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Moisan MA, Lajoie G, Constant P, Martineau C, Maire V. How tree traits modulate tree methane fluxes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173730. [PMID: 38839018 DOI: 10.1016/j.scitotenv.2024.173730] [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: 02/11/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Trees can play different roles in the regulation of fluxes of methane (CH4), a greenhouse gas with a warming potential 83 times greater than that of carbon dioxide. Forest soils have the greatest potential for methane uptake compared to other land uses. In addition to their influence on soil CH4 fluxes, trees can act directly as a source or sink of CH4, by transporting CH4 produced in the soil and harbouring the key microorganisms involved in CH4 production and consumption (methanogens and methanotrophs). Tree CH4 fluxes can vary between species characterized by different traits that influence transport and modify the availability of CH4 reaction substrates as well as the habitat for methanogens and methanotrophs. Despite their important role in modulating CH4 fluxes from forest ecosystems, the identity and role of tree traits influencing these fluxes are poorly consolidated in the literature. The objectives of this paper are to 1) Review the functional traits of trees associated with their role in the regulation of CH4 emissions; 2) Assess the importance of inter-specific variability in CH4 fluxes via a global analysis of tree methane fluxes in the literature. Our review highlights that differences in CH4 fluxes between tree species and individuals can be explained by a diversity of traits influencing CH4 transport and microbial production of CH4 such as wood density and secondary metabolites. We propose a functional classification for trees based on the key traits associated with a function in CH4 emissions. We identified the fast-growing species with low wood density, species adapted to flood and species vulnerable to rot as functional groups which can be net sources of CH4 in conditions favorable to CH4 production. The global analysis further demonstrated the importance of taxonomy, with other factors such as land type and season in explaining variability in tree CH4 fluxes.
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Affiliation(s)
- Marie-Ange Moisan
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada; Département des Sciences de l'environnement, Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada; Centre de Recherche sur les Interactions Bassins Versants - Écosystèmes Aquatiques (RIVE), Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada.
| | - Geneviève Lajoie
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke St E, Montréal H1X 2B2, Canada; Jardin Botanique de Montréal, 4101 Sherbrooke St E, Montréal H1X 2B2, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
| | - Christine Martineau
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada
| | - Vincent Maire
- Département des Sciences de l'environnement, Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada; Centre de Recherche sur les Interactions Bassins Versants - Écosystèmes Aquatiques (RIVE), Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada
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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; 9:e0031424. [PMID: 38940520 PMCID: PMC11264602 DOI: 10.1128/msystems.00314-24] [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: 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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Bicaldo IEC, Padilla KSAR, Tu TH, Chen WT, Mendoza-Pascual MU, Vicera CVB, de Leon JR, Poblete KN, Austria ES, Lopez MLD, Kobayashi Y, Shiah FK, Papa RDS, Okuda N, Wang PL, Lin LH. The methane-oxidizing microbial communities of three maar lakes in tropical monsoon Asia. Front Microbiol 2024; 15:1410666. [PMID: 39044952 PMCID: PMC11263035 DOI: 10.3389/fmicb.2024.1410666] [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: 04/01/2024] [Accepted: 05/21/2024] [Indexed: 07/25/2024] Open
Abstract
Methane-oxidizing bacteria (MOB) is a group of planktonic microorganisms that use methane as their primary source of cellular energy. For tropical lakes in monsoon Asia, there is currently a knowledge gap on MOB community diversity and the factors influencing their abundance. Herewith, we present a preliminary assessment of the MOB communities in three maar lakes in tropical monsoon Asia using Catalyzed Reporter Deposition, Fluorescence In-Situ Hybridization (CARD-FISH), 16S rRNA amplicon sequencing, and pmoA gene sequencing. Correlation analysis between MOB abundances and lakes' physicochemical parameters following seasonal monsoon events were performed to explain observed spatial and temporal patterns in MOB diversity. The CARD-FISH analyses detected the three MOB types (I, II, and NC10) which aligned with the results from 16S rRNA amplicons and pmoA gene sequencing. Among community members based on 16S rRNA genes, Proteobacterial Type I MOB (e.g., Methylococcaceae and Methylomonadaceae), Proteobacterial Type II (Methylocystaceae), Verrucomicrobial (Methylacidiphilaceae), Methylomirabilota/NC10 (Methylomirabilaceae), and archaeal ANME-1a were found to be the dominant methane-oxidizers in three maar lakes. Analysis of microbial diversity and distribution revealed that the community compositions in Lake Yambo vary with the seasons and are more distinct during the stratified period. Temperature, DO, and pH were significantly and inversely linked with type I MOB and Methylomirabilota during stratification. Only MOB type I was influenced by monsoon changes. This research sought to establish a baseline for the diversity and ecology of planktonic MOB in tropical monsoon Asia to better comprehend their contribution to the CH4 cycle in tropical freshwater ecosystems.
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Affiliation(s)
- Iona Eunice C. Bicaldo
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Karol Sophia Agape R. Padilla
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
- Department of Science and Technology, Science Education Institute, Taguig, Philippines
| | - Tzu-Hsuan Tu
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wan Ting Chen
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
| | - Milette U. Mendoza-Pascual
- Department of Environmental Science, School of Science and Engineering, Ateneo Research Institute for Science and Engineering, Ateneo de Manila University, Quezon City, Philippines
| | | | - Justine R. de Leon
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | | | | | - Mark Louie D. Lopez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Yuki Kobayashi
- Center for Ecological Research, Kyoto University, Shiga, Japan
| | - Fuh-Kwo Shiah
- Research Center for Environmental Changes, Academia Sinica, Taipei, Taiwan
| | - Rey Donne S. Papa
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, University of Santo Tomas, Manila, Philippines
| | - Noboru Okuda
- Center for Ecological Research, Kyoto University, Shiga, Japan
- Research Center for Inland Seas, Kobe University, Kobe, Japan
- Research Institute for Humanity and Nature, Kamigamo Motoyama, Kita Ward, Kyoto, Japan
| | - Pei-Ling Wang
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
| | - Li-Hung Lin
- Department of Geosciences, National Taiwan University, Taipei, Taiwan
- Research Center for Future Earth, National Taiwan University, Taipei, Taiwan
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Rocha RA, Alexandrov K, Scott C. Rare earth elements in biology: From biochemical curiosity to solutions for extractive industries. Microb Biotechnol 2024; 17:e14503. [PMID: 38829373 PMCID: PMC11146143 DOI: 10.1111/1751-7915.14503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/28/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024] Open
Abstract
Rare earth elements (REEs) are critical for our modern lifestyles and the transition to a low-carbon economy. Recent advances in our understanding of the role of REEs in biology, particularly methylotrophy, have provided opportunities to explore biotechnological innovations to improve REE mining and recycling. In addition to bacterial accumulation and concentration of REEs, biological REE binders, including proteins (lanmodulin, lanpepsy) and small molecules (metallophores and cofactors) have been identified that enable REE concentration and separation. REE-binding proteins have also been used in several mechanistically distinct REE biosensors, which have potential application in mining and medicine. Notably, the role of REEs in biology has only been known for a decade, suggesting their considerable scope for developing new understanding and novel applications.
