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Rasmussen AN, Tolar BB, Bargar JR, Boye K, Francis CA. Diverse and unconventional methanogens, methanotrophs, and methylotrophs in metagenome-assembled genomes from subsurface sediments of the Slate River floodplain, Crested Butte, CO, USA. mSystems 2024:e0031424. [PMID: 38940520 DOI: 10.1128/msystems.00314-24] [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: 02/29/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024] Open
Abstract
We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling-particularly methane-cycling-microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.
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Affiliation(s)
- Anna N Rasmussen
- Department of Earth System Science, Stanford University, Stanford, California, USA
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Bradley B Tolar
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - John R Bargar
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kristin Boye
- SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher A Francis
- Department of Earth System Science, Stanford University, Stanford, California, USA
- Oceans Department, Stanford University, Stanford, California, USA
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Schorn S, Graf JS, Littmann S, Hach PF, Lavik G, Speth DR, Schubert CJ, Kuypers MMM, Milucka J. Persistent activity of aerobic methane-oxidizing bacteria in anoxic lake waters due to metabolic versatility. Nat Commun 2024; 15:5293. [PMID: 38906896 PMCID: PMC11192741 DOI: 10.1038/s41467-024-49602-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Lacustrine methane emissions are strongly mitigated by aerobic methane-oxidizing bacteria (MOB) that are typically most active at the oxic-anoxic interface. Although oxygen is required by the MOB for the first step of methane oxidation, their occurrence in anoxic lake waters has raised the possibility that they are capable of oxidizing methane further anaerobically. Here, we investigate the activity and growth of MOB in Lake Zug, a permanently stratified freshwater lake. The rates of anaerobic methane oxidation in the anoxic hypolimnion reached up to 0.2 µM d-1. Single-cell nanoSIMS measurements, together with metagenomic and metatranscriptomic analyses, linked the measured rates to MOB of the order Methylococcales. Interestingly, their methane assimilation activity was similar under hypoxic and anoxic conditions. Our data suggest that these MOB use fermentation-based methanotrophy as well as denitrification under anoxic conditions, thus offering an explanation for their widespread presence in anoxic habitats such as stratified water columns. Thus, the methane sink capacity of anoxic basins may have been underestimated by not accounting for the anaerobic MOB activity.
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Affiliation(s)
- Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Daan R Speth
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Carsten J Schubert
- Department of Surface Waters, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Kastanienbaum, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Zurich, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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Chen KH, Feng J, Bodelier PLE, Yang Z, Huang Q, Delgado-Baquerizo M, Cai P, Tan W, Liu YR. Metabolic coupling between soil aerobic methanotrophs and denitrifiers in rice paddy fields. Nat Commun 2024; 15:3471. [PMID: 38658559 PMCID: PMC11043409 DOI: 10.1038/s41467-024-47827-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Paddy fields are hotspots of microbial denitrification, which is typically linked to the oxidation of electron donors such as methane (CH4) under anoxic and hypoxic conditions. While several anaerobic methanotrophs can facilitate denitrification intracellularly, whether and how aerobic CH4 oxidation couples with denitrification in hypoxic paddy fields remains virtually unknown. Here we combine a ~3300 km field study across main rice-producing areas of China and 13CH4-DNA-stable isotope probing (SIP) experiments to investigate the role of soil aerobic CH4 oxidation in supporting denitrification. Our results reveal positive relationships between CH4 oxidation and denitrification activities and genes across various climatic regions. Microcosm experiments confirm that CH4 and methanotroph addition promote gene expression involved in denitrification and increase nitrous oxide emissions. Moreover, 13CH4-DNA-SIP analyses identify over 70 phylotypes harboring genes associated with denitrification and assimilating 13C, which are mostly belonged to Rubrivivax, Magnetospirillum, and Bradyrhizobium. Combined analyses of 13C-metagenome-assembled genomes and 13C-metabolomics highlight the importance of intermediates such as acetate, propionate and lactate, released during aerobic CH4 oxidation, for the coupling of CH4 oxidation with denitrification. Our work identifies key microbial taxa and pathways driving coupled aerobic CH4 oxidation and denitrification, with important implications for nitrogen management and greenhouse gas regulation in agroecosystems.
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Affiliation(s)
- Kang-Hua Chen
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiao Feng
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Paul L E Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB, Wageningen, The Netherlands
| | - Ziming Yang
- Department of Chemistry, Oakland University, Rochester, MI, 48309, USA
| | - Qiaoyun Huang
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, 41012, Spain
| | - Peng Cai
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenfeng Tan
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yu-Rong Liu
- National Key Laboratory of Agricultural Microbiology and College of Resources and Environment, Huazhong Agricultural University, Wuhan, 430070, China.
- State Environmental Protection Key Laboratory of Soil Health and Green Remediation and Hubei Key Laboratory of Soil Environment and Pollution Remediation, Huazhong Agricultural University, Wuhan, 430070, China.
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Huang H, Zan S, Shao K, Chen H, Fan J. Spatial distribution characteristics and interaction effects of DOM and microbial communities in kelp cultivation areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170511. [PMID: 38309352 DOI: 10.1016/j.scitotenv.2024.170511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
The influence of macroalgae cultivation on aquaculture carbon sinks is significant, with microbial carbon (C) pumps contributing to a stable inert dissolved carbon pool in this context. Concurrently, dissolved organic matter (DOM) exchange at the marine sediment-water interface profoundly affects global ecosystem element cycling. However, the interactions between DOM and bacterial communities at the sediment-water interface in kelp cultivation areas, especially regarding microbial function prediction, have not been fully explored. This study analyzed the DOM characteristics, environmental factors, and bacterial community structure in the Tahewan kelp--Saccharina japonica cultivated area and compared them with those in non-cultivated areas. The results indicated significantly higher dissolved organic carbon (DOC) concentrations in the kelp culture area, particularly in surface seawater and overlying water. The dominant bacterial phyla in both regions included Pseudomonadota, Actinomycetota, and Bacteroidota in both regions, while Desulfobacterota was more prevalent in the sediment environment of the cultivated region. Parallel factor analysis (EEM-PARAFAC) was used to identify DOM components, among which component C2 (a microbial humic-like substance DOM) was highly resistant to microbial degradation. We infer that C2 has similar properties to recalcitrant dissolved organic matter (RDOM). Analysis of the predicted functional genes based on 16S rRNA gene data showed that methanol oxidation, methylotrophy, and methanotrophy were significant in the bottom seawater of the cultivation area. The carbon (C), nitrogen (N), and sulfur (S) cycle functional genes in the sediment environment of the kelp cultivation area were more active than those in other areas, especially in which sulfate reduction and denitrification were the two main processes. Furthermore, a DOM priming effect was identified in the cultivated sediment environment, where kelp-released labile dissolved organic matter (LDOM) stimulates rapid degradation of the original RDOM, potentially enhancing C sequestration.
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Affiliation(s)
- Huiling Huang
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Shuaijun Zan
- Groundwater Provincial Engineering Research Center for Urban Water Recycling and Environmental Safety, Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Kuishuang Shao
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China
| | - Hanjun Chen
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China
| | - Jingfeng Fan
- College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, China; State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian, China.
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Wang YL, Ikuma K, Brooks SC, Varonka MS, Deonarine A. Non-mercury methylating microbial taxa are integral to understanding links between mercury methylation and elemental cycles in marine and freshwater sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123573. [PMID: 38365074 DOI: 10.1016/j.envpol.2024.123573] [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: 10/04/2023] [Revised: 01/09/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024]
Abstract
The goal of this study was to explore the role of non-mercury (Hg) methylating taxa in mercury methylation and to identify potential links between elemental cycles and Hg methylation. Statistical approaches were utilized to investigate the microbial community and biochemical functions in relation to methylmercury (MeHg) concentrations in marine and freshwater sediments. Sediments were collected from the methylation zone (top 15 cm) in four Hg-contaminated sites. Both abiotic (e.g., sulfate, sulfide, iron, salinity, total organic matter, etc.) and biotic factors (e.g., hgcA, abundances of methylating and non-methylating taxa) were quantified. Random forest and stepwise regression were performed to assess whether non-methylating taxa were significantly associated with MeHg concentration. Co-occurrence and functional network analyses were constructed to explore associations between taxa by examining microbial community structure, composition, and biochemical functions across sites. Regression analysis showed that approximately 80% of the variability in sediment MeHg concentration was predicted by total mercury concentration, the abundances of Hg methylating taxa, and the abundances of the non-Hg methylating taxa. The co-occurrence networks identified Paludibacteraceae and Syntrophorhabdaceae as keystone non Hg methylating taxa in multiple sites, indicating the potential for syntrophic interactions with Hg methylators. Strong associations were also observed between methanogens and sulfate-reducing bacteria, which were likely symbiotic associations. The functional network results suggested that non-Hg methylating taxa play important roles in sulfur respiration, nitrogen respiration, and the carbon metabolism-related functions methylotrophy, methanotrophy, and chemoheterotrophy. Interestingly, keystone functions varied by site and did not involve carbon- and sulfur-related functions only. Our findings highlight associations between methylating and non-methylating taxa and sulfur, carbon, and nitrogen cycles in sediment methylation zones, with implications for predicting and understanding the impact of climate and land/sea use changes on Hg methylation.
