plates were immerged in both surface and bottom of the seawater column, at five sites, along strong TM contamination gradients, in Toulon Bay. The PC plates were incubated during 4 weeks to enable colonization by biofilm-forming microorganisms on artificial surfaces. Biofilms from the PC plates, as well as surrounding seawaters, were collected and analyzed by 16S rRNA amplicon gene sequencing to describe prokaryotic community diversity, structure and functions, and to determine the relationships between bacterioplankton and biofilm communities. Our results showed that prokaryotic biofilm structure was not significantly affected by the measured environmental variables, while the functional profiles of biofilms were significantly impacted by Cu, Mn, Zn, and salinity. Biofilms from the contaminated sites were dominated by tolerant taxa to contaminants and specialized hydrocarbon-degrading microorganisms. Functions related to major xenobiotics biodegradation and metabolism, such as methane metabolism, degradation of aromatic compounds, and benzoate degradation, as well as functions involved in quorum sensing signaling, extracellular polymeric substances (EPS) matrix, and biofilm formation were significantly over-represented in the contaminated site relative to the uncontaminated one. Taken together, our results suggest that biofilms may be able to survive to strong multi-chemical contamination because of the presence of tolerant taxa in biofilms, as well as the functional responses of biofilm communities. Moreover, biofilm communities exhibited significant variations of structure and functional profiles along the seawater column, potentially explained by the contribution of taxa from surrounding sediments. Finally, we found that both structure and functions were significantly distinct between the biofilm and bacterioplankton, highlighting major differences between the both lifestyles, and the divergence of their responses facing to a multi-chemical contamination.
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Affiliation(s)
- Clément Coclet
- Université de Toulon, Laboratoire MAPIEM, EA 4323, Toulon, France
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Sébastien D’Onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Gaël Durrieu
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Emilie Pasero
- Microbia Environnement Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Christophe Le Poupon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
| | - Dario Omanović
- Division for Marine and Environmental Research, Ruðer Bošković Institute, Zagreb, Croatia
| | | | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography, UM110, La Garde, France
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Bermanec V, Paradžik T, Kazazić SP, Venter C, Hrenović J, Vujaklija D, Duran R, Boev I, Boev B. Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123437. [PMID: 32712355 DOI: 10.1016/j.jhazmat.2020.123437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/28/2020] [Accepted: 07/06/2020] [Indexed: 05/12/2023]
Abstract
Novel hyper-resistant bacteria were isolated from the Crven Dol mine (Allchar, North Macedonia), arsenic-rich extreme environment. Bacteria were recovered from a secondary mineral mixture, an alteration of hydrothermal realgar rich in arsenates (pharmacolite, hornesite, and talmessite). The sample was recovered from the dark part of the mine at 28 m depth. Three bacterial strains and a bacterial consortium were isolated for their capacity to survive exposure to 32 g/L (209 mM) of arsenite, and 176 g/L (564 mM) of arsenate. The 16S rRNA gene analysis identified bacterial isolates as Stenotrophomonas sp. and two Microbacterium spp. This analysis also revealed that bacterial consortium comprise two Bacteriodetes exhibiting similarity to Olivibacter ginsengisoli and to uncultured bacterium, and one γ-proteobacteria with similarity to Luteimonas sp. Among all isolates Stenotrophomonas sp. exhibited the highest tolerance to As compound as well as the capacity to accumulate As inside the cells. Analysis of genes involved in As-resistance showed that recovered isolates possess the genes encoding the ArsB, Acr3(1) and Acr3(2) proteins, indicating that at least a part of their resistance could be ascribed to As-efflux systems described in isolates obtained from human-polluted environments.
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Affiliation(s)
| | - Tina Paradžik
- Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia.
| | | | - Chantelle Venter
- Stellenbosch University, Department of Physiological Sciences, Faculty of Science, Stellenbosch, South Africa.
| | - Jasna Hrenović
- University of Zagreb, Faculty of Science, Zagreb, Croatia.
| | | | - Robert Duran
- Université de Pau et des Pays de l'Adour/E2S UPPA, IPREM UMR CNRS 5254, Pau, France.
| | - Ivan Boev
- Goce Delčev University of Štip, Štip, Macedonia.
| | - Blažo Boev
- Goce Delčev University of Štip, Štip, Macedonia.
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Hemmat-Jou MH, Safari-Sinegani AA, Che R, Mirzaie-Asl A, Tahmourespour A, Tahmasbian I. Toxic trace element resistance genes and systems identified using the shotgun metagenomics approach in an Iranian mine soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4845-4856. [PMID: 32949366 DOI: 10.1007/s11356-020-10824-x] [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: 03/01/2020] [Accepted: 09/13/2020] [Indexed: 05/27/2023]
Abstract
This study aimed to identify the microbial communities, resistance genes, and resistance systems in an Iranian mine soil polluted with toxic trace elements (TTE). The polluted soil samples were collected from a mining area and compared against non-polluted (control) collected soils from the vicinity of the mine. The soil total DNA was extracted and sequenced, and bioinformatic analysis of the assembled metagenomes was conducted to identify soil microbial biodiversity, TTE resistance genes, and resistance systems. The results of the employed shotgun approach indicated that the relative abundance of Proteobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus was significantly higher in the TTE-polluted soils compared with those in the control soils, while the relative abundance of Actinobacteria and Acidobacteria was significantly lower in the polluted soils. The high concentration of TTE increased the ratio of archaea to bacteria and decreased the alpha diversity in the polluted soils compared with the control soils. Canonical correspondence analysis (CCA) demonstrated that heavy metal pollution was the major driving factor in shaping microbial communities compared with any other soil characteristics. In the identified heavy metal resistome (HV-resistome) of TTE-polluted soils, major functional pathways were carbohydrates metabolism, stress response, amino acid and derivative metabolism, clustering-based subsystems, iron acquisition and metabolism, cell wall synthesis and capsulation, and membrane transportation. Ten TTE resistance systems were identified in the HV-resistome of TTE-polluted soils, dominated by "P-type ATPases," "cation diffusion facilitators," and "heavy metal efflux-resistance nodulation cell division (HME-RND)." Most of the resistance genes (69%) involved in resistance systems are affiliated to cell wall, outer membrane, periplasm, and cytoplasmic membrane. The finding of this study provides insight into the microbial community in Iranian TTE-polluted soils and their resistance genes and systems.