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Affiliation(s)
- Raquel A. Rocha
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- CSIRO Advanced Engineering Biology Future Science Platform, Black Mountain Science and Innovation ParkCanberraAustralian Capital TerritoryAustralia
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Colin Scott
- ARC Centre of Excellence in Synthetic BiologyCanberraAustralian Capital TerritoryAustralia
- CSIRO Advanced Engineering Biology Future Science Platform, Black Mountain Science and Innovation ParkCanberraAustralian Capital TerritoryAustralia
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5
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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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6
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Liu C, Schmitz RA, Pol A, Hogendoorn C, Verhagen D, Peeters SH, van Alen TA, Cremers G, Mesman RA, Op den Camp HJM. Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil. Environ Microbiol 2024; 26:e16602. [PMID: 38454738 DOI: 10.1111/1462-2920.16602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arjan Pol
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Daniël Verhagen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Mesman
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
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Tucci FJ, Rosenzweig AC. Direct Methane Oxidation by Copper- and Iron-Dependent Methane Monooxygenases. Chem Rev 2024; 124:1288-1320. [PMID: 38305159 PMCID: PMC10923174 DOI: 10.1021/acs.chemrev.3c00727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Methane is a potent greenhouse gas that contributes significantly to climate change and is primarily regulated in Nature by methanotrophic bacteria, which consume methane gas as their source of energy and carbon, first by oxidizing it to methanol. The direct oxidation of methane to methanol is a chemically difficult transformation, accomplished in methanotrophs by complex methane monooxygenase (MMO) enzyme systems. These enzymes use iron or copper metallocofactors and have been the subject of detailed investigation. While the structure, function, and active site architecture of the copper-dependent particulate methane monooxygenase (pMMO) have been investigated extensively, its putative quaternary interactions, regulation, requisite cofactors, and mechanism remain enigmatic. The iron-dependent soluble methane monooxygenase (sMMO) has been characterized biochemically, structurally, spectroscopically, and, for the most part, mechanistically. Here, we review the history of MMO research, focusing on recent developments and providing an outlook for future directions of the field. Engineered biological catalysis systems and bioinspired synthetic catalysts may continue to emerge along with a deeper understanding of the molecular mechanisms of biological methane oxidation. Harnessing the power of these enzymes will necessitate combined efforts in biochemistry, structural biology, inorganic chemistry, microbiology, computational biology, and engineering.
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Affiliation(s)
- Frank J Tucci
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Wutkowska M, Tláskal V, Bordel S, Stein LY, Nweze JA, Daebeler A. Leveraging genome-scale metabolic models to understand aerobic methanotrophs. THE ISME JOURNAL 2024; 18:wrae102. [PMID: 38861460 PMCID: PMC11195481 DOI: 10.1093/ismejo/wrae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/20/2024] [Accepted: 06/10/2024] [Indexed: 06/13/2024]
Abstract
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
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Affiliation(s)
- Magdalena Wutkowska
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
| | - Vojtěch Tláskal
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
| | - Sergio Bordel
- Department of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of Valladolid, Valladolid 47011, Spain
- Institute of Sustainable Processes, Valladolid 47011, Spain
| | - Lisa Y Stein
- Department of Biological Sciences, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Justus Amuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
- Department of Science Laboratory Technology, Faculty of Physical Sciences, University of Nigeria, Nsukka 410001, Nigeria
| | - Anne Daebeler
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, 370 05 České Budějovice, Czech Republic
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9
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Woern C, Grossmann L. Microbial gas fermentation technology for sustainable food protein production. Biotechnol Adv 2023; 69:108240. [PMID: 37647973 DOI: 10.1016/j.biotechadv.2023.108240] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023]
Abstract
The development of novel, sustainable, and robust food production technologies represents one of the major pillars to address the most significant challenges humanity is going to face on earth in the upcoming decades - climate change, population growth, and resource depletion. The implementation of microfoods, i.e., foods formulated with ingredients from microbial cultivation, into the food supply chain has a huge potential to contribute towards energy-efficient and nutritious food manufacturing and represents a means to sustainably feed a growing world population. This review recapitulates and assesses the current state in the establishment and usage of gas fermenting bacteria as an innovative feedstock for protein production. In particular, we focus on the most promising representatives of this taxon: the hydrogen-oxidizing bacteria (hydrogenotrophs) and the methane-oxidizing bacteria (methanotrophs). These unicellular microorganisms can aerobically metabolize gaseous hydrogen and methane, respectively, to provide the required energy for building up cell material. A protein yield over 70% in the dry matter cell mass can be reached with no need for arable land and organic substrates making it a promising alternative to plant- and animal-based protein sources. We illuminate the holistic approach to incorporate protein extracts obtained from the cultivation of gas fermenting bacteria into microfoods. Herein, the fundamental properties of the bacteria, cultivation methods, downstream processing, and potential food applications are discussed. Moreover, this review covers existing and future challenges as well as sustainability aspects associated with the production of microbial protein through gas fermentation.
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Affiliation(s)
- Carlos Woern
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA
| | - Lutz Grossmann
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA.