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Affiliation(s)
- Yong-Li Wang
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, Lubbock, TX, United States
| | - Kaoru Ikuma
- Department of Civil, Construction & Environmental Engineering, Iowa State University, Ames, IA, United States
| | - Scott C Brooks
- Oak Ridge National Laboratory, Environmental Science Division, Oak Ridge, TN, United States
| | - Matthew S Varonka
- U.S. Geological Survey, Geology, Energy & Minerals Science Center, Reston, VA, United States
| | - Amrika Deonarine
- Department of Civil, Environmental & Construction Engineering, Texas Tech University, Lubbock, TX, United States.
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6
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Phi MT, Singer H, Zäh F, Haisch C, Schneider S, Op den Camp HJM, Daumann LJ. Assessing Lanthanide-Dependent Methanol Dehydrogenase Activity: The Assay Matters. Chembiochem 2024; 25:e202300811. [PMID: 38269599 DOI: 10.1002/cbic.202300811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Indexed: 01/26/2024]
Abstract
Artificial dye-coupled assays have been widely adopted as a rapid and convenient method to assess the activity of methanol dehydrogenases (MDH). Lanthanide(Ln)-dependent XoxF-MDHs are able to incorporate different lanthanides (Lns) in their active site. Dye-coupled assays showed that the earlier Lns exhibit a higher enzyme activity than the late Lns. Despite widespread use, there are limitations: oftentimes a pH of 9 and activators are required for the assay. Moreover, Ln-MDH variants are not obtained by isolation from the cells grown with the respective Ln, but by incubation of an apo-MDH with the Ln. Herein, we report the cultivation of Ln-dependent methanotroph Methylacidiphilum fumariolicum SolV with nine different Lns, the isolation of the respective MDHs and the assessment of the enzyme activity using the dye-coupled assay. We compare these results with a protein-coupled assay using its physiological electron acceptor cytochrome cGJ (cyt cGJ ). Depending on the assay, two distinct trends are observed among the Ln series. The specific enzyme activity of La-, Ce- and Pr-MDH, as measured by the protein-coupled assay, exceeds that measured by the dye-coupled assay. This suggests that early Lns also have a positive effect on the interaction between XoxF-MDH and its cyt cGJ thereby increasing functional efficiency.
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Affiliation(s)
- Manh Tri Phi
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Helena Singer
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Felix Zäh
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Christoph Haisch
- Faculty of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
| | - Huub J M Op den Camp
- Department of Microbiology, Research Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, München, Germany
- Chair of Bioinorganic Chemistry, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
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7
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Xu X, Wu W, Li X, Zhao C, Qin Y. Metagenomics coupled with thermodynamic analysis revealed a potential way to improve the nitrogen removal efficiency of the aerobic methane oxidation coupled to denitrification process under the hypoxic condition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168953. [PMID: 38056669 DOI: 10.1016/j.scitotenv.2023.168953] [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: 09/25/2023] [Revised: 11/25/2023] [Accepted: 11/25/2023] [Indexed: 12/08/2023]
Abstract
Aerobic methane (CH4) oxidation coupled to denitrification (AME-D) is a promising wastewater treatment process for CH4 utilization and nitrogen removal. However, it is unclear which CH4-derived carbons are suitable for the AME-D process and how these organics are metabolized. In this study, metagenomics coupled with a thermodynamic model were used to explore the microorganisms and their metabolic mechanisms in an AME-D membrane biofilm reactor (MBfR) with high nitrogen removal efficiency. Results revealed that the aerobic methanotrophs of Methylomonas with the CH4-based fermentation potential were highly enriched and played an important role in CH4 conversion in the MBfR. Bacteria of Xanthomonadaceae, Methylophilaceae, Bacteroidetes, Rhodocyclaceae, Hyphomicrobium were the main denitrifiers. C1 compounds (methanol, formaldehyde and formate) and CH4-based fermentation products are promising cross-feeding intermediates of the AME-D. Specially, by means of integrating the CH4-based fermentation with denitrification, the minimum amount of CH4 required to remove per mole of nitrate can be further reduced to 1.25 mol-CH4 mol-1-NO3-, even lower than that of methanol. Compared to the choice to secrete methanol, type I aerobic methanotrophs require a 15 % reduction in the amount of oxygen required to secrete fermentation metabolites, but a 72 % increase in the amount of CH4-C released. Based on this trade-off, optimizing oxygen supply strategies will help to construct engineered microbiomes focused on aerobic methanotrophs with CH4-based fermentation potential. This study gives an insight into C and N conversions in the AME-D process and highlights the role of CH4-based fermentation in improving the nitrogen removal efficiency of the AME-D process.
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Affiliation(s)
- Xingkun Xu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Weixiang Wu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang University, Hangzhou 310058, China
| | - Xinyu Li
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Changxun Zhao
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Yong Qin
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China.
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Ma X, Sun C, Xian M, Guo J, Zhang R. Progress in research on the biosynthesis of 1,2,4-butanetriol by engineered microbes. World J Microbiol Biotechnol 2024; 40:68. [PMID: 38200399 DOI: 10.1007/s11274-024-03885-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
1,2,4-butanetriol (BT) is a polyol with unique chemical properties, which has a stereocenter and can be divided into D-BT (the S-enantiomer) and L-BT (the R-enantiomer). BT can be used for the synthesis of 1,2,4-butanetriol trinitrate, 3-hydroxytetrahydrofuran, polyurethane, and other chemicals. It is widely used in the military industry, medicine, tobacco, polymer. At present, the BT is mainly synthesized by chemical methods, which are accompanied by harsh reaction conditions, poor selectivity, many by-products, and environmental pollution. Therefore, BT biosynthesis methods with the advantages of mild reaction conditions and green sustainability have become a current research hotspot. In this paper, the research status of microbial synthesis of BT was summarized from the following three aspects: (1) the biosynthetic pathway establishment for BT from xylose; (2) metabolic engineering strategies employed for improving BT production from xylose; (3) other substrates for BT production. Finally, the challenges and prospects of biosynthetic BT were discussed for future methods to improve competitiveness for industrial production.
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Affiliation(s)
- Xiangyu Ma
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Jing Guo
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
| | - Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
- Shandong Energy Institute, Qingdao, 266101, China.
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China.
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Deng Y, Liang C, Zhu X, Zhu X, Chen L, Pan H, Xun F, Tao Y, Xing P. Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments. ISME COMMUNICATIONS 2024; 4:ycae032. [PMID: 38524764 PMCID: PMC10960969 DOI: 10.1093/ismeco/ycae032] [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: 01/03/2024] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024]
Abstract
Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with 13CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the 13C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe3+), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.
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Affiliation(s)
- Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Chulin Liang
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xiaomeng Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Lei Chen
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Hongan Pan
- School of Geography, Nanjing Normal University, Nanjing 210023, Jiangsu, China
| | - Fan Xun
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ye Tao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
| | - Peng Xing
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, Jiangsu, China
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10
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Gorniak L, Bechwar J, Westermann M, Steiniger F, Wegner CE. Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph. Microbiol Spectr 2023; 11:e0086723. [PMID: 37909735 PMCID: PMC10848612 DOI: 10.1128/spectrum.00867-23] [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: 03/07/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Since its discovery, Ln-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding Ln recycling and circular economy. The physiological role of Ln is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) Ln affect metabolism have rarely been done. We noticed unexpectedly pronounced changes in gene expression caused by different Ln supplementation. Our research suggests that strain RH AL1 distinguishes different Ln elements and that the effect of Ln reaches into many aspects of metabolism, for instance, chemotaxis, motility, and polyhydroxyalkanoate metabolism. Our findings regarding Ln accumulation suggest a distinction between individual Ln elements and provide insights relating to intracellular Ln homeostasis. Understanding comprehensively how microbes distinguish and handle different Ln elements is key for turning knowledge into application regarding Ln-centered biometallurgy.
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Affiliation(s)
- Linda Gorniak
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | - Julia Bechwar
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
| | | | - Frank Steiniger
- Electron Microscopy Center, Jena University Hospital, Jena, Germany
| | - Carl-Eric Wegner
- Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University, Jena, Germany
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11
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Rao L, Gu D, Xiang X, Zeng J, Wu Y, Lin X, Christie P. Impact of lignin constituents on the bacterial community and polycyclic aromatic hydrocarbon co-metabolism in an agricultural soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 333:122105. [PMID: 37356789 DOI: 10.1016/j.envpol.2023.122105] [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: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Lignin is a complex biopolymer comprising phenolic monomers with different degrees of methoxylation and may potentially enhance the degradation of soil pollutants such as polycyclic aromatic hydrocarbons (PAHs) through co-metabolism. However, the contribution of lignin constituents, including phenolic and methoxy subunits, to PAH biodegradation remains unclear. Here, p-hydroxybenzoate (pHBA), vanillate and methanol were selected to simulate phenolic units and methoxy groups of lignin. Soil microcosms receiving these compounds were established to evaluate their regulation on the bacterial community and PAH co-metabolism. There were different effects of different components on the biodegradation of a four-ring PAH, benzo(a)anthracene (BaA), as characterized using an isotopic tracer. Only vanillate significantly stimulated BaA mineralization to CO2, with pHBA and methanol leading to no appreciable change in the allocation of BaA in soil compartments. The lignin constituents had differential impacts on the soil bacterial community, with substantial enrichment of methylotrophs occurring in methanol-supplemented microcosms. Both vanillate and pHBA selected several aromatic degraders. Vanillate caused additional enrichment of methylotrophs, suggesting structure-dependent stimulation of bacterial functional guilds by lignin monomers. Compared with its constituents, lignin produced more extensive responses in terms of bacterial diversity and composition and the fate of BaA. However, it was difficult to link BaA co-metabolism to any specific bacterial taxa in the presence of lignin or its subunits. The results indicate that the co-metabolism effects of lignin may not be directly associated with phenolic or methoxy metabolism but with its regulation of the soil microbiome.