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Affiliation(s)
| | | | - Rongxiao Che
- Institute of International Rivers and Eco-security, Yunnan University, Kunming, 650091, China
| | - Asghar Mirzaie-Asl
- Department of Biotechnology, Bu-Ali Sina University, Hamedan, 6517838695, Iran
| | - Arezoo Tahmourespour
- Department of Basic Medical Sciences, Islamic Azad University (Isfahan Branch), Isfahan, Iran
| | - Iman Tahmasbian
- Department of Agriculture and Fisheries, Queensland Government, Toowoomba, QLD, 4350, Australia
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Xu Y, Teng Y, Wang X, Li R, Christie P. Exploring bacterial community structure and function associated with polychlorinated biphenyl biodegradation in two hydrogen-amended soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140839. [PMID: 32726695 DOI: 10.1016/j.scitotenv.2020.140839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/07/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen (H2) is a universal energy source supplying survival energy for numerous microbial functions. Diffusive fluxes of H2 released by rhizobacterial symbiont nodules in which H2 is an obligate by-product of dinitrogen fixation may act as an additional energy input shaping microbial community structure and function in soils. However, the effects of H2 at the soil-nodule interface on soil contaminant degradation processes are poorly understood. Here, we mimicked the hydrogen conditions present at the soil-nodule interface (10,000 ppmv) to test the impact of elevated H2 concentrations on soil microbial removal of 3, 3', 4, 4'-tetrachlorobiphenyl (PCB77) and examined the associated bacterial communities and their functions by conducting a microcosm experiment using two different soil types at three PCB contamination levels (0.5, 1.0 and 5.0 mg kg-1). After incubation for 84 days the PCB77 removal rates in the elevated H2 treatments in the Paddy soil were significantly promoted (by 4.88 to 6.41%) compared with the control (0.5 ppmv H2) but no significant effect was observed in a Fluvo-aquic soil. This is consistent with changes in the abundance of functional genes for PCB-degraders as shown by quantitative real-time PCR (Q-PCR) and phylogenetic investigation of bacterial communities by reconstruction of unobserved states (PICRUSt). 16S amplicon sequencing was conducted to explore bacterial community structure and correlate the genera to potential PCB degradation. The abundance of a total of four potentially PCB-degrading bacterial genera (Bacillus, Streptomyces, Ramlibacter and Paenibacillus) increased with increasing H2 level. In addition, the abundance of hydrogenase in the elevated H2 treatments was higher than in the control across different contamination levels in both soil types. Thus, elevated H2 stimulated soil PCB degradation with direct effects (aerobic PCB-degrading bacteria directly utilized H2 as an energy source for growth and thus enhanced PCB degradation efficiency) and indirect effects (aerobic PCB-degrading bacteria acted synergistically with other hydrogenotrophs to enhance PCB degradation efficiency by exchange of substances and energy). These results help to further understand the role of elevated hydrogen amendment in the PCB biodegradation process and provide evidence that H2 supports metabolic and energetic flexibility in microorganisms supplying a range of ecosystem services.
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Affiliation(s)
- Yongfeng Xu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
| | - Xiaomi Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Ran Li
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Chamberlain CA, Hatch M, Garrett TJ. Oxalobacter formigenes produces metabolites and lipids undetectable in oxalotrophic Bifidobacterium animalis. Metabolomics 2020; 16:122. [PMID: 33219444 DOI: 10.1007/s11306-020-01747-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/11/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION In the search for new potential therapies for pathologies of oxalate, such as kidney stone disease and primary hyperoxaluria, the intestinal microbiome has generated significant interest. Resident oxalate-degrading bacteria inhabit the gastrointestinal tract and reduce absorption of dietary oxalate, thereby potentially lowering the potency of oxalate as a risk factor for kidney stone formation. Although several species of bacteria have been shown to degrade oxalate, select strains of Oxalobacter formigenes (O. formigenes) have thus far demonstrated the unique ability among oxalotrophs to initiate a net intestinal oxalate secretion into the lumen from the bloodstream, allowing them to feed on both dietary and endogenous metabolic oxalate. There is significant interest in this function as a potential therapeutic application for circulating oxalate reduction, although its mechanism of action is still poorly understood. Since this species-exclusive, oxalate-regulating function is reported to be dependent on the use of a currently unidentified secreted bioactive compound, there is much interest in whether O. formigenes produces unique biochemicals that are not expressed by other oxalotrophs which lack the ability to transport oxalate. Hence, this study sought to analyze and compare the metabolomes of O. formigenes and another oxalate degrader, Bifidobacterium animalis subsp. lactis (B. animalis), to determine whether O. formigenes could produce features undetectable in another oxalotroph, thus supporting the theory of a species-exclusive secretagogue compound. METHODS A comparative metabolomic analysis of O. formigenes strain HC1 (a human isolate) versus B. animalis, another oxalate-degrading human intestinal microbe, was performed by ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS). Bacteria were cultured independently in anaerobic conditions, harvested, lysed, and extracted by protein precipitation. Metabolite extracts were chromatographically separated and analyzed by UHPLC-HRMS using reverse phase gradient elution (ACE Excel 2 C18-Pentafluorophenyl column) paired with a Q Exactive™ mass spectrometer. OBJECTIVES The purpose of this study was to assess whether O. formigenes potentially produces unique biochemicals from other oxalate degraders to better understand its metabolic profile and provide support for the theoretical production of a species-exclusive secretagogue compound responsible for enhancing intestinal oxalate secretion. RESULTS We report a panel of metabolites and lipids detected in the O. formigenes metabolome which were undetectable in B. animalis, several of which were identified either by mass-to-charge ratio and retention time matching to our method-specific metabolite library or MS/MS fragmentation. Furthermore, re-examination of data from our previous work showed most of these features were also undetected in the metabolomes of Lactobacillus acidophilus and Lactobacillus gasseri, two other intestinal oxalate degraders. CONCLUSIONS Our observation of O. formigenes metabolites and lipids which were undetectable in other oxalotrophs suggests that this bacterium likely holds the ability to produce biochemicals not expressed by at least a selection of other oxalate degraders. These findings provide support for the hypothesized biosynthesis of a species-exclusive secretagogue responsible for the stimulation of net intestinal oxalate secretion.
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Affiliation(s)
- Casey A Chamberlain
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Marguerite Hatch
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA.
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Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F. Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2. Microb Genom 2020; 6:mgen000447. [PMID: 33034553 PMCID: PMC7660254 DOI: 10.1099/mgen.0.000447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/14/2020] [Indexed: 11/30/2022] Open
Abstract
Thiomonas bacteria are ubiquitous at acid mine drainage sites and play key roles in the remediation of water at these locations by oxidizing arsenite to arsenate, favouring the sorption of arsenic by iron oxides and their coprecipitation. Understanding the adaptive capacities of these bacteria is crucial to revealing how they persist and remain active in such extreme conditions. Interestingly, it was previously observed that after exposure to arsenite, when grown in a biofilm, some strains of Thiomonas bacteria develop variants that are more resistant to arsenic. Here, we identified the mechanisms involved in the emergence of such variants in biofilms. We found that the percentage of variants generated increased in the presence of high concentrations of arsenite (5.33 mM), especially in the detached cells after growth under biofilm-forming conditions. Analysis of gene expression in the parent strain CB2 revealed that genes involved in DNA repair were upregulated in the conditions where variants were observed. Finally, we assessed the phenotypes and genomes of the subsequent variants generated to evaluate the number of mutations compared to the parent strain. We determined that multiple point mutations accumulated after exposure to arsenite when cells were grown under biofilm conditions. Some of these mutations were found in what is referred to as ICE19, a genomic island (GI) carrying arsenic-resistance genes, also harbouring characteristics of an integrative and conjugative element (ICE). The mutations likely favoured the excision and duplication of this GI. This research aids in understanding how Thiomonas bacteria adapt to highly toxic environments, and, more generally, provides a window to bacterial genome evolution in extreme environments.