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10
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Liu C, Mesman R, Pol A, Angius F, Op den Camp HJM. Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV. Antonie Van Leeuwenhoek 2023; 116:1227-1245. [PMID: 37737555 PMCID: PMC10542722 DOI: 10.1007/s10482-023-01879-0] [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: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
The outer membrane (OM) protects Gram-negative bacteria against a hostile environment. The proteins embedded in the OM fulfil a number of tasks that are crucial to the bacterial cell. In this study, we identified and characterised a major outer membrane protein (WP_009059494) from Methylacidiphilum fumariolicum SolV. PRED-TMBB and AlphaFold2 predicted this protein to form a porin with a β-barrel structure consisting of ten antiparallel β-sheets and with a small amphipathic N-terminal α-helix in the periplasm. We purified soluble recombinant protein WP_009059494 from E. coli using Tris-HCl buffer with SDS. Antibodies were raised against two peptides in the two large extracellular loops of protein WP_009059494 and immunogold localisation showed this protein to be mainly present in the OM of strain SolV. In addition, this protein is tightly associated with the OM, and is resistant to extraction. Only a small amount can be isolated from the cell envelope using harsh conditions (SDS and boiling). Despite this resistance to extraction, WP_009059494 most likely is an outer membrane protein. A regular lattice could not be detected by negative staining TEM of strain SolV and isolated protein WP_009059494. Considering the specific ecological niche of strain SolV living in a geothermal environment with low pH and high temperatures, this major protein WP_009059494 may act as barrier to resist the extreme conditions found in its natural environment. In addition, we found an absence of the BamB, BamC and BamE proteins of the canonical BAM complex, in Methylacidiphilum and Methylacidimicrobium species. This suggests that these bacteria use a simple BAM complex for folding and transport of OM proteins.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Rob Mesman
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Nijmegen, The Netherlands.
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11
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Venetz J, Żygadłowska OM, Lenstra WK, van Helmond NAGM, Nuijten GHL, Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM, Veraart AJ. Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin. Environ Microbiol 2023; 25:2277-2288. [PMID: 37381163 DOI: 10.1111/1462-2920.16448] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 05/31/2023] [Indexed: 06/30/2023]
Abstract
The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.
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Affiliation(s)
- Jessica Venetz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Olga M Żygadłowska
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Wytze K Lenstra
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Guylaine H L Nuijten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Anna J Wallenius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Caroline P Slomp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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12
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Awala SI, Gwak JH, Kim Y, Seo C, Strazzulli A, Kim SG, Rhee SK. Methylacidiphilum caldifontis gen. nov., sp. nov., a thermoacidophilic methane-oxidizing bacterium from an acidic geothermal environment, and descriptions of the family Methylacidiphilaceae fam. nov. and order Methylacidiphilales ord. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37791995 DOI: 10.1099/ijsem.0.006085] [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] [Indexed: 10/05/2023] Open
Abstract
Strain IT6T, a thermoacidophilic and facultative methane-oxidizing bacterium, was isolated from a mud-water mixture collected from Pisciarelli hot spring in Pozzuoli, Italy. The novel strain is white when grown in liquid or solid media and forms Gram-negative rod-shaped, non-flagellated, non-motile cells. It conserves energy by aerobically oxidizing methane and hydrogen while deriving carbon from carbon dioxide fixation. Strain IT6T had three complete pmoCAB operons encoding particulate methane monooxygenase and genes encoding group 1d and 3b [NiFe] hydrogenases. Simple carbon-carbon substrates such as ethanol, 2-propanol, acetone, acetol and propane-1,2-diol were used as alternative electron donors and carbon sources. Optimal growth occurred at 50-55°C and between pH 2.0-3.0. The major fatty acids were C18 : 0, C15 : 0 anteiso, C14 : 0 iso, C16 : 0 and C14 : 0, and the main polar lipids were phosphatidylethanolamine, aminophospholipid, phosphatidylglycerol, diphosphatidylglycerol, some unidentified phospholipids and glycolipids, and other unknown polar lipids. Strain IT6T has a genome size of 2.19 Mbp and a G+C content of 40.70 mol%. Relative evolutionary divergence using 120 conserved single-copy marker genes (bac120) and phylogenetic analyses based on bac120 and 16S rRNA gene sequences showed that strain IT6T is affiliated with members of the proposed order 'Methylacidiphilales' of the class Verrucomicrobiia in the phylum Verrucomicrobiota. It shared a 16S rRNA gene sequence identity of >96 % with cultivated isolates in the genus 'Methylacidiphilum' of the family 'Methylacidiphilaceae', which are thermoacidophilic methane-oxidizing bacteria. 'Methylacidiphilum sp.' Phi (100 %), 'Methylacidiphilum infernorum' V4 (99.02 %) and 'Methylacidiphilum sp.' RTK17.1 (99.02 %) were its closest relatives. Its physiological and genomic properties were consistent with those of other isolated 'Methylacidiphilum' species. Based on these results, we propose the name Methylacidiphilum caldifontis gen. nov., sp. nov. to accommodate strain IT6T (=KCTC 92103T=JCM 39288T). We also formally propose that the names Methylacidiphilaceae fam. nov. and Methylacidiphilales ord. nov. to accommodate the genus Methylacidiphilum gen. nov.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Chanmee Seo
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Song-Gun Kim
- University of Science and Technology, Yuseong-gu, Daejeon 305-850, Republic of Korea
- Biological Resource Center/ Korean Collection for Type Culture (KCTC), Korea Research Institute of Bioscience and Biotechnology, 181 Ipsingil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju 28644, Republic of Korea
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13
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Zhang L, Sun X, Wang L, Zhang H, Chu H, Li Y. Soil edaphic factors and climate seasonality explain the turnover of methanotrophic communities in riparian wetlands. ENVIRONMENTAL RESEARCH 2023; 233:116447. [PMID: 37331554 DOI: 10.1016/j.envres.2023.116447] [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: 05/06/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/20/2023]
Abstract
Aerobic CH4-oxidizing bacteria (methanotrophs) represent a biological model system for the removal of atmospheric CH4, which is sensitive to the dynamics of water tables. However, little attention has been given to the turnover of methanotrophic communities across wet and dry periods in riparian wetlands. Here, by sequencing the pmoA gene, we investigated the turnover of soil methanotrophic communities across wet and dry periods in typical riparian wetlands that experience intensive agricultural practices. The results demonstrated that the methanotrophic abundance and diversity were significantly higher in the wet period than in the dry period, probably owing to the climatic seasonal succession and associated variation in soil edaphic factors. The co-occurrence patterns of the interspecies association analysis demonstrated that the key ecological clusters (i.e., Mod#1, Mod#2, Mod#4, Mod#5) showed contrasting correlations with soil edaphic properties between wet and dry periods. The linear regression slope of the relationships between the relative abundance of Mod#1 and the carbon to nitrogen ratio was higher in the wet period than in the dry period, whereas the linear regression slope of the relationships between the relative abundance of Mod#2 and soil nitrogen content (i.e., dissolved organic nitrogen, nitrate, and total nitrogen) was higher in the dry period than in the wet period. Moreover, Stegen's null model combined with phylogenetic group-based assembly analysis demonstrated that the methanotrophic community exhibited a higher proportion of drift (55.0%) and a lower contribution of dispersal limitation (24.5%) in the wet period than in the dry period (43.8% and 35.7%, respectively). Overall, these findings demonstrate that the turnover of methanotrophic communities across wet and dry periods were soil edaphic factors and climate dependent.
