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Zhan H, Wan Y, Sun Y, Xu Z, Zhang F, Yang K, Zhu W, Cheung CP, Tang W, Ng EK, Wong SK, Yeoh YK, Kl Chan F, Miao Y, Zuo T, Zeng Z, Ng SC. Gut mycobiome alterations in obesity in geographically different regions. Gut Microbes 2024; 16:2367297. [PMID: 38899956 PMCID: PMC11195487 DOI: 10.1080/19490976.2024.2367297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
The gut fungi play important roles in human health and are involved in energy metabolism. This study aimed to examine gut mycobiome composition in obese subjects in two geographically different regions in China and to identify specific gut fungi associated with obesity. A total of 217 subjects from two regions with different urbanization levels [Hong Kong (HK): obese, n = 59; lean, n = 59; Kunming (KM): obese, n = 50; lean, n = 49. Mean body mass index (BMI) for obesity = 33.7] were recruited. We performed deep shotgun metagenomic sequencing on fecal samples to compare gut mycobiome composition and trophic functions in lean and obese subjects across these two regions. The gut mycobiome of obese subjects in both HK and KM were altered compared to those of lean subjects, characterized by a decrease in the relative abundance of Nakaseomyces, Schizosaccharomyces pombe, Candida dubliniensis and an increase in the abundance of Lanchanceathermotolerans, Saccharomyces paradox, Parastagonospora nodorum and Myceliophthorathermophila. Reduced fungal - bacterial and fungal - fungal correlations as well as increased negative fungal-bacterial correlations were observed in the gut of obese subjects. Furthermore, the anti-obesity effect of fungus S. pombe was further validated using a mouse model. Supplementing high-fat diet-induced obese mice with the fungus for 12 weeks led to a significant reduction in body weight gain (p < 0.001), and an improvement in lipid and glucose metabolism compared to mice without intervention. In conclusion, the gut mycobiome composition and functionalities of obese subjects were altered. These data shed light on the potential of utilizing fungus-based therapeutics for the treatment of obesity. S. pombe may serve as a potential fungal probiotic in the prevention of diet-induced obesity and future human trials are needed.
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Affiliation(s)
- Hui Zhan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yating Wan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yang Sun
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
- Yunnan Geriatric Medical Center, Kunming, Yunnan, China
| | - Zhilu Xu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fen Zhang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Keli Yang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenyi Zhu
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Enders Kw Ng
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Simon Kh Wong
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yun Kit Yeoh
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
| | - Francis Kl Chan
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Yunnan, China
| | - Tao Zuo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhong Zeng
- Department of Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Siew C Ng
- Microbiota I-Center (MagIC) Limited, Hong Kong SAR, China
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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Nivetha N, Srivarshine B, Sowmya B, Rajendiran M, Saravanan P, Rajeshkannan R, Rajasimman M, Pham THT, Shanmugam V, Dragoi EN. A comprehensive review on bio-stimulation and bio-enhancement towards remediation of heavy metals degeneration. CHEMOSPHERE 2023; 312:137099. [PMID: 36372332 DOI: 10.1016/j.chemosphere.2022.137099] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/20/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
Pollution of heavy metals is one of the risky contaminations that should be managed for all intents and purposes of general well-being concerns. The bioaccumulation of these heavy metals inside our bodies and pecking orders will influence our people in the future. Bioremediation is a bio-mechanism where residing organic entities use and reuse the squanders that are reused to one more form. This could be accomplished by taking advantage of the property of explicit biomolecules or biomass that is equipped for restricting by concentrating the necessary heavy metal particles. The microorganisms can't obliterate the metal yet can change it into a less harmful substance. In this unique circumstance, this review talks about the sources, poisonousness, impacts, and bioremediation strategies of five heavy metals: lead, mercury, arsenic, chromium, and manganese. The concentrations here are the ordinary strategies for bioremediation such as biosorption methods, the use of microbes, green growth, and organisms, etc. This review demonstrates the toxicity of heavy metal contamination degradation by biotransformation through bacterioremediation and biodegradation through mycoremediation.
