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Yuan Y, Gao J, Wang Z, Xu H, Zeng L, Fu X, Zhao Y. Exposure to zinc and dialkyldimethyl ammonium compound alters bacterial community structure and resistance gene levels in partial sulfur autotrophic denitrification coupled with the Anammox process. JOURNAL OF HAZARDOUS MATERIALS 2024; 476:135070. [PMID: 38944986 DOI: 10.1016/j.jhazmat.2024.135070] [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: 04/10/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Dialkyldimethyl ammonium compound (DADMAC) is widely used in daily life as a typical disinfectant and often co-exists with the heavy metal zinc in sewage environments. This study investigated the effects of co-exposure to zinc (1 mg/L) and DADMAC (0.2-5 mg/L) on the performance, bacterial community, and resistance genes (RGs) in a partial sulfur autotrophic denitrification coupled with anaerobic ammonium oxidation (PSAD-Anammox) system in a sequencing batch moving bed biofilm reactor for 150 days. Co-exposure to zinc and low concentration (0.2 mg/L) DADMAC did not affect the nitrogen removal ability of the PASD-Anammox system, but increased the abundance and transmission risk of free RGs in water. Co-exposure to zinc and medium-to-high (2-5 mg/L) DADMAC led to fluctuations in and inhibition of nitrogen removal, which might be related to the enrichment of heterotrophic denitrifying bacteria dominated by Denitratisoma. Co-exposure to zinc and high concentration DADMAC (5 mg/L) stimulated the secretion of extracellular polymeric substances and increased the proliferation risk of intracellular RGs in sludge. This study provided insights into the application of PSAD-Anammox system and the ecological risks of wastewater containing zinc and DADMAC.
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Affiliation(s)
- Yukun Yuan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Jingfeng Gao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China.
| | - Zhiqi Wang
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China; Institute of NBC Defense, P.O. Box 1048, Beijing 102205, China
| | - Hongxin Xu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Liqin Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Xiaoyu Fu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
| | - Yifan Zhao
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, Beijing 100124, China
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Lyons TW, Tino CJ, Fournier GP, Anderson RE, Leavitt WD, Konhauser KO, Stüeken EE. Co-evolution of early Earth environments and microbial life. Nat Rev Microbiol 2024; 22:572-586. [PMID: 38811839 DOI: 10.1038/s41579-024-01044-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/31/2024]
Abstract
Two records of Earth history capture the evolution of life and its co-evolving ecosystems with interpretable fidelity: the geobiological and geochemical traces preserved in rocks and the evolutionary histories captured within genomes. The earliest vestiges of life are recognized mostly in isotopic fingerprints of specific microbial metabolisms, whereas fossils and organic biomarkers become important later. Molecular biology provides lineages that can be overlayed on geologic and geochemical records of evolving life. All these data lie within a framework of biospheric evolution that is primarily characterized by the transition from an oxygen-poor to an oxygen-rich world. In this Review, we explore the history of microbial life on Earth and the degree to which it shaped, and was shaped by, fundamental transitions in the chemical properties of the oceans, continents and atmosphere. We examine the diversity and evolution of early metabolic processes, their couplings with biogeochemical cycles and their links to the oxygenation of the early biosphere. We discuss the distinction between the beginnings of metabolisms and their subsequent proliferation and their capacity to shape surface environments on a planetary scale. The evolution of microbial life and its ecological impacts directly mirror the Earth's chemical and physical evolution through cause-and-effect relationships.
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Affiliation(s)
- Timothy W Lyons
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA.
| | - Christopher J Tino
- Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.
| | - Gregory P Fournier
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rika E Anderson
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- Biology Department, Carleton College, Northfield, MN, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Eva E Stüeken
- Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
- School of Earth and Environmental Sciences, University of St Andrews, St Andrews, UK
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Qiao Y, Lin Z, Li L, Jiang W, Ge J, Chen J, Lu L, Tian S. Serendipita indica Drives Sulfur-Related Microbiota in Enhancing Growth of Hyperaccumulator Sedum alfredii and Facilitating Soil Cadmium Remediation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:14726-14739. [PMID: 39116417 DOI: 10.1021/acs.est.4c01418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Endophytic fungus Serendipita indica can bolster plant growth and confer protection against various biotic and abiotic stresses. However, S. indica-reshaped rhizosphere microecology interactions and root-soil interface processes in situ at the submicrometer scale remain poorly understood. We combined amplicon sequencing and high-resolution nano X-ray fluorescence (nano-XRF) imaging of the root-soil interface to reveal cadmium (Cd) rhizosphere processes. S. indica can successfully colonize the roots of Sedum alfredii Hance, which induces a remarkable increase in shoot biomass by 211.32% and Cd accumulation by 235.72%. Nano-XRF images showed that S. indica colonization altered the Cd distribution in the rhizosphere and facilitated the proximity of more Cd and sulfur (S) to enter the roots and transport to the shoot. Furthermore, the rhizosphere-enriched microbiota demonstrated a more stable network structure after the S. indica inoculation. Keystone species were strongly associated with growth promotion and Cd absorption. For example, Comamonadaceae are closely related to the organic acid cycle and S bioavailability, which could facilitate Cd and S accumulation in plants. Meanwhile, Sphingomonadaceae could release auxin and boost plant biomass. In summary, we construct a mutualism system for beneficial fungi and hyperaccumulation plants, which facilitates high-efficient remediation of Cd-contaminated soils by restructuring the rhizosphere microbiota.
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Affiliation(s)
- Yabei Qiao
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
| | - Zhi Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
| | - Luxi Li
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Wei Jiang
- Xianghu Laboratory, Biotechnology Institute, Hangzhou 311231, P. R. China
| | - Jun Ge
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
| | - Jiuzhou Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
| | - Lingli Lu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Science, Zhejiang University, Hangzhou 310058, P. R. China
- Zhejiang Provincial Key Laboratory of Subtropic Soil and Plant Nutrition, Zhejiang University, Hangzhou 310058, P. R. China
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Rai AK, Basak N, Chandra P, Sundha P, Kaur H, Bedwal S, Patel S, Kumar S, Choubey K, Meena RL, Sharma PC, Yadav RK. Occurrence of Sphingomonas olei with elemental S oxidation capability in sodic soil: Potential role in sodicity reclamation and plant growth promotion. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116396. [PMID: 38696872 DOI: 10.1016/j.ecoenv.2024.116396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/04/2024]
Abstract
The success of the sodic soil reclamation using elemental S (S°) depends on the population of the native S° oxidizers. Augmenting the native flora of the sodic soils with effective S° oxidizers can enhance the success of the sodic soil reclamation. Present study reports for the first time the S° oxidation potential of the Sphingomonas olei strain 20UP7 isolated from sodic soils with pHs 9.8 and ECe 3.6 dS m-1. Inoculation with S. olei strain 20UP7 caused 13.0-24.2 % increase in S° oxidation in different sodic soils (pHs 9.1-10.5). It improved the concentration of the Ca2+, Mg2+, PO43- and declined the HCO3- and total alkalinity of the soil solution. This isolate also showed appreciable P and Zn solubilization, indole acetic acid, ammonia, and titratable acidity production in the growth media. It tended to the formation of biofilm around sulphur particles. The PCR amplification with gene-specific primers showed the occurrence of soxA, soxB, and soxY genes with a single band corresponding to length of 850, 460, and 360 base pairs, respectively. The integration of the S. olei strain 20UP7 with S° caused 21.7-25.4 % increase in the rice and wheat yield compared to the soil treated with S° alone. This study concludes that the S. olei, native to high saline-sodic soils can be utilized for improving the sodicity reclamation and plant growth promotion using elemental S based formulations.
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Affiliation(s)
- Arvind Kumar Rai
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Nirmalendu Basak
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India.
| | - Priyanka Chandra
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India.
| | - Parul Sundha
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Harshpreet Kaur
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Sandeep Bedwal
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India; Department of Soil Science, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana 125004, India
| | - Subedar Patel
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Sanjay Kumar
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Kajal Choubey
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
| | - Rameshwar Lal Meena
- ICAR-Central Soil Salinity Research Institute, Karnal, Haryana 132001, India
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Rey-Velasco X, Lucena T, Belda A, Gasol JM, Sánchez O, Arahal DR, Pujalte MJ. Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean. Front Microbiol 2024; 15:1407904. [PMID: 38863746 PMCID: PMC11165706 DOI: 10.3389/fmicb.2024.1407904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.
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Affiliation(s)
| | - Teresa Lucena
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Ana Belda
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - Josep M. Gasol
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
| | - María J. Pujalte
- Departamento de Microbiología y Ecología, Universitat de València, València, Spain
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Geng L, Yang L, Liu T, Zhang S, Sun X, Wang W, Pan H, Yan L. Higher diversity of sulfur-oxidizing bacteria based on soxB gene sequencing in surface water than in spring in Wudalianchi volcanic group, NE China. Int Microbiol 2024:10.1007/s10123-024-00526-6. [PMID: 38740654 DOI: 10.1007/s10123-024-00526-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/26/2024] [Accepted: 05/03/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION Sulfur-oxidizing bacteria (SOB) play a key role in the biogeochemical cycling of sulfur. OBJECTIVES To explore SOB diversity, distribution, and physicochemical drivers in five volcanic lakes and two springs in the Wudalianchi volcanic field, China. METHODS This study analyzed microbial communities in samples via high-throughput sequencing of the soxB gene. Physical-chemical parameters were measured, and QIIME 2 (v2019.4), R, Vsearch, MEGA7, and Mothur processed the data. Alpha diversity indices and UPGMA clustering assessed community differences, while heat maps visualized intra-sample variations. Canoco 5.0 analyzed community-environment correlations, and NMDS, Adonis, and PcoA explored sample dissimilarities and environmental factor correlations. SPSS v.18.0 tested for statistical significance. RESULTS The diversity of SOB in surface water was higher than in springs (more than 7.27 times). We detected SOB affiliated to β-proteobacteria (72.3 %), α-proteobacteria (22.8 %), and γ-proteobacteria (4.2 %) distributed widely in these lakes and springs. Rhodoferax and Cupriavidus were most frequent in all water samples, while Rhodoferax and Bradyrhizobium are dominant in surface waters but rare in springs. SOB genera in both habitats were positively correlated. Co-occurrence analysis identified Bradyrhizobium, Blastochloris, Methylibium, and Metyhlobacterium as potential keystone taxa. Redundancy analysis (RDA) revealed positive correlations between SOB diversity and total carbon (TC), Fe2+, and total nitrogen (TN) in all water samples. CONCLUSION The diversity and community structure of SOB in volcanic lakes and springs in the Wudalianchi volcanic group were clarified. Moreover, the diversity and abundance of SOB decreased with the variation of water openness, from open lakes to semi-enclosed lakes and enclosed lakes.