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Affiliation(s)
- Kelle C. Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Hawaiʻi Institute of Marine Biology, University of Hawaiʻi at Mānoa, Kāneʻohe, HI, USA
| | - Stephanie Fouteau
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Aline Huber
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Sandrine Koechler
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Martina Peres
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Hugo Varet
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
- Hub Bioinformatique et Biostatistique, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI, USR 3756, IP CNRS), Institut Pasteur, Paris, France
| | - Caroline Proux
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Julien Deschamps
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Rachel Torchet
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Stephane Cruveiller
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
| | - Jean-Yves Coppée
- Plateforme Transcriptome et Epigenome, BioMics, Centre de Ressources et Recherches Technologiques, Institut Pasteur, Paris, France
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, Institut de Botanique, CNRS – Université de Strasbourg, Strasbourg, France
- Present address: Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France
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Giddings LA, Chlipala G, Kunstman K, Green S, Morillo K, Bhave K, Peterson H, Driscoll H, Maienschein-Cline M. Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PLoS One 2020; 15:e0237599. [PMID: 32785287 PMCID: PMC7423320 DOI: 10.1371/journal.pone.0237599] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/29/2020] [Indexed: 01/20/2023] Open
Abstract
The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.
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Affiliation(s)
- Lesley-Ann Giddings
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- Department of Chemistry, Smith College, Northampton, Massachusetts, United States of America
| | - George Chlipala
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Kevin Kunstman
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Stefan Green
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Katherine Morillo
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Kieran Bhave
- Department of Chemistry & Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
| | - Holly Peterson
- Department of Geology, Guilford College, Greensboro, North Carolina, United States of America
| | - Heather Driscoll
- Vermont Genetics Network, Department of Biology, Norwich University, Northfield, Vermont, United States of America
| | - Mark Maienschein-Cline
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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Jaiswal S, Shukla P. Alternative Strategies for Microbial Remediation of Pollutants via Synthetic Biology. Front Microbiol 2020; 11:808. [PMID: 32508759 PMCID: PMC7249858 DOI: 10.3389/fmicb.2020.00808] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Continuous contamination of the environment with xenobiotics and related recalcitrant compounds has emerged as a serious pollution threat. Bioremediation is the key to eliminating persistent contaminants from the environment. Traditional bioremediation processes show limitations, therefore it is necessary to discover new bioremediation technologies for better results. In this review we provide an outlook of alternative strategies for bioremediation via synthetic biology, including exploring the prerequisites for analysis of research data for developing synthetic biological models of microbial bioremediation. Moreover, cell coordination in synthetic microbial community, cell signaling, and quorum sensing as engineered for enhanced bioremediation strategies are described, along with promising gene editing tools for obtaining the host with target gene sequences responsible for the degradation of recalcitrant compounds. The synthetic genetic circuit and two-component regulatory system (TCRS)-based microbial biosensors for detection and bioremediation are also briefly explained. These developments are expected to increase the efficiency of bioremediation strategies for best results.
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Pothier MP, Lenoble V, Garnier C, Misson B, Rentmeister C, Poulain AJ. Dissolved organic matter controls of arsenic bioavailability to bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137118. [PMID: 32059299 DOI: 10.1016/j.scitotenv.2020.137118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/14/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
The presence of arsenic in irrigation and drinking waters is a threat to worldwide human health. Dissolved organic matter (DOM) is a ubiquitous and photoreactive sorbent of arsenic, capable of both suppressing and enhancing its mobility. Microbes can control the mobilization of mineral-bound arsenic, through redox processes thought to occur intracellularly. The role that DOM plays on the bioavailability of arsenic to microbes is often invoked but remains untested experimentally. Here, using a whole-cell biosensor, we tested the role of DOM on As(III) and As(V) bioavailability. Using cation amendments, we explored the nature of As-DOM interactions. We found As bioavailability to be dependent on [As]/[DOM] ratio and on the strength of As binding to DOM which varied as a function of time. We further tested the role of DOM on As(III) photooxidation and showed that As(III) photooxidation rate is limited by the strength of its interactions with DOM and sensitive to ionic competitive desorption. Our study demonstrates the dynamic control that photoreactive DOM poses on the bioavailability and reactivity of As in the environment and highlights the kinetic controls that DOM can possibly exert on As toxicity at various levels in foodwebs.
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Affiliation(s)
- Martin P Pothier
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Véronique Lenoble
- Univ. Toulon, Aix Marseille Univ., CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France
| | - Cédric Garnier
- Univ. Toulon, Aix Marseille Univ., CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France
| | - Benjamin Misson
- Univ. Toulon, Aix Marseille Univ., CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France
| | - Charlotte Rentmeister
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Alexandre J Poulain
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
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Zhai W, Qin T, Li L, Guo T, Yin X, Khan MI, Hashmi MZ, Liu X, Tang X, Xu J. Abundance and diversity of microbial arsenic biotransformation genes in the sludge of full-scale anaerobic digesters from a municipal wastewater treatment plant. ENVIRONMENT INTERNATIONAL 2020; 138:105535. [PMID: 32220815 DOI: 10.1016/j.envint.2020.105535] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/24/2020] [Accepted: 01/26/2020] [Indexed: 06/10/2023]
Abstract
Arsenic (As) is a potential contaminant in sewage sludge that may affect waste treatment and limit the use of these waste materials as soil amendments. Anaerobic digestion (AD) is an important and effective process for the treatment of sewage sludge and the chemical speciation of As is particularly important in sludge AD. However, the biotransformation genes of As in sludge during AD has not been fully explored. In this study, the influent and effluent sludge of anaerobic digester in a wastewater treatment plant (WWTP) was collected to investigate the species transformations of As, the abundance and diversity of As biotransformation genes was explored by real-time PCR (qPCR) and metagenomic sequencing, separately. The results showed that arsenite [As(III)] and arsenate [As(V)] were predominant in the influent sludge, whereas the relative abundance of monomethylarsenic acid (MMA) increased by 25.7% after digestion. As biotransformation genes were highly abundant, and the As(III) S-adenosylmethionine methyltransferase (arsM) gene was the predominant which significantly increased after AD by qPCR analysis. Metagenomic analysis indicated that the diversity of the arsM-like sequences also increased significantly after AD. Most of the arsM-like sequences in all the influent and effluent sludge samples were related to Bacteroidetes and Alphaproteobacteria. Furthermore, co-occurrence network analysis indicated a strong correlation between the microbial communities and As. This study provides a direct and reliable reference on As biotransformation genes and microbial community in the AD of sludge.