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Affiliation(s)
- Leizhen Rao
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Decheng Gu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230031, China
| | - Xingjia Xiang
- Anhui Province Key Laboratory of Wetland Ecological Protection and Restoration, School of Resources and Environmental Engineering, Anhui University, Hefei, 230031, China
| | - Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
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12
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Xiao Y, Wu K, Batool SS, Wang Q, Chen H, Zhai X, Yu Z, Huang J. Enzymatic properties of alcohol dehydrogenase PedE_M.s. derived from Methylopila sp. M107 and its broad metal selectivity. Front Microbiol 2023; 14:1191436. [PMID: 37560521 PMCID: PMC10409515 DOI: 10.3389/fmicb.2023.1191436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
As an important metabolic enzyme in methylotrophs, pyrroloquinoline quinone (PQQ)-dependent alcohol dehydrogenases play significant roles in the global carbon and nitrogen cycles. In this article, a calcium (Ca2+)-dependent alcohol dehydrogenase PedE_M.s., derived from the methylotroph Methylopila sp. M107 was inserted into the modified vector pCM80 and heterologously expressed in the host Methylorubrum extorquens AM1. Based on sequence analysis, PedE_M.s., a PQQ-dependent dehydrogenase belonging to a methanol/ethanol family, was successfully extracted and purified. Showing by biochemical results, its enzymatic activity was detected as 0.72 U/mg while the Km value was 0.028 mM while employing ethanol as optimal substrate. The activity of PedE_M.s. could be enhanced by the presence of potassium (K+) and calcium (Ca2+), while acetonitrile and certain common detergents have been found to decrease the activity of PedE_M.s.. In addition, its optimum temperature and pH were 30°C and pH 9.0, respectively. Chiefly, as a type of Ca2+-dependent alcohol dehydrogenase, PedE_M.s. maintained 60-80% activity in the presence of 10 mM lanthanides and displayed high affinity for ethanol compared to other PedE-type enzymes. The 3D structure of PedE_M.s. was predicted by AlphaFold, and it had an 8-bladed propeller-like super-barrel. Meanwhile, we could speculate that PedE_M.s. contained the conserved residues Glu213, Asn300, and Asp350 through multiple sequence alignment by Clustal and ESpript. The analysis of enzymatic properties of PedE_M.s. enriches our knowledge of the methanol/ethanol family PQQ-dependent dehydrogenase. This study provides new ideas to broaden the application of alcohol dehydrogenase in alcohol concentration calculation, biosensor preparation, and other industries.
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Affiliation(s)
- Ying Xiao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Syeda Sundas Batool
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Qingqun Wang
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xingyu Zhai
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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13
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Identification of a TonB-Dependent Receptor Involved in Lanthanide Switch by the Characterization of Laboratory-Adapted Methylosinus trichosporium OB3b. Appl Environ Microbiol 2023; 89:e0141322. [PMID: 36645275 PMCID: PMC9888264 DOI: 10.1128/aem.01413-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Two methanol dehydrogenases (MDHs), MxaFI and XoxF, have been characterized in methylotrophic and methanotrophic bacteria. MxaFI contains a calcium ion in its active site, whereas XoxF contains a lanthanide ion. Importantly, the expression of MxaFI and XoxF is inversely regulated by lanthanide bioavailability, i.e., the "lanthanide switch." To reveal the genetic and environmental factors affecting the lanthanide switch, we focused on two Methylosinus trichosporium OB3b mutants isolated during routine cultivation. In these mutants, MxaF was constitutively expressed, but lanthanide-dependent XoxF1 was not, even in the presence of 25 μM cerium ions, which is sufficient for XoxF expression in the wild type. Genotyping showed that both mutants harbored a loss-of-function mutation in the CQW49_RS02145 gene, which encodes a TonB-dependent receptor. Gene disruption and complementation experiments demonstrated that CQW49_RS02145 was required for XoxF1 expression in the presence of 25 μM cerium ions. Phylogenetic analysis indicated that CQW49_RS02145 was homologous to the Methylorubrum extorquens AM1 lanthanide transporter gene (lutH). These findings suggest that CQW49_RS02145 is involved in lanthanide uptake across the outer membrane. Furthermore, we demonstrated that supplementation with cerium and glycerol caused severe growth arrest in the wild type. CQW49_RS02145 underwent adaptive laboratory evolution in the presence of cerium and glycerol ions, resulting in a mutation that partially mitigated the growth arrest. This finding implies that loss-of-function mutations in CQW49_RS02145 can be attributed to residual glycerol from the frozen stock. IMPORTANCE Lanthanides are widely used in many industrial applications, including catalysts, magnets, and polishing. Recently, lanthanide-dependent metabolism was characterized in methane-utilizing bacteria. Despite the global demand for lanthanides, few studies have investigated the mechanism of lanthanide uptake by these bacteria. In this study, we identify a lanthanide transporter in Methylosinus trichosporium OB3b and indicate the potential interaction between intracellular lanthanide and glycerol. Understanding the genetic and environmental factors affecting lanthanide uptake should not only help improve the use of lanthanides for the bioconversion of methane into valuable products like methanol but also be of value for developing biomining to extract lanthanides under neutral conditions.
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14
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Hemmann JL, Keller P, Hemmerle L, Vonderach T, Ochsner AM, Bortfeld-Miller M, Günther D, Vorholt JA. Lanpepsy is a novel lanthanide-binding protein involved in the lanthanide response of the obligate methylotroph Methylobacillus flagellatus. J Biol Chem 2023; 299:102940. [PMID: 36702252 PMCID: PMC9988556 DOI: 10.1016/j.jbc.2023.102940] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Lanthanides were recently discovered as metals required in the active site of certain methanol dehydrogenases. Since then, the characterization of the lanthanome, that is, proteins involved in sensing, uptake, and utilization of lanthanides, has become an active field of research. Initial exploration of the response to lanthanides in methylotrophs has revealed that the lanthanome is not conserved and that multiple mechanisms for lanthanide utilization must exist. Here, we investigated the lanthanome in the obligate model methylotroph Methylobacillus flagellatus. We used a proteomic approach to analyze differentially regulated proteins in the presence of lanthanum. While multiple known proteins showed induction upon growth in the presence of lanthanum (Xox proteins, TonB-dependent receptor), we also identified several novel proteins not previously associated with lanthanide utilization. Among these was Mfla_0908, a periplasmic 19 kDa protein without functional annotation. The protein comprises two characteristic PepSY domains, which is why we termed the protein lanpepsy (LanP). Based on bioinformatic analysis, we speculated that LanP could be involved in lanthanide binding. Using dye competition assays, quantification of protein-bound lanthanides by inductively coupled plasma mass spectrometry, as well as isothermal titration calorimetry, we demonstrated the presence of multiple lanthanide binding sites that showed selectivity over the chemically similar calcium ion. LanP thus represents the first member of the PepSY family that binds lanthanides. Although the physiological role of LanP is still unclear, its identification is of interest for applications toward the sustainable purification and separation of rare-earth elements.
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Affiliation(s)
- Jethro L Hemmann
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Philipp Keller
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lucas Hemmerle
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Thomas Vonderach
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Andrea M Ochsner
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Detlef Günther
- Laboratory of Inorganic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Julia A Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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15
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Yao X, Wang J, Hu B. How methanotrophs respond to pH: A review of ecophysiology. Front Microbiol 2023; 13:1034164. [PMID: 36687570 PMCID: PMC9853399 DOI: 10.3389/fmicb.2022.1034164] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/09/2022] [Indexed: 01/08/2023] Open
Abstract
Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.
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Affiliation(s)
- Xiangwu Yao
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Jiaqi Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China
| | - Baolan Hu
- Department of Environmental Engineering, Zhejiang University, Hangzhou, China,Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou, China,*Correspondence: Baolan Hu ✉
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16
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Timsy T, Behrendt U, Ulrich A, Foesel BU, Spanner T, Neumann-Schaal M, Wolf J, Schloter M, Horn MA, Kolb S. Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. Int J Syst Evol Microbiol 2022; 72. [PMID: 36861375 DOI: 10.1099/ijsem.0.005581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Abstract
Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.
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Affiliation(s)
- Timsy Timsy
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Bärbel U Foesel
- Research Unit Molecular Epidemiology, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Spanner
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Meina Neumann-Schaal
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Research Group Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Marcus A Horn
- Institute of Microbiology, Leibniz University of Hannover, Hannover, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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17
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Isolation and Characterization of Homologically Expressed Methanol Dehydrogenase from Methylorubrum extorquens AM1 for the Development of Bioelectrocatalytical Systems. Int J Mol Sci 2022; 23:ijms231810337. [PMID: 36142248 PMCID: PMC9499683 DOI: 10.3390/ijms231810337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/27/2022] [Accepted: 09/02/2022] [Indexed: 12/05/2022] Open
Abstract
(Ca2+)-dependent pyrroloquinolinequinone (PQQ)-dependent methanol dehydrogenase (MDH) (EC: 1.1.2.7) is one of the key enzymes of primary C1-compound metabolism in methylotrophy. PQQ-MDH is a promising catalyst for electrochemical biosensors and biofuel cells. However, the large-scale use of PQQ-MDH in bioelectrocatalysis is not possible due to the low yield of the native enzyme. Homologously overexpressed MDH was obtained from methylotrophic bacterium Methylorubrum extorquens AM1 by cloning the gene of only one subunit, mxaF. The His-tagged enzyme was easily purified by immobilized metal ion affinity chromatography (36% yield). A multimeric form (α6β6) of recombinant PQQ-MDH possessing enzymatic activity (0.54 U/mg) and high stability was demonstrated for the first time. pH-optimum of the purified protein was about 9–10; the enzyme was activated by ammonium ions. It had the highest affinity toward methanol (KM = 0.36 mM). The recombinant MDH was used for the fabrication of an amperometric biosensor. Its linear range for methanol concentrations was 0.002–0.1 mM, the detection limit was 0.7 µM. The properties of the invented biosensor are competitive to the analogs, meaning that this enzyme is a promising catalyst for industrial methanol biosensors. The developed simplified technology for PQQ-MDH production opens up new opportunities for the development of bioelectrocatalytic systems.