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Affiliation(s)
- N Nivetha
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - B Srivarshine
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | - B Sowmya
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India
| | | | - Panchamoorthy Saravanan
- Department of Petrochemical Technology, UCE - BIT Campus, Anna University, Tiruchirappalli, Tamil Nadu, India
| | - R Rajeshkannan
- Department of Chemical Engineering, Annamalai University, Tamilnadu, India
| | - M Rajasimman
- Department of Chemical Engineering, Annamalai University, Tamilnadu, India
| | - Thi Hong Trang Pham
- Institute for Global Health Innovations, Duy Tan University, Da Nang, 550000, Viet Nam; Faculty of Natural Science, Duy Tan University, Da Nang, 550000, Viet Nam
| | - VenkatKumar Shanmugam
- School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore, 632014, Tamil Nadu, India.
| | - Elena-Niculina Dragoi
- "Cristofor Simionescu" Faculty of Chemical Engineering and Environmental Protection, "Gheorghe Asachi" Technical University, Iasi, Bld Mangeron No 73, 700050, Romania
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Bose H, Sahu RP, Sar P. Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 841:156486. [PMID: 35667424 DOI: 10.1016/j.scitotenv.2022.156486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 107 gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO43-, SO42- and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO42- and NO3- reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO43- and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3- reduction to ammonium), and S (assimilatory SO42- reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.
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Affiliation(s)
- Himadri Bose
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Rajendra Prasad Sahu
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
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Park JH, Kim SJ, Nam IH, Ryu J, Jung GY, Han YS. Microbial mediated reaction of dimethylarsinic acid in wetland water and sediments. WATER RESEARCH 2022; 222:118873. [PMID: 35914499 DOI: 10.1016/j.watres.2022.118873] [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: 03/25/2022] [Revised: 06/29/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
The biogeochemical reactions of dimethylarsinic acid (DMAs(V)) were investigated using simulated wetland systems in a laboratory. DMAs(V) was injected into the wetland water, and the As concentrations in the water, plants, and sediments were monitored. Aqueous and solid-phase As speciation was evaluated, and the results revealed that the DMAs(V) was completely transported to the sediments and plants. X-ray absorption spectroscopic measurement of the As in the sediment revealed that approximately 85-95% of As existed as inorganic As species, demonstrating the important role of microorganisms in the biogeochemical reaction of DMAs(V). The influences of microbes were further investigated in smaller batches under aerobic and anaerobic conditions. The microbial batch results showed that DMAs(V) demethylation reduced the total aqueous As concentration, demonstrating that As(V) has higher affinity to wetland sediment than DMAs(V). The redox conditions were also revealed as an important controlling factor of the As reaction and, under anaerobic conditions, we observed the presence of the most toxic form of inorganic As(III) in the aqueous phase. Although this study reports one example from a specific wetland, the important roles of the redox conditions and microbial influences were identified from the comprehensive analysis of As speciation and mass balance.
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Affiliation(s)
- Ji-Hyun Park
- Department of Environmental and IT Engineering, Chungnam National University, Daehak-ro 99, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - So-Jeong Kim
- Mineral Resources Division, Korea Institute of Geoscience and Mineral Resources, Gwahak-ro 124, Yuseong-gu, Daejeon 34132, Republic of Korea
| | - In-Hyun Nam
- Mineral Resources Division, Korea Institute of Geoscience and Mineral Resources, Gwahak-ro 124, Yuseong-gu, Daejeon 34132, Republic of Korea
| | - Jungho Ryu
- Mineral Resources Division, Korea Institute of Geoscience and Mineral Resources, Gwahak-ro 124, Yuseong-gu, Daejeon 34132, Republic of Korea
| | - Gi-Yong Jung
- Mineral Resources Division, Korea Institute of Geoscience and Mineral Resources, Gwahak-ro 124, Yuseong-gu, Daejeon 34132, Republic of Korea
| | - Young-Soo Han
- Department of Environmental and IT Engineering, Chungnam National University, Daehak-ro 99, Yuseong-gu, Daejeon 34134, Republic of Korea; Department of Environmental Engineering, Chungnam National University, Daehak-ro 99, Yuseong-gu, Daejeon 34134, Republic of Korea.