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Affiliation(s)
- Lirong Geng
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Tao Liu
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Xindi Sun
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China
- Key Laboratory of Low‑carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Hong Pan
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin, 150090, Heilongjiang, China
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, Heilongjiang, China.
- Key Laboratory of Low‑carbon Green Agriculture in Northeastern China, Ministry of Agriculture and Rural Affairs P. R. China, Heilongjiang Bayi Agricultural University, Daqing, 163319, China.
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Sun X, Chen Q, Häggblom MM, Liu G, Kong T, Huang D, Chen Z, Li F, Li B, Sun W. Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats. THE ISME JOURNAL 2024; 18:wrae110. [PMID: 38900902 PMCID: PMC11283718 DOI: 10.1093/ismejo/wrae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/09/2024] [Accepted: 06/19/2024] [Indexed: 06/22/2024]
Abstract
Arsenate [As(V)] reduction is a major cause of arsenic (As) release from soils, which threatens more than 200 million people worldwide. While heterotrophic As(V) reduction has been investigated extensively, the mechanism of chemolithotrophic As(V) reduction is less studied. Since As is frequently found as a sulfidic mineral in the environment, microbial mediated sulfur oxidation coupled to As(V) reduction (SOAsR), a chemolithotrophic process, may be more favorable in sites impacted by oligotrophic mining (e.g. As-contaminated mine tailings). While SOAsR is thermodynamically favorable, knowledge regarding this biogeochemical process is still limited. The current study suggested that SOAsR was a more prevalent process than heterotrophic As(V) reduction in oligotrophic sites, such as mine tailings. The water-soluble reduced sulfur concentration was predicted to be one of the major geochemical parameters that had a substantial impact on SOAsR potentials. A combination of DNA stable isotope probing and metagenome binning revealed members of the genera Sulfuricella, Ramlibacter, and Sulfuritalea as sulfur oxidizing As(V)-reducing bacteria (SOAsRB) in mine tailings. Genome mining further expanded the list of potential SOAsRB to diverse phylogenetic lineages such as members associated with Burkholderiaceae and Rhodocyclaceae. Metagenome analysis using multiple tailing samples across southern China confirmed that the putative SOAsRB were the dominant As(V) reducers in these sites. Together, the current findings expand our knowledge regarding the chemolithotrophic As(V) reduction process, which may be harnessed to facilitate future remediation practices in mine tailings.
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Affiliation(s)
- Xiaoxu Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Qizhi Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Max M Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, United States
| | - Guoqiang Liu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 511443, China
| | - Tianle Kong
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Duanyi Huang
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
| | - Zhenyu Chen
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- School of Environment, Key Laboratory of Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Normal University, Xinxiang 453007, China
| | - Fangbai Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Baoqin Li
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Weimin Sun
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- Guangdong-Hong Kong-Macao Joint Laboratory for Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
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Mosley OE, Gios E, Handley KM. Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers. ISME COMMUNICATIONS 2024; 4:ycae047. [PMID: 38650708 PMCID: PMC11033732 DOI: 10.1093/ismeco/ycae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.
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Affiliation(s)
- Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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Kop LFM, Koch H, Jetten MSM, Daims H, Lücker S. Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses. ISME COMMUNICATIONS 2024; 4:ycad017. [PMID: 38317822 PMCID: PMC10839748 DOI: 10.1093/ismeco/ycad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.
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Affiliation(s)
- Linnea F M Kop
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Hanna Koch
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, Tulln an der Donau 3430, Austria
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Holger Daims
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria
| | - Sebastian Lücker
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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10
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Thangaraj S, Kim HR, Heo JM, Son S, Ryu J, Park JW, Kim JH, Kim SY, Jung HK, Kim IN. Unraveling prokaryotic diversity distribution and functional pattern on nitrogen and methane cycling in the subtropical Western North Pacific Ocean. MARINE POLLUTION BULLETIN 2023; 196:115569. [PMID: 37922593 DOI: 10.1016/j.marpolbul.2023.115569] [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: 04/10/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 11/07/2023]
Abstract
Prokaryotes play an important role in marine nitrogen and methane cycles. However, their community changes and metabolic modifications to the concurrent impact of ocean warming (OW), acidification (OA), deoxygenation (OD), and anthropogenic‑nitrogen-deposition (AND) from the surface to the deep ocean remains unknown. We examined here the amplicon sequencing approach across the surface (0-200 m; SL), intermediate (200-1000 m; IL), and deep layers (1000-2200 m; DL), and characterized the simultaneous impacts of OW, OA, OD, and AND on the Western North Pacific Ocean prokaryotic changes and their functional pattern in nitrogen and methane cycles. Results showed that SL possesses higher ammonium oxidation community/metabolic composition assumably the reason for excess nitrogen input from AND and modification of their kinetic properties to OW adaptation. Expanding OD at IL showed hypoxic conditions in the oxygen minimum layer, inducing higher microbial respiration that elevates the dimerization of nitrification genes for higher nitrous oxide production. The aerobic methane-oxidation composition was dominant in SL presumably the reason for adjustment in prokaryotic optimal temperature to OW, while anaerobic oxidation composition was dominant at IL due to the evolutionary changes coupling with higher nitrification. Our findings refocus on climate-change impacts on the open ocean ecosystem from the surface to the deep-environment integrating climate-drivers as key factors for higher nitrous-oxide and methane emissions.
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Affiliation(s)
- Satheeswaran Thangaraj
- Department of Marine Science, Incheon National University, Incheon, South Korea; Freddy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel; Interuniversity Institute for Marine Sciences, Eilat, Israel; Department of Physiology, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Hyo-Ryeon Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Jang-Mu Heo
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Seunghyun Son
- Cooperative Institute for Satellite Earth System Studies (CISESS) / Earth System Science Interdisciplinary Center (ESSIC), University of Maryland, USA
| | - Jongseong Ryu
- Department of Marine Biotechnology, Anyang University, Incheon, South Korea
| | - Jong-Woo Park
- Tidal Flat Research Center, National Institute of Fisheries Science, Gunsan, South Korea
| | - Ju-Hyoung Kim
- Department of Aquaculture and Aquatic Science, Kunsan National University, Gunsan, South Korea
| | - Seo-Young Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea
| | - Hae-Kun Jung
- Environment and Fisheries Resources Research Division, East Sea Fisheries Institute, National Institute of Fisheries Science, Gangneung, South Korea
| | - Il-Nam Kim
- Department of Marine Science, Incheon National University, Incheon, South Korea.
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11
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Zhang J, Yang Q, Yue W, Yang B, Zhou W, Chen L, Huang X, Zhang W, Dong J, Ling J. Seagrass Thalassia hemprichii and associated bacteria co-response to the synergistic stress of ocean warming and ocean acidification. ENVIRONMENTAL RESEARCH 2023; 236:116658. [PMID: 37454799 DOI: 10.1016/j.envres.2023.116658] [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: 03/11/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
Seagrass meadows play vital ecological roles in the marine ecosystem. Global climate change poses considerable threats to seagrass survival. However, it is unclear how seagrass and its associated bacteria will respond under future complex climate change scenarios. This study explored the effects of ocean warming (+2 °C) and ocean acidification (-0.4 units) on seagrass physiological indexes and bacterial communities (sediment and rhizosphere bacteria) of the seagrass Thalassia hemprichii during an experimental exposure of 30 days. Results demonstrated that the synergistic effect of ocean warming and ocean acidification differed from that of one single factor on seagrass and the associated bacterial community. The seagrass showed a weak resistance to ocean warming and ocean acidification, which manifested through the increase in the activity of typical oxidoreductase enzymes. Moreover, the synergistic effect of ocean warming and ocean acidification caused a significant decrease in seagrass's chlorophyll content. Although the bacterial community diversity exhibited higher resistance to ocean warming and ocean acidification, further bacterial functional analysis revealed the synergistic effect of ocean warming and ocean acidification led to significant increases in SOX-related genes abundance which potentially supported the seagrass in resisting climate stress by producing sulfates and oxidizing hydrogen sulfide. More stable bacterial communities were detected in the seagrass rhizosphere under combined ocean warming and ocean acidification. While for one single environmental stress, simpler networks were detected in the rhizosphere. In addition, the observed significant correlations between several modules of the bacterial community and the physiological indexes of the seagrass indicate the possible intimate interaction between seagrass and bacteria under ocean warming and ocean acidification. This study extends our understanding regarding the role of seagrass associated bacterial communities and sheds light on both the prediction and preservation of the seagrass meadow ecosystems in response to global climate change.
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Affiliation(s)
- Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Qingsong Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Weizhong Yue
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Bing Yang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Weiguo Zhou
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Luxiang Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Xiaofang Huang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wenqian Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China
| | - Junde Dong
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China.
| | - Juan Ling
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China; Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, 572000, PR China; Guangdong Provincial Observation and Research Station for Coastal Upwelling Ecosystem, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Shantou, 515041, PR China; Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, PR China.
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12
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Wang YH, Liu JC, Du YH, Xu JH, Du ZJ, Ye MQ. Psychromarinibacter sediminicola sp. nov., a novel moderately halophilic, metabolically diverse bacterium isolated from a solar saltern sediment, and comparison between members of family Roseobacteraceae. Arch Microbiol 2023; 205:331. [PMID: 37698663 DOI: 10.1007/s00203-023-03672-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. This study compared and analyzed the phylogenetic, genomic, biochemical, and chemo taxonomical properties of seven species from three genera (Psychromarinibacter, Lutimaribacter, and Maritimibacter) of the family Roseobacteraceae. Moreover, a novel strain, named C21-152T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) between genomes of the novel strain and Psychromarinibacter halotolerans MCCC 1K03203T were 97.19, 78.49, 73.45, and 21.90%, respectively. Genome sequencing of strain C21-152T revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152T was resistant to many antibiotics and had the ability to survive below 13% salinity. This strain had versatile survival strategies in saline environments including salt-in, compatible solute production and compatible solute transport. Some of its physiological features enriched and complemented the knowledge of the characteristics of the genus Psychromarinibacter. Optimum growth of strain C21-152T occurred at 37 ℃, with 5-6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152T should represent a novel specie of the genus Psychromarinibacter, for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152T (= MCCC 1H00808T = KCTC 92746T = SDUM1063002T).
