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Teng ZJ, Li J, Wang P, Li CY, Peng M, Qin QL, Chen XL, Chen Y, Fu HH, Wang N, Zhang YZ. Meta-omics analysis reveals the marine arsenic cycle driven by bacteria. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135137. [PMID: 39024770 DOI: 10.1016/j.jhazmat.2024.135137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/16/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
Arsenic is a toxic element widely distributed in the Earth's crust and ranked as a class I human carcinogen. Microbial metabolism makes significant contributions to arsenic detoxification, migration and transformation. Nowadays, research on arsenic is primarily in areas affected by arsenic pollution associated with human health activities. However, the biogeochemical traits of arsenic in the global marine ecosystem remain to be explicated. In this study, we revealed that seawater environments were primarily governed by the process of arsenate reduction to arsenite, while arsenite methylation was predominant in marine sediments which may serve as significant sources of arsenic emission into the atmosphere. Significant disparities existed in the distribution patterns of the arsenic cycle between surface and deep seawaters at middle and low latitudes, whereas these situations tend to be similar in the Arctic and Antarctic oceans. Significant variations were also observed in the taxonomic diversity and core microbial community of arsenic cycling across different marine environments. Specifically, γ-proteobacteria played a pivotal role in the arsenic cycle in the whole marine environment. Temperature, dissolved oxygen and phosphate were the crucial factors that related to these differentiations in seawater environments. Overall, our study contributes to a deeper understanding of the marine arsenic cycle.
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Affiliation(s)
- Zhao-Jie Teng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Jian Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ming Peng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qi-Long Qin
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; School of Life Sciences, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, Qingdao 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266373, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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3
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Biotechnology Advances in Bioremediation of Arsenic: A Review. Molecules 2023; 28:molecules28031474. [PMID: 36771138 PMCID: PMC9921067 DOI: 10.3390/molecules28031474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/16/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Arsenic is a highly toxic metalloid widespread in the Earth's crust, and its contamination due to different anthropogenic activities (application of agrochemicals, mining, waste management) represents an emerging environmental issue. Therefore, different sustainable and effective remediation methods and approaches are needed to prevent and protect humans and other organisms from detrimental arsenic exposure. Among numerous arsenic remediation methods, those supported by using microbes as sorbents (microbial remediation), and/or plants as green factories (phytoremediation) are considered as cost-effective and environmentally-friendly bioremediation. In addition, recent advances in genetic modifications and biotechnology have been used to develop (i) more efficient transgenic microbes and plants that can (hyper)accumulate or detoxify arsenic, and (ii) novel organo-mineral materials for more efficient arsenic remediation. In this review, the most recent insights from arsenic bio-/phytoremediation are presented, and the most relevant physiological and molecular mechanisms involved in arsenic biological routes, which can be useful starting points in the creation of more arsenic-tolerant microbes and plants, as well as their symbiotic associations are discussed.
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Raiyani NM, Singh SP. Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:43245-43266. [PMID: 36650368 DOI: 10.1007/s11356-023-25196-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023]
Abstract
Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.
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Affiliation(s)
- Nirali M Raiyani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot, 360 005, Gujarat, India.
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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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6
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Tercier-Waeber ML, Confalonieri F, Abdou M, Dutruch L, Bossy C, Fighera M, Bakker E, Graziottin F, van der Wal P, Schäfer J. Advanced multichannel submersible probe for autonomous high-resolution in situ monitoring of the cycling of the potentially bioavailable fraction of a range of trace metals. CHEMOSPHERE 2021; 282:131014. [PMID: 34118619 DOI: 10.1016/j.chemosphere.2021.131014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 06/12/2023]
Abstract
We report here on the development and application of a submersible, compact, low power consumption, integrated multichannel trace metal sensing probe (TracMetal). This probe is unique in that it allows high-resolution, simultaneous in-situ measurements of the potentially bioavailable (so-called dynamic) fraction of Hg(II), As(III), Cd(II), Pb(II), Cu(II), Zn(II). The TracMetal incorporates nanostructured Au-plated and Hg-plated gel-integrated microelectrode arrays. In addition to be selective to the fraction of metal potentially bioavailable, they offer protection against fouling and ill-controlled convective interferences. Sensitivities in the low pM for Hg(II) and sub-nM for the other target trace metals is achieved with precision ≤ 12%. The TracMetal is capable of autonomous operation during deployment, with routines for repetitive measurements (1-2 h-1), data storage and management, data computer visualization, and wireless data transfer. The system was successfully applied in the Arcachon Bay, to study the temporal variation of the dynamic fraction of the trace metals targeted. The in situ autonomous TracMetal measurements were combined with in situ measurements of the master bio-physicochemical parameters and sample collection for complementary measurements of the dissolved metal concentrations, organic matter concentrations and proxy for biological activities. The integration of all data revealed that various biotic and abiotic processes control the temporal variation of the dynamic fractions of the target metals (Medyn). The difference in the percentage of the dynamic forms of the metals studied and the short-term processes influencing their variation highlight the TracMetal potentiality as metal bioavailability-assessment sentinel to achieve comprehensive environmental monitoring of dynamic aquatic systems.