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18
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Xu X, Qin Y, Li X, Ma Z, Wu W. Heterogeneity of CH 4-derived carbon induced by O 2:CH 4 mediates the bacterial community assembly processes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154442. [PMID: 35288141 DOI: 10.1016/j.scitotenv.2022.154442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
The mechanism by which O2:CH4 controls microbial community assembly in the process of aerobic methane oxidation coupled to denitrification (AMED) remains largely uncharacterized, which hinders the design of engineering microbiomes for the AMED. In this study, the changes in the bacterial community in fed-batch serum bottle reactors under different O2:CH4 ratios were systematically characterized. The ratios of CH4 consumption to the amount of nitrate removal in the treatment with O2:CH4 = 1.5:1, O2:CH4 = 0.5:1, and O2:CH4 = 0.25:1 were 13.1 ± 3.4, 4.7 ± 1.1, and 5.9 ± 3.0 mol-CH4 mol-1-NO3-, respectively. The α-diversity of the bacterial community increased as O2:CH4 decreased. Significantly different selection patterns were found for the high and low O2:CH4 ratios. The coherence process dominated the selection at high O2:CH4 ratios, while the diversification process played a role when O2:CH4 was low. Differences were also observed in the composition of CH4-derived carbon between treatments with O2:CH4 = 1.5:1 and O2:CH4 = 0.5:1. Compared with the treatments with O2:CH4 = 1.5:1, the concentrations of methanol, formaldehyde, acetate, and ethanol in the treatment with O2:CH4 = 0.5:1 were significantly higher, while the concentration of formate was significantly lower. The heterogeneity of CH4-derived carbon induced by O2:CH4 was likely to be responsible for the differences in the selection patterns. Our findings bridge the gaps between the observations of bacterial community perturbations and ecological community assembly theories, highlighting the potential of the bottom-up design approach to improve the nitrate removal rate of the AME-D.
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Affiliation(s)
- Xingkun Xu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Yong Qin
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China.
| | - Xinyu Li
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China
| | - Zhuang Ma
- Zhejiang Transper Environmental Protection Technology Co., Ltd., Hangzhou 310058, China
| | - Weixiang Wu
- Institute of Environment Pollution Control and Treatment, Zhejiang University, Hangzhou 310058, China; Zhejiang Province Key Laboratory for Water Pollution Control and Environmental Safety Technology, Zhejiang University, Hangzhou 310058, China
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19
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Affiliation(s)
- Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Republic of Korea.
| | - Arslan Sarwar
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, Yongin-si, Republic of Korea
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20
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Sakarika M, Ganigué R, Rabaey K. Methylotrophs: from C1 compounds to food. Curr Opin Biotechnol 2022; 75:102685. [DOI: 10.1016/j.copbio.2022.102685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/12/2021] [Accepted: 12/30/2021] [Indexed: 01/11/2023]
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21
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Schmitz RA, Mohammadi SS, van Erven T, Berben T, Jetten MSM, Pol A, Op den Camp HJM. Methanethiol Consumption and Hydrogen Sulfide Production by the Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum SolV. Front Microbiol 2022; 13:857442. [PMID: 35422776 PMCID: PMC9003020 DOI: 10.3389/fmicb.2022.857442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Methanotrophs aerobically oxidize methane to carbon dioxide to make a living and are known to degrade various other short chain carbon compounds as well. Volatile organic sulfur compounds such as methanethiol (CH3SH) are important intermediates in the sulfur cycle. Although volatile organic sulfur compounds co-occur with methane in various environments, little is known about how these compounds affect methanotrophy. The enzyme methanethiol oxidase catalyzing the oxidation of methanethiol has been known for decades, but only recently the mtoX gene encoding this enzyme was identified in a methylotrophic bacterium. The presence of a homologous gene in verrucomicrobial methanotrophs prompted us to examine how methanotrophs cope with methanethiol. Here, we show that the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV consumes methanethiol and produces H2S, which is concurrently oxidized. Consumption of methanethiol is required since methanethiol inhibits methane oxidation. Cells incubated with ∼15 μM methanethiol from the start clearly showed inhibition of growth. After depletion of methanethiol, growth resumed within 1 day. Genes encoding a putative methanethiol oxidase were found in a variety of methanotrophs. Therefore, we hypothesize that methanethiol degradation is a widespread detoxification mechanism in methanotrophs in a range of environments.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands.,Environmental Chemistry, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zurich, Switzerland
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Timo van Erven
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Research, Radboud University, Nijmegen, Netherlands
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Daszczyńska A, Krucoń T, Stasiuk R, Koblowska M, Matlakowska R. Lanthanide-Dependent Methanol Metabolism of a Proteobacteria-Dominated Community in a Light Lanthanide-Rich Deep Environment. Int J Mol Sci 2022; 23:ijms23073947. [PMID: 35409305 PMCID: PMC8999231 DOI: 10.3390/ijms23073947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln3+)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by Alpha-, Beta-, and Gammaproteobacteria represented by the four orders Methylococcales, Nitrosomonadales, Rhizobiales, and Xanthomonadales. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with Nitrosomonadales and Rhizobiales, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.
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Affiliation(s)
- Agnieszka Daszczyńska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Tomasz Krucoń
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Robert Stasiuk
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Renata Matlakowska
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (A.D.); (R.S.)
- Correspondence:
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23
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Cerbin S, Pérez G, Rybak M, Wejnerowski Ł, Konowalczyk A, Helmsing N, Naus-Wiezer S, Meima-Franke M, Pytlak Ł, Raaijmakers C, Nowak W, Bodelier PLE. Methane-Derived Carbon as a Driver for Cyanobacterial Growth. Front Microbiol 2022; 13:837198. [PMID: 35432228 PMCID: PMC9010870 DOI: 10.3389/fmicb.2022.837198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 11/23/2022] Open
Abstract
Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH4 oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO2) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ13C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO2 released by MOB. On the other hand, 13C-CH4 labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.
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Affiliation(s)
- Slawek Cerbin
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- *Correspondence: Slawek Cerbin,
| | - Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Michał Rybak
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Łukasz Wejnerowski
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Adam Konowalczyk
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Nico Helmsing
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Suzanne Naus-Wiezer
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Łukasz Pytlak
- Montanuniversität Leoben, Applied Geosciences and Geophysics, Leoben, Austria
| | - Ciska Raaijmakers
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
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24
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Bajpai A, Mahawar H, Dubey G, Atoliya N, Parmar R, Devi MH, Kollah B, Mohanty SR. Prospect of pink pigmented facultative methylotrophs in mitigating abiotic stress and climate change. J Basic Microbiol 2022; 62:889-899. [DOI: 10.1002/jobm.202200087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Apekcha Bajpai
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- Department of Microbiology Barkatullah University Bhopal India
| | - Himanshu Mahawar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
- ICAR‐Directorate of Weed Research Jabalpur India
| | - Garima Dubey
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Nagvanti Atoliya
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Rakesh Parmar
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Mayanglambam H. Devi
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Bharati Kollah
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
| | - Santosh R. Mohanty
- Indian Institute of Soil Science Indian Council of Agricultural Research Bhopal India
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Reis PCJ, Thottathil SD, Prairie YT. The role of methanotrophy in the microbial carbon metabolism of temperate lakes. Nat Commun 2022; 13:43. [PMID: 35013226 PMCID: PMC8748455 DOI: 10.1038/s41467-021-27718-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 12/07/2021] [Indexed: 11/30/2022] Open
Abstract
Previous stable isotope and biomarker evidence has indicated that methanotrophy is an important pathway in the microbial loop of freshwater ecosystems, despite the low cell abundance of methane-oxidizing bacteria (MOB) and the low methane concentrations relative to the more abundant dissolved organic carbon (DOC). However, quantitative estimations of the relative contribution of methanotrophy to the microbial carbon metabolism of lakes are scarce, and the mechanism allowing methanotrophy to be of comparable importance to DOC-consuming heterotrophy remained elusive. Using incubation experiments, microscopy, and multiple water column profiles in six temperate lakes, we show that MOB play a much larger role than their abundances alone suggest because of their larger cell size and higher specific activity. MOB activity is tightly constrained by the local methane:oxygen ratio, with DOC-rich lakes with large hypolimnetic volume fraction showing a higher carbon consumption through methanotrophy than heterotrophy at the whole water column level. Our findings suggest that methanotrophy could be a critical microbial carbon consumption pathway in many temperate lakes, challenging the prevailing view of a DOC-centric microbial metabolism in these ecosystems.