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Affiliation(s)
- Yu-Hui Wang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Jun-Cheng Liu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Heng Du
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jin-Hao Xu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China.
- Shenzhen Research Institute of Shandong University, Shenzhen, 518057, Guangdong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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13
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Konrad R, Vergara-Barros P, Alcorta J, Alcamán-Arias ME, Levicán G, Ridley C, Díez B. Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana. Microorganisms 2023; 11:1803. [PMID: 37512975 PMCID: PMC10385741 DOI: 10.3390/microorganisms11071803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.
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Affiliation(s)
- Ricardo Konrad
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
| | - Pablo Vergara-Barros
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
| | - María E Alcamán-Arias
- Department of Oceanography, University of Concepcion, Concepcion 4030000, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
- Escuela de Medicina, Universidad Espíritu Santo, Guayaquil 0901952, Ecuador
| | - Gloria Levicán
- Biology Department, Chemistry and Biology Faculty, University of Santiago of Chile, Santiago 9170022, Chile
| | - Christina Ridley
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago 8331150, Chile
- Millennium Institute Center for Genome Regulation (CGR), Santiago 8370186, Chile
- Center for Climate and Resilience Research (CR)2, Santiago 8370449, Chile
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14
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Mateos K, Chappell G, Klos A, Le B, Boden J, Stüeken E, Anderson R. The evolution and spread of sulfur cycling enzymes reflect the redox state of the early Earth. SCIENCE ADVANCES 2023; 9:eade4847. [PMID: 37418533 PMCID: PMC10328410 DOI: 10.1126/sciadv.ade4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 02/06/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
The biogeochemical sulfur cycle plays a central role in fueling microbial metabolisms, regulating the Earth's redox state, and affecting climate. However, geochemical reconstructions of the ancient sulfur cycle are confounded by ambiguous isotopic signals. We use phylogenetic reconciliation to ascertain the timing of ancient sulfur cycling gene events across the tree of life. Our results suggest that metabolisms using sulfide oxidation emerged in the Archean, but those involving thiosulfate emerged only after the Great Oxidation Event. Our data reveal that observed geochemical signatures resulted not from the expansion of a single type of organism but were instead associated with genomic innovation across the biosphere. Moreover, our results provide the first indication of organic sulfur cycling from the Mid-Proterozoic onwards, with implications for climate regulation and atmospheric biosignatures. Overall, our results provide insights into how the biological sulfur cycle evolved in tandem with the redox state of the early Earth.
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Affiliation(s)
- Katherine Mateos
- Carleton College, Northfield, MN, USA
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Garrett Chappell
- Carleton College, Northfield, MN, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aya Klos
- Carleton College, Northfield, MN, USA
| | - Bryan Le
- Carleton College, Northfield, MN, USA
| | - Joanne Boden
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Eva Stüeken
- University of St. Andrews, School of Earth and Environmental Sciences, Bute Building, Queen’s Terrace, St Andrews, Fife KY16 9TS, UK
| | - Rika Anderson
- Carleton College, Northfield, MN, USA
- NASA NExSS Virtual Planetary Laboratory, University of Washington, Seattle, WA, USA
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15
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Lima LFO, Alker AT, Papudeshi B, Morris MM, Edwards RA, de Putron SJ, Dinsdale EA. Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale. MICROBIAL ECOLOGY 2023; 86:392-407. [PMID: 35965269 PMCID: PMC10293411 DOI: 10.1007/s00248-022-02094-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.
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Affiliation(s)
- Laís F. O. Lima
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Biological Sciences, University of California Davis, Davis, CA USA
| | - Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, CA USA
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
| | | | - Robert A. Edwards
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
| | | | - Elizabeth A. Dinsdale
- Department of Biology, San Diego State University, San Diego, CA USA
- College of Science and Engineering, Flinders University, Adelaide, South Australia Australia
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16
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Baltar F, Martínez-Pérez C, Amano C, Vial M, Robaina-Estévez S, Reinthaler T, Herndl GJ, Zhao Z, Logares R, Morales SE, González JM. A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean. Nat Microbiol 2023; 8:1137-1148. [PMID: 37095175 DOI: 10.1038/s41564-023-01374-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 03/24/2023] [Indexed: 04/26/2023]
Abstract
The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the 'Tara Oceans' and 'Malaspina' expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean.
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Affiliation(s)
- Federico Baltar
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.
| | - Clara Martínez-Pérez
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Chie Amano
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Marion Vial
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | | | - Thomas Reinthaler
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University, AB Den Burg, The Netherlands
| | - Zihao Zhao
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain.
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17
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Nosalova L, Piknova M, Kolesarova M, Pristas P. Cold Sulfur Springs-Neglected Niche for Autotrophic Sulfur-Oxidizing Bacteria. Microorganisms 2023; 11:1436. [PMID: 37374938 DOI: 10.3390/microorganisms11061436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Since the beginning of unicellular life, dissimilation reactions of autotrophic sulfur bacteria have been a crucial part of the biogeochemical sulfur cycle on Earth. A wide range of sulfur oxidation states is reflected in the diversity of metabolic pathways used by sulfur-oxidizing bacteria. This metabolically and phylogenetically diverse group of microorganisms inhabits a variety of environments, including extreme environments. Although they have been of interest to microbiologists for more than 150 years, meso- and psychrophilic chemolithoautotrophic sulfur-oxidizing microbiota are less studied compared to the microbiota of hot springs. Several recent studies suggested that cold sulfur waters harbor unique, yet not described, bacterial taxa.
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Affiliation(s)
- Lea Nosalova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Maria Piknova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Mariana Kolesarova
- Department of Microbiology, Faculty of Science, Institute of Biology and Ecology, Pavol Jozef Safarik University in Kosice, 041 54 Kosice, Slovakia
| | - Peter Pristas
- Centre of Biosciences, Institute of Animal Physiology, Slovak Academy of Sciences, 040 01 Kosice, Slovakia
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18
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Mo S, Yan B, Gao T, Li J, Kashif M, Song J, Bai L, Yu D, Liao J, Jiang C. Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB. Sci Rep 2023; 13:8126. [PMID: 37208450 DOI: 10.1038/s41598-023-34995-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/11/2023] [Indexed: 05/21/2023] Open
Abstract
Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB ( https://smdb.gxu.edu.cn/ )-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.
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Affiliation(s)
- Shuming Mo
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, 530007, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Bing Yan
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, 530007, China
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China
| | - Tingwei Gao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Beihai, 536000, China
| | - Jinhui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Muhammad Kashif
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, 530007, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jingjing Song
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535011, China
| | - Lirong Bai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535011, China
| | - Dahui Yu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535011, China.
| | - Jianping Liao
- Guangxi Key Lab of Human-Machine Interaction and Intelligent Decision, Nanning Normal University, Nanning, 530299, China.
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, China.
| | - Chengjian Jiang
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Research Center for Biological Science and Technology, Guangxi Academy of Sciences, Nanning, 530007, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, 535011, China.
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19
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Whaley-Martin KJ, Chen LX, Nelson TC, Gordon J, Kantor R, Twible LE, Marshall S, McGarry S, Rossi L, Bessette B, Baron C, Apte S, Banfield JF, Warren LA. O 2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters. Nat Commun 2023; 14:2006. [PMID: 37037821 PMCID: PMC10086054 DOI: 10.1038/s41467-023-37426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/14/2023] [Indexed: 04/12/2023] Open
Abstract
The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S2O32-] via the complete Sox pathway coupled to O2. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO3-, resulting in higher [S2O32-] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.
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Affiliation(s)
- Kelly J Whaley-Martin
- University of Toronto, Toronto, ON, Canada
- Environmental Resources management (ERM), Toronto, ON, Canada
| | - Lin-Xing Chen
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | | | - Rose Kantor
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | | | - Stephanie Marshall
- Environmental Resources management (ERM), Toronto, ON, Canada
- McMaster University, Hamilton, ON, Canada
| | - Sam McGarry
- Glencore, Sudbury Integrated Nickel Operations, Sudbury, ON, Canada
| | | | | | | | - Simon Apte
- CSIRO Land and Water, Clayton, NSW, Australia
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
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20
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Gao P, Fan K. Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review. Arch Microbiol 2023; 205:162. [PMID: 37010699 DOI: 10.1007/s00203-023-03520-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/18/2023] [Accepted: 03/26/2023] [Indexed: 04/04/2023]
Abstract
Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.
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Affiliation(s)
- Peike Gao
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
| | - Keyan Fan
- College of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
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21
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Mo S, He S, Sang Y, Li J, Kashif M, Zhang Z, Su G, Jiang C. Integration of Microbial Transformation Mechanism of Polyphosphate Accumulation and Sulfur Cycle in Subtropical Marine Mangrove Ecosystems with Spartina alterniflora Invasion. MICROBIAL ECOLOGY 2023; 85:478-494. [PMID: 35157108 DOI: 10.1007/s00248-022-01979-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
Excessive phosphorus can lead to eutrophication in marine and coastal ecosystems. Sulfur metabolism-associated microorganisms stimulate biological phosphorous removal. However, the integrating co-biotransformation mechanism of phosphorus and sulfur in subtropical marine mangrove ecosystems with Spartina alterniflora invasion is poorly understood. In this study, an ecological model of the coupling biotransformation of sulfur and phosphorus is constructed using metagenomic analysis and quantitative polymerase chain reaction strategies. Phylogenetic analysis profiling, a distinctive microbiome with high frequencies of Gammaproteobacteria and Deltaproteobacteria, appears to be an adaptive characteristic of microbial structures in subtropical mangrove ecosystems. Functional analysis reveals that the levels of sulfate reduction, sulfur oxidation, and poly-phosphate (Poly-P) aggregation decrease with increasing depth. However, at depths of 25-50 cm in the mangrove ecosystems with S. alterniflora invasion, the abundance of sulfate reduction genes, sulfur oxidation genes, and polyphosphate kinase (ppk) significantly increased. A strong positive correlation was found among ppk, sulfate reduction, sulfur oxidation, and sulfur metabolizing microorganisms, and the content of sulfide was significantly and positively correlated with the abundance of ppk. Further microbial identification suggested that Desulfobacterales, Anaerolineales, and Chromatiales potentially drove the coupling biotransformation of phosphorus and sulfur cycling. In particular, Desulfobacterales exhibited dominance in the microbial community structure. Our findings provided insights into the simultaneous co-biotransformation of phosphorus and sulfur bioconversions in subtropical marine mangrove ecosystems with S. alterniflora invasion.