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Current knowledge on molecular mechanisms of microorganism-mediated bioremediation for arsenic contamination: A review. Microbiol Res 2022; 258:126990. [DOI: 10.1016/j.micres.2022.126990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 11/30/2022]
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Nie Z, Hu L, Zhang D, Qian Y, Long Y, Shen D, Fang C, Yao J, Liu J. Drivers and ecological consequences of arsenite detoxification in aged semi-aerobic landfill. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126597. [PMID: 34252667 DOI: 10.1016/j.jhazmat.2021.126597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Microbial populations responsible for arsenite [As(III)] detoxification were examined in aged refuse treated with 75 μM As(III) under semi-aerobic conditions. As(III) was rapidly oxidized to As(V) via microbial activity, and substantial As was fixed in the solid phase. The abundance of arsenite oxidase genes (aioA) was about four times higher in the moderate As(III) stressed treatment than in the untreated control. Network analysis of microbial community 16S rRNA genes based on MRT (random matrix theory) further illuminated details about microbe-microbe interactions, and showed six ecological clusters. A total of 166 "core" taxa were identified by within-module connectivity and among-module connectivity values. When compared with the control treatment without As(III), 12 putative keystone operational taxonomic units were positively correlated with As(III) oxidation, of which 10 of these were annotated to genera level. Eight genera were associated with As(III) detoxification: Pseudomonas, Paenalcaligenes, Proteiniphilum, Moheibacter, Mobilitalea, Anaerosporobacter, Syntrophomonas and Pusillimonas. Most of those putative keystone taxa were rare species in landfill, which suggests that low-abundance taxa might significantly contribute to As(III) oxidation.
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Affiliation(s)
- Zhiyuan Nie
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Lifang Hu
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China.
| | - Dongchen Zhang
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Yating Qian
- College of Quality and Safety Engineering, Institution of Industrial Carbon Metrology, China Jiliang University, Hangzhou 310018, China
| | - Yuyang Long
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China.
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Chengran Fang
- College of Civil Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Jun Yao
- College of Life Science, Taizhou University, Jiaojiang 318000, China
| | - Jinbao Liu
- Zhejiang Tongji Vocational College of Science and Technology, Hangzhou 311231, China
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Irshad S, Xie Z, Mehmood S, Nawaz A, Ditta A, Mahmood Q. Insights into conventional and recent technologies for arsenic bioremediation: A systematic review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:18870-18892. [PMID: 33586109 DOI: 10.1007/s11356-021-12487-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/11/2021] [Indexed: 05/22/2023]
Abstract
Arsenic (As) bioremediation has been an economical and sustainable approach, being practiced widely under several As-contaminated environments. Bioremediation of As involves the use of bacteria, fungi, yeast, plants, and genetically modified organisms for detoxification/removal of As from the contaminated site. The understanding of multi-factorial biological components involved in these approaches is complex and more and more efforts are on their way to make As bioremediation economical and efficient. In this regard, we systematically reviewed the recent literature (n=200) from the last two decades regarding As bioremediation potential of conventional and recent technologies including genetically modified plants for phytoremediation and integrated approaches. Also, the responsible mechanisms behind different approaches have been identified. From the literature, it was found that As bioremediation through biosorption, bioaccumulation, phytoextraction, and volatilization involving As-resistant microbes has proved a very successful technology. However, there are various pathways of As tolerance of which the mechanisms have not been fully understood. Recently, phytosuction separation technology has been introduced and needs further exploration. Also, integrated approaches like phytobial, constructed wetlands using As-resistant bacteria with plant growth-promoting activities have not been extensively studied. It is speculated that the integrated bioremediation approaches with practical applicability and reliability would prove most promising for As remediation. Further technological advancements would help explore the identified research gaps in different approaches and lead us toward sustainability and perfection in As bioremediation.