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Affiliation(s)
- Paula C J Reis
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada.
| | - Shoji D Thottathil
- Department of Environmental Science, SRM University AP, Amaravati, Andhra Pradesh, 522 502, India
| | - Yves T Prairie
- Département des Sciences Biologiques, Groupe de Recherche Interuniversitaire en Limnologie, Université du Québec à Montréal, Montréal, QC, H2X 1Y4, Canada
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Shi LD, Lv PL, McIlroy SJ, Wang Z, Dong XL, Kouris A, Lai CY, Tyson GW, Strous M, Zhao HP. Methane-dependent selenate reduction by a bacterial consortium. THE ISME JOURNAL 2021; 15:3683-3692. [PMID: 34183781 PMCID: PMC8630058 DOI: 10.1038/s41396-021-01044-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/08/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023]
Abstract
Methanotrophic microorganisms play a critical role in controlling the flux of methane from natural sediments into the atmosphere. Methanotrophs have been shown to couple the oxidation of methane to the reduction of diverse electron acceptors (e.g., oxygen, sulfate, nitrate, and metal oxides), either independently or in consortia with other microbial partners. Although several studies have reported the phenomenon of methane oxidation linked to selenate reduction, neither the microorganisms involved nor the underlying trophic interaction has been clearly identified. Here, we provide the first detailed evidence for interspecies electron transfer between bacterial populations in a bioreactor community where the reduction of selenate is linked to methane oxidation. Metagenomic and metaproteomic analyses of the community revealed a novel species of Methylocystis as the most abundant methanotroph, which actively expressed proteins for oxygen-dependent methane oxidation and fermentation pathways, but lacked the genetic potential for selenate reduction. Pseudoxanthomonas, Piscinibacter, and Rhodocyclaceae populations appeared to be responsible for the observed selenate reduction using proteins initially annotated as periplasmic nitrate reductases, with fermentation by-products released by the methanotrophs as electron donors. The ability for the annotated nitrate reductases to reduce selenate was confirmed by gene knockout studies in an isolate of Pseudoxanthomonas. Overall, this study provides novel insights into the metabolic flexibility of the aerobic methanotrophs that likely allows them to thrive across natural oxygen gradients, and highlights the potential role for similar microbial consortia in linking methane and other biogeochemical cycles in environments where oxygen is limited.
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Affiliation(s)
- Ling-Dong Shi
- grid.13402.340000 0004 1759 700XMOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Pan-Long Lv
- grid.13402.340000 0004 1759 700XMOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Simon J. McIlroy
- grid.489335.00000000406180938Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD Australia ,grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD Australia
| | - Zhen Wang
- grid.13402.340000 0004 1759 700XMOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
| | - Xiao-Li Dong
- grid.22072.350000 0004 1936 7697Department of Geoscience, University of Calgary, Calgary, AB Canada
| | - Angela Kouris
- grid.22072.350000 0004 1936 7697Department of Geoscience, University of Calgary, Calgary, AB Canada
| | - Chun-Yu Lai
- grid.13402.340000 0004 1759 700XMOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China ,grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD Australia
| | - Gene W. Tyson
- grid.489335.00000000406180938Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, QLD Australia
| | - Marc Strous
- grid.22072.350000 0004 1936 7697Department of Geoscience, University of Calgary, Calgary, AB Canada
| | - He-Ping Zhao
- grid.13402.340000 0004 1759 700XMOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China
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Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase. mBio 2021; 12:e0170821. [PMID: 34544276 PMCID: PMC8546591 DOI: 10.1128/mbio.01708-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH4), H2, H2S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (Vmax) of 0.15 ± 0.01 μmol · min-1 · mg protein-1 and an affinity constant (Km) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.
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Korlević M, Markovski M, Zhao Z, Herndl GJ, Najdek M. Seasonal Dynamics of Epiphytic Microbial Communities on Marine Macrophyte Surfaces. Front Microbiol 2021; 12:671342. [PMID: 34603223 PMCID: PMC8482799 DOI: 10.3389/fmicb.2021.671342] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Surfaces of marine macrophytes are inhabited by diverse microbial communities. Most studies focusing on epiphytic communities of macrophytes did not take into account temporal changes or applied low sampling frequency approaches. The seasonal dynamics of epiphytic microbial communities was determined in a meadow of Cymodocea nodosa invaded by Caulerpa cylindracea and in a monospecific settlement of C. cylindracea at monthly intervals. For comparison the ambient prokaryotic picoplankton community was also characterized. At the OTU level, the microbial community composition differed between the ambient water and the epiphytic communities exhibiting host-specificity. Also, successional changes were observed connected to the macrophyte growth cycle. Taxonomic analysis, however, showed similar high rank taxa (phyla and classes) in the ambient water and the epiphytic communities, with the exception of Desulfobacterota, which were only found on C. cylindracea. Cyanobacteria showed seasonal changes while other high rank taxa were present throughout the year. In months of high Cyanobacteria presence the majority of cyanobacterial sequences were classified as Pleurocapsa. Phylogenetic groups present throughout the year (e.g., Saprospiraceae, Rhodobacteraceae, members without known relatives within Gammaproteobacteria, Desulfatitalea, and members without known relatives within Desulfocapsaceae) constituted most of the sequences, while less abundant taxa showed seasonal patterns connected to the macrophyte growth cycle. Taken together, epiphytic microbial communities of the seagrass C. nodosa and the macroalga C. cylindracea appear to be host-specific and contain taxa that undergo successional changes.
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Affiliation(s)
- Marino Korlević
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Marsej Markovski
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
| | - Zihao Zhao
- 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.,Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, Netherlands
| | - Mirjana Najdek
- Center for Marine Research, Ruđer Bošković Institute, Rovinj, Croatia
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Wang Y, Ma F, Yang J, Guo H, Su D, Yu L. Adaption and Degradation Strategies of Methylotrophic 1,4-Dioxane Degrading Strain Xanthobacter sp. YN2 Revealed by Transcriptome-Scale Analysis. Int J Mol Sci 2021; 22:ijms221910435. [PMID: 34638775 PMCID: PMC8508750 DOI: 10.3390/ijms221910435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Biodegradation of 1,4-dioxane (dioxane) contamination has gained much attention for decades. In our previous work, we isolated a highly efficient dioxane degrader, Xanthobacter sp. YN2, but the underlying mechanisms of its extraordinary degradation performance remained unresolved. In this study, we performed a comparative transcriptome analysis of YN2 grown on dioxane and citrate to elucidate its genetic degradation mechanism and investigated the transcriptomes of different dioxane degradation stages (T0, T24, T48). We also analyzed the transcriptional response of YN2 over time during which the carbon source switched from citrate to dioxane. The results indicate that strain YN2 was a methylotroph, which provides YN2 a major advantage as a pollutant degrader. A large number of genes involved in dioxane metabolism were constitutively expressed prior to dioxane exposure. Multiple genes related to the catabolism of each intermediate were upregulated by treatment in response to dioxane. Glyoxylate metabolism was essential during dioxane degradation by YN2, and the key intermediate glyoxylate was metabolized through three routes: glyoxylate carboligase pathway, malate synthase pathway, and anaplerotic ethylmalonyl-CoA pathway. Genes related to quorum sensing and transporters were significantly upregulated during the early stages of degradation (T0, T24) prior to dioxane depletion, while the expression of genes encoding two-component systems was significantly increased at late degradation stages (T48) when total organic carbon in the culture was exhausted. This study is the first to report the participation of genes encoding glyoxalase, as well as methylotrophic genes xoxF and mox, in dioxane metabolism. The present study reveals multiple genetic and transcriptional strategies used by YN2 to rapidly increase biomass during growth on dioxane, achieve high degradation efficiency and tolerance, and adapt to dioxane exposure quickly, which provides useful information regarding the molecular basis for efficient dioxane biodegradation.
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Affiliation(s)
- Yingning Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
- Correspondence:
| | - Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Haijuan Guo
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056107, China;
| | - Delin Su
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
| | - Lan Yu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China; (Y.W.); (J.Y.); (D.S.); (L.Y.)
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Comparative Genomics Revealing Insights into Niche Separation of the Genus Methylophilus. Microorganisms 2021; 9:microorganisms9081577. [PMID: 34442656 PMCID: PMC8399692 DOI: 10.3390/microorganisms9081577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/15/2021] [Accepted: 07/22/2021] [Indexed: 11/22/2022] Open
Abstract
The genus Methylophilus uses methanol as a carbon and energy source, which is widely distributed in terrestrial, freshwater and marine ecosystems. Here, three strains (13, 14 and QUAN) related to the genus Methylophilus, were newly isolated from Lake Fuxian sediments. The draft genomes of strains 13, 14 and QUAN were 3.11 Mb, 3.02 Mb, 3.15 Mb with a G+C content of 51.13, 50.48 and 50.33%, respectively. ANI values between strains 13 and 14, 13 and QUAN, and 14 and QUAN were 81.09, 81.06 and 91.46%, respectively. Pan-genome and core-genome included 3994 and 1559 genes across 18 Methylophilus genomes, respectively. Phylogenetic analysis based on 1035 single-copy genes and 16S rRNA genes revealed two clades, one containing strains isolated from aquatic and the other from the leaf surface. Twenty-three aquatic-specific genes, such as 2OG/Fe(II) oxygenase and diguanylate cyclase, reflected the strategy to survive in oxygen-limited water and sediment. Accordingly, 159 genes were identified specific to leaf association. Besides niche separation, Methylophilus could utilize the combination of ANRA and DNRA to convert nitrate to ammonia and reduce sulfate to sulfur according to the complete sulfur metabolic pathway. Genes encoding the cytochrome c protein and riboflavin were detected in Methylophilus genomes, which directly or indirectly participate in electron transfer.