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Affiliation(s)
- Shuming Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Sheng He
- Guangxi Key Laboratory of Birth Defects Research and Prevention, Guangxi Key Laboratory of Reproductive Health and Birth Defect prevention, Guangxi Zhuang Autonomous Region Women and Children Health Care Hospital, Nanning, 530033, China
| | - Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Jinhui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Zufan Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Guijiao Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, 530004, China.
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22
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Lin YT, Xu T, Ip JCH, Sun Y, Fang L, Luan T, Zhang Y, Qian PY, Qiu JW, Qian PY, Qiu JW. Interactions among deep-sea mussels and their epibiotic and endosymbiotic chemoautotrophic bacteria: Insights from multi-omics analysis. Zool Res 2023; 44:106-125. [PMID: 36419378 PMCID: PMC9841196 DOI: 10.24272/j.issn.2095-8137.2022.279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Endosymbiosis with Gammaproteobacteria is fundamental for the success of bathymodioline mussels in deep-sea chemosynthesis-based ecosystems. However, the recent discovery of Campylobacteria on the gill surfaces of these mussels suggests that these host-bacterial relationships may be more complex than previously thought. Using the cold-seep mussel ( Gigantidas haimaensis) as a model, we explored this host-bacterial system by assembling the host transcriptome and genomes of its epibiotic Campylobacteria and endosymbiotic Gammaproteobacteria and quantifying their gene and protein expression levels. We found that the epibiont applies a sulfur oxidizing (SOX) multienzyme complex with the acquisition of soxB from Gammaproteobacteria for energy production and switched from a reductive tricarboxylic acid (rTCA) cycle to a Calvin-Benson-Bassham (CBB) cycle for carbon assimilation. The host provides metabolic intermediates, inorganic carbon, and thiosulfate to satisfy the materials and energy requirements of the epibiont, but whether the epibiont benefits the host is unclear. The endosymbiont adopts methane oxidation and the ribulose monophosphate pathway (RuMP) for energy production, providing the major source of energy for itself and the host. The host obtains most of its nutrients, such as lysine, glutamine, valine, isoleucine, leucine, histidine, and folate, from the endosymbiont. In addition, host pattern recognition receptors, including toll-like receptors, peptidoglycan recognition proteins, and C-type lectins, may participate in bacterial infection, maintenance, and population regulation. Overall, this study provides insights into the complex host-bacterial relationships that have enabled mussels and bacteria to thrive in deep-sea chemosynthetic ecosystems.
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Affiliation(s)
- Yi-Tao Lin
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ting Xu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jack Chi-Ho Ip
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Yanan Sun
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China
| | - Ling Fang
- Instrumental Analysis & Research Center, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China
| | - Tiangang Luan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510875, China,Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Yu Zhang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China,E-mail:
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,Department of Ocean Science, Hong Kong University of Science and Technology, Hong Kong SAR, China,
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong 511458, China,
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23
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Gadson O, Bevilacqua JG, Fishman CB, Hahn AS, McAdam AC, Bleacher J, Johnson SS. Metagenome-Assembled Genome of a Putative Chemoheterotroph from Volcanic Terrain in Hawaii. Microbiol Resour Announc 2022; 11:e0055622. [PMID: 36264256 PMCID: PMC9671002 DOI: 10.1128/mra.00556-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/02/2022] [Indexed: 11/18/2022] Open
Abstract
Here, we present the draft genome for a new putative species, Gaiellasilicea maunaloa, most closely related to Gaiella occulta, within the phylum Actinobacteria. This group contains Gram-negative, aerobic mesophilic species. This metagenome-assembled genome (MAG) contributes to knowledge of life in volcanic environments and may inform investigations of life beyond Earth.
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Affiliation(s)
- O. Gadson
- Department of Biology, Georgetown University, Washington, DC, USA
| | - J. G. Bevilacqua
- Department of Biology, Georgetown University, Washington, DC, USA
| | - C. B. Fishman
- Department of Biology, Georgetown University, Washington, DC, USA
- Gladstone Institutes, University of California San Francisco, San Francisco, California, USA
| | - A. S. Hahn
- Koonkie Inc., Menlo Park, California, USA
| | - A. C. McAdam
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | | | - S. S. Johnson
- Department of Biology, Georgetown University, Washington, DC, USA
- Science, Technology, and International Affairs Program, Georgetown University, Washington, DC, USA
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24
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Liu R, Shan Y, Xi S, Zhang X, Sun C. A deep-sea sulfate-reducing bacterium generates zero-valent sulfur via metabolizing thiosulfate. MLIFE 2022; 1:257-271. [PMID: 38818226 PMCID: PMC10989961 DOI: 10.1002/mlf2.12038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 06/01/2024]
Abstract
Zero-valent sulfur (ZVS) is a crucial intermediate in the sulfur geobiochemical circulation and is widespread in deep-sea cold seeps. Sulfur-oxidizing bacteria are thought to be the major contributors to the formation of ZVS. However, ZVS production mediated by sulfate-reducing bacteria (SRB) has rarely been reported. In this study, we isolated and cultured a typical SRB designated Oceanidesulfovibrio marinus CS1 from deep-sea cold seep sediment in the South China Sea. We show that O. marinus CS1 forms ZVS in the medium supplemented with thiosulfate. Proteomic and protein activity assays revealed that thiosulfate reductase (PhsA) and the sulfide:quinone oxidoreductase (SQR) played key roles in driving ZVS formation in O. marinus CS1. During this process, thiosulfate firstly was reduced by PhsA to form sulfide, then sulfide was oxidized by SQR to produce ZVS. The expressions of PhsA and SQR were significantly upregulated when O. marinus CS1 was cultured in a deep-sea cold seep, strongly indicating that strain CS1 might form ZVS in the deep-sea environment. Notably, homologs of phsA and sqr were widely identified from microbes living in sediments of deep-sea cold seep in the South China Sea by the metagenomic analysis. We thus propose that SRB containing phsA and sqr genes potentially contribute to the formation of ZVS in deep-sea cold seep environments.
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Affiliation(s)
- Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
| | - Shichuan Xi
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- College of Earth Science, University of Chinese Academy of SciencesBeijingChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Xin Zhang
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
- CAS Key Laboratory of Marine Geology and EnvironmentCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine BiologyCenter of Deep Sea Research, Institute of Oceanology, Chinese Academy of SciencesQingdaoChina
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and TechnologyQingdaoChina
- Center of Ocean Mega‐Science, Chinese Academy of SciencesQingdaoChina
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25
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Liu H, Luo L, Jiang G, Li G, Zhu C, Meng W, Zhang J, Jiao Q, Du P, Li X, Fahad S, Jie X, Liu S. Sulfur enhances cadmium bioaccumulation in Cichorium intybus by altering soil properties, heavy metal availability and microbial community in contaminated alkaline soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155879. [PMID: 35568178 DOI: 10.1016/j.scitotenv.2022.155879] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/25/2022] [Accepted: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Cadmium (Cd) contamination seriously threatens the soil health and food safety. Combination of amendment and accumulator plant is a green and effective technique to improve phytoremediation of Cd-contaminated alkaline soil. In this study, a potting experiment was conducted to investigate the effect of sulfur on Cd phytoextraction by Cichorium intybus (chicory). Soil chemical and microbial properties were determined to reveal the mechanism of sulfur-assisting Cd phytoremediation by chicory. Soil pH decreased from 7.77 to the lowest 7.30 with sulfur addition (0.6, 0.9 and 1.2 g kg-1, LS, MS and HS treatment); Electric conductivity, sulfate anion and available cadmium concentration increased gradually with increasing sulfur doses. Cd concentration of shoot and root significantly increased from 1.47 to 4.43 mg kg-1, 6.15 to 20.16 mg kg-1 by sulfur treatment relative to CK, which were attributed to increased available Cd concentration induced by decreased pH. Sulfur treatments significantly increased the Cd bioconcentration factor by 64.1%, 118.6%, 201.0% for shoot, 76.3%, 145.6% and 227.7% for root under LS, MS and HS relative to CK treatment, respectively (P < 0.05). However, only MS treatment significantly improved the Cd removal efficiency by 82.9% in comparison of CK treatment (P < 0.05). Microbial community diversity measured by 16SrRNA showed that Thiobacillus and Actinobacteria were the key and dominant strains of soil microbial communities after sulfur addition, which played a pivotal role in the process of sulfur oxidation involved in decrease of soil pH and the transformation of Cd forms. Correlation analysis and path analysis by structural equation model indicated that soil sulfate anion and Thiobacillus directly affected Cd removal efficiency by chicory in Cd-contaminated alkaline soil. This suggests that combination of sulfur and chicory may provide a way to promote Cd bioaccumulation for phytoremediation of Cd-contaminated alkaline soil.
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Affiliation(s)
- Haitao Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Lan Luo
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Guiying Jiang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China.
| | - Gezi Li
- College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Changwei Zhu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Weiwei Meng
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingjing Zhang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiujuan Jiao
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengqiang Du
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 570228, China; Department of Agronomy, Faculty of Agricultural Sciences, The University of Haripur, Haripur 22620, Pakistan
| | - Xiaolei Jie
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China
| | - Shiliang Liu
- College of Resources and Environment, Henan Agricultural University, Zhengzhou 450002, China.
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26
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Pu Q, Zhang K, Poulain AJ, Liu J, Zhang R, Abdelhafiz MA, Meng B, Feng X. Mercury drives microbial community assembly and ecosystem multifunctionality across a Hg contamination gradient in rice paddies. JOURNAL OF HAZARDOUS MATERIALS 2022; 435:129055. [PMID: 35650726 DOI: 10.1016/j.jhazmat.2022.129055] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Soil microbial communities are critical for maintaining terrestrial ecosystems and fundamental ecological processes. Mercury (Hg) is a heavy metal that is toxic to microorganisms, but its effects on microbial community assembly and ecosystem multifunctionality in rice paddy ecosystems remain largely unknown. In the current study, we analyzed the microbial community structure and ecosystem multifunctionality of paddy soils across a Hg contamination gradient. The results demonstrated that Hg contamination significantly altered the microbial community structure. The microbial communities were predominantly driven by deterministic selection rather than stochastic processes. The random forest model and variation partition analysis demonstrated that the Hg level was the most important predictor of microbial profiles. Ecosystem multifunctionality decreased across the Hg concentration gradient, and multifunctionality was significantly correlated with soil biodiversity, suggesting that Hg-induced reductions in soil biodiversity led to reduced ecosystem services. A structural equation model showed that Hg contamination directly and indirectly affected ecosystem multifunctionality. The present work broadens our knowledge of the assembly of the microbiome in rice paddies across a Hg contamination gradient and highlights the significance of soil biodiversity in regulating ecosystem functions, especially in Hg-polluted rice paddies.