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Affiliation(s)
- Weiwei Zhai
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Tianyue Qin
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Liguan Li
- Department of Civil Engineering, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Ting Guo
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Xiaole Yin
- Department of Civil Engineering, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Muhammad Imran Khan
- Institute of Soil & Environmental Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | | | - Xingmei Liu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
| | - Xianjin Tang
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China
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Barral-Fraga L, Barral MT, MacNeill KL, Martiñá-Prieto D, Morin S, Rodríguez-Castro MC, Tuulaikhuu BA, Guasch H. Biotic and Abiotic Factors Influencing Arsenic Biogeochemistry and Toxicity in Fluvial Ecosystems: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17072331. [PMID: 32235625 PMCID: PMC7177459 DOI: 10.3390/ijerph17072331] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 01/20/2023]
Abstract
This review is focused on the biogeochemistry of arsenic in freshwaters and, especially, on the key role that benthic microalgae and prokaryotic communities from biofilms play together in through speciation, distribution, and cycling. These microorganisms incorporate the dominant iAs (inorganic arsenic) form and may transform it to other arsenic forms through metabolic or detoxifying processes. These transformations have a big impact on the environmental behavior of arsenic because different chemical forms exhibit differences in mobility and toxicity. Moreover, exposure to toxicants may alter the physiology and structure of biofilms, leading to changes in ecosystem function and trophic relations. In this review we also explain how microorganisms (i.e., biofilms) can influence the effects of arsenic exposure on other key constituents of aquatic ecosystems such as fish. At the end, we present two real cases of fluvial systems with different origins of arsenic exposure (natural vs. anthropogenic) that have improved our comprehension of arsenic biogeochemistry and toxicity in freshwaters, the Pampean streams (Argentina) and the Anllóns River (Galicia, Spain). We finish with a briefly discussion of what we consider as future research needs on this topic. This work especially contributes to the general understanding of biofilms influencing arsenic biogeochemistry and highlights the strong impact of nutrient availability on arsenic toxicity for freshwater (micro) organisms.
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Affiliation(s)
- Laura Barral-Fraga
- Grup de recerca en Ecologia aquàtica continental (GRECO), Departament de Ciències Ambientals, Universitat de Girona, 17071 Girona, Spain;
- LDAR24—Laboratoire Départemental d’Analyse et de Recherche du Département de la Dordogne, 24660 Coulounieix-Chamiers, Périgueux, France
- Correspondence:
| | - María Teresa Barral
- Instituto CRETUS, Departmento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.T.B.); (D.M.-P.)
| | - Keeley L. MacNeill
- Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA;
| | - Diego Martiñá-Prieto
- Instituto CRETUS, Departmento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (M.T.B.); (D.M.-P.)
| | - Soizic Morin
- INRAE—Institut National de Recherche en Agriculture, Alimentation et Environnement, UR EABX—Equipe ECOVEA, 33612 Cestas Cedex, France;
| | - María Carolina Rodríguez-Castro
- INEDES—Instituto de Ecología y Desarrollo Sustentable (UNLu-CONICET), Universidad Nacional de Luján, 6700 Buenos Aires, Argentina;
- CONICET—Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires C1425FQB CABA, Argentina
| | - Baigal-Amar Tuulaikhuu
- School of Agroecology, Mongolian University of Life Sciences, Khoroo 11, Ulaanbaatar 17024, Mongolia;
| | - Helena Guasch
- Grup de recerca en Ecologia aquàtica continental (GRECO), Departament de Ciències Ambientals, Universitat de Girona, 17071 Girona, Spain;
- CEAB—Centre d’Estudis Avançats de Blanes, CSIC, Blanes, 17300 Girona, Spain
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In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis. Res Microbiol 2020; 171:37-43. [DOI: 10.1016/j.resmic.2019.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/26/2019] [Accepted: 09/26/2019] [Indexed: 11/23/2022]
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Prabha R, Singh DP, Gupta S, Gupta VK, El-Enshasy HA, Verma MK. Rhizosphere Metagenomics of Paspalum scrobiculatum L. (Kodo Millet) Reveals Rhizobiome Multifunctionalities. Microorganisms 2019; 7:microorganisms7120608. [PMID: 31771141 PMCID: PMC6956225 DOI: 10.3390/microorganisms7120608] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Multifunctionalities linked with the microbial communities associated with the millet crop rhizosphere has remained unexplored. In this study, we are analyzing microbial communities inhabiting rhizosphere of kodo millet and their associated functions and its impact over plant growth and survival. Metagenomics of Paspalum scrobiculatum L.(kodo millet) rhizopshere revealed taxonomic communities with functional capabilities linked to support growth and development of the plants under nutrient-deprived, semi-arid and dry biotic conditions. Among 65 taxonomically diverse phyla identified in the rhizobiome, Actinobacteria were the most abundant followed by the Proteobacteria. Functions identified for different genes/proteins led to revelations that multifunctional rhizobiome performs several metabolic functions including carbon fixation, nitrogen, phosphorus, sulfur, iron and aromatic compound metabolism, stress response, secondary metabolite synthesis and virulence, disease, and defense. Abundance of genes linked with N, P, S, Fe and aromatic compound metabolism and phytohormone synthesis—along with other prominent functions—clearly justifies growth, development, and survival of the plants under nutrient deprived dry environment conditions. The dominance of actinobacteria, the known antibiotic producing communities shows that the kodo rhizobiome possesses metabolic capabilities to defend themselves against biotic stresses. The study opens avenues to revisit multi-functionalities of the crop rhizosphere for establishing link between taxonomic abundance and targeted functions that help plant growth and development in stressed and nutrient deprived soil conditions. It further helps in understanding the role of rhizosphere microbiome in adaptation and survival of plants in harsh abiotic conditions.
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Affiliation(s)
- Ratna Prabha
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
| | - Dhananjaya P. Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Indian Council of Agricultural Research, Kushmaur, Maunath Bhanjan 275101, UP, India
- Correspondence:
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock 18057, Germany;
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, Tallinn University of Technology, 12618 Tallinn, Estonia;
| | - Hesham A. El-Enshasy
- Institute of Bioproduct Development, Universiti Teknologi Malaysia, Skudai 81310, Johor Bahru, Johor, Malaysia;
| | - Mukesh K. Verma
- Chhattisgarh Swami Vivekananda Technical University, Bhilai, Chhattisgarh 491107, India; (R.P.); (M.K.V.)