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Affiliation(s)
- Mary-Lou Tercier-Waeber
- University of Geneva, Dept. of Inorganic and Analytical Chemistry, 1211 Geneva 4, Switzerland.
| | | | - Melina Abdou
- University of Geneva, Dept. of Inorganic and Analytical Chemistry, 1211 Geneva 4, Switzerland; University of Bordeaux, UMR CNRS 5805 EPOC, 33615 Pessac, France
| | - Lionel Dutruch
- University of Bordeaux, UMR CNRS 5805 EPOC, 33615 Pessac, France
| | - Cécile Bossy
- University of Bordeaux, UMR CNRS 5805 EPOC, 33615 Pessac, France
| | - Marianna Fighera
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Eric Bakker
- University of Geneva, Dept. of Inorganic and Analytical Chemistry, 1211 Geneva 4, Switzerland
| | | | - Peter van der Wal
- Ecole Polytechnique Fédérale de Lausanne (EPFL), Neuchâtel, Switzerland
| | - Jörg Schäfer
- University of Bordeaux, UMR CNRS 5805 EPOC, 33615 Pessac, France
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7
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Kuramae EE, Derksen S, Schlemper TR, Dimitrov MR, Costa OYA, da Silveira APD. Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. Microorganisms 2020; 8:E725. [PMID: 32414048 PMCID: PMC7285511 DOI: 10.3390/microorganisms8050725] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/11/2023] Open
Abstract
Bacteria from the genera Paraburkholderia and Herbaspirillum can promote the growth of Sorghum bicolor, but the underlying mechanisms are not yet known. In a pot experiment, sorghum plants grown on sterilized substrate were inoculated with Paraburkholderia tropica strain IAC/BECa 135 and Herbaspirillum frisingense strain IAC/BECa 152 under phosphate-deficient conditions. These strains significantly increased Sorghum bicolor cultivar SRN-39 root and shoot biomass. Shotgun metagenomic analysis of the rhizosphere revealed successful colonization by both strains; however, the incidence of colonization was higher in plants inoculated with P. tropica strain IAC/BECa 135 than in those inoculated with H. frisingense strain IAC/BECa 152. Conversely, plants inoculated with H. frisingense strain IAC/BECa 152 showed the highest increase in biomass. Genomic analysis of the two inoculants implied a high degree of rhizosphere fitness of P. tropica strain IAC/BECa 135 through environmental signal processing, biofilm formation, and nutrient acquisition. Both genomes contained genes related to plant growth-promoting bacterial (PGPB) traits, including genes related to indole-3-acetate (IAA) synthesis, nitrogen fixation, nodulation, siderophore production, and phosphate solubilization, although the P. tropica strain IAC/BECa 135 genome contained a slightly more extensive repertoire. This study provides evidence that complementary mechanisms of growth promotion in Sorghum might occur, i.e., that P. tropica strain IAC/BECa 135 acts in the rhizosphere and increases the availability of nutrients, while H. frisingense strain IAC/BECa 152 influences plant hormone signaling. While the functional and taxonomic profiles of the rhizobiomes were similar in all treatments, significant differences in plant biomass were observed, indicating that the rhizobiome and the endophytic microbial community may play equally important roles in the complicated plant-microbial interplay underlying increased host plant growth.