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Lee H, Baek JI, Lee JY, Jeong J, Kim H, Lee DH, Kim DM, Lee SG. Syntrophic co-culture of a methanotroph and heterotroph for the efficient conversion of methane to mevalonate. Metab Eng 2021; 67:285-292. [PMID: 34298134 DOI: 10.1016/j.ymben.2021.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/07/2021] [Accepted: 07/18/2021] [Indexed: 10/20/2022]
Abstract
As the bioconversion of methane becomes increasingly important for bio-industrial and environmental applications, methanotrophs have received much attention for their ability to convert methane under ambient conditions. This includes the extensive reporting of methanotroph engineering for the conversion of methane to biochemicals. To further increase methane usability, we demonstrated a highly flexible and efficient modular approach based on a synthetic consortium of methanotrophs and heterotrophs mimicking the natural methane ecosystem to produce mevalonate (MVA) from methane. In the methane-conversion module, we used Methylococcus capsulatus Bath as a highly efficient methane biocatalyst and optimized the culture conditions for the production of high amounts of organic acids. In the MVA-synthesis module, we used Escherichia coli SBA01, an evolved strain with high organic acid tolerance and utilization ability, to convert organic acids to MVA. Using recombinant E. coli SBA01 possessing genes for the MVA pathway, 61 mg/L (0.4 mM) of MVA was successfully produced in 48 h without any addition of nutrients except methane. Our platform exhibited high stability and reproducibility with regard to cell growth and MVA production. We believe that this versatile system can be easily extended to many other value-added processes and has a variety of potential applications.
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Affiliation(s)
- Hyewon Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ji In Baek
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, 34134, Republic of Korea
| | - Jin-Young Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jiyeong Jeong
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Haseong Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon, 34113, Republic of Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, 34134, Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science & Technology (UST), Daejeon, 34113, Republic of Korea.
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Karthikeyan OP, Smith TJ, Dandare SU, Parwin KS, Singh H, Loh HX, Cunningham MR, Williams PN, Nichol T, Subramanian A, Ramasamy K, Kumaresan D. Metal(loid) speciation and transformation by aerobic methanotrophs. MICROBIOME 2021; 9:156. [PMID: 34229757 PMCID: PMC8262016 DOI: 10.1186/s40168-021-01112-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/09/2021] [Indexed: 05/06/2023]
Abstract
Manufacturing and resource industries are the key drivers for economic growth with a huge environmental cost (e.g. discharge of industrial effluents and post-mining substrates). Pollutants from waste streams, either organic or inorganic (e.g. heavy metals), are prone to interact with their physical environment that not only affects the ecosystem health but also the livelihood of local communities. Unlike organic pollutants, heavy metals or trace metals (e.g. chromium, mercury) are non-biodegradable, bioaccumulate through food-web interactions and are likely to have a long-term impact on ecosystem health. Microorganisms provide varied ecosystem services including climate regulation, purification of groundwater, rehabilitation of contaminated sites by detoxifying pollutants. Recent studies have highlighted the potential of methanotrophs, a group of bacteria that can use methane as a sole carbon and energy source, to transform toxic metal (loids) such as chromium, mercury and selenium. In this review, we synthesise recent advances in the role of essential metals (e.g. copper) for methanotroph activity, uptake mechanisms alongside their potential to transform toxic heavy metal (loids). Case studies are presented on chromium, selenium and mercury pollution from the tanneries, coal burning and artisanal gold mining, respectively, which are particular problems in the developing economy that we propose may be suitable for remediation by methanotrophs. Video Abstract.
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Affiliation(s)
- Obulisamy Parthiba Karthikeyan
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
- Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI USA
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX USA
| | - Thomas J. Smith
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | - Shamsudeen Umar Dandare
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Kamaludeen Sara Parwin
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore, India
| | - Heetasmin Singh
- Department of Chemistry, University of Guyana, Georgetown, Guyana
| | - Hui Xin Loh
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Mark R Cunningham
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Paul Nicholas Williams
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
| | - Tim Nichol
- Biomolecular Sciences Research Centre, Sheffield Hallam University, Sheffield, UK
| | | | | | - Deepak Kumaresan
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, 19 Chlorine Gardens, Belfast, UK
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Costa RB, Lens PNL, Foresti E. Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies. Crit Rev Biotechnol 2021; 42:145-161. [PMID: 34157918 DOI: 10.1080/07388551.2021.1931014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NOx consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.
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Affiliation(s)
- R B Costa
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil.,National University of Ireland, Galway, Ireland
| | - P N L Lens
- National University of Ireland, Galway, Ireland
| | - E Foresti
- Department of Hydraulics and Sanitation, São Carlos School of Engineering (EESC), University of São Paulo (USP), São Carlos, Brazil
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Extracellular and Intracellular Lanthanide Accumulation in the Methylotrophic Beijerinckiaceae Bacterium RH AL1. Appl Environ Microbiol 2021; 87:e0314420. [PMID: 33893117 PMCID: PMC8316094 DOI: 10.1128/aem.03144-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Recent work with Methylorubrum extorquens AM1 identified intracellular, cytoplasmic lanthanide storage in an organism that harnesses these metals for its metabolism. Here, we describe the extracellular and intracellular accumulation of lanthanides in the Beijerinckiaceae bacterium RH AL1, a newly isolated and recently characterized methylotroph. Using ultrathin-section transmission electron microscopy (TEM), freeze fracture TEM (FFTEM), and energy-dispersive X-ray spectroscopy, we demonstrated that strain RH AL1 accumulates lanthanides extracellularly at outer membrane vesicles (OMVs) and stores them in the periplasm. High-resolution elemental analyses of biomass samples revealed that strain RH AL1 can accumulate ions of different lanthanide species, with a preference for heavier lanthanides. Its methanol oxidation machinery is supposedly adapted to light lanthanides, and their selective uptake is mediated by dedicated uptake mechanisms. Based on transcriptome sequencing (RNA-seq) analysis, these presumably include the previously characterized TonB-ABC transport system encoded by the lut cluster but potentially also a type VI secretion system. A high level of constitutive expression of genes coding for lanthanide-dependent enzymes suggested that strain RH AL1 maintains a stable transcript pool to flexibly respond to changing lanthanide availability. Genes coding for lanthanide-dependent enzymes are broadly distributed taxonomically. Our results support the hypothesis that central aspects of lanthanide-dependent metabolism partially differ between the various taxa. IMPORTANCE Although multiple pieces of evidence have been added to the puzzle of lanthanide-dependent metabolism, we are still far from understanding the physiological role of lanthanides. Given how widespread lanthanide-dependent enzymes are, only limited information is available with respect to how lanthanides are taken up and stored in an organism. Our research complements work with commonly studied model organisms and showed the localized storage of lanthanides in the periplasm. This storage occurred at comparably low concentrations. Strain RH AL1 is able to accumulate lanthanide ions extracellularly and to selectively utilize lighter lanthanides. The Beijerinckiaceae bacterium RH AL1 might be an attractive target for developing biorecovery strategies to obtain these economically highly demanded metals in environmentally friendly ways.
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De Anda V, Chen LX, Dombrowski N, Hua ZS, Jiang HC, Banfield JF, Li WJ, Baker BJ. Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways. Nat Commun 2021; 12:2404. [PMID: 33893309 PMCID: PMC8065059 DOI: 10.1038/s41467-021-22736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/18/2021] [Indexed: 02/02/2023] Open
Abstract
Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.
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Affiliation(s)
- Valerie De Anda
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
| | - Lin-Xing Chen
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Nina Dombrowski
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, Den Burg, Netherlands
| | - Zheng-Shuang Hua
- Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, People's Republic of China
| | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, People's Republic of China.
| | - Brett J Baker
- Department of Marine Science, University of Texas Austin, Port Aransas, TX, 78373, USA.
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Roszczenko-Jasińska P, Krucoń T, Stasiuk R, Matlakowska R. Occurrence of XoxF-type methanol dehydrogenases in bacteria inhabiting light lanthanide-rich shale rock. FEMS Microbiol Ecol 2021; 97:6047175. [PMID: 33547466 DOI: 10.1093/femsec/fiaa259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/22/2020] [Indexed: 11/12/2022] Open
Abstract
This study analyzed the occurrence of lanthanide-dependent (XoxF type) methanol dehydrogenases in the bacterial community dominated by Proteobacteria inhabiting shale rock. In total, 22 sequence matches of XoxF were identified in the metaproteome of the community. This enzyme was produced by bacteria represented by orders such as Rhizobiales, Rhodobacterales, Rhodospiralles, Burkholderiales and Nitrosomonadales. Among the identified XoxF proteins, seven belonged to XoxF1 clade and 15 to XoxF5 clade. This study is the first to show the occurrence of XoxF proteins in the metaproteome of environmental lithobiontic bacterial community colonizing an underground rock rich in light lanthanides. The presented results broaden our understanding of the ecology of XoxF producing bacteria as well as the distribution and diversity of these enzymes in the natural environment.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Faculty of Biology, Department of Bacterial Genetics, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Tomasz Krucoń
- Faculty of Biology, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Robert Stasiuk
- Faculty of Biology, Department of Geomicrobiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Renata Matlakowska
- Faculty of Biology, Department of Geomicrobiology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
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Featherston ER, Mattocks JA, Tirsch JL, Cotruvo JA. Heterologous expression, purification, and characterization of proteins in the lanthanome. Methods Enzymol 2021; 650:119-157. [PMID: 33867019 DOI: 10.1016/bs.mie.2021.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recent work has revealed that certain lanthanides-in particular, the more earth-abundant, lighter lanthanides-play essential roles in pyrroloquinoline quinone (PQQ) dependent alcohol dehydrogenases from methylotrophic and non-methylotrophic bacteria. More recently, efforts of several laboratories have begun to identify the molecular players (the lanthanome) involved in selective uptake, recognition, and utilization of lanthanides within the cell. In this chapter, we present protocols for the heterologous expression in Escherichia coli, purification, and characterization of many of the currently known proteins that comprise the lanthanome of the model facultative methylotroph, Methylorubrum extorquens AM1. In addition to the methanol dehydrogenase XoxF, these proteins include the associated c-type cytochrome, XoxG, and solute binding protein, XoxJ. We also present new, streamlined protocols for purification of the highly selective lanthanide-binding protein, lanmodulin, and a solute binding protein for PQQ, PqqT. Finally, we discuss simple, spectroscopic methods for determining lanthanide- and PQQ-binding stoichiometry of proteins. We envision that these protocols will be useful to investigators identifying and characterizing novel members of the lanthanome in many organisms.