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Affiliation(s)
- Liyan Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Xiangxin Sun
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, China.
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14
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Li R, Fan X, Jiang Y, Wang R, Guo R, Zhang Y, Fu S. From anaerobic digestion to single cell protein synthesis: A promising route beyond biogas utilization. WATER RESEARCH 2023; 243:120417. [PMID: 37517149 DOI: 10.1016/j.watres.2023.120417] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023]
Abstract
The accumulation of a large amount of organic solid waste and the lack of sufficient protein supply worldwide are two major challenges caused by rapid population growth. Anaerobic digestion is the main force of organic waste treatment, and the high-value utilization of its products (biogas and digestate) has been widely concerned. These products can be used as nutrients and energy sources for microorganisms such as microalgae, yeast, methane-oxidizing bacteria(MOB), and hydrogen-oxidizing bacteria(HOB) to produce single cell protein(SCP), which contributes to the achievement of sustainable development goals. This new model of energy conversion can construct a bioeconomic cycle from waste to nutritional products, which treats waste without additional carbon emissions and can harvest high-value biomass. Techno-economic analysis shows that the SCP from biogas and digestate has higher profit than biogas electricity generation, and its production cost is lower than the SCP using special raw materials as the substrate. In this review, the case of SCP-rich microorganisms using anaerobic digestion products for growth was investigated. Some of the challenges faced by the process and the latest developments were analyzed, and their potential economic and environmental value was verified.
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Affiliation(s)
- Rui Li
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China
| | - XiaoLei Fan
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China
| | - YuFeng Jiang
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China
| | - RuoNan Wang
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China
| | - RongBo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China.
| | - Yifeng Zhang
- Department of Environmental and Resource Engineering, Technical University of Denmark, Lyngby DK-2800, Denmark
| | - ShanFei Fu
- Shandong Industrial Engineering Laboratory of Biogas Production and Utilization, Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, NO. 189 Songling Road, Qingdao 266101, PR China; Shandong Energy Institute, Qingdao 266101, PR China; Qingdao New Energy Shandong Laboratory, Qingdao 266101, PR China.
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15
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [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: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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16
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Ratnadevi CM, Erikstad HA, Kruse T, Birkeland NK. Methylacidiphilum kamchatkense gen. nov., sp. nov., an extremely acidophilic and moderately thermophilic methanotroph belonging to the phylum Verrucomicrobiota. Int J Syst Evol Microbiol 2023; 73. [PMID: 37755432 DOI: 10.1099/ijsem.0.006060] [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] [Indexed: 09/28/2023] Open
Abstract
The thermo-acidophilic aerobic methanotrophic Verrucomicrobia bacterium, designated strain Kam1T was isolated from an acidic geothermal mud spring in Kamchatka, Russia. Kam1T is Gram-stain-negative, with non-motile cells and non-spore-forming rods, and a diameter of 0.45-0.65 µm and length of 0.8-1.0 µm. Its growth is optimal at the temperature of 55 °C (range, 37-60 °C) and pH of 2.5 (range, pH 1-6), and its maximal growth rate is ~0.11 h-1 (doubling time ~6.3 h). Its cell wall contains peptidoglycan with meso-diaminopimelic acid. In addition to growing on methane and methanol, strain Kam1T grows on acetone and 2-propanol. Phylogenetically, it forms a distinct group together with other Methylacidiphilum strains and with the candidate genus Methylacidimicrobium as a sister group. These findings support the classification of the strain Kam1T as a representative of a novel species and genus of the phylum Verrucomicrobiota. For this strain, we propose the name Methylacidiphilum kamchatkense sp. nov. as the type species within Methylacidiphilum gen. nov. Strain Kam1T (JCM 30608T=KCTC 4682T) is the type strain.
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Affiliation(s)
| | - Helge-André Erikstad
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Thomas Kruse
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
- Present address: NORCE, Industrial biotechnology, Prof. Olav Hanssensvei 15, 4021 Stavanger, Norway
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17
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Houghton KM, Carere CR, Stott MB, McDonald IR. Thermophilic methane oxidation is widespread in Aotearoa-New Zealand geothermal fields. Front Microbiol 2023; 14:1253773. [PMID: 37720161 PMCID: PMC10502179 DOI: 10.3389/fmicb.2023.1253773] [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: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 09/19/2023] Open
Abstract
Geothermal areas represent substantial point sources for greenhouse gas emissions such as methane. While it is known that methanotrophic microorganisms act as a biofilter, decreasing the efflux of methane in most soils to the atmosphere, the diversity and the extent to which methane is consumed by thermophilic microorganisms in geothermal ecosystems has not been widely explored. To determine the extent of biologically mediated methane oxidation at elevated temperatures, we set up 57 microcosms using soils from 14 Aotearoa-New Zealand geothermal fields and show that moderately thermophilic (>40°C) and thermophilic (>60°C) methane oxidation is common across the region. Methane oxidation was detected in 54% (n = 31) of the geothermal soil microcosms tested at temperatures up to 75°C (pH 1.5-8.1), with oxidation rates ranging from 0.5 to 17.4 μmol g-1 d-1 wet weight. The abundance of known aerobic methanotrophs (up to 60.7% Methylacidiphilum and 11.2% Methylothermus) and putative anaerobic methanotrophs (up to 76.7% Bathyarchaeota) provides some explanation for the rapid rates of methane oxidation observed in microcosms. However, not all methane oxidation was attributable to known taxa; in some methane-consuming microcosms we detected methanotroph taxa in conditions outside of their known temperature range for growth, and in other examples, we observed methane oxidation in the absence of known methanotrophs through 16S rRNA gene sequencing. Both of these observations suggest unidentified methane oxidizing microorganisms or undescribed methanotrophic syntrophic associations may also be present. Subsequent enrichment cultures from microcosms yielded communities not predicted by the original diversity studies and showed rates inconsistent with microcosms (≤24.5 μmol d-1), highlighting difficulties in culturing representative thermophilic methanotrophs. Finally, to determine the active methane oxidation processes, we attempted to elucidate metabolic pathways from two enrichment cultures actively oxidizing methane using metatranscriptomics. The most highly expressed genes in both enrichments (methane monooxygenases, methanol dehydrogenases and PqqA precursor peptides) were related to methanotrophs from Methylococcaceae, Methylocystaceae and Methylothermaceae. This is the first example of using metatranscriptomics to investigate methanotrophs from geothermal environments and gives insight into the metabolic pathways involved in thermophilic methanotrophy.