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32
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Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies. Curr Microbiol 2019; 77:657-674. [DOI: 10.1007/s00284-019-01771-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 11/27/2022]
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33
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Zhang S, Hu Z, Wang H. Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment. ENVIRONMENT INTERNATIONAL 2019; 129:308-319. [PMID: 31150973 DOI: 10.1016/j.envint.2019.05.028] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/15/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.
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Affiliation(s)
- Shuangfei Zhang
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou 515063, China.
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34
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Tan S, Liu J, Fang Y, Hedlund BP, Lian ZH, Huang LY, Li JT, Huang LN, Li WJ, Jiang HC, Dong HL, Shu WS. Insights into ecological role of a new deltaproteobacterial order Candidatus Acidulodesulfobacterales by metagenomics and metatranscriptomics. THE ISME JOURNAL 2019; 13:2044-2057. [PMID: 30962514 PMCID: PMC6776010 DOI: 10.1038/s41396-019-0415-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/15/2019] [Accepted: 03/24/2019] [Indexed: 12/21/2022]
Abstract
Several abundant but yet uncultivated bacterial groups exist in extreme iron- and sulfur-rich environments, and the physiology, biodiversity, and ecological roles of these bacteria remain a mystery. Here we retrieved four metagenome-assembled genomes (MAGs) from an artificial acid mine drainage (AMD) system, and propose they belong to a new deltaproteobacterial order, Candidatus Acidulodesulfobacterales. The distribution pattern of Ca. Acidulodesulfobacterales in AMDs across Southeast China correlated strongly with ferrous iron. Reconstructed metabolic pathways and gene expression profiles showed that they were likely facultatively anaerobic autotrophs capable of nitrogen fixation. In addition to dissimilatory sulfate reduction, encoded by dsrAB, dsrD, dsrL, and dsrEFH genes, these microorganisms might also oxidize sulfide, depending on oxygen concentration and/or oxidation reduction potential. Several genes with homology to those involved in iron metabolism were also identified, suggesting their potential role in iron cycling. In addition, the expression of abundant resistance genes revealed the mechanisms of adaptation and response to the extreme environmental stresses endured by these organisms in the AMD environment. These findings shed light on the distribution, diversity, and potential ecological role of the new order Ca. Acidulodesulfobacterales in nature.
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Affiliation(s)
- Sha Tan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jun Liu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
| | - Yun Fang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA
| | - Zheng-Han Lian
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
- Guangdong Magigene Biotechnology Co. Ltd., 510000, Guangzhou, China
| | - Li-Ying Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Li-Nan Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074, Wuhan, China
| | - Hai-Liang Dong
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA.
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 100083, Beijing, China.
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
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35
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Ward LM, Cardona T, Holland-Moritz H. Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2). Front Microbiol 2019; 10:1658. [PMID: 31396180 PMCID: PMC6664022 DOI: 10.3389/fmicb.2019.01658] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 12/15/2022] Open
Abstract
Genome-resolved environmental metagenomic sequencing has uncovered substantial previously unrecognized microbial diversity relevant for understanding the ecology and evolution of the biosphere, providing a more nuanced view of the distribution and ecological significance of traits including phototrophy across diverse niches. Recently, the capacity for bacteriochlorophyll-based anoxygenic photosynthesis has been proposed in the uncultured bacterial WPS-2 phylum (recently proposed as Candidatus Eremiobacterota) that are in close association with boreal moss. Here, we use phylogenomic analysis to investigate the diversity and evolution of phototrophic WPS-2. We demonstrate that phototrophic WPS-2 show significant genetic and metabolic divergence from other phototrophic and non-phototrophic lineages. The genomes of these organisms encode a new family of anoxygenic Type II photochemical reaction centers and other phototrophy-related proteins that are both phylogenetically and structurally distinct from those found in previously described phototrophs. We propose the name Candidatus Baltobacterales for the order-level aerobic WPS-2 clade which contains phototrophic lineages, from the Greek for "bog" or "swamp," in reference to the typical habitat of phototrophic members of this clade.
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Affiliation(s)
- Lewis M. Ward
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, United States
| | - Tanai Cardona
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hannah Holland-Moritz
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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36
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Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G. Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. Front Microbiol 2019; 10:1514. [PMID: 31333619 PMCID: PMC6620896 DOI: 10.3389/fmicb.2019.01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2T, and Thioalkalivibrio thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lucia Cavalca
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Milena Colombo
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - J Merijn Schuurmans
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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37
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Cavalca L, Zecchin S, Zaccheo P, Abbas B, Rotiroti M, Bonomi T, Muyzer G. Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy. Front Microbiol 2019; 10:1480. [PMID: 31312188 PMCID: PMC6614289 DOI: 10.3389/fmicb.2019.01480] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/13/2019] [Indexed: 11/13/2022] Open
Abstract
Arsenic contamination of groundwater aquifers is an issue of global concern. Among the affected sites, in several Italian groundwater aquifers arsenic levels above the WHO limits for drinking water are present, with consequent issues of public concern. In this study, for the first time, the role of microbial communities in metalloid cycling in groundwater samples from Northern Italy lying on Pleistocene sediments deriving from Alps mountains has been investigated combining environmental genomics and cultivation approaches. 16S rRNA gene libraries revealed a high number of yet uncultured species, which in some of the study sites accounted for more of the 50% of the total community. Sequences related to arsenic-resistant bacteria (arsenate-reducing and arsenite-oxidizing) were abundant in most of the sites, while arsenate-respiring bacteria were negligible. In some of the sites, sulfur-oxidizing bacteria of the genus Sulfuricurvum accounted for more than 50% of the microbial community, whereas iron-cycling bacteria were less represented. In some aquifers, arsenotrophy, growth coupled to autotrophic arsenite oxidation, was suggested by detection of arsenite monooxygenase (aioA) and 1,5-ribulose bisphosphate carboxylase (RuBisCO) cbbL genes of microorganisms belonging to Rhizobiales and Burkholderiales. Enrichment cultures established from sampled groundwaters in laboratory conditions with 1.5 mmol L-1 of arsenite as sole electron donor were able to oxidize up to 100% of arsenite, suggesting that this metabolism is active in groundwaters. The presence of heterotrophic arsenic resistant bacteria was confirmed by enrichment cultures in most of the sites. The overall results provided a first overview of the microorganisms inhabiting arsenic-contaminated aquifers in Northern Italy and suggested the importance of sulfur-cycling bacteria in the biogeochemistry of arsenic in these ecosystems. The presence of active arsenite-oxidizing bacteria indicates that biological oxidation of arsenite, in combination with arsenate-adsorbing materials, could be employed for metalloid removal.