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Affiliation(s)
- Qiang Pu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Kun Zhang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alexandre J Poulain
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Jiang Liu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Rui Zhang
- Biology Department, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada
| | - Mahmoud A Abdelhafiz
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Geology Department, Faculty of Science, Al-Azhar University, Assiut 71524, Egypt
| | - Bo Meng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China; Center for Excellence in Quaternary Science and Global Change, Chinese Academy of Sciences, Xi'an 710061, China
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Liu H, Zeng W, Li J, Zhan M, Fan Z, Peng Y. Effect of S 2O 32--S addition on Anammox coupling sulfur autotrophic denitrification and mechanism analysis using N and O dual isotope effects. WATER RESEARCH 2022; 218:118404. [PMID: 35462259 DOI: 10.1016/j.watres.2022.118404] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic ammonia oxidation (Anammox) coupling sulfur autotrophic denitrification is an effective method for the advanced nitrogen removal from the wastewater with limited carbon source. The influence of S2O32--S addition on Anammox coupling sulfur autotrophic denitrification was investigated by adding different concentrations of S2O32--S (0, 39, 78, 156 and 312 mg/L) to the Anammox system. The contribution of sulfur autotrophic denitrification and Anammox to nitrogen removal at S2O32--S concentrations of 156 mg/L was 75% ∼83% and 17%∼25%, respectively, and the mixed system achieved completely nitrogen removal. However, Anammox bioactivity was completely inhibited at S2O32--S concentrations up to 312 mg/L, and only sulfur autotrophic denitrification occurred. The isotopic effects of NO2--N (δ15NNO2 and δ18ONO2) and NO3--N (δ15NNO3 and δ18ONO3) during Anammox coupling sulfur autotrophic denitrification showed a gradual decrease trend with the increase of S2O32--S addition. The ratios of δ15NNO2:δ18ONO2 and δ15NNO3:δ18ONO3 was maintained at 1.30-2.41 and 1.36-2.52, respectively, which revealed that Anammox was dominant nitrogen removal pathway at S2O32--S concentrations less than 156 mg/L. Microbial diversity gradually decreased with the increase of S2O32--S. The S2O32--S addition enhanced the S2O32--driven autotrophic denitrification and weakened the Anammox, leading to a gradually decreasing trend of the proportion of Candidatus Brocadia as Anammox bacteria from the initial 27% to 4% (S2O32--S of 156 mg/L). Yet Norank-f-Hydrogenophilaceae (more than 50%) and Thiobacillus (54%) as functional bacteria of autotrophic denitrification obviously increased. The appropriate amount of S2O32--S addition promoted the performance of Anammox coupling sulfur autotrophic denitrification achieved completely nitrogen removal.
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Affiliation(s)
- Hong Liu
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Wei Zeng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China.
| | - Jianmin Li
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Mengjia Zhan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Zhiwei Fan
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Yongzhen Peng
- National Engineering Laboratory for Advanced Municipal Wastewater Treatment and Reuse Technology, Department of Environmental Engineering, Beijing University of Technology, No. 100 Pingleyuan, Chaoyang District, Beijing 100124, China
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Li X, Yang M, Mu T, Miao D, Liu J, Xing J. Composition and key-influencing factors of bacterial communities active in sulfur cycling of soda lake sediments. Arch Microbiol 2022; 204:317. [PMID: 35567694 DOI: 10.1007/s00203-022-02925-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/20/2022] [Accepted: 04/15/2022] [Indexed: 11/28/2022]
Abstract
Bacteria are important participants in sulfur cycle of the extremely haloalkaline environment, e.g. soda lake. The effects of physicochemical factors on the composition of sulfide-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in soda lake have remained elusive. Here, we surveyed the community structure of total bacteria, SOB and SRB based on 16S rRNA, soxB and dsrB gene sequencing, respectively, in five soda lakes with different physicochemical factors. The results showed that the dominant bacteria belonged to the phyla Proteobacteria, Bacteroidetes, Halanaerobiaeota, Firmicutes and Actinobacteria. SOB and SRB were widely distributed in lakes with different physicochemical characteristics, and the community composition were different. In general, salinity and inorganic nitrogen sources (NH4+-N, NO3--N) were the most significant factors. Specifically, the communities of SOB, mainly including Thioalkalivibrio, Burkholderia, Paracoccus, Bradyrhizobium, and Hydrogenophaga genera, were remarkably influenced by the levels of NH4+-N and salinity. Yet, for SRB communities, including Desulfurivibrio, Candidatus Electrothrix, Desulfonatronospira, Desulfonatronum, Desulfonatronovibrio, Desulfonatronobacter and so on, the most significant determinants were salinity and NO3--N. Besides, Rhodoplanes played a significant role in the interaction between SOB and SRB. From our results, the knowledge regarding the community structures of SOB and SRB in extremely haloalkaline environment was extended.
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Affiliation(s)
- Xiangyuan Li
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.,College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Maohua Yang
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Tingzhen Mu
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Delu Miao
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jinlong Liu
- College of Bioscience and Bioengineering, Hebei University of Science and Technology, Shijiazhuang, 050018, Hebei, China
| | - Jianmin Xing
- CAS Key Laboratory of Green Process and Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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Wei D, Liu L, Shi J, Yan W, Chen X, Li X. Biodesulfurization of thiosulfate by a Pseudomonas strain PSP1 and the investigation of underlying metabolic mechanisms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:33764-33773. [PMID: 35029825 DOI: 10.1007/s11356-022-18648-7] [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: 09/29/2021] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
The increasing public expectations for good air quality have necessitated the development of biodeodorization technology. Among different malodorous pollutants, H2S has attracted extensive attention and diverse biodesulfurization technology has been developed for efficient H2S removal. In this study, a novel heterotrophic Pseudomonas strain, PSP1, was isolated from biogas slurry and its biodesulfurization ability was investigated. Culture conditions of 30 °C and 200 rpm were determined as the optimal for both cell growth and thiosulfate conversion. Under such conditions, the highest OD600 value was observed as 6.74 and 50 mM thiosulfate within 10 h. PSP1 was found to convert thiosulfate to sulfane which could be decomposed into elemental sulfur and therefore achieved desulfurization. However, this process was relatively weak as more than 60% thiosulfate was converted into soluble tetrathionate. The whole genome sequencing and functional annotation identified the genes in PSP1 associated with sulfur metabolism and the RT-qPCR analysis quantified the expression level of corresponding genes. The expression level of tsdA, which was responsible for tetrathionate production, was around 60 folds higher than genes for sulfane production (e.g. TST1, cysI). Further research would focus on the enhancement of sulfane production pathway through metabolic engineering tools.
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Affiliation(s)
- Dong Wei
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Li Liu
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Jiping Shi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Weizhi Yan
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China
| | - Xiaojia Chen
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Xiang Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
- Shanghai Engineering Research Center of Biotransformation of Organic Solid Waste, Shanghai, 200241, China.
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30
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Li L, Zhang B, Li L, Borthwick AGL. Microbial selenate detoxification linked to elemental sulfur oxidation: Independent and synergic pathways. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126932. [PMID: 34419844 DOI: 10.1016/j.jhazmat.2021.126932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/01/2021] [Accepted: 08/15/2021] [Indexed: 06/13/2023]
Abstract
Elevated selenium levels in the environment, with soluble selenate [Se(VI)] as the common chemical species, pose a severe threat to human health. Anaerobic Se(VI) bioreduction is a promising approach for selenium detoxification, and various organic/inorganic electron donors have proved effective in supporting this bioprocess. Nevertheless, autotrophic Se(VI) bioreduction driven by solid inorganic electron donors is still not fully understood. This work is the first to employ elemental sulfur [S(0)] as electron donor to support Se(VI) bioreduction. A batch trial with mixed culture demonstrated the feasibility of this bioprocess, with Se(VI) removal efficiency of 92.4 ± 0.7% at an initial Se(VI) concentration of 10 mg/L within 36 h. Continuous column tests showed that increased initial concentration, flow rate, and introduction of NO3--N depressed Se(VI) removal. Se(VI) was mainly bioreduced to solid elemental Se with trace selenite in the effluent, while S(0) was oxidized to SO42-. Enrichment of Thiobacillus, Desulfurivibrio, and Sulfuricurvum combined with upregulation of genes serA, tatC, and soxB indicated Se(VI) bioreduction was coupled to S(0) oxidation. Thiobacillus performed S(0) oxidation and Se(VI) reduction independently. Intermediate metabolites as volatile fatty acids, hydrogen and methane from S(0) oxidation were utilized by heterotrophic Se(VI) reducers for Se(VI) detoxification, indicative of microbial synergy.
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Affiliation(s)
- Liuliu Li
- School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China; Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Baogang Zhang
- School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China; Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China.
| | - Lei Li
- School of Water Resources and Environment, China University of Geosciences Beijing, Beijing 100083, China; Key Laboratory of Groundwater Circulation and Evolution (China University of Geosciences Beijing), Ministry of Education, Beijing 100083, China
| | - Alistair G L Borthwick
- St Edmund Hall, Queen's Lane, Oxford OX1 4AR, UK; School of Engineering, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JL, UK; School of Engineering, Computing and Mathematics, University of Plymouth, Drakes Circus, Plymouth PL4 8AA, UK
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31
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Ma WJ, Cheng YF, Jin RC. Comprehensive evaluation of the long-term effect of Cu 2+ on denitrifying granular sludge and feasibility of in situ recovery by phosphate. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126901. [PMID: 34419849 DOI: 10.1016/j.jhazmat.2021.126901] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/18/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
With increased industrial development, vast heavy metals are inevitably discharged into wastewater. Cu2+ is one of the most hazardous heavy metals in biotreatment. However, the potential effect of Cu2+ on denitrifying granular sludge is still unknown. This work assesses the response of denitrifying granular sludge to Cu2+ stress from multiple aspects. The denitrifying granular sludge could tolerate 5 mg L-1 Cu2+, while the nitrogen removal efficiency decreased to 48.5% under 10 mg L-1 Cu2+. Enzyme activity and carbohydrate metabolism were inhibited, and the denitrifying bacteria were washed out under Cu2+ stress. The resulting deteriorated state was reversed by phosphate. The nitrogen removal efficiency recovered to 99% after 10 days, and the enzyme activity also recovered to the original level. Membrane transport, transcription and cellular processes were promoted. Overall, the results of this work provide a feasible strategy to rapidly restore the metabolic activity of denitrifying granular sludge under Cu2+ stress.