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Affiliation(s)
- Karen M. Houghton
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Matthew B. Stott
- Te Pū Ao | GNS Science, Wairakei Research Centre, Taupō, New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
| | - Ian R. McDonald
- Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
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18
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Liu C, Angius F, Pol A, Mesman RA, Versantvoort W, Op den Camp HJM. Identification and characterization of an abundant lipoprotein from Methylacidiphilum fumariolicum SolV. Arch Microbiol 2023; 205:261. [PMID: 37306788 DOI: 10.1007/s00203-023-03603-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/17/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Bacterial lipoproteins are characterized by the presence of a conserved N-terminal lipid-modified cysteine residue that allows the hydrophilic protein to anchor into bacterial cell membranes. These lipoproteins play essential roles in a wide variety of physiological processes. Based on transcriptome analysis of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV, we identified a highly expressed lipoprotein, WP_009060351 (139 amino acids), in its genome. The first 86 amino acids are specific for the methanotrophic genera Methylacidiphilum and Methylacidmicrobium, while the last 53 amino acids are present only in lipoproteins of members from the phylum Verrucomicrobiota (Hedlund). Heterologous expression of WP_009060351 in Escherichia coli revealed a 25-kDa dimeric protein and a 60-kDa tetrameric protein. Immunoblotting showed that WP_009060351 was present in the total membrane protein and peptidoglycan fractions of M. fumariolicum SolV. The results suggest an involvement of lipoprotein WP_009060351 in the linkage between the outer membrane and the peptidoglycan.
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Affiliation(s)
- Changqing Liu
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Federica Angius
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Arjan Pol
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Rob A Mesman
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Faculty of Science, Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands.
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19
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Schmitz RA, Peeters SH, Mohammadi SS, Berben T, van Erven T, Iosif CA, van Alen T, Versantvoort W, Jetten MSM, Op den Camp HJM, Pol A. Simultaneous sulfide and methane oxidation by an extremophile. Nat Commun 2023; 14:2974. [PMID: 37221165 DOI: 10.1038/s41467-023-38699-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Hydrogen sulfide (H2S) and methane (CH4) are produced in anoxic environments through sulfate reduction and organic matter decomposition. Both gases diffuse upwards into oxic zones where aerobic methanotrophs mitigate CH4 emissions by oxidizing this potent greenhouse gas. Although methanotrophs in myriad environments encounter toxic H2S, it is virtually unknown how they are affected. Here, through extensive chemostat culturing we show that a single microorganism can oxidize CH4 and H2S simultaneously at equally high rates. By oxidizing H2S to elemental sulfur, the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV alleviates the inhibitory effects of H2S on methanotrophy. Strain SolV adapts to increasing H2S by expressing a sulfide-insensitive ba3-type terminal oxidase and grows as chemolithoautotroph using H2S as sole energy source. Genomic surveys revealed putative sulfide-oxidizing enzymes in numerous methanotrophs, suggesting that H2S oxidation is much more widespread in methanotrophs than previously assumed, enabling them to connect carbon and sulfur cycles in novel ways.
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Affiliation(s)
- Rob A Schmitz
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, 8092, Zurich, Switzerland
| | - Stijn H Peeters
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Sepehr S Mohammadi
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Timo van Erven
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Carmen A Iosif
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands.
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ, Nijmegen, The Netherlands
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20
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Wang J, Wang C, Chu YX, Tian G, He R. Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:263-274. [PMID: 36917925 DOI: 10.1016/j.wasman.2023.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH4 emission from landfills. Here, stable isotope probing microcosms with CH4 or CH4 and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH4 oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO42-) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH4 in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH4 and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH4 and sulfur compounds.
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Affiliation(s)
- Jing Wang
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Chen Wang
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Yi-Xuan Chu
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China; School of Civil Engineering and Architecture, Zhejiang University of Science and Technology, Hangzhou 310023, China
| | - Guangming Tian
- Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ruo He
- Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Department of Environmental Engineering, Zhejiang University, Hangzhou 310058, China.
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21
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Hwangbo M, Shao Y, Hatzinger PB, Chu KH. Acidophilic methanotrophs: Occurrence, diversity, and possible bioremediation applications. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 37041665 DOI: 10.1111/1758-2229.13156] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Methanotrophs have been identified and isolated from acidic environments such as wetlands, acidic soils, peat bogs, and groundwater aquifers. Due to their methane (CH4 ) utilization as a carbon and energy source, acidophilic methanotrophs are important in controlling the release of atmospheric CH4 , an important greenhouse gas, from acidic wetlands and other environments. Methanotrophs have also played an important role in the biodegradation and bioremediation of a variety of pollutants including chlorinated volatile organic compounds (CVOCs) using CH4 monooxygenases via a process known as cometabolism. Under neutral pH conditions, anaerobic bioremediation via carbon source addition is a commonly used and highly effective approach to treat CVOCs in groundwater. However, complete dechlorination of CVOCs is typically inhibited at low pH. Acidophilic methanotrophs have recently been observed to degrade a range of CVOCs at pH < 5.5, suggesting that cometabolic treatment may be an option for CVOCs and other contaminants in acidic aquifers. This paper provides an overview of the occurrence, diversity, and physiological activities of methanotrophs in acidic environments and highlights the potential application of these organisms for enhancing contaminant biodegradation and bioremediation.