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Affiliation(s)
- Lucia Cavalca
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Sarah Zecchin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente (DeFENS), Università degli Studi di Milano, Milan, Italy
| | - Patrizia Zaccheo
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia (DiSAA), Università degli Studi di Milano, Milan, Italy
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Marco Rotiroti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Tullia Bonomi
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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Lima MA, Urbieta MS, Donati E. Arsenic-tolerant microbial consortia from sediments of Copahue geothermal system with potential applications in bioremediation. J Basic Microbiol 2019; 59:680-691. [PMID: 30997929 DOI: 10.1002/jobm.201800628] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/02/2019] [Accepted: 04/11/2019] [Indexed: 11/09/2022]
Abstract
Although arsenic (As) is recognized as a toxic element for living species, some microorganisms have the ability to tolerate and transform it; recent studies have proposed to take advantage of such capacity to develop sustainable bioremediation strategies. In this study, we evaluated the adaptation to increasing concentrations of As(III) and As(V) of three metabolically different microbial cultures (heterotrophic, autotrophic-acidophilic, and anaerobic) obtained from a sample with low-soluble As content from the Copahue geothermal system. At the end of the adaptation process, the heterotrophic culture was able to grow at 20 mM and 450 mM of As(III) and As(V), respectively; the autotrophic-acidophilic culture showed tolerance to 15 mM of As(III) and 150 mM of As(V), whereas the anaerobic culture only developed in As(V) at concentrations up to 50 mM. The most tolerant consortia were characterized by their growth performance, complexity, and the presence of genes related to As metabolism and resistance. Regarding the consortia complexity, the predominant genera identified were: Paenibacillus in both heterotrophic consortia, Acidithiobacillus in the autotrophic-acidophilic consortium tolerant to As(III), Acidiphilium in the autotrophic-acidophilic consortium tolerant to As(V), and Thiomonas and Clostridium in the anaerobic consortium. This study is the first report of As tolerance microorganisms obtained from Copahue and reasserts the versatility and flexibility of the community of this natural extreme environment; also, it opens the door to the study of possible uses of these consortia in the design of biotechnological processes where the As concentration may fluctuate.
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Affiliation(s)
- María Alejandra Lima
- Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI, CCT La Plata - CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Sofía Urbieta
- Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI, CCT La Plata - CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Edgardo Donati
- Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI, CCT La Plata - CONICET, UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Crognale S, Casentini B, Amalfitano S, Fazi S, Petruccioli M, Rossetti S. Biological As(III) oxidation in biofilters by using native groundwater microorganisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 651:93-102. [PMID: 30227294 DOI: 10.1016/j.scitotenv.2018.09.176] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 09/13/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Arsenic (As) contamination in drinking water represents a worldwide threat to human health. During last decades, the exploitation of microbial As-transformations has been proposed for bioremediation applications. Among biological methods for As-contaminated water treatment, microbial As(III)-oxidation is one of the most promising approaches since it can be coupled to commonly used adsorption removal technologies, without requiring the addition of chemicals and producing toxic by-products. Despite the As(III) oxidation capability has been described in several bacterial pure or enrichment cultures, very little is known about the real potentialities of this process when mixed microbial communities, naturally occurring in As contaminated waters, are used. This study highlighted the contribution of native groundwater bacteria to As(III)-oxidation in biofilters, under conditions suitable for a household-scale treatment system. This work elucidated the influence of a variety of experimental conditions (i.e., various filling materials, flow rates, As(III) inflow concentration, As(III):As(V) ratio, filter volumes) on the microbially-mediated As(III)-oxidation process in terms of oxidation efficiency and rate. The highest oxidation efficiencies (up to 90% in 3 h) were found on coarse sand biofilters treating total initial As concentration of 100 μg L-1. The detailed microbial characterization of the As(III) oxidizing biofilms revealed the occurrence of several OTUs affiliated with families known to oxidize As(III) (e.g., Burkholderiaceae, Comamonadaceae, Rhodobacteraceae, Xanthomonadaceae). Furthermore, As-related functional genes increased in biofilter systems in line with the observed oxidative performances.
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Affiliation(s)
- Simona Crognale
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Barbara Casentini
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Stefano Amalfitano
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Stefano Fazi
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Agroforestry and Biological systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Simona Rossetti
- Water Research Institute, National Research Council of Italy (IRSA - CNR), Via Salaria, km 29.300, Monterotondo, Rome 00015, Italy.
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Laroche E, Casiot C, Fernandez-Rojo L, Desoeuvre A, Tardy V, Bruneel O, Battaglia-Brunet F, Joulian C, Héry M. Dynamics of Bacterial Communities Mediating the Treatment of an As-Rich Acid Mine Drainage in a Field Pilot. Front Microbiol 2018; 9:3169. [PMID: 30627121 PMCID: PMC6309452 DOI: 10.3389/fmicb.2018.03169] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022] Open
Abstract
Passive treatment based on iron biological oxidation is a promising strategy for Arsenic (As)-rich acid mine drainage (AMD) remediation. In the present study, we characterized by 16S rRNA metabarcoding the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ, over a 6 months monitoring period. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biofilm (“biogenic precipitate”) whose composition varied in time and space. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure quite similar to the natural biofilm developing in situ in the AMD. Over the monitoring period, iron-oxidizing bacteria always largely dominated the biogenic precipitate, with distinct populations (Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum), whose relative proportions extensively varied among time and space. A spatial structuring was observed inside the trays (arranged in series) composing the bioreactor. This spatial dynamic could be linked to the variation of the physico-chemistry of the AMD water between the raw water entering and the treated water exiting the pilot. According to redundancy analysis (RDA), the following parameters exerted a control on the bacterial communities potentially involved in the water treatment process: dissolved oxygen, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the stable presence of two distinct monophylogenetic groups of Thiomonas related bacteria. The ubiquity and the physiological diversity of the bacteria identified, as well as the presence of bacteria of biotechnological relevance, suggested that this treatment system could be applied to the treatment of other AMD.