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Affiliation(s)
- Wen-Jie Ma
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ya-Fei Cheng
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ren-Cun Jin
- Laboratory of Water Pollution Remediation, School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.
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32
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Marlow JJ, Hoer D, Jungbluth SP, Reynard LM, Gartman A, Chavez MS, El-Naggar MY, Tuross N, Orphan VJ, Girguis PR. Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:e2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample's methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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Affiliation(s)
- Jeffrey J Marlow
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
| | - Daniel Hoer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Sean P Jungbluth
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94720
| | - Linda M Reynard
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Amy Gartman
- US Geological Survey Pacific Coastal and Marine Science Center, Santa Cruz, CA 95060
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138;
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33
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Li M, Fang A, Yu X, Zhang K, He Z, Wang C, Peng Y, Xiao F, Yang T, Zhang W, Zheng X, Zhong Q, Liu X, Yan Q. Microbially-driven sulfur cycling microbial communities in different mangrove sediments. CHEMOSPHERE 2021; 273:128597. [PMID: 33077194 DOI: 10.1016/j.chemosphere.2020.128597] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 05/13/2023]
Abstract
Microbially-driven sulfur cycling is a vital biogeochemical process in the sulfur-rich mangrove ecosystem. It is critical to evaluate the potential impact of sulfur transformation in mangrove ecosystems. To reveal the diversity, composition, and structure of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) and underlying mechanisms, we analyzed the physicochemical properties and sediment microbial communities from an introduced mangrove species (Sonneratia apetala), a native mangrove species (Kandelia obovata) and the mudflat in Hanjiang River Estuary in Guangdong (23.27°N, 116.52°E), China. The results indicated that SOB was dominated by autotrophic Thiohalophilus and chemoautotrophy Chromatium in S. apetala and K. obovata, respectively, while Desulfatibacillum was the dominant genus of SRB in K. obovata sediments. Also, the redundancy analysis indicated that temperature, redox potential (ORP), and SO42- were the significant factors influencing the sulfur cycling microbial communities with elemental sulfur (ES) as the key factor driver for SOB and total carbon (TC) for SRB in mangrove sediments. Additionally, the morphological transformation of ES, acid volatile sulfide (AVS) and SO42- explained the variation of sulfur cycling microbial communities under sulfur-rich conditions, and we found mangrove species-specific dominant Thiohalobacter, Chromatium and Desulfatibacillum, which could well use ES and SO42-, thus promoting the sulfur cycling in mangrove sediments. Meanwhile, the change of nutrient substances (TN, TC) explained why SOB were more susceptible to environmental changes than SRB. Sulfate reducing bacteria produces sulfide in anoxic sediments at depth that then migrate upward, toward fewer reducing conditions, where it's oxidized by sulfur oxidizing bacteria. This study indicates the high ability of SOB and SRB in ES, SO42-,S2- and S2- generation and transformation in sulfur-rich mangrove ecosystems, and provides novel insights into sulfur cycling in other wetland ecosystems from a microbial perspective.
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Affiliation(s)
- Mingyue Li
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Anqi Fang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaoli Yu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Keke Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China; College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Yisheng Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Fanshu Xiao
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
| | - Tony Yang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Wei Zhang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiafei Zheng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qiuping Zhong
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Xingyu Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Qingyun Yan
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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Segura A, Udaondo Z, Molina L. PahT regulates carbon fluxes in Novosphingobium sp. HR1a and influences its survival in soil and rhizospheres. Environ Microbiol 2021; 23:2969-2991. [PMID: 33817928 PMCID: PMC8360164 DOI: 10.1111/1462-2920.15509] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/29/2021] [Accepted: 04/03/2021] [Indexed: 01/23/2023]
Abstract
Novosphingobium sp. HR1a is a good biodegrader of PAHs and aromatic compounds, and also a good colonizer of rhizospheric environments. It was previously demonstrated that this microbe is able to co-metabolize nutrients existing in root exudates together with the PAHs. We have revealed here that PahT, a regulator of the IclR-family, regulates the central carbon fluxes favouring the degradation of PAHs and mono-aromatic compounds, the ethanol and acetate metabolism and the uptake, phosphorylation and further degradation of mono- and oligo-saccharides through a phosphoenolpyruvate transferase system (PTS). As final products of these fluxes, pyruvate and acetyl-CoA are obtained. The pahT gene is located within a genomic region containing two putative transposons that carry all the genes for PAH catabolism; PahT also regulates these genes. Furthermore, encoded in this genomic region, there are genes that are involved in the recycling of phosphoenolpyruvate, from the obtained pyruvate, which is the motor molecule involved in the saccharide uptake by the PTS system. The co-metabolism of PAHs with different carbon sources, together with the activation of the thiosulfate utilization and an alternative cytochrome oxidase system, also regulated by PahT, represents an advantage for Novosphingobium sp. HR1a to survive in rhizospheric environments.
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Affiliation(s)
- Ana Segura
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Zulema Udaondo
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Lázaro Molina
- Environmental Protection Department, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Profesor Albareda 1, Granada, 18008, Spain
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35
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Chen YH, Yang SH, Tandon K, Lu CY, Chen HJ, Shih CJ, Tang SL. Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis. Microb Genom 2021; 7:000574. [PMID: 33952388 PMCID: PMC8209720 DOI: 10.1099/mgen.0.000574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/31/2021] [Indexed: 11/21/2022] Open
Abstract
Endolithic microbial symbionts in the coral skeleton may play a pivotal role in maintaining coral health. However, compared to aerobic micro-organisms, research on the roles of endolithic anaerobic micro-organisms and microbe-microbe interactions in the coral skeleton are still in their infancy. In our previous study, we showed that a group of coral-associated Prosthecochloris (CAP), a genus of anaerobic green sulphur bacteria, was dominant in the skeleton of the coral Isopora palifera. Though CAP is diverse, the 16S rRNA phylogeny presents it as a distinct clade separate from other free-living Prosthecochloris. In this study, we build on previous research and further characterize the genomic and metabolic traits of CAP by recovering two new high-quality CAP genomes - Candidatus Prosthecochloris isoporae and Candidatus Prosthecochloris sp. N1 - from the coral I. palifera endolithic cultures. Genomic analysis revealed that these two CAP genomes have high genomic similarities compared with other Prosthecochloris and harbour several CAP-unique genes. Interestingly, different CAP species harbour various pigment synthesis and sulphur metabolism genes, indicating that individual CAPs can adapt to a diversity of coral microenvironments. A novel high-quality genome of sulfate-reducing bacterium (SRB)- Candidatus Halodesulfovibrio lyudaonia - was also recovered from the same culture. The fact that CAP and various SRB co-exist in coral endolithic cultures and coral skeleton highlights the importance of SRB in the coral endolithic community. Based on functional genomic analysis of Ca. P. sp. N1, Ca. P. isoporae and Ca. H. lyudaonia, we also propose a syntrophic relationship between the SRB and CAP in the coral skeleton.
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Affiliation(s)
- Yu-Hsiang Chen
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan, ROC
- Bioinformatics Program, Institute of Information Science,Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Shan-Hua Yang
- Institute of Fisheries Science, National Taiwan University, Taipei, Taiwan, ROC
| | - Kshitij Tandon
- Bioinformatics Program, Institute of Information Science,Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, ROC
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
- Molecular and Biological Agricultural Sciences, Program Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan, ROC
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Sen-Lin Tang
- Bioinformatics Program, Institute of Information Science,Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan, ROC
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
- Molecular and Biological Agricultural Sciences, Program Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan, ROC
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36
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Tang X, Zou L, Su S, Lu Y, Zhai W, Manzoor M, Liao Y, Nie J, Shi J, Ma LQ, Xu J. Long-Term Manure Application Changes Bacterial Communities in Rice Rhizosphere and Arsenic Speciation in Rice Grains. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1555-1565. [PMID: 33449628 DOI: 10.1021/acs.est.0c03924] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bioavailability and speciation of arsenic (As) are impacted by fertilization and bacteria in the rice rhizosphere. In this study, we investigated the effects of long-term manure application on As bioavailability, microbial community structure, and functional genes in a rice paddy field. The results showed that manure application did not affect total As in the soil but increased soluble As forms by 19%, increasing arsenite (As(III)) accumulation in rice grains and roots by 34 and 64% compared to a control. A real-time quantitative polymerase chain reaction (qPCR) and high-throughput sequencing analysis demonstrated that manure application increased the relative abundance of Rhizobium, Burkholderia, Sphingobium, and Sphingomonas containing arsenate reductase genes (arsC) in the rhizosphere soil, consistent with the 529% increase in arsC, which may have promoted arsenate (As(V)) reduction and increased As availability in pore water. In addition, manure application significantly altered the iron (Fe)-plaque microbial community structure and diversity. The microbes, particularly, Bradyrhizobium, Burkholderia, and Ralstonia, were mostly associated with As, Fe, and sulfur (S) cycles. This result was consistent with changes in the functional genes related to As, Fe, and S transformation. Although manure application promoted As(V) reduction (arsC) in Fe-plaque by 682%, it inhibited Fe and S reduction by decreasing FeIII reduction bacteria (Geobacteraceae) and the sulfate-reducing gene (dsrA) abundance. Further, manure application changed the composition of the microbial community that contained the arsC gene. In short, caution needs to be excised even in the soil with a low As concentration as manure application increased As(III) accumulation in rice grains.
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Affiliation(s)
- Xianjin Tang
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lina Zou
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiming Su
- Key Laboratory of Agro-Environment, Ministry of Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanhong Lu
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Weiwei Zhai
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Maria Manzoor
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yulin Liao
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jun Nie
- Soil and Fertilizer Institute of Hunan Province, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Jiyan Shi
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lena Q Ma
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianming Xu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, and Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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37
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Zhang T, Xiao X, Chen S, Zhao J, Chen Z, Feng J, Liang Q, Phelps TJ, Zhang C. Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea. Front Microbiol 2021; 11:612135. [PMID: 33391242 PMCID: PMC7772427 DOI: 10.3389/fmicb.2020.612135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.