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Affiliation(s)
- Sana Irshad
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Zuoming Xie
- School of Environmental Studies, China University of Geosciences, Wuhan, 430074, People's Republic of China
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, People's Republic of China
| | - Sajid Mehmood
- Guangdong Provincial Key Laboratory for Radionuclides Pollution Control and Resources, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Asad Nawaz
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, People's Republic of China
| | - Allah Ditta
- Department of Environmental Sciences, Shaheed Benazir Bhutto University Sheringal, Upper Dir, Khyber Pakhtunkhwa, 18000, Pakistan.
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
| | - Qaisar Mahmood
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan.
- School of Biotechnology and Food Engineering, Huanghuai University, Zhumadian, 463000, China.
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Martin-Pozas T, Sanchez-Moral S, Cuezva S, Jurado V, Saiz-Jimenez C, Perez-Lopez R, Carrey R, Otero N, Giesemann A, Well R, Calaforra JM, Fernandez-Cortes A. Biologically mediated release of endogenous N 2O and NO 2 gases in a hydrothermal, hypoxic subterranean environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141218. [PMID: 32777502 DOI: 10.1016/j.scitotenv.2020.141218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
Abstract
The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO2-rich fluids. Anomalous concentrations of N2O and NO2 were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO2 and CH4 during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O2, temperature, and GHG concentration. Both the N2O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N2O and NO2 emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH2OH, NO, and NO2- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | - Soledad Cuezva
- Plants and Ecosystems, Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium.
| | - Valme Jurado
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil Conservation, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Raul Perez-Lopez
- Geological Hazard Division, Geological Survey of Spain (IGME), 28003 Madrid, Spain.
| | - Raul Carrey
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Neus Otero
- Grup MAiMA, SGR Mineralogia Aplicada, Geoquímica i Geomicrobiologia, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Recerca de l'Aigua (IdRA), UB, 08001 Barcelona, Spain.
| | - Anette Giesemann
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Reinhard Well
- Thünen Institute of Climate-Smart Agriculture, Federal Research Institute for Rural Areas, Forestry and Fisheries, 38116 Braunschweig, Germany.
| | - Jose M Calaforra
- Department of Biology and Geology, University of Almeria, 04120 Almeria, Spain.
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Han YH, Yin DX, Jia MR, Wang SS, Chen Y, Rathinasabapathi B, Chen DL, Ma LQ. Arsenic-resistance mechanisms in bacterium Leclercia adecarboxylata strain As3-1: Biochemical and genomic analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 690:1178-1189. [PMID: 31470481 DOI: 10.1016/j.scitotenv.2019.07.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/06/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Microbial arsenic transformation is important in As biogeochemical cycles in the environment. In this study, a new As-resistant bacterial strain Leclercia adecarboxylata As3-1 was isolated and its associated mechanisms in As resistance and detoxification were evaluated based on genome sequencing and gene annotations. After subjecting strain As3-1 to medium containing arsenate (AsV), AsV reduction occurred and an AsV-enhanced bacterial growth was observed. Strain As3-1 lacked arsenite (AsIII) oxidation ability and displayed lower AsIII resistance than AsV, probably due to its higher AsIII accumulation. Polymerase chain reaction and phylogenetic analysis showed that strain As3-1 harbored a typical AsV reductase gene (arsC) on the plasmids. Genome sequencing and gene annotations identified four operons phoUpstBACS, arsHRBC, arsCRDABC and ttrRSBCA, with 8 additional genes outside the operons that might have involved in As resistance and detoxification in strain As3-1. These included 5 arsC genes explaining why strain As3-1 tolerated high AsV concentrations. Besides ArsC, TtrB, TtrC and TtrA proteins could also be involved in AsV reduction and consequent energy acquisition for bacterial growth. Our data provided a new example of diverse As-regulating systems and AsV-enhanced growth without ArrA in bacteria. The information helps to understand the role of As in selecting microbial systems that can transform and utilize As.