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Affiliation(s)
- Emily R Featherston
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Jonathan L Tirsch
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Joseph A Cotruvo
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States.
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Vu HN, Subuyuj GA, Crisostomo RV, Skovran E. Transposon mutagenesis for methylotrophic bacteria using Methylorubrum extorquens AM1 as a model system. Methods Enzymol 2021; 650:159-184. [PMID: 33867020 DOI: 10.1016/bs.mie.2021.01.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transposon mutagenesis utilizes transposable genetic elements that integrate into a recipient genome to generate random insertion mutations which are easily identified. This forward genetic approach has proven powerful in elucidating complex processes, such as various pathways in methylotrophy. In the past decade, many methylotrophic bacteria have been shown to possess alcohol dehydrogenase enzymes that use lanthanides (Lns) as cofactors. Using Methylorubrum extorquens AM1 as a model organism, we discuss the experimental designs, protocols, and results of three transposon mutagenesis studies to identify genes involved in different aspects of Ln-dependent methanol oxidation. These studies include a selection for transposon insertions that prevent toxic intracellular formaldehyde accumulation, a fluorescence-imaging screen to identify regulatory processes for a primary Ln-dependent methanol dehydrogenase, and a phenotypic screen for genes necessary for function of a Ln-dependent ethanol dehydrogenase. We anticipate that the methods described in this chapter can be applied to understand other metabolic systems in diverse bacteria.
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Affiliation(s)
- Huong N Vu
- Department of Biological Sciences, San José State University, San José, CA, United States
| | - Gabriel A Subuyuj
- Department of Biological Sciences, San José State University, San José, CA, United States
| | | | - Elizabeth Skovran
- Department of Biological Sciences, San José State University, San José, CA, United States.
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Huang J, Zheng Y, Groom JD, Yu Z, Chistoserdova L. Expression, purification and properties of the enzymes involved in lanthanide-dependent alcohol oxidation: XoxF4, XoxF5, ExaF/PedH, and XoxG4. Methods Enzymol 2021; 650:81-96. [PMID: 33867026 DOI: 10.1016/bs.mie.2021.01.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this chapter we describe logistics, protocols and conditions for expression, purification and characterization of Ln3+-dependent alcohol dehydrogenases representing three distinct phylogenetic clades of these enzymes, classified as XoxF4, XoxF5 and ExaF/PedH. We present data on the biochemical properties of a dozen enzymes, all generated by our group, in a comparative fashion. These enzymes display a range of properties in terms of substrate and metal specificities, pH and ammonium requirement, as well as catalytic constants. In addition, we describe a single novel cytochrome, XoxG4, that likely serves as a natural electron acceptor from XoxF5 in methanotrophs of the Gammaproteobacteria class.
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Affiliation(s)
- Jing Huang
- Department of Parasitology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Joseph D Groom
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States
| | - Zheng Yu
- Department of Microbiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA, United States.
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Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
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Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
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Methane utilizing plant growth-promoting microbial diversity analysis of flooded paddy ecosystem of India. World J Microbiol Biotechnol 2021; 37:56. [PMID: 33619649 DOI: 10.1007/s11274-021-03018-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/01/2021] [Indexed: 01/10/2023]
Abstract
Methane utilizing bacteria (MUB) are known to inhabit the flooded paddy ecosystem where they play an important role in regulating net methane (CH4) emission. We hypothesize that efficient MUB having plant growth-promoting (PGP) attributes can be used for developing novel bio-inoculant for flooded paddy ecosystem which might not only reduce methane emission but also assist in improving the plant growth parameters. Hence, soil and plant samples were collected from the phyllosphere, rhizosphere, and non-rhizosphere of five rice-growing regions of India at the tillering stage and investigated for efficient methane-oxidizing and PGP bacteria. Based on the monooxygenase activity and percent methane utilization on NMS medium with methane as the sole C source, 123 isolates were identified and grouped phylogenetically into 13 bacteria and 2 yeast genera. Among different regions, a significantly higher number of isolates were obtained from lowland flooded paddy ecosystems of Aduthurai (33.33%) followed by Ernakulum (20.33%) and Brahmaputra valley (19.51%) as compared to upland irrigated regions of Gaya (17.07%) and Varanasi (8.94%). Among sub-samples, a significantly higher number of isolates were found inhabiting the phyllosphere (58.54%) followed by non-rhizosphere (25.20%) and rhizosphere (15.45%). Significantly higher utilization of methane and PGP attributes were observed in 30 isolates belonging to genera Hyphomicrobium, Burkholderia, Methylobacterium, Paenibacillus, Pseudomonas, Rahnella, and Meyerozyma. M. oryzae MNL7 showed significantly better growth with 74.33% of CH4 utilization at the rate of 302.9 ± 5.58 and exhibited half-maximal growth rate, Ks of 1.92 ± 0.092 mg CH4 L-1. Besides the ability to utilize CH4, P. polymyxa MaAL70 possessed PGP attributes such as solubilization of P, K, and Zn, fixation of atmospheric N and production of indole acetic acid (IAA). Both these promising isolates can be explored in the future for developing novel biofertilizers for flooded paddies.
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Sarmiento-Pavía PD, Sosa-Torres ME. Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases. J Biol Inorg Chem 2021; 26:177-203. [PMID: 33606117 DOI: 10.1007/s00775-021-01852-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 12/19/2022]
Abstract
Among the several alcohol dehydrogenases, PQQ-dependent enzymes are mainly found in the α, β, and γ-proteobacteria. These proteins are classified into three main groups. Type I ADHs are localized in the periplasm and contain one Ca2+-PQQ moiety, being the methanol dehydrogenase (MDH) the most representative. In recent years, several lanthanide-dependent MDHs have been discovered exploding the understanding of the natural role of lanthanide ions. Type II ADHs are localized in the periplasm and possess one Ca2+-PQQ moiety and one heme c group. Finally, type III ADHs are complexes of two or three subunits localized in the cytoplasmic membrane and possess one Ca2+-PQQ moiety and four heme c groups, and in one of these proteins, an additional [2Fe-2S] cluster has been discovered recently. From the bioinorganic point of view, PQQ-dependent alcohol dehydrogenases have been revived recently mainly due to the discovery of the lanthanide-dependent enzymes. Here, we review the three types of PQQ-dependent ADHs with special focus on their structural features and electron transfer processes. The PQQ-Alcohol dehydrogenases are classified into three main groups. Type I and type II ADHs are located in the periplasm, while type III ADHs are in the cytoplasmic membrane. ADH-I have a Ca-PQQ or a Ln-PQQ, ADH-II a Ca-PQQ and one heme-c and ADH-III a Ca-PQQ and four hemes-c. This review focuses on their structural features and electron transfer processes.
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Affiliation(s)
- Pedro D Sarmiento-Pavía
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico
| | - Martha E Sosa-Torres
- Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, 04510, Ciudad de México, Mexico.
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Mass spectrometry-based approaches to study lanthanides and lanthanide-dependent proteins in the phyllosphere. Methods Enzymol 2021; 650:215-236. [PMID: 33867023 DOI: 10.1016/bs.mie.2021.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rare-earth elements (REEs) were recently discovered to be biologically significant. The finding was originally made with the methanol dehydrogenase XoxF, which depends on REEs for its activity, and reports of lanthanide-utilizing bacteria have since expanded. Environmental proteomics allows the identification of proteins specifically induced by the presence of lanthanides or can provide insights into the preferred use of lanthanide-dependent and -independent isoenzymes, for example. Here we describe protocols for the growth and subsequent mass spectrometry-based proteome analysis of bacteria obtained from controlled artificial media and from the phyllosphere of the model plant Arabidopsis thaliana. In addition, the use of inductively coupled plasma mass spectrometry (ICP-MS) is described for the quantification of REEs in biological samples.