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Affiliation(s)
- Eiko E. Kuramae
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
- Utrecht University, Institute of Environmental Biology, Ecology and biodiversity, 3508 TC Utrecht, The Netherlands
| | - Stan Derksen
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Thiago R. Schlemper
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Maurício R. Dimitrov
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Ohana Y. A. Costa
- Netherlands Institute of Ecology (NIOO-KNAW), Microbial Ecology Department, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands; (S.D.); (T.R.S.); (M.R.D.); (O.Y.A.C.)
| | - Adriana P. D. da Silveira
- Center of Soil and Environmental Resources, Agronomic Institute of Campinas (IAC), Av. Barão de Itapura 1481, 13020-902 Campinas, Brazil
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8
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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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9
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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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Wang HL, Zhang J, Sun QL, Lian C, Sun L. A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields. PLoS One 2017; 12:e0181048. [PMID: 28704556 PMCID: PMC5507547 DOI: 10.1371/journal.pone.0181048] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 06/26/2017] [Indexed: 12/02/2022] Open
Abstract
Currently, little is known about the microbial diversity in the sediments of Pacmanus and Desmos hydrothermal fields in Manus Basin. In this study, Illumina-based sequencing of 16S rRNA gene amplicons and metagenomic analysis were conducted to investigate the microbial populations and metabolic profiles in the sediments from four different regions in Pacmanus and Desmos hydrothermal fields. It was found that Gammaproteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal populations, respectively. The autotrophic prokaryotes in the four communities probably fixed CO2 via four major pathways, i.e. Calvin-Benson-Bassham cycle, reductive acetyl-CoA cycle, rTCA cycle, and 3-hydroxypropionate/4-hydroxybutyrate cycle. Ammonia-oxidizing Thaumarchaeota, nitrifiers, denitrifiers, and sulfur oxidizers belonging to the subgroups of Proteobacteria (e.g., alpha, beta, gamma, and epsilon), Nitrospira, and Nitrospina, and sulfate-reducing Desulfobacterales likely played critical roles in nitrogen and sulfur cycling, in which ammonia, sulfur compounds, and hydrogen could be utilized as potential energy sources. These findings revealed new insights into the operational mechanism of the microbial communities associated with Pacmanus and Desmos hydrothermal fields.
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Affiliation(s)
- Hai-liang Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qing-lei Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chao Lian
- Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Li Sun
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- * E-mail:
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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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12
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Gutleben J, Chaib De Mares M, van Elsas JD, Smidt H, Overmann J, Sipkema D. The multi-omics promise in context: from sequence to microbial isolate. Crit Rev Microbiol 2017; 44:212-229. [PMID: 28562180 DOI: 10.1080/1040841x.2017.1332003] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The numbers and diversity of microbes in ecosystems within and around us is unmatched, yet most of these microorganisms remain recalcitrant to in vitro cultivation. Various high-throughput molecular techniques, collectively termed multi-omics, provide insights into the genomic structure and metabolic potential as well as activity of complex microbial communities. Nonetheless, pure or defined cultures are needed to (1) decipher microbial physiology and thus test multi-omics-based ecological hypotheses, (2) curate and improve database annotations and (3) realize novel applications in biotechnology. Cultivation thus provides context. In turn, we here argue that multi-omics information awaits integration into the development of novel cultivation strategies. This can build the foundation for a new era of omics information-guided microbial cultivation technology and reduce the inherent trial-and-error search space. This review discusses how information that can be extracted from multi-omics data can be applied for the cultivation of hitherto uncultured microorganisms. Furthermore, we summarize groundbreaking studies that successfully translated information derived from multi-omics into specific media formulations, screening techniques and selective enrichments in order to obtain novel targeted microbial isolates. By integrating these examples, we conclude with a proposed workflow to facilitate future omics-aided cultivation strategies that are inspired by the microbial complexity of the environment.
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Affiliation(s)
- Johanna Gutleben
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Maryam Chaib De Mares
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Jan Dirk van Elsas
- b Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES) , Rijksuniversiteit Groningen , Groningen , The Netherlands
| | - Hauke Smidt
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
| | - Jörg Overmann
- c Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen , Braunschweig , Germany
| | - Detmer Sipkema
- a Laboratory of Microbiology , Wageningen University & Research , Wageningen , The Netherlands
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13
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Kurth D, Amadio A, Ordoñez OF, Albarracín VH, Gärtner W, Farías ME. Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis. Sci Rep 2017; 7:1024. [PMID: 28432307 PMCID: PMC5430908 DOI: 10.1038/s41598-017-00896-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/16/2017] [Indexed: 11/09/2022] Open
Abstract
Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.