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Affiliation(s)
- Yong-He Han
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Fujian Key Laboratory of Pollution Control and Resource Reuse, Fuzhou 350007, China
| | - Dai-Xia Yin
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Meng-Ru Jia
- School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Shan-Shan Wang
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China
| | - Yanshan Chen
- School of the Environment, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Bala Rathinasabapathi
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, United States
| | - Deng-Long Chen
- Quangang Petrochemical Research Institute, Fujian Normal University, Quanzhou, Fujian 362801, China; Innovative Center for Eco-Friendly Polymeric Materials, Quanzhou, Fujian 362801, China.
| | - Lena Q Ma
- College of Environmental Science and Engineering, Fujian Normal University, Fuzhou, Fujian 350007, China; Soil and Water Sciences Department, University of Florida, Gainesville, FL 32611, United States.
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Kumari N, Rana A, Jagadevan S. Arsenite biotransformation by Rhodococcus sp.: Characterization, optimization using response surface methodology and mechanistic studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 687:577-589. [PMID: 31216511 DOI: 10.1016/j.scitotenv.2019.06.077] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 05/11/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
A large population of the world is under increased health risk due to consumption of arsenic contaminated groundwater. The present study investigates the arsenic resistance and arsenic biotransforming ability in three bacterial species, namely Bacillus arsenicus, Rhodococcus sp. and Alcaligenes faecalis for employing them in potential groundwater bioremediation programmes. The tolerance to pH levels for the 3 organisms are 6-9 for A. faecalis, 5-10 for Rhodococcus and 5-9 for B. arsenicus. The arsenic bio-oxidation capacity was qualitatively confirmed by using the silver nitrate method and all three bacteria were able to convert arsenite to arsenate. The arsenite tolerance capacity (MIC values) were found to be 3 mM, 7 mM and 12 mM for B. arsenicus, A. faecalis and Rhodococcus sp. respectively. The changes in cellular morphology of these strains under various arsenic stress conditions were studied using advanced cell imaging techniques such as scanning electron microscopy and Atomic Force Microscopy. Rhodococcus sp. emerged as a potential candidate for bioremediation application. A response surface methodology was employed to optimize key parameters affecting arsenic removal (pH, Iron (II) soluble, concentration of humic acid and initial arsenic concentration) and at optimized conditions, experimental runs demonstrated 48.34% removal of As (III) (initial concentration = 500 μg/L) in a duration of 6 h, with complete removal after 48 h. Evidences from this work indicate that arsenic removal occurs through bioaccumulation, biotransformation and biosorption. The present study makes the first attempt to investigate the arsenic removal capability of Rhodococcus sp. in synthetic groundwater by employing bacterial whole cell assays. This study also sheds light on the arsenic tolerance and detoxification mechanisms employed by these bacteria, knowledge of which could be crucial in the successful implementation of in-situ bioremediation programmes.
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Affiliation(s)
- Nisha Kumari
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004, India
| | - Anu Rana
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004, India
| | - Sheeja Jagadevan
- Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand 826004, India.