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Yang Q, Guo X, Liu Y, Jiang H. Biocatalytic C-C Bond Formation for One Carbon Resource Utilization. Int J Mol Sci 2021; 22:ijms22041890. [PMID: 33672882 PMCID: PMC7918591 DOI: 10.3390/ijms22041890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/31/2021] [Accepted: 02/05/2021] [Indexed: 12/22/2022] Open
Abstract
The carbon-carbon bond formation has always been one of the most important reactions in C1 resource utilization. Compared to traditional organic synthesis methods, biocatalytic C-C bond formation offers a green and potent alternative for C1 transformation. In recent years, with the development of synthetic biology, more and more carboxylases and C-C ligases have been mined and designed for the C1 transformation in vitro and C1 assimilation in vivo. This article presents an overview of C-C bond formation in biocatalytic C1 resource utilization is first provided. Sets of newly mined and designed carboxylases and ligases capable of catalyzing C-C bond formation for the transformation of CO2, formaldehyde, CO, and formate are then reviewed, and their catalytic mechanisms are discussed. Finally, the current advances and the future perspectives for the development of catalysts for C1 resource utilization are provided.
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Affiliation(s)
- Qiaoyu Yang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoxian Guo
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
| | - Yuwan Liu
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (Q.Y.); (X.G.)
- National Technology Innovation Center of Synthetic Biology, Tianjin 300308, China
- Correspondence: (Y.L.); (H.J.)
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Picone N, Blom P, Wallenius AJ, Hogendoorn C, Mesman R, Cremers G, Gagliano AL, D'Alessandro W, Quatrini P, Jetten MSM, Pol A, Op den Camp HJM. Methylacidimicrobium thermophilum AP8, a Novel Methane- and Hydrogen-Oxidizing Bacterium Isolated From Volcanic Soil on Pantelleria Island, Italy. Front Microbiol 2021; 12:637762. [PMID: 33643272 PMCID: PMC7907005 DOI: 10.3389/fmicb.2021.637762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
The Favara Grande is a geothermal area located on Pantelleria Island, Italy. The area is characterized high temperatures in the top layer of the soil (60°C), low pH (3–5) and hydrothermal gas emissions mainly composed of carbon dioxide (CO2), methane (CH4), and hydrogen (H2). These geothermal features may provide a suitable niche for the growth of chemolithotrophic thermoacidophiles, including the lanthanide-dependent methanotrophs of the phylum Verrucomicrobia. In this study, we started enrichment cultures inoculated with soil of the Favara Grande at 50 and 60°C with CH4 as energy source and medium containing sufficient lanthanides at pH 3 and 5. From these cultures, a verrucomicrobial methanotroph could be isolated via serial dilution and floating filters techniques. The genome of strain AP8 was sequenced and based on phylogenetic analysis we propose to name this new species Methylacidimicrobium thermophilum AP8. The transcriptome data at μmax (0.051 ± 0.001 h−1, doubling time ~14 h) of the new strain showed a high expression of the pmoCAB2 operon encoding the membrane-bound methane monooxygenase and of the gene xoxF1, encoding the lanthanide-dependent methanol dehydrogenase. A second pmoCAB operon and xoxF2 gene were not expressed. The physiology of strain AP8 was further investigated and revealed an optimal growth in a pH range of 3–5 at 50°C, representing the first thermophilic strain of the genus Methylacidimicrobium. Moreover, strain AP8 had a KS(app) for methane of 8 ± 1 μM. Beside methane, a type 1b [NiFe] hydrogenase enabled hydrogen oxidation at oxygen concentrations up to 1%. Taken together, our results expand the knowledge on the characteristics and adaptations of verrucomicrobial methanotrophs in hydrothermal environments and add a new thermophilic strain to the genus Methylacidimicrobium.
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Affiliation(s)
- Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Pieter Blom
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Rob Mesman
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | | | | | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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Schmitz RA, Peeters SH, Versantvoort W, Picone N, Pol A, Jetten MSM, Op den Camp HJM. Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles. FEMS Microbiol Rev 2021; 45:6125968. [PMID: 33524112 PMCID: PMC8498564 DOI: 10.1093/femsre/fuab007] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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Sanders-Smith R, Segovia BT, Forbes C, Hessing-Lewis M, Morien E, Lemay MA, O'Connor MI, Parfrey LW. Host-Specificity and Core Taxa of Seagrass Leaf Microbiome Identified Across Tissue Age and Geographical Regions. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.605304] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The seagrass Zostera marina is a widespread foundational species in temperate coastal ecosystems that supports diverse communities of epiphytes and grazers. Bacteria link the production of seagrass to higher trophic levels and are thought to influence seagrass biology and health. Yet, we lack a clear understanding of the factors that structure the seagrass microbiome, or whether there is a consistent microbial community associated with seagrass that underpins functional roles. We sampled surface microbiome (epibiota) from new and old growth seagrass leaves and the surrounding seawater in eight meadows among four regions along the Central Coast of British Columbia, Canada to assess microbiome variability across space and as leaves age. We found that the seagrass leaf microbiome differs strongly from seawater. Microbial communities in new and old growth leaves are different from each other and from artificial seagrass leaves we deployed in one meadow. The microbiome on new leaves is less diverse and there is a small suite of core OTUs (operational taxonomic units) consistently present across regions. The overall microbial community for new leaves is more dispersed but with little regional differentiation, while the epiphytes on old leaves are regionally distinct. Many core OTUs on old leaves are commonly associated with marine biofilms. Together these observations suggest a stronger role for host filtering in new compared to old leaves, and a stronger influence of the environment and environmental colonization in old leaves. We found 11 core microbial taxa consistently present on old and new leaves and at very low relative abundance on artificial leaves and in the water column. These 11 taxa appear to be strongly associated with Z. marina. These core taxa may perform key functions important for the host such as detoxifying seagrass waste products, enhancing plant growth, and controlling epiphyte cover.
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Pastawan V, Suganuma S, Mizuno K, Wang L, Tani A, Mitsui R, Nakamura K, Shimada M, Hayakawa T, Fitriyanto NA, Nakagawa T. Regulation of lanthanide-dependent methanol oxidation pathway in the legume symbiotic nitrogen-fixing bacterium Bradyrhizobium sp. strain Ce-3. J Biosci Bioeng 2020; 130:582-587. [DOI: 10.1016/j.jbiosc.2020.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
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Zheng Y, Wang H, Yu Z, Haroon F, Hernández ME, Chistoserdova L. Metagenomic Insight into Environmentally Challenged Methane-Fed Microbial Communities. Microorganisms 2020; 8:microorganisms8101614. [PMID: 33092280 PMCID: PMC7589939 DOI: 10.3390/microorganisms8101614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/16/2020] [Accepted: 10/18/2020] [Indexed: 11/16/2022] Open
Abstract
In this study, we aimed to investigate, through high-resolution metagenomics and metatranscriptomics, the composition and the trajectories of microbial communities originating from a natural sample, fed exclusively with methane, over 14 weeks of laboratory incubation. This study builds on our prior data, suggesting that multiple functional guilds feed on methane, likely through guild-to-guild carbon transfer, and potentially through intraguild and intraspecies interactions. We observed that, under two simulated dioxygen partial pressures—low versus high—community trajectories were different, with considerable variability among the replicates. In all microcosms, four major functional guilds were prominently present, representing Methylococcaceae (the true methanotrophs), Methylophilaceae (the nonmethanotrophic methylotrophs), Burkholderiales, and Bacteroidetes. Additional functional guilds were detected in multiple samples, such as members of Opitutae, as well as the predatory species, suggesting additional complexity for methane-oxidizing communities. Metatranscriptomic analysis suggested simultaneous expression of the two alternative types of methanol dehydrogenases in both Methylococcaceae and Methylophilaceae, while high expression of the oxidative/nitrosative stress response genes suggested competition for dioxygen among the community members. The transcriptomic analysis further suggested that Burkholderiales likely feed on acetate that is produced by Methylococcaceae under hypoxic conditions, while Bacteroidetes likely feed on biopolymers produced by both Methylococcaceae and Methylophilaceae.
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Affiliation(s)
- Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (Y.Z.); (H.W.)
| | - Huan Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; (Y.Z.); (H.W.)
| | - Zheng Yu
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA;
| | - Fauzi Haroon
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Maria E. Hernández
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA;
- Biotechnological Management of Resources Network, Institute of Ecology A. C., 91070 Xalapa, Mexico
- Correspondence: (M.E.H.); (L.C.)
| | - Ludmila Chistoserdova
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA;
- Correspondence: (M.E.H.); (L.C.)
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50
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Mattocks JA, Cotruvo JA. Biological, biomolecular, and bio-inspired strategies for detection, extraction, and separations of lanthanides and actinides. Chem Soc Rev 2020; 49:8315-8334. [PMID: 33057507 DOI: 10.1039/d0cs00653j] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lanthanides and actinides are elements of ever-increasing technological importance in the modern world. However, the similar chemical and physical properties within these groups make purification of individual elements a challenge. Current industrial standards for the extraction, separation, and purification of these metals from natural sources, recycled materials, and industrial waste are inefficient, relying upon harsh conditions, repetitive steps, and ligands with only modest selectivity. Biological, biomolecular, and bio-inspired strategies towards improving these separations and making them more environmentally sustainable have been researched for many years; however, these methods often have insufficient selectivity for practical application. Recent developments in the understanding of how lanthanides are selectively acquired and used by certain bacteria offer the opportunity for a newer, more efficient take on these designs, as well as the possibility for fundamentally new designs and strategies. Herein, we review current cell-based and biomolecular (primarily small-molecule and protein-based) methods for detection, extraction, and separations of f-block elements. We discuss how the increasing knowledge regarding the selective recognition, uptake, trafficking, and storage of these elements in biological systems has informed and will continue to promote development of novel approaches to achieve these ends.
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Affiliation(s)
- Joseph A Mattocks
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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