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Affiliation(s)
- Elia Laroche
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France.,BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - Corinne Casiot
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Lidia Fernandez-Rojo
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Angélique Desoeuvre
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Vincent Tardy
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | - Odile Bruneel
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
| | | | - Catherine Joulian
- BRGM, Geomicrobiology and Environmental Monitoring Unit, Orléans, France
| | - Marina Héry
- HydroSciences Montpellier, CNRS, IRD, University of Montpellier, Montpellier, France
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Gupta A, Dutta A, Sarkar J, Panigrahi MK, Sar P. Low-Abundance Members of the Firmicutes Facilitate Bioremediation of Soil Impacted by Highly Acidic Mine Drainage From the Malanjkhand Copper Project, India. Front Microbiol 2018; 9:2882. [PMID: 30619102 PMCID: PMC6297179 DOI: 10.3389/fmicb.2018.02882] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
Sulfate- and iron-reducing heterotrophic bacteria represented minor proportion of the indigenous microbial community of highly acidic, oligotrophic acid mine drainage (AMD), but they can be successfully stimulated for in situ bioremediation of an AMD impacted soil (AIS). These anaerobic microorganisms although played central role in sulfate- and metal-removal, they remained inactive in the AIS due to the paucity of organic carbon and extreme acidity of the local environment. The present study investigated the scope for increasing the abundance and activity of inhabitant sulfate- and iron-reducing bacterial populations of an AIS from Malanjkhand Copper Project. An AIS of pH 3.5, high soluble SO4 2- (7838 mg/l) and Fe (179 mg/l) content was amended with nutrients (cysteine and lactate). Thorough geochemical analysis, 16S rRNA gene amplicon sequencing and qPCR highlighted the intrinsic metabolic abilities of native bacteria in AMD bioremediation. Following 180 days incubation, the nutrient amended AIS showed marked increase in pH (to 6.6) and reduction in soluble -SO4 2- (95%), -Fe (50%) and other heavy metals. Concomitant to physicochemical changes a vivid shift in microbial community composition was observed. Members of the Firmicutes present as a minor group (1.5% of total community) in AIS emerged as the single most abundant taxon (∼56%) following nutrient amendments. Organisms affiliated to Clostridiaceae, Peptococcaceae, Veillonellaceae, Christensenellaceae, Lachnospiraceae, Bacillaceae, etc. known for their fermentative, iron and sulfate reducing abilities were prevailed in the amended samples. qPCR data corroborated with this change and further revealed an increase in abundance of dissimilatory sulfite reductase gene (dsrB) and specific bacterial taxa. Involvement of these enhanced populations in reductive processes was validated by further enrichments and growth in sulfate- and iron-reducing media. Amplicon sequencing of these enrichments confirmed growth of Firmicutes members and proved their sulfate- and iron-reduction abilities. This study provided a better insight on ecological perspective of Firmicutes members within the AMD impacted sites, particularly their involvement in sulfate- and iron-reduction processes, in situ pH management and bioremediation.
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Affiliation(s)
- Abhishek Gupta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Avishek Dutta
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Jayeeta Sarkar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Mruganka Kumar Panigrahi
- Department of Geology and Geophysics, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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42
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Genome-centric view of carbon processing in thawing permafrost. Nature 2018; 560:49-54. [PMID: 30013118 DOI: 10.1038/s41586-018-0338-1] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/05/2018] [Indexed: 11/09/2022]
Abstract
As global temperatures rise, large amounts of carbon sequestered in permafrost are becoming available for microbial degradation. Accurate prediction of carbon gas emissions from thawing permafrost is limited by our understanding of these microbial communities. Here we use metagenomic sequencing of 214 samples from a permafrost thaw gradient to recover 1,529 metagenome-assembled genomes, including many from phyla with poor genomic representation. These genomes reflect the diversity of this complex ecosystem, with genus-level representatives for more than sixty per cent of the community. Meta-omic analysis revealed key populations involved in the degradation of organic matter, including bacteria whose genomes encode a previously undescribed fungal pathway for xylose degradation. Microbial and geochemical data highlight lineages that correlate with the production of greenhouse gases and indicate novel syntrophic relationships. Our findings link changing biogeochemistry to specific microbial lineages involved in carbon processing, and provide key information for predicting the effects of climate change on permafrost systems.
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43
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Plewniak F, Crognale S, Rossetti S, Bertin PN. A Genomic Outlook on Bioremediation: The Case of Arsenic Removal. Front Microbiol 2018; 9:820. [PMID: 29755441 PMCID: PMC5932151 DOI: 10.3389/fmicb.2018.00820] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/10/2018] [Indexed: 01/07/2023] Open
Abstract
Microorganisms play a major role in biogeochemical cycles. As such they are attractive candidates for developing new or improving existing biotechnological applications, in order to deal with the accumulation and pollution of organic and inorganic compounds. Their ability to participate in bioremediation processes mainly depends on their capacity to metabolize toxic elements and catalyze reactions resulting in, for example, precipitation, biotransformation, dissolution, or sequestration. The contribution of genomics may be of prime importance to a thorough understanding of these metabolisms and the interactions of microorganisms with pollutants at the level of both single species and microbial communities. Such approaches should pave the way for the utilization of microorganisms to design new, efficient and environmentally sound remediation strategies, as exemplified by the case of arsenic contamination, which has been declared as a major risk for human health in various parts of the world.
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Affiliation(s)
- Frédéric Plewniak
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
| | - Simona Crognale
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Simona Rossetti
- Istituto di Ricerca sulle Acque, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe N Bertin
- Génétique Moléculaire, Génomique et Microbiologie, UMR7156 CNRS, Université de Strasbourg, Strasbourg, France
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44
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Metatranscriptome sequencing and analysis of agriculture soil provided significant insights about the microbial community structure and function. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.egg.2017.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Survey of sulfur-oxidizing bacterial community in the Pearl River water using soxB, sqr, and dsrA as molecular biomarkers. 3 Biotech 2018; 8:73. [PMID: 29354384 DOI: 10.1007/s13205-017-1077-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022] Open
Abstract
In this study, we surveyed the abundance and diversity of three sulfur oxidation genes (sqr, soxB, and dsrA) using quantitative assays and Miseq high-throughput sequencing. The quantitative assays revealed that soxB is more abundant than sqr and dsrA and is the main contributor to sulfur oxidation. In the diversity analysis, the SOB community mainly comprised the classes Nitrospira, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The genera Gallionella, Hydrogenophaga, Limnohabitans, Methylomonas, Nitrospira, Rhodoferax, and Sulfuritalea were abundant in the communities for sqr; Dechloromonas, Limnohabitans, Paracoccus, Sulfuritalea, Sulfitobacter, and Thiobacillus were abundant in communities for soxB; Sulfuritalea, Sulfurisoma, and Thiobacillus were abundant in communities for dsrA. This study presented a high diversity of SOB species and functional sulfur-oxidizing genes in Pearl River via high-throughput sequencing, suggesting that the aquatic ecosystem has great potential to scavenge the sulfur pollutants by itself.