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Affiliation(s)
- Tingting Zhang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Xi Xiao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Songze Chen
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
| | - Jing Zhao
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Zongheng Chen
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China
| | - Junxi Feng
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China
| | - Qianyong Liang
- Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, China.,Gas Hydrate Engineering Technology Center, China Geological Survey, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Tommy J Phelps
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Earth and Planetary Sciences, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, China
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38
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Yang Y, Lu H, Shao Z, Liu S, Zhang Y, Jiang D, Gu L, He Q, Chai H. Electron buffer formation through coupling thiosulfate-dependent denitratation with anammox in a single-stage sequencing batch reactor. BIORESOURCE TECHNOLOGY 2020; 312:123560. [PMID: 32473471 DOI: 10.1016/j.biortech.2020.123560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/15/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
The combination of thiosulfate-dependent denitratation and anammox in a single-stage reactor provides a feasible way to improve total nitrogen removal. The molar ratios of NH4+/NO3- and S2O32-/NO3- were confirmed to be two key factors affecting the reactor performance. The optimal total nitrogen removal efficiency of 99.4% was achieved at NH4+/NO3- of 0.75 and S2O32-/NO3- of 0.85. The multiple thiosulfate oxidation pathways contribute to electron buffers generated in the system. A novel isotope labeling method using 15N was applied to reveal N transformation pathways and a 3-step model was proposed. The nitrate was first converted to nitrite or nitric oxide (NO) by sulfur-oxidizing bacteria. In the second step, both nitrite and NO were utilized by anammox bacteria. Finally, the nitrate generated from anammox could be removed using sulfur deposits as electron donors. The findings provide a potential solution for mainstream nitrogen removal.
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Affiliation(s)
- Yan Yang
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Guangzhou, China
| | - Zhiyu Shao
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China
| | - Shiyi Liu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China
| | - Yuxin Zhang
- College of Materials Science and Engineering, Chongqing University, Chongqing 400044, China
| | - Debin Jiang
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing 400067, China
| | - Li Gu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China
| | - Hongxiang Chai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, China; National Centre for International Research of Low-carbon and Green Buildings, Chongqing University, Chongqing 400045, China.
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39
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Ai T, Zhan H, Zou L, Fu J, Fu Q, He Q, Ai H. Potential applications of endogenous sulfide for enhanced denitrification of low C/N domestic wastewater in anodic mixotrophic denitrification microbial fuel cell: The mechanism of electrons transfer and microbial community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137830. [PMID: 32349200 DOI: 10.1016/j.scitotenv.2020.137830] [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: 01/23/2020] [Revised: 03/01/2020] [Accepted: 03/07/2020] [Indexed: 06/11/2023]
Abstract
Anodic mixotrophic denitrification microbial fuel cell (MFC) was developed for pollutants removal and electricity generation in treatment of low C/N domestic wastewater. The experimental results show that the MFC achieved up to 100% of acetate, 100% of sulfide, and more than 91% of nitrate removal efficiency in all the MFCs. Particularly, thiosulfate was generated as the main intermediate of sulfide oxidation, and the sulfate generation ratio ranged from 66.93% to 73.76%. Those electrons produced during the acetate and sulfide oxidation were mainly used for denitrification and electricity generation. The microbial community analysis revealed that heterotrophic denitrifying bacteria (HDB) and sulfide-based autotrophic denitrifying bacteria (SADB) were the dominant bacteria for pollutants removal, and those facultative autotrophic bacterium (FAB) were key functional genera for high sulfate generation under both low and high sulfide concentrations. Meanwhile, the microbial functional prediction revealed that sulfide oxidation gene of Sqr and Sox were highly expressed. Moreover, a preliminary sulfide-based autotrophic denitrification (SAD) potential estimation indicated that the sulfide generated in the WWTPs had great potential for denitrification.
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Affiliation(s)
- Tao Ai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Hao Zhan
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Linzhi Zou
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Junyu Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Qibin Fu
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Qiang He
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China
| | - Hainan Ai
- Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, Chongqing University, Chongqing 400045, PR China.
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40
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Krause S, Molari M, Gorb EV, Gorb SN, Kossel E, Haeckel M. Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor. Sci Rep 2020; 10:9484. [PMID: 32528001 PMCID: PMC7289819 DOI: 10.1038/s41598-020-66361-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/25/2020] [Indexed: 12/14/2022] Open
Abstract
The fate of plastic debris entering the oceans is largely unconstrained. Currently, intensified research is devoted to the abiotic and microbial degradation of plastic floating near the ocean surface for an extended period of time. In contrast, the impacts of environmental conditions in the deep sea on polymer properties and rigidity are virtually unknown. Here, we present unique results of plastic items identified to have been introduced into deep-sea sediments at a water depth of 4150 m in the eastern equatorial Pacific Ocean more than two decades ago. The results, including optical, spectroscopic, physical and microbial analyses, clearly demonstrate that the bulk polymer materials show no apparent sign of physical or chemical degradation. Solely the polymer surface layers showed reduced hydrophobicity, presumably caused by microbial colonization. The bacterial community present on the plastic items differed significantly (p < 0.1%) from those of the adjacent natural environment by a dominant presence of groups requiring steep redox gradients (Mesorhizobium, Sulfurimonas) and a remarkable decrease in diversity. The establishment of chemical gradients across the polymer surfaces presumably caused these conditions. Our findings suggest that plastic is stable over extended times under deep-sea conditions and that prolonged deposition of polymer items at the seafloor may induce local oxygen depletion at the sediment-water interface.
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Affiliation(s)
- S Krause
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - M Molari
- HGF-MPG Joint Research Group on Deep Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - E V Gorb
- Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - S N Gorb
- Zoological Institute, Christian-Albrechts-University, Kiel, Germany
| | - E Kossel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - M Haeckel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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41
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Zhang J, Liu R, Xi S, Cai R, Zhang X, Sun C. A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea. ISME JOURNAL 2020; 14:2261-2274. [PMID: 32457501 PMCID: PMC7608252 DOI: 10.1038/s41396-020-0684-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 11/09/2022]
Abstract
Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (−O3S–S–S–SO3−), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.
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Affiliation(s)
- Jing Zhang
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, 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.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, 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.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Shichuan Xi
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, 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.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Xin Zhang
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.,CAS Key Laboratory of Marine Geology and Environment & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, 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. .,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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42
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Lu J, Zhang B, He C, Borthwick AGL. The role of natural Fe(II)-bearing minerals in chemoautotrophic chromium (VI) bio-reduction in groundwater. JOURNAL OF HAZARDOUS MATERIALS 2020; 389:121911. [PMID: 31879105 DOI: 10.1016/j.jhazmat.2019.121911] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/04/2019] [Accepted: 12/15/2019] [Indexed: 06/10/2023]
Abstract
To date, comparatively little is known about the role of natural Fe(II)-bearing minerals in bioremediation of chromium (VI) contaminated aquifers subject to chemoautotrophic conditions. This work employed four kinds of Fe(II)-bearing minerals (pyrite, mackinawite, wustite, and magnetite) as inorganic electron donors to support Cr(VI) bio-reduction. In batch experiments, mackinawite (FeS) performed best, with Cr(VI) removal efficiency of 98.1 ± 1.21 % in 96 h. Continuous column experiments lasting 180 d implied that groundwater chemistry and hydrodynamics influenced the Cr(VI) removal process. A breakthrough study suggested that biotic and abiotic contributions to Cr(VI) reduction were 76.0 ± 1.12 % and 24.1 ± 1.43 %, respectively. Cr(VI) was reduced to insoluble Cr(III), whereas Fe(II) and S(-II) in mackinawite were finally oxidized to Fe(III) and sulfate. Mackinawite evolved progressively into pyrrhotite. High-throughput 16S rRNA gene sequencing indicated that mackinawite-driven Cr(VI) reduction was mediated through synergistic interactions of microbial consortia; i.e. autotrophs as Acidovorax synthesized volatile fatty acids as metabolic intermediates, which were consumed by Cr(VI) reducers as Geobacter. Genes encoding enzymes for S oxidation (soxB) and Cr(VI) reduction (chrA, yieF) were upregulated. Cytochrome c participating in Fe(II) oxidation increased significantly. This work advances the development of sustainable techniques for Cr(VI) polluted groundwater remediation.
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Affiliation(s)
- Jianping Lu
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Baogang Zhang
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China.
| | - Chao He
- School of Water Resources and Environment, MOE Key Laboratory of Groundwater Circulation and Environmental Evolution, China University of Geosciences (Beijing), Beijing, 100083, PR China
| | - Alistair G L Borthwick
- St Edmund Hall, Queen's Lane, Oxford, OX1 4AR, UK; School of Engineering, The University of Edinburgh, The King's Buildings, Edinburgh, EH9 3JL, UK
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43
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Sabuda MC, Brazelton WJ, Putman LI, McCollom TM, Hoehler TM, Kubo MDY, Cardace D, Schrenk MO. A dynamic microbial sulfur cycle in a serpentinizing continental ophiolite. Environ Microbiol 2020; 22:2329-2345. [PMID: 32249550 DOI: 10.1111/1462-2920.15006] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 03/19/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022]
Abstract
Serpentinization is the hydration and oxidation of ultramafic rock, which occurs as oceanic lithosphere is emplaced onto continental margins (ophiolites), and along the seafloor as faulting exposes this mantle-derived material to circulating hydrothermal fluids. This process leads to distinctive fluid chemistries as molecular hydrogen (H2 ) and hydroxyl ions (OH- ) are produced and reduced carbon compounds are mobilized. Serpentinizing ophiolites also serve as a vector to transport sulfur compounds from the seafloor onto the continents. We investigated hyperalkaline, sulfur-rich, brackish groundwater in a serpentinizing continental ophiolite to elucidate the role of sulfur compounds in fuelling in situ microbial activities. Here we illustrate that key sulfur-cycling taxa, including Dethiobacter, Desulfitispora and 'Desulforudis', persist throughout this extreme environment. Biologically catalysed redox reactions involving sulfate, sulfide and intermediate sulfur compounds are thermodynamically favourable in the groundwater, which indicates they may be vital to sustaining life in these characteristically oxidant- and energy-limited systems. Furthermore, metagenomic and metatranscriptomic analyses reveal a complex network involving sulfate reduction, sulfide oxidation and thiosulfate reactions. Our findings highlight the importance of the complete inorganic sulfur cycle in serpentinizing fluids and suggest sulfur biogeochemistry provides a key link between terrestrial serpentinizing ecosystems and their submarine heritage.