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Affiliation(s)
- Daniel Kurth
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Ariel Amadio
- E.E.A. Rafaela, Instituto Nacional de Tecnología Agropecuaria (INTA), CCT Santa Fe, CONICET, Rafaela, Argentina
| | - Omar F Ordoñez
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
| | - Virginia H Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
| | - Wolfgang Gärtner
- Max-Planck Institute for Chemical Energy Conversion, Mülheim an der Ruhr, Germany
| | - María E Farías
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT Tucumán, CONICET, San Miguel de Tucumán, Argentina.
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14
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Gillan DC, Van Camp C, Mergeay M, Provoost A, Thomas N, Vermard L, Billon G, Wattiez R. Paleomicrobiology to investigate copper resistance in bacteria: isolation and description ofCupriavidus necatorB9 in the soil of a medieval foundry. Environ Microbiol 2017; 19:770-787. [DOI: 10.1111/1462-2920.13645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/04/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Max Mergeay
- Molecular & Cellular Biology; Unit of Microbiology SCK•CEN; Mol Belgium
| | - Ann Provoost
- Molecular & Cellular Biology; Unit of Microbiology SCK•CEN; Mol Belgium
| | - Nicolas Thomas
- Médiévistique occidentale, Université Paris 1 Panthéon-Sorbonne-CNRS; Inrap-UMR 8589 Lamop France
- Institut National de Recherches Archéologiques Préventives (INRAP); France
| | - Laurent Vermard
- Institut National de Recherches Archéologiques Préventives (INRAP); France
| | - Gabriel Billon
- Université de Lille 1, Sciences & Technologies, LASIR (UMR CNRS 8516); Villeneuve d'Ascq France
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15
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Wasmund K, Cooper M, Schreiber L, Lloyd KG, Baker BJ, Petersen DG, Jørgensen BB, Stepanauskas R, Reinhardt R, Schramm A, Loy A, Adrian L. Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling. mBio 2016; 7:e00266-16. [PMID: 27143384 PMCID: PMC4959651 DOI: 10.1128/mbio.00266-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The marine subsurface sediment biosphere is widely inhabited by bacteria affiliated with the class Dehalococcoidia (DEH), phylum Chloroflexi, and yet little is known regarding their metabolisms. In this report, genomic content from a single DEH cell (DEH-C11) with a 16S rRNA gene that was affiliated with a diverse cluster of 16S rRNA gene sequences prevalent in marine sediments was obtained from sediments of Aarhus Bay, Denmark. The distinctive gene content of this cell suggests metabolic characteristics that differ from those of known DEH and Chloroflexi The presence of genes encoding dissimilatory sulfite reductase (Dsr) suggests that DEH could respire oxidized sulfur compounds, although Chloroflexi have never been implicated in this mode of sulfur cycling. Using long-range PCR assays targeting DEH dsr loci, dsrAB genes were amplified and sequenced from various marine sediments. Many of the amplified dsrAB sequences were affiliated with the DEH Dsr clade, which we propose equates to a family-level clade. This provides supporting evidence for the potential for sulfite reduction by diverse DEH species. DEH-C11 also harbored genes encoding reductases for arsenate, dimethyl sulfoxide, and halogenated organics. The reductive dehalogenase homolog (RdhA) forms a monophyletic clade along with RdhA sequences from various DEH-derived contigs retrieved from available metagenomes. Multiple facts indicate that this RdhA may not be a terminal reductase. The presence of other genes indicated that nutrients and energy may be derived from the oxidation of substituted homocyclic and heterocyclic aromatic compounds. Together, these results suggest that marine DEH play a previously unrecognized role in sulfur cycling and reveal the potential for expanded catabolic and respiratory functions among subsurface DEH. IMPORTANCE Sediments underlying our oceans are inhabited by microorganisms in cell numbers similar to those estimated to inhabit the oceans. Microorganisms in sediments consist of various diverse and uncharacterized groups that contribute substantially to global biogeochemical cycles. Since most subsurface microorganisms continue to evade cultivation, possibly due to very slow growth, we obtained and analyzed genomic information from a representative of one of the most widespread and abundant, yet uncharacterized bacterial groups of the marine subsurface. We describe several key features that may contribute to their widespread distribution, such as respiratory flexibility and the potential to use oxidized sulfur compounds, which are abundant in marine environments, as electron acceptors. Together, these data provide important information that can be used to assist in designing enrichment strategies or other postgenomic studies, while also improving our understanding of the diversity and distribution of dsrAB genes, which are widely used functional marker genes for sulfur-cycling microbes.