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Affiliation(s)
- Myung Hwangbo
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Yiru Shao
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
| | - Paul B Hatzinger
- Aptim Federal Services, LLC, 17 Princess Road, Lawrenceville, New Jersey, USA
| | - Kung-Hui Chu
- Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, Texas, USA
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22
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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: 7] [Impact Index Per Article: 7.0] [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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23
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Cui Z, Li R, Li F, Jin L, Wu H, Cheng C, Ma Y, Wang Z, Wang Y. Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau. Front Microbiol 2023; 14:1070815. [PMID: 36876117 PMCID: PMC9981654 DOI: 10.3389/fmicb.2023.1070815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/01/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction Fritillaria przewalskii Maxim. is a Chinese endemic species with high medicinal value distributed in the northeastern part of the Tibetan Plateau. F. przewalskii root-associated rhizosphere bacterial communities shaped by soil properties may maintain the stability of soil structure and regulate F. przewalskii growth, but the rhizosphere bacterial community structure of wild F. przewalskii from natural populations is not clear. Methods In the current study, soil samples from 12 sites within the natural range of wild F. przewalskii were collected to investigate the compositions of bacterial communities via high-throughput sequencing of 16S rRNA genes and multivariate statistical analysis combined with soil properties and plant phenotypic characteristics. Results Bacterial communities varied between rhizosphere and bulk soil, and also between sites. Co-occurrence networks were more complex in rhizosphere soil (1,169 edges) than in bulk soil (676 edges). There were differences in bacterial communities between regions, including diversity and composition. Proteobacteria (26.47-37.61%), Bacteroidetes (10.53-25.22%), and Acidobacteria (10.45-23.54%) were the dominant bacteria, and all are associated with nutrient cycling. In multivariate statistical analysis, both soil properties and plant phenotypic characteristics were significantly associated with the bacterial community (p < 0.05). Soil physicochemical properties accounted for most community differences, and pH was a key factor (p < 0.01). Interestingly, when the rhizosphere soil environment remained alkaline, the C and N contents were lowest, as was the biomass of the medicinal part bulb. This might relate to the specific distribution of genera, such as Pseudonocardia, Ohtaekwangia, Flavobacterium (relative abundance >0.01), which all have significantly correlated with the biomass of F. przewalskii (p < 0.05). Discussion F. przewalskii is evidently averse to alkaline soil with high potassium contents, but this requires future verification. The results of the present study may provide theoretical guidance and new insights for the cultivation and domestication of F. przewalskii.
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Affiliation(s)
- Zhijia Cui
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Ran Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Fan Li
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Haixu Wu
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Chunya Cheng
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Yi Ma
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Zhenheng Wang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China.,Northwest Collaborative Innovation Center for Traditional Chinese Medicine Co-Constructed by Gansu Province & MOE of PRC, Lanzhou, Gansu, China
| | - Yuanyuan Wang
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
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24
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Howe KL, Seitz KW, Campbell LG, Baker BJ, Thrash JC, Rabalais NN, Rogener MK, Joye SB, Mason OU. Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column. FEMS Microbiol Ecol 2022; 99:6909064. [PMID: 36520069 PMCID: PMC9874027 DOI: 10.1093/femsec/fiac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 12/20/2022] [Indexed: 12/23/2022] Open
Abstract
The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.
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Affiliation(s)
- Kathryn L Howe
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Kiley W Seitz
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States
| | - Lauren G Campbell
- Department of Earth, Ocean, and Atmospheric Science, Florida State University, 32306, Tallahassee, United States
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, 78373, Port Aransas, United States,Department of Integrative Biology, University of Texas at Austin, 78712, Austin, United States
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, 90089, Los Angeles, United States
| | - Nancy N Rabalais
- Department of Oceanography and Coastal Sciences, Louisiana State University, 70803, Baton Rouge, United States,Louisiana Universities Marine Consortium, 70344, Chauvin, United States
| | - Mary-Kate Rogener
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, 30602, Athens, United States
| | - Olivia U Mason
- Corresponding author: Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, United States. E-mail:
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25
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Neira G, Vergara E, Holmes DS. Genome-guided prediction of acid resistance mechanisms in acidophilic methanotrophs of phylogenetically deep-rooted Verrucomicrobia isolated from geothermal environments. Front Microbiol 2022; 13:900531. [PMID: 36212841 PMCID: PMC9543262 DOI: 10.3389/fmicb.2022.900531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Verrucomicrobia are a group of microorganisms that have been proposed to be deeply rooted in the Tree of Life. Some are methanotrophs that oxidize the potent greenhouse gas methane and are thus important in decreasing atmospheric concentrations of the gas, potentially ameliorating climate change. They are widespread in various environments including soil and fresh or marine waters. Recently, a clade of extremely acidophilic Verrucomicrobia, flourishing at pH < 3, were described from high-temperature geothermal ecosystems. This novel group could be of interest for studies about the emergence of life on Earth and to astrobiologists as homologs for possible extraterrestrial life. In this paper, we describe predicted mechanisms for survival of this clade at low pH and suggest its possible evolutionary trajectory from an inferred neutrophilic ancestor. Extreme acidophiles are defined as organisms that thrive in extremely low pH environments (≤ pH 3). Many are polyextremophiles facing high temperatures and high salt as well as low pH. They are important to study for both providing fundamental insights into biological mechanisms of survival and evolution in such extreme environments and for understanding their roles in biotechnological applications such as industrial mineral recovery (bioleaching) and mitigation of acid mine drainage. They are also, potentially, a rich source of novel genes and pathways for the genetic engineering of microbial strains. Acidophiles of the Verrucomicrobia phylum are unique as they are the only known aerobic methanotrophs that can grow optimally under acidic (pH 2–3) and moderately thermophilic conditions (50–60°C). Three moderately thermophilic genera, namely Methylacidiphilum, Methylacidimicrobium, and Ca. Methylacidithermus, have been described in geothermal environments. Most of the investigations of these organisms have focused on their methane oxidizing capabilities (methanotrophy) and use of lanthanides as a protein cofactor, with no extensive study that sheds light on the mechanisms that they use to flourish at extremely low pH. In this paper, we extend the phylogenetic description of this group of acidophiles using whole genome information and we identify several mechanisms, potentially involved in acid resistance, including “first line of defense” mechanisms that impede the entry of protons into the cell. These include the presence of membrane-associated hopanoids, multiple copies of the outer membrane protein (Slp), and inner membrane potassium channels (kup, kdp) that generate a reversed membrane potential repelling the intrusion of protons. Acidophilic Verrucomicrobia also display a wide array of proteins potentially involved in the “second line of defense” where protons that evaded the first line of defense and entered the cell are expelled or neutralized, such as the glutamate decarboxylation (gadAB) and phosphate-uptake systems. An exclusive N-type ATPase F0-F1 was identified only in acidophiles of Verrucomicrobia and is predicted to be a specific adaptation in these organisms. Phylogenetic analyses suggest that many predicted mechanisms are evolutionarily conserved and most likely entered the acidophilic lineage of Verrucomicrobia by vertical descent from a common ancestor. However, it is likely that some defense mechanisms such as gadA and kup entered the acidophilic Verrucomicrobia lineage by horizontal gene transfer.