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Arsène-Ploetze F, Chiboub O, Lièvremont D, Farasin J, Freel KC, Fouteau S, Barbe V. Adaptation in toxic environments: comparative genomics of loci carrying antibiotic resistance genes derived from acid mine drainage waters. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:1470-1483. [PMID: 29090447 DOI: 10.1007/s11356-017-0535-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/19/2017] [Indexed: 06/07/2023]
Abstract
Several studies have suggested the existence of a close relationship between antibiotic-resistant phenotypes and resistance to other toxic compounds such as heavy metals, which involve co-resistance or cross-resistance mechanisms. A metagenomic library was previously constructed in Escherichia coli with DNA extracted from the bacterial community inhabiting an acid mine drainage (AMD) site highly contaminated with heavy metals. Here, we conducted a search for genes involved in antibiotic resistance using this previously constructed library. In particular, resistance to antibiotics was observed among five clones carrying four different loci originating from CARN5 and CARN2, two genomes reconstructed from the metagenomic data. Among the three CARN2 loci, two carry genes homologous to those previously proposed to be involved in antibiotic resistance. The third CARN2 locus carries a gene encoding a membrane transporter with an unknown function and was found to confer bacterial resistance to rifampicin, gentamycin, and kanamycin. The genome of Thiomonas delicata DSM 16361 and Thiomonas sp. X19 were sequenced in this study. Homologs of genes carried on these three CARN2 loci were found in these genomes, two of these loci were found in genomic islands. Together, these findings confirm that AMD environments contaminated with several toxic metals also constitute habitats for bacteria that function as reservoirs for antibiotic resistance genes.
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Affiliation(s)
- Florence Arsène-Ploetze
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France.
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de Strasbourg, Strasbourg, France.
| | - Olfa Chiboub
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Didier Lièvremont
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
- Institut de Chimie de Strasbourg, UMR7177 CNRS-Université de Strasbourg, Strasbourg, France
| | - Julien Farasin
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Kelle C Freel
- Laboratoire Génétique Moléculaire, Génomique et Microbiologie, UMR7156, CNRS-Université de Strasbourg, Strasbourg, France
| | - Stephanie Fouteau
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
| | - Valérie Barbe
- Laboratoire de Biologie Moléculaire pour l'Etude des Génomes, (LBioMEG), CEA/DRF/IBFJ/Genoscope, Evry, France
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Mesa V, Gallego JLR, González-Gil R, Lauga B, Sánchez J, Méndez-García C, Peláez AI. Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage. Front Microbiol 2017; 8:1756. [PMID: 28955322 PMCID: PMC5600952 DOI: 10.3389/fmicb.2017.01756] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/29/2017] [Indexed: 12/20/2022] Open
Abstract
Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.
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Affiliation(s)
- Victoria Mesa
- Department of Functional Biology - IUBA, University of OviedoOviedo, Spain.,Vedas Research and Innovation, Vedas CIIMedellín, Colombia
| | - Jose L R Gallego
- Department of Mining Exploitation and Prospecting - IUBA, University of OviedoMieres, Spain
| | - Ricardo González-Gil
- Department of Biology of Organisms and Systems - University of OviedoOviedo, Spain
| | - Béatrice Lauga
- Equipe Environnement et Microbiologie, CNRS/Université de Pau et des Pays de l'Adour, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux, UMR5254Pau, France
| | - Jesús Sánchez
- Department of Functional Biology - IUBA, University of OviedoOviedo, Spain
| | | | - Ana I Peláez
- Department of Functional Biology - IUBA, University of OviedoOviedo, Spain
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Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment. Appl Environ Microbiol 2017; 83:AEM.00729-17. [PMID: 28667104 PMCID: PMC5561297 DOI: 10.1128/aem.00729-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 06/20/2017] [Indexed: 02/06/2023] Open
Abstract
During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and contaminant mobility. Results demonstrate that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the important role that the taxonomically diverse microbial community played in this transition. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs.
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49
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Chauhan NS, Nain S, Sharma R. Identification of Arsenic Resistance Genes from Marine Sediment Metagenome. Indian J Microbiol 2017; 57:299-306. [PMID: 28904414 DOI: 10.1007/s12088-017-0658-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 07/03/2017] [Indexed: 02/02/2023] Open
Abstract
A metagenomic library of sea sediment metagenome containing 245,000 recombinant clones representing ~ 2.45 Gb of sea sediment microbial DNA was constructed. Two unique arsenic resistance clones, A7 and A12, were identified by selection on sodium arsenite containing medium. Clone A7 showed a six-fold higher resistance to arsenate [As(V)], a three-fold higher resistance to arsenite [As(III)] and significantly increased resistance to antimony [Sb(III)], while clone A12 showed increased resistance only to sodium arsenite and not to the other two metalloids. The clones harbored inserts of 8.848 Kb and 6.771 Kb, respectively. Both the clones possess A + T rich nucleotide sequence with similarity to sequences from marine psychrophilic bacteria. Sequence and transposon-mutagenesis based analysis revealed the presence of a putative arsenate reductase (ArsC), a putative arsenite efflux pump (ArsB/ACR) and a putative NADPH-dependent FMN reductase (ArsH) in both the clones and also a putative transcriptional regulatory protein (ArsR) in pA7. The increased resistance of clone A7 to As(V), As(III) and Sb(III) indicates functional expression of ArsC and ArsB proteins from pA7. The absence of increased As(V) resistance in clone A12 may be due to the expression of a possible inactive ArsC, as conserved Arg60 residue in this protein was replaced by Glu60, while the absence of Sb(III) resistance may be due to the presence of an ACR3p-type arsenite pump, which is known to lack antimony transport ability.
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Affiliation(s)
- Nar Singh Chauhan
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Department of Biochemistry, Present Address: Maharishi Dayanand University, Rohtak, Haryana India
| | - Sonam Nain
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research, Sukhdev Vihar, Mathura Road, Delhi, 110020 India.,Academy of Scientific and Industrial Research (AcSIR), New Delhi, India
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Zhu YG, Xue XM, Kappler A, Rosen BP, Meharg AA. Linking Genes to Microbial Biogeochemical Cycling: Lessons from Arsenic. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:7326-7339. [PMID: 28602082 PMCID: PMC5871744 DOI: 10.1021/acs.est.7b00689] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur, and nitrogen affects the redox and bioavailability of arsenic species. In this critical review we illustrate the biogeochemical processes and genes involved in arsenic biotransformations. We discuss how current and future metagenomic-, metatranscriptomic-, metaproteomic-, and metabolomic-based methods will help to decipher individual microbial arsenic transformation processes, and their connections to other biogeochemical cycle. These insights will allow future use of microbial metabolic capabilities for new biotechnological solutions to environmental problems. To understand the complex nature of inorganic and organic arsenic species and the fate of environmental arsenic will require integrating systematic approaches with biogeochemical modeling. Finally, from the lessons learned from these studies of arsenic biogeochemistry, we will be able to predict how the environment changes arsenic, and, in response, how arsenic biotransformations change the environment.
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Affiliation(s)
- Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xi-Mei Xue
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Tübingen 72076, Germany
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida 33199, United States
| | - Andrew A Meharg
- Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 5HN, United Kingdom
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