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Affiliation(s)
- Kenneth Wasmund
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Myriel Cooper
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Lars Schreiber
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Karen G Lloyd
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Brett J Baker
- Department of Marine Science, University of Texas-Austin, Marine Science Institute, Port Aransas, Texas, USA
| | - Dorthe G Petersen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | | | | | - Andreas Schramm
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry meets Microbiology, University of Vienna, Vienna, Austria
| | - Lorenz Adrian
- Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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16
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Gillan DC. Metal resistance systems in cultivated bacteria: are they found in complex communities? Curr Opin Biotechnol 2016; 38:123-30. [DOI: 10.1016/j.copbio.2016.01.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 12/11/2022]
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17
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Andres J, Bertin PN. The microbial genomics of arsenic. FEMS Microbiol Rev 2016; 40:299-322. [DOI: 10.1093/femsre/fuv050] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2015] [Indexed: 12/17/2022] Open
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18
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Caruso G, La Ferla R, Azzaro M, Zoppini A, Marino G, Petochi T, Corinaldesi C, Leonardi M, Zaccone R, Fonda Umani S, Caroppo C, Monticelli L, Azzaro F, Decembrini F, Maimone G, Cavallo RA, Stabili L, Hristova Todorova N, K. Karamfilov V, Rastelli E, Cappello S, Acquaviva MI, Narracci M, De Angelis R, Del Negro P, Latini M, Danovaro R. Microbial assemblages for environmental quality assessment: Knowledge, gaps and usefulness in the European Marine Strategy Framework Directive. Crit Rev Microbiol 2015; 42:883-904. [DOI: 10.3109/1040841x.2015.1087380] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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19
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Zhang W, Wang Y, Bougouffa S, Tian R, Cao H, Li Y, Cai L, Wong YH, Zhang G, Zhou G, Zhang X, Bajic VB, Al-Suwailem A, Qian PY. Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool. Environ Microbiol 2015; 17:4089-104. [DOI: 10.1111/1462-2920.12978] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/01/2015] [Accepted: 07/02/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Weipeng Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yong Wang
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
| | - Salim Bougouffa
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Renmao Tian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Huiluo Cao
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yongxin Li
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Lin Cai
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Yue Him Wong
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Gen Zhang
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Guowei Zhou
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
| | - Xixiang Zhang
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Abdulaziz Al-Suwailem
- King Abdullah University of Science and Technology; Thuwal The Kingdom of Saudi Arabia
| | - Pei-Yuan Qian
- KAUST Global Partnership Program; Division of Life Science; Hong Kong University of Science and Technology; Clear Water Bay Hong Kong China
- Sanya Institute of Deep Sea Science and Engineering; Chinese Academy of Sciences; Sanya Hainan China
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20
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Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J. Representing virus-host interactions and other multi-organism processes in the Gene Ontology. BMC Microbiol 2015; 15:146. [PMID: 26215368 PMCID: PMC4517558 DOI: 10.1186/s12866-015-0481-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/10/2015] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. METHODS To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. CONCLUSIONS Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.
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Affiliation(s)
- R E Foulger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - D Osumi-Sutherland
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
| | - B K McIntosh
- Department of Biochemistry and Biophysics, Texas Agrilife Research, Texas A&M University, College Station, TX, 77843, USA.
| | - C Hulo
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Masson
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - S Poux
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - P Le Mercier
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 Rue Michel-Servet, 1211, Geneva 4, Switzerland.