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Affiliation(s)
- Mary C Sabuda
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Lindsay I Putman
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Tom M McCollom
- Laboratory for Atmospheric and Space Physics, UCB 600, University of Colorado-Boulder, Boulder, CO, 80309, USA
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Michael D Y Kubo
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,SETI Institute, Mountain View, CA, 94043, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Matthew O Schrenk
- Department of Earth and Environmental Sciences, Michigan State University, East Lansing, MI, 48824, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
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44
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Li W, Zhang M, Kang D, Chen W, Yu T, Xu D, Zeng Z, Li Y, Zheng P. Mechanisms of sulfur selection and sulfur secretion in a biological sulfide removal (BISURE) system. ENVIRONMENT INTERNATIONAL 2020; 137:105549. [PMID: 32086075 DOI: 10.1016/j.envint.2020.105549] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/06/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Biological desulfurization technology is a sustainable process for the sulfide removal from biogas, which has multiple advantages. In this study, a biological sulfide removal (BISURE) system was established to investigate the working performances and process mechanisms. The results showed that the sulfide removal rate was 2.30 kg-S/(m3 d), the sulfide removal efficiency was higher than 98%, the sulfur production rate was 1.76 kg-S/(m3 d), the sulfur selectivity was 75.02 ± 3.63% and the main form of products (sulfur compounds) was Rosickyite-S and S8. The performance of BISURE system was supported by the dominant genus (abundance more than 60%) of sulfur-oxidizing bacteria (SOB) which shifted to Thiovirga at the high SLR. The sqr and dsrA genes could serve as the indicators for the pathway of two-step sulfide oxidation, i.e. "partial sulfide oxidation (PSO, sulfide → sulfur)" and "complete sulfide oxidation (CSO, sulfur → sulfate)". The sulfur selectivity was improved by enhancing PSO and inhibiting CSO with the indication of two genes. The cellular sulfur secretion was revealed, and the "outer-membrane vesicles (OMVs)-dependent" sulfur-secreting hypothesis was proposed to explain the transportation of elemental sulfur from inside to outside of SOB cells. The findings of this work provide a new perspective to understand the sulfur selection of sulfide bio-oxidation and the sulfur secretion of SOB cells so as to promote the development of biological desulfurization technology.
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Affiliation(s)
- Wenji Li
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Meng Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Da Kang
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenda Chen
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tao Yu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dongdong Xu
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhuo Zeng
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yiyu Li
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ping Zheng
- Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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45
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Magnuson E, Mykytczuk NC, Pellerin A, Goordial J, Twine SM, Wing B, Foote SJ, Fulton K, Whyte LG. Thiomicrorhabdus
streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high Arctic. Environ Microbiol 2020; 23:3384-3400. [DOI: 10.1111/1462-2920.14916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 12/10/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Elisse Magnuson
- Natural Resource Sciences McGill University Montreal QC Canada
| | | | - Andre Pellerin
- Centre for Geomicrobiology Aarhus University Aarhus Denmark
| | - Jacqueline Goordial
- Natural Resource Sciences McGill University Montreal QC Canada
- School of Environmental Sciences University of Guelph Guelph, ON Canada
| | - Susan M. Twine
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Boswell Wing
- Earth and Planetary Sciences McGill University Montreal QC Canada
| | - Simon J. Foote
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Kelly Fulton
- Institute for Biological Sciences National Research Council Ottawa Ontario
| | - Lyle G. Whyte
- Natural Resource Sciences McGill University Montreal QC Canada
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46
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Mori Y, Tada C, Fukuda Y, Nakai Y. Diversity of Sulfur-oxidizing Bacteria at the Surface of Cattle Manure Composting Assessed by an Analysis of the Sulfur Oxidation Gene soxB. Microbes Environ 2020; 35:ME18066. [PMID: 32713897 PMCID: PMC7511791 DOI: 10.1264/jsme2.me18066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/16/2020] [Indexed: 11/24/2022] Open
Abstract
Sulfur-oxidizing bacterial diversity at the surface of cattle manure was characterized throughout the composting process using a sulfur oxidation gene (soxB) clone library approach. In the mesophilic phase, clones related to the genera Hydrogenophaga and Hydrogenophilus were characteristically detected. In the thermophilic phase, clones related to the genera Hydrogenophaga and Thiohalobacter were predominant. In the cooling phase, the predominant soxB sequences were related to the genus Pseudaminobacter and a new sulfur-oxidizing bacterium belonging to the class Alphaproteobacteria. The present study showed changes in the community composition of sulfur-oxidizing bacteria at the surface of compost throughout the composting process.
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Affiliation(s)
- Yumi Mori
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
- Research Institute for Bioresource and Biotechnology, Ishikawa Prefectural University, 1–308 Suematsu, Nonoichi, Ishikawa 921–8836, Japan
| | - Chika Tada
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
| | - Yasuhiro Fukuda
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
| | - Yutaka Nakai
- Laboratory of Sustainable Animal Environmental Science, Graduate School of Agricultural Science, Tohoku University, 232–3 Yomogida, Naruko-onsen, Osaki, Miyagi 989–6711, Japan
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47
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Yang L, Zhao D, Yang J, Wang W, Chen P, Zhang S, Yan L. Acidithiobacillus thiooxidans and its potential application. Appl Microbiol Biotechnol 2019; 103:7819-7833. [PMID: 31463545 DOI: 10.1007/s00253-019-10098-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 08/12/2019] [Accepted: 08/21/2019] [Indexed: 11/26/2022]
Abstract
Acidithiobacillus thiooxidans (A. thiooxidans) is a widespread, mesophilic, obligately aerobic, extremely acidophilic, rod-shaped, and chemolithoautotrophic gram-negative gammaproteobacterium. It can obtain energy and electrons from the oxidation of reducible sulfur, and it can fix carbon dioxide and assimilate nitrate, nitrite, and ammonium to satisfy carbon and nitrogen requirement. This bacterium exists as different genomovars and its genome size range from 3.02 to 3.97 Mb. Here, we highlight the recent advances in the understanding of the general biological features of A. thiooxidans, as well as the genetic diversity and the sulfur oxidation pathway system. Additionally, the potential applications of A. thiooxidans were summarized including the recycling of metals from metal-bearing ores, electric wastes, and sludge, the improvement of alkali-salinity soils, and the removal of sulfur from sulfur-containing solids and gases.
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Affiliation(s)
- Lei Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Dan Zhao
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Jian Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Weidong Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Peng Chen
- School of Pharmacy, Lanzhou University, Donggang West Road No. 199, Lanzhou, 730020, People's Republic of China
| | - Shuang Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Lei Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
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48
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A combined approach of 16S rRNA and a functional marker gene, soxB to reveal the diversity of sulphur-oxidising bacteria in thermal springs. Arch Microbiol 2019; 201:951-967. [PMID: 31025055 DOI: 10.1007/s00203-019-01666-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/05/2019] [Accepted: 04/19/2019] [Indexed: 10/27/2022]
Abstract
With the advent of new molecular tools, new taxa of sulphur-oxidising bacteria (SOB) in diverse environments are being discovered. However, there is a significant gap of knowledge about the ecology and diversity of SOB in thermal springs. Here, the species diversity and phylogenetic affiliations of SOB were investigated using 16S rRNA and functional gene marker, soxB in thermal springs of Thane district of Maharashtra, India. Most SOB detected by 16S rDNA sequences belong to different operational taxonomic units (OTU's): Firmicutes, α-, β-, γ-Proteobacteria and Actinobacteria with the dominance of first class. However, the soxB gene clone library sequences had shown affiliation with the β-, γ- and α-Proteobacteria. β-Proteobacteria-related sequences were dominant, with 53.3% clones belonging to genus Hydrogenophaga. The thiosulphate oxidation assay carried out for different isolates having distinct identity showed the mean sulphate-sulphur production from 117.86 ± 0.50 to 218.82 ± 2.56 mg SO4-S l-1 after 9 days of incubation. Also, sulphur oxidation by the genus Nitratireductor, Caldimonas, Geobacillus, Paenibacillus, Brevibacillus, Tristrella and Chelatococcus has been reported for the first time that reveals ecological widening over which thiotrophs are distributed.
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49
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Li X, Yu H, Sun X, Yang J, Wang D, Shen L, Pan Y, Wu Y, Wang Q, Zhao Y. Effects of sulfur application on cadmium bioaccumulation in tobacco and its possible mechanisms of rhizospheric microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2019; 368:308-315. [PMID: 30685719 DOI: 10.1016/j.jhazmat.2018.12.099] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/15/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
A potting experiment was conducted to investigate the effect of sulfur application on the bioaccumulation by tobacco and its mechanisms of rhizospheric microorganisms. Cadmium content in tobacco was analyzed using atomic absorption spectrometer, while bacterial community and related gene in soil were analyzed via high-throughput sequencing and quantitative PCR techniques, respectively. The obtained results indicated that tobacco had the ability to accumulate cadmium under no sulfur application conditions, with cadmium contents of 35.4, 23.6, and 26.3 mg kg-1 in leaves, stems, and roots, respectively. Under high-sulfur treatment, these values increased to 66.4, 46.1, and 42.6 mg kg-1, respectively, probably due to the increase of the available cadmium content (from 1.1 to 3.3 mg kg-1) in the soil through a decrease of the soil pH value, which was contributed by the sulfur oxidation reaction. dsrA and soxB genes might play an important role in sulfur oxidation, and Thiobacillus sp. was the dominant bacterial genus during the sulfur oxidation process. In addition, sulfur application exerted little effect on the diversity and structure of the soil bacterial community. The combined results indicate that sulfur application is an effective and safe method for Cd phytoextraction by tobacco.
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Affiliation(s)
- Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hao Yu
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaowei Sun
- Henan Academy of Forestry, Zhengzhou, 450008, China
| | - Jiantao Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Daichang Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lianfeng Shen
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yanshuo Pan
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Qiang Wang
- College of Resources and Environment, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Zhao
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China.
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50
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Watanabe T, Kojima H, Umezawa K, Hori C, Takasuka TE, Kato Y, Fukui M. Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera. Front Microbiol 2019; 10:316. [PMID: 30858836 PMCID: PMC6397845 DOI: 10.3389/fmicb.2019.00316] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/06/2019] [Indexed: 01/08/2023] Open
Abstract
Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
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Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukako Kato
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
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