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Affiliation(s)
- Gonzalo Neira
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
| | - Eva Vergara
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - David S. Holmes
- Center for Bioinformatics and Genome Biology, Centro Ciencia & Vida, Fundación Ciencia & Vida, Santiago, Chile
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
- *Correspondence: David S. Holmes
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26
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Venturini AM, Dias NMS, Gontijo JB, Yoshiura CA, Paula FS, Meyer KM, Nakamura FM, da França AG, Borges CD, Barlow J, Berenguer E, Nüsslein K, Rodrigues JLM, Bohannan BJM, Tsai SM. Increased soil moisture intensifies the impacts of forest-to-pasture conversion on methane emissions and methane-cycling communities in the Eastern Amazon. ENVIRONMENTAL RESEARCH 2022; 212:113139. [PMID: 35337832 DOI: 10.1016/j.envres.2022.113139] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Climatic changes are altering precipitation patterns in the Amazon and may influence soil methane (CH4) fluxes due to the differential responses of methanogenic and methanotrophic microorganisms. However, it remains unclear if these climate feedbacks can amplify land-use-related impacts on the CH4 cycle. To better predict the responses of soil CH4-cycling microorganisms and emissions under altered moisture levels in the Eastern Brazilian Amazon, we performed a 30-day microcosm experiment manipulating the moisture content (original moisture; 60%, 80%, and 100% of field capacity - FC) of forest and pasture soils. Gas samples were collected periodically for gas chromatography analysis, and methanogenic archaeal and methanotrophic bacterial communities were assessed using quantitative PCR and metagenomics. Positive and negative daily CH4 fluxes were observed for forest and pasture, indicating that these soils can act as both CH4 sources and sinks. Cumulative emissions and the abundance of methanogenesis-related genes and taxonomic groups were affected by land use, moisture, and their interaction. Pasture soils at 100% FC had the highest abundance of methanogens and CH4 emissions, 22 times higher than forest soils under the same treatment. Higher ratios of methanogens to methanotrophs were found in pasture than in forest soils, even at field capacity conditions. Land use and moisture were significant factors influencing the composition of methanogenic and methanotrophic communities. The diversity and evenness of methanogens did not change throughout the experiment. In contrast, methanotrophs exhibited the highest diversity and evenness in pasture soils at 100% FC. Taken together, our results suggest that increased moisture exacerbates soil CH4 emissions and microbial responses driven by land-use change in the Amazon. This is the first report on the microbial CH4 cycle in Amazonian upland soils that combined one-month gas measurements with advanced molecular methods.
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Affiliation(s)
- Andressa M Venturini
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Princeton Institute for International and Regional Studies, Princeton University, Princeton, NJ, 08544, USA.
| | - Naissa M S Dias
- Environmental Biogeochemistry Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Júlia B Gontijo
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Caio A Yoshiura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Fabiana S Paula
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil; Department of Biological Oceanography, Oceanographic Institute, University of São Paulo, São Paulo, SP, 05508-120, Brazil
| | - Kyle M Meyer
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA; Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, 94720, USA
| | - Fernanda M Nakamura
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Aline G da França
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Clovis D Borges
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Erika Berenguer
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK; Environmental Change Institute, University of Oxford, Oxford, OX1 3QY, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, 95616, USA
| | - Brendan J M Bohannan
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, 97403, USA
| | - Siu M Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, 13416-000, Brazil
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27
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Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland. Microorganisms 2022; 10:microorganisms10081653. [PMID: 36014071 PMCID: PMC9416152 DOI: 10.3390/microorganisms10081653] [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: 04/21/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.
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28
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Daumann LJ, Pol A, Op den Camp HJM, Martinez-Gomez NC. A perspective on the role of lanthanides in biology: Discovery, open questions and possible applications. Adv Microb Physiol 2022; 81:1-24. [PMID: 36167440 DOI: 10.1016/bs.ampbs.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Because of their use in high technologies like computers, smartphones and renewable energy applications, lanthanides (belonging to the group of rare earth elements) are essential for our daily lives. A range of applications in medicine and biochemical research made use of their photo-physical properties. The discovery of a biological role for lanthanides has boosted research in this new field. Several methanotrophs and methylotrophs are strictly dependent on the presence of lanthanides in the growth medium while others show a regulatory response. After the first demonstration of a lanthanide in the active site of the XoxF-type pyrroloquinoline quinone methanol dehydrogenases, follow-up studies showed the same for other pyrroloquinoline quinone-containing enzymes. In addition, research focused on the effect of lanthanides on regulation of gene expression and uptake mechanism into bacterial cells. This review briefly describes the discovery of the role of lanthanides in biology and focuses on open questions in biological lanthanide research and possible application of lanthanide-containing bacteria and enzymes in recovery of these special elements.
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Affiliation(s)
- Lena J Daumann
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Arjan Pol
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, RIBES, Radboud University, Nijmegen, The Netherlands.
| | - N Cecilia Martinez-Gomez
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States
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She W, Yang J, Wu G, Jiang H. The synergy of environmental and microbial variations caused by hydrologic management affects the carbon emission in the Three Gorges Reservoir. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153446. [PMID: 35092771 DOI: 10.1016/j.scitotenv.2022.153446] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/16/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
The synergy of environmental and microbiological changes caused by hydrologic management on carbon emissions of river reservoirs remains unknown. Here, we investigated physiochemistry parameters, compositions of dissolved organic matter (DOM), carbon fluxes (CH4 and CO2), and microbial communities in the surface waters of the Three Gorges Reservoir (TGR) within one whole hydrological year. The results showed that hydrologic management significantly changed physiochemistry and DOM composition of the TGR water, and further influenced microbial community composition and functions. DOM content during the drainage period was much lower than during the impoundment period. During the impoundment period, humification extent of DOM became decreasing, while biotransformation extent became increasing compared with the drainage period. DOM composition and water pH exhibited significant correlation with the fluxes of CH4 and CO2, respectively. Microbial community composition and function significantly differed between the drainage and impoundment periods. Most of the differential microbial taxa were affiliated with functional groups involved in carbon cycle such as methanotrophy and phototrophy, which showed significant correlation with carbon fluxes. CH4 and CO2 fluxes can be mostly explained by synergy of microbial function with DOM composition and water pH, respectively. Such synergistic effect may account for the observed temporal variations of CH4 fluxes and spatial variations of CO2, and for the relatively low annual carbon emissions in the TGR. In summary, the synergy of environmental and microbial variations caused by hydrologic management affects carbon emissions from river reservoirs.