| | - J Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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21
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Fierer N, Barberán A, Laughlin DC. Seeing the forest for the genes: using metagenomics to infer the aggregated traits of microbial communities. Front Microbiol 2014; 5:614. [PMID: 25429288 PMCID: PMC4228856 DOI: 10.3389/fmicb.2014.00614] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 10/28/2014] [Indexed: 02/03/2023] Open
Abstract
Most environments harbor large numbers of microbial taxa with ecologies that remain poorly described and characterizing the functional capabilities of whole communities remains a key challenge in microbial ecology. Shotgun metagenomic analyses are increasingly recognized as a powerful tool to understand community-level attributes. However, much of this data is under-utilized due, in part, to a lack of conceptual strategies for linking the metagenomic data to the most relevant community-level characteristics. Microbial ecologists could benefit by borrowing the concept of community-aggregated traits (CATs) from plant ecologists to glean more insight from the ever-increasing amount of metagenomic data being generated. CATs can be used to quantify the mean and variance of functional traits found in a given community. A CAT-based strategy will often yield far more useful information for predicting the functional attributes of diverse microbial communities and changes in those attributes than the more commonly used analytical strategies. A more careful consideration of what CATs to measure and how they can be quantified from metagenomic data, will help build a more integrated understanding of complex microbial communities.
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Affiliation(s)
- Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA ; Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO, USA
| | - Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, CO, USA
| | - Daniel C Laughlin
- Environmental Research Institute, School of Science, University of Waikato Hamilton, New Zealand
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22
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Torto-Alalibo T, Purwantini E, Lomax J, Setubal JC, Mukhopadhyay B, Tyler BM. Genetic resources for advanced biofuel production described with the Gene Ontology. Front Microbiol 2014; 5:528. [PMID: 25346727 PMCID: PMC4193338 DOI: 10.3389/fmicb.2014.00528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/22/2014] [Indexed: 12/12/2022] Open
Abstract
Dramatic increases in research in the area of microbial biofuel production coupled with high-throughput data generation on bioenergy-related microbes has led to a deluge of information in the scientific literature and in databases. Consolidating this information and making it easily accessible requires a unified vocabulary. The Gene Ontology (GO) fulfills that requirement, as it is a well-developed structured vocabulary that describes the activities and locations of gene products in a consistent manner across all kingdoms of life. The Microbial ENergy processes Gene Ontology () project is extending the GO to include new terms to describe microbial processes of interest to bioenergy production. Our effort has added over 600 bioenergy related terms to the Gene Ontology. These terms will aid in the comprehensive annotation of gene products from diverse energy-related microbial genomes. An area of microbial energy research that has received a lot of attention is microbial production of advanced biofuels. These include alcohols such as butanol, isopropanol, isobutanol, and fuels derived from fatty acids, isoprenoids, and polyhydroxyalkanoates. These fuels are superior to first generation biofuels (ethanol and biodiesel esterified from vegetable oil or animal fat), can be generated from non-food feedstock sources, can be used as supplements or substitutes for gasoline, diesel and jet fuels, and can be stored and distributed using existing infrastructure. Here we review the roles of genes associated with synthesis of advanced biofuels, and at the same time introduce the use of the GO to describe the functions of these genes in a standardized way.
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Affiliation(s)
- Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
| | - Jane Lomax
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome CampusCambridge, UK
| | - João C. Setubal
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Departamento de Bioquímica, Instituto de Química, Universidade de São PauloSão Paulo, Brazil
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Department of Biological Sciences, Oregon State UniversityCorvallis, OR, USA
| | - Brett M. Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State UniversityBlacksburg, VA, USA
- Center for Genome Research and Biocomputing, Oregon State UniversityCorvallis, OR, USA
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23
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Luo J, Bai Y, Liang J, Qu J. Metagenomic approach reveals variation of microbes with arsenic and antimony metabolism genes from highly contaminated soil. PLoS One 2014; 9:e108185. [PMID: 25299175 PMCID: PMC4191978 DOI: 10.1371/journal.pone.0108185] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/18/2014] [Indexed: 11/18/2022] Open
Abstract
Microbes have great potential for arsenic (As) and antimony (Sb) bioremediation in heavily contaminated soil because they have the ability to biotransform As and Sb to species that have less toxicity or are more easily removed. In this study, we integrated a metagenomic method with physicochemical characterization to elucidate the composition of microbial community and functional genes (related to As and Sb) in a high As (range from 34.11 to 821.23 mg kg−1) and Sb (range from 226.67 to 3923.07 mg kg−1) contaminated mine field. Metagenomic analysis revealed that microbes from 18 phyla were present in the 5 samples of soil contaminated with high As and Sb. Moreover, redundancy analysis (RDA) of the relationship between the 18 phyla and the concentration of As and Sb demonstrated that 5 phyla of microbes, i.e. Actinobacteria, Firmicutes, Nitrospirae, Tenericutes and Gemmatimonadetes were positively correlated with As and Sb concentration. The distribution, diversity and abundance of functional genes (including arsC, arrA, aioA, arsB and ACR3) were much higher for the samples containing higher As and Sb concentrations. Based on correlation analysis, the results showed a positive relationship between arsC-like (R2 = 0.871) and aioA-like (R2 = 0.675) gene abundance and As concentration, and indicated that intracellular As(V) reduction and As(III) oxidation could be the dominant As detoxification mechanism enabling the microbes to survive in the environment. This study provides a direct and reliable reference on the diversity of microbial community and functional genes in an extremely high concentration As- and Sb-contaminated environment.