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Enhanced Arsenic Tolerance in Triticum aestivum Inoculated with Arsenic-Resistant and Plant Growth Promoter Microorganisms from a Heavy Metal-Polluted Soil. Microorganisms 2019; 7:microorganisms7090348. [PMID: 31547348 PMCID: PMC6780836 DOI: 10.3390/microorganisms7090348] [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: 08/14/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 12/16/2022] Open
Abstract
In soils multi-contaminated with heavy metal and metalloids, the establishment of plant species is often hampered due to toxicity. This may be overcome through the inoculation of beneficial soil microorganisms. In this study, two arsenic-resistant bacterial isolates, classified as Pseudomonas gessardii and Brevundimonas intermedia, and two arsenic-resistant fungi, classified as Fimetariella rabenhortii and Hormonema viticola, were isolated from contaminated soil from the Puchuncaví valley (Chile). Their ability to produce indoleacetic acid and siderophores and mediate phosphate solubilization as plant growth-promoting properties were evaluated, as well as levels of arsenic resistance. A real time PCR applied to Triticum aestivum that grew in soil inoculated with the bacterial and fungal isolates was performed to observe differences in the relative expression of heavy metal stress defense genes. The minimum inhibitory concentration of the bacterial strains to arsenate was up to 7000 mg·L−1 and that of the fungal strains was up to 2500 mg·L−1. P. gessardi was able to produce siderophores and solubilize phosphate; meanwhile, B. intermedia and both fungi produced indoleacetic acid. Plant dry biomass was increased and the relative expression of plant metallothionein, superoxide dismutase, ascorbate peroxidase and phytochelatin synthase genes were overexpressed when P. gessardii plus B. intermedia were inoculated.
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Shri M, Singh PK, Kidwai M, Gautam N, Dubey S, Verma G, Chakrabarty D. Recent advances in arsenic metabolism in plants: current status, challenges and highlighted biotechnological intervention to reduce grain arsenic in rice. Metallomics 2019; 11:519-532. [PMID: 30672944 DOI: 10.1039/c8mt00320c] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Arsenic (As), classified as a “metalloid” element, is well known for its carcinogenicity and other toxic effects to humans.
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Affiliation(s)
- Manju Shri
- Academy of Scientific and Innovative Research (AcSIR)
- Ghaziabad
- India
| | - Pradyumna Kumar Singh
- Academy of Scientific and Innovative Research (AcSIR)
- Ghaziabad
- India
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
| | - Maria Kidwai
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
- India
| | - Neelam Gautam
- Academy of Scientific and Innovative Research (AcSIR)
- Ghaziabad
- India
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
| | - Sonali Dubey
- Academy of Scientific and Innovative Research (AcSIR)
- Ghaziabad
- India
| | - Giti Verma
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
- India
| | - Debasis Chakrabarty
- Academy of Scientific and Innovative Research (AcSIR)
- Ghaziabad
- India
- Genetics and Molecular Biology Division
- CSIR-National Botanical Research Institute
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Sathe SS, Mahanta C, Mishra P. Simultaneous influence of indigenous microorganism along with abiotic factors controlling arsenic mobilization in Brahmaputra floodplain, India. JOURNAL OF CONTAMINANT HYDROLOGY 2018; 213:1-14. [PMID: 29598853 DOI: 10.1016/j.jconhyd.2018.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/13/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
In the dynamic cycling of oxic and anoxic aqueous alluvial aquifer environments, varying Arsenic (As) concentrations are controlled by both abiotic and biotic factors. Studies have shown a significant form of toxic As (III) being released through the reductive dissolution of iron-oxy/hydroxide minerals and microbial reduction mechanisms, which leads to a serious health concern. The present study was performed in order to assess the abiotic and biotic factors influencing As release into the alluvial aquifer groundwater in Brahmaputra floodplain, India. The groundwater chemistry, characterization of the sediments, isolation, identification and characterization of prominent As releasing indigenous bacterium were conducted. The measured solid and liquid phases of total As concentration were ranged between 0.02 and 17.2 mg kg-1 and 8 to 353 μg L-1, respectively. The morphology and mineralogy showed the presence of detrital and authigenic mineral assemblages whereas primary and secondary As bearing Realgar and Claudetite minerals were identified, respectively. Furthermore, significant non-labile As fraction was found associated with the amorphous oxides of Fe, Mn and Al. The observed groundwater chemistry and sediment color, deduced a sub-oxic reducing aquifer conditions in As-contaminated regions. In addition, 16S rDNA sequencing results of the isolated bacterium showed the prominent Pseudomonas aeruginosa responsible for the mobilization of As, reducing condition, biomineralization and causing grey color to the sediments at the shallower and deeper aquifers in the study area. These findings suggest that microbial metabolic activities are equally responsible in iron-oxy/hydroxide reductive dissolution, controlling As mobilization in dynamic fluvial flood plains.