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Affiliation(s)
- Jinming Luo
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jinsong Liang
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jiuhui Qu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail:
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24
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Bik HM. Deciphering diversity and ecological function from marine metagenomes. THE BIOLOGICAL BULLETIN 2014; 227:107-116. [PMID: 25411370 DOI: 10.1086/bblv227n2p107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metagenomic sequencing now represents a common, powerful approach for investigating diversity and functional relationships in marine ecosystems. High-throughput datasets generated from random fragments of environmental DNA can provide a less biased view of organismal abundance (versus PCR-based amplicon sequencing) and enable novel exploration of microbial genomes by recovering genome assemblies from uncultured species, identifying ecological functions, and reconstructing metabolic pathways. This review highlights the current state of knowledge in marine metagenomics, focusing on biological insights gained from recent environmental studies and detailing commonly employed methods for data collection and analysis.
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Affiliation(s)
- Holly M Bik
- UC Davis Genome Center, University of California-Davis, One Shields Ave, Davis, California 95616
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25
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Diversity of marine microbes in a changing Mediterranean Sea. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-014-0333-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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26
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Chen M, Wang W, Feng Y, Zhu X, Zhou H, Tan Z, Li X. Impact resistance of different factors on ammonia removal by heterotrophic nitrification-aerobic denitrification bacterium Aeromonas sp. HN-02. BIORESOURCE TECHNOLOGY 2014; 167:456-461. [PMID: 25006021 DOI: 10.1016/j.biortech.2014.06.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 06/03/2023]
Abstract
To give reference for the application of heterotrophic nitrification-aerobic denitrification bacteria in actual wastewater treatment, the impact resistance of extreme pH, low temperature, heavy metals and high salinity on ammonia removal by a typical heterotrophic nitrifying-aerobic denitrifying bacterium Aeromonas sp. HN-02 was investigated. The results showed that HN-02 demonstrated strong acid- and alkali-resistance. In addition, it remained active at 5°C, and the removal rates of ammonia and COD were 0.90 mg L(-1)h(-1) and 22.34 mg L(-1)h(-1), respectively. Under the same extent of immediate temperature drop, the temperature correction coefficients of ammonia, COD removal rates and cell growth rate were close. Moreover, HN-02 could survive in the solution containing 0.5 mg L(-1) Cu(2+) or 8 mg L(-1) Zn(2+), or 0.5 mg L(-1) of equivalent Cu(2+)-Zn(2+). Furthermore, efficient ammonia removal was retained at salinity below 20 g L(-1), thus it could be identified as a halotolerant bacterium. At last, stronger stress resulted in higher ΔCOD/ΔTN ratio.
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Affiliation(s)
- Maoxia Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Wenchao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Ye Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Xiaohua Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Houzhen Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
| | - Zhouliang Tan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China.