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Affiliation(s)
- Sandip S Sathe
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
| | - Chandan Mahanta
- Department of Civil Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pushpanjali Mishra
- Department of Computer Science and Engineering, Sri Ramswaroop Memorial College of Engineering and Management, Lucknow 227105, Uttar Pradesh, India
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14
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Saba, Andreasen R, Li Y, Rehman Y, Ahmed M, Meyer R, Sabri A. Prospective role of indigenousExiguobacterium profundumPT2 in arsenic biotransformation and biosorption by planktonic cultures and biofilms. J Appl Microbiol 2018; 124:431-443. [DOI: 10.1111/jam.13636] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/10/2017] [Accepted: 11/02/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Saba
- Department of Microbiology and Molecular Genetics; University of the Punjab; Lahore Pakistan
- Interdisciplinary Nanoscience Centre; Aarhus University; Aarhus Denmark
- The Women University Multan; Multan Pakistan
| | - R. Andreasen
- Department of Geoscience; Aarhus University; Aarhus Denmark
| | - Y. Li
- Bio-Optics Institute; School of Physics and Electronics; Henan University; Henan China
| | - Y. Rehman
- Department of Microbiology and Molecular Genetics; University of the Punjab; Lahore Pakistan
| | - M. Ahmed
- Department of Microbiology and Molecular Genetics; University of the Punjab; Lahore Pakistan
| | - R.L. Meyer
- Interdisciplinary Nanoscience Centre; Aarhus University; Aarhus Denmark
| | - A.N. Sabri
- Department of Microbiology and Molecular Genetics; University of the Punjab; Lahore Pakistan
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Khowal S, Siddiqui MZ, Ali S, Khan MT, Khan MA, Naqvi SH, Wajid S. A report on extensive lateral genetic reciprocation between arsenic resistant Bacillus subtilis and Bacillus pumilus strains analyzed using RAPD-PCR. Mol Phylogenet Evol 2016; 107:443-454. [PMID: 27956257 DOI: 10.1016/j.ympev.2016.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/26/2016] [Accepted: 12/08/2016] [Indexed: 12/16/2022]
Abstract
The study involves isolation of arsenic resistant bacteria from soil samples. The characterization of bacteria isolates was based on 16S rRNA gene sequences. The phylogenetic consanguinity among isolates was studied employing rpoB and gltX gene sequence. RAPD-PCR technique was used to analyze genetic similarity between arsenic resistant isolates. In accordance with the results Bacillus subtilis and Bacillus pumilus strains may exhibit extensive horizontal gene transfer. Arsenic resistant potency in Bacillus sonorensis and high arsenite tolerance in Bacillus pumilus strains was identified. The RAPD-PCR primer OPO-02 amplified a 0.5kb DNA band specific to B. pumilus 3ZZZ strain and 0.75kb DNA band specific to B. subtilis 3PP. These unique DNA bands may have potential use as SCAR (Sequenced Characterized Amplified Region) molecular markers for identification of arsenic resistant B. pumilus and B. subtilis strains.
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Affiliation(s)
- Sapna Khowal
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Md Zulquarnain Siddiqui
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Shadab Ali
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Mohd Taha Khan
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India
| | - Mather Ali Khan
- 247, Bond Life Sciences Centre, 1201 Rollins Street, University of Missouri-Columbia, Columbia, MO 65211, USA
| | | | - Saima Wajid
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi 110 062, India.
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