| | - Xudong Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China; Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, PR China
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27
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Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RHEM, van Veen JA, Kuramae EE. Impact of long-term N, P, K, and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil. FEMS Microbiol Ecol 2014; 90:195-205. [PMID: 25046442 DOI: 10.1111/1574-6941.12384] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/09/2023] Open
Abstract
Soil abiotic and biotic interactions govern important ecosystem processes. However, the mechanisms behind these interactions are complex, and the links between specific environmental factors, microbial community structures, and functions are not well understood. Here, we applied DNA shotgun metagenomic techniques to investigate the effect of inorganic fertilizers N, P, K, and NPK on the bacterial community composition and potential functions in grassland soils in a 54-year experiment. Differences in total and available nutrients were found in the treatment soils; interestingly, Al, As, Mg, and Mn contents were variable in N, P, K, and NPK treatments. Bacterial community compositions shifted and Actinobacteria were overrepresented under the four fertilization treatments compared to the control. Redundancy analysis of the soil parameters and the bacterial community profiles showed that Mg, total N, Cd, and Al were linked to community variation. Using correlation analysis, Acidobacteria, Bacteroidetes, and Verrucomicrobia were linked similarly to soil parameters, and Actinobacteria and Proteobacteria were linked separately to different suites of parameters. Surprisingly, we found no fertilizers effect on microbial functional profiles which supports functional redundancy as a mechanism for stabilization of functions during changes in microbial composition. We suggest that functional profiles are more resistant to environmental changes than community compositions in the grassland ecosystem.
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Affiliation(s)
- Yao Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, The Netherlands
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28
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Li X, Zhang L, Wang G. Genomic evidence reveals the extreme diversity and wide distribution of the arsenic-related genes in Burkholderiales. PLoS One 2014; 9:e92236. [PMID: 24632831 PMCID: PMC3954881 DOI: 10.1371/journal.pone.0092236] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/19/2014] [Indexed: 11/18/2022] Open
Abstract
So far, numerous genes have been found to associate with various strategies to resist and transform the toxic metalloid arsenic (here, we denote these genes as "arsenic-related genes"). However, our knowledge of the distribution, redundancies and organization of these genes in bacteria is still limited. In this study, we analyzed the 188 Burkholderiales genomes and found that 95% genomes harbored arsenic-related genes, with an average of 6.6 genes per genome. The results indicated: a) compared to a low frequency of distribution for aio (arsenite oxidase) (12 strains), arr (arsenate respiratory reductase) (1 strain) and arsM (arsenite methytransferase)-like genes (4 strains), the ars (arsenic resistance system)-like genes were identified in 174 strains including 1,051 genes; b) 2/3 ars-like genes were clustered as ars operon and displayed a high diversity of gene organizations (68 forms) which may suggest the rapid movement and evolution for ars-like genes in bacterial genomes; c) the arsenite efflux system was dominant with ACR3 form rather than ArsB in Burkholderiales; d) only a few numbers of arsM and arrAB are found indicating neither As III biomethylation nor AsV respiration is the primary mechanism in Burkholderiales members; (e) the aio-like gene is mostly flanked with ars-like genes and phosphate transport system, implying the close functional relatedness between arsenic and phosphorus metabolisms. On average, the number of arsenic-related genes per genome of strains isolated from arsenic-rich environments is more than four times higher than the strains from other environments. Compared with human, plant and animal pathogens, the environmental strains possess a larger average number of arsenic-related genes, which indicates that habitat is likely a key driver for bacterial arsenic resistance.
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Linshuang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Gejiao Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan, P. R. China
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29
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Dittami SM, Eveillard D, Tonon T. A metabolic approach to study algal-bacterial interactions in changing environments. Mol Ecol 2014; 23:1656-60. [PMID: 24447216 DOI: 10.1111/mec.12670] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/10/2014] [Accepted: 01/10/2014] [Indexed: 12/16/2022]
Abstract
Increasing evidence exists that bacterial communities interact with and shape the biology of algae and that their evolutionary histories are connected. Despite these findings, physiological studies were and still are generally carried out with axenic or at least antibiotic-treated cultures. Here, we argue that considering interactions between algae and associated bacteria is key to understanding their biology and evolution. To deal with the complexity of the resulting 'holobiont' system, a metabolism-centred approach that uses combined metabolic models for algae and associated bacteria is proposed. We believe that these models will be valuable tools both to study algal-bacterial interactions and to elucidate processes important for the acclimation of the holobiont to environmental changes.
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Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff Cedex, F-29688, France; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff Cedex, F-29688, France
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Genome Sequence of Halomonas sp. Strain A3H3, Isolated from Arsenic-Rich Marine Sediments. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00819-13. [PMID: 24115546 PMCID: PMC3795216 DOI: 10.1128/genomea.00819-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the genome sequence of Halomonas sp. strain A3H3, a bacterium with a high tolerance to arsenite, isolated from multicontaminated sediments of the l’Estaque harbor in Marseille, France. The genome is composed of a 5,489,893-bp chromosome and a 157,085-bp plasmid.
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