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Affiliation(s)
- Weiyu She
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Jian Yang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China; State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, China University of Geosciences, Wuhan 430074, China.
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30
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Cai Y, Yun J, Jia Z. Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction. Microorganisms 2022; 10:microorganisms10050955. [PMID: 35630399 PMCID: PMC9145241 DOI: 10.3390/microorganisms10050955] [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: 04/05/2022] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023] Open
Abstract
Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin–Benson–Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N2 fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.
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Affiliation(s)
- Yuanfeng Cai
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Correspondence: (Y.C.); (Z.J.); Tel.: +86-25-8688-1850 (Y.C.); +86-25-8688-1311 (Z.J.)
| | - Juanli Yun
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
- Correspondence: (Y.C.); (Z.J.); Tel.: +86-25-8688-1850 (Y.C.); +86-25-8688-1311 (Z.J.)
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31
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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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Schäfer A, Vetsova VA, Schneider EK, Kappes M, Seitz M, Daumann LJ, Weis P. Ion Mobility Studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:722-730. [PMID: 35300493 DOI: 10.1021/jasms.2c00023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the past decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently convert alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here, we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry, and quantum-chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas-phase structures of [PQQH2]-, [PQQH2+H2O]-, [PQQH2+MeOH]-, [PQQ-15c5+H]+, and [PQQ-15c5+Ln+NO3]2+ (Ln = La to Lu, except Pm). In the latter case, a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in the future such investigations will help to guide the design and understanding of lanthanide-based biomimetic complexes optimized for catalytic function.
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Affiliation(s)
- Alexander Schäfer
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Violeta A Vetsova
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Erik K Schneider
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
| | - Manfred Kappes
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
- Karlsruhe Institute of Technology Institute of Nanotechnology Hermann von Helmholtz Pl 1,76344 Eggenstein Leopoldshafen, Germany
| | - Michael Seitz
- University of Tübingen Institute of Inorganic Chemistry Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Lena J Daumann
- Department of Chemistry Ludwig Maximilian University of Munich Butenandtstraße 5-13, 81377 Munich, Germany
| | - Patrick Weis
- Karlsruhe Institute of Technology Institute of Physical Chemistry Fritz-Haber-Weg 2, 76128 Karlsruhe, Germany
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Sakoula D, Smith GJ, Frank J, Mesman RJ, Kop LFM, Blom P, Jetten MSM, van Kessel MAHJ, Lücker S. Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. THE ISME JOURNAL 2022; 16:958-971. [PMID: 34743174 PMCID: PMC8941013 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Garrett J Smith
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Rob J Mesman
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Linnea F M Kop
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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Berenjkar P, Sparling R, Lozecznik S, Yuan Q. Methane oxidation in a landfill biowindow under wide seasonally fluctuating climatic conditions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:24623-24638. [PMID: 34825333 DOI: 10.1007/s11356-021-17566-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
In the current study, a pilot biowindow was constructed in a closed cell of a Canadian Landfill, undergoing high seasonal fluctuations in the temperature from -30 in winter to 35 in summer. The biowindow was filled with biosolids compost amended with yard waste and leaf compost with the ratio of 4:1 as the substrate layer. Two years of monitoring of methane (CH4) oxidation in the biowindow led to remarkable expected observations including a thick, solid winter frost cover affecting gas exchange in winter and temperatures above 45 ℃ in the biowindow in late summer. A high influx compared to the reported values was observed into the biowindow with an average value of 1137 g.m-2.d-1, consisting of 64% of CH4 and 36% of carbon dioxide (CO2) in the landfill gas. The variations in the temperature and moisture content (MC) of the compost layer in addition to the influx fluctuations affected CH4 oxidation efficiency; however, a high average CH4 oxidation rate of 237 g.m-2.d-1 was obtained, with CH4 being mostly oxidized at top layers. The laboratory batch experiments verified that thermophilic methane-oxidizing bacteria (MOB) were active throughout the study period and oxidized CH4 with a higher rate than mesophilic MOB. The methanotrophic potential of the compost mixture showed an average value of 282 µmol.g-1.d-1 in the entire period of the study which is in the range of the highest reported maximum CH4 oxidation rates. The adopted compost mixture was suitable for CH4 oxidation if the MC was above 30%. The significance of MC variations on CH4 oxidation rate depended on the temperature range within the biowindow. At temperatures below 2 ℃, between 29 and 31℃, and above 45 ℃, MC was not a controlling factor for mesophilic CH4 oxidation.
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Affiliation(s)
- Parvin Berenjkar
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | | | - Qiuyan Yuan
- Department of Civil Engineering, University of Manitoba, Winnipeg, MB, R3T 5V6, Canada.
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Kambara H, Shinno T, Matsuura N, Matsushita S, Aoi Y, Kindaichi T, Ozaki N, Ohashi A. Environmental Factors Affecting the Community of Methane-oxidizing Bacteria. Microbes Environ 2022; 37. [PMID: 35342121 PMCID: PMC8958294 DOI: 10.1264/jsme2.me21074] [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] [Indexed: 01/04/2023] Open
Abstract
Methane-oxidizing bacteria (MOB) are ubiquitous and play an important role in the mitigation of global warming by reducing methane. MOB are commonly classified into Type I and Type II, belonging to Gammaproteobacteria and Alphaproteobacteria, respectively, and the diversity of MOB has been examined. However, limited information is currently available on favorable environments for the respective MOB. To investigate the environmental factors affecting the dominant type in the MOB community, we performed MOB enrichment using down-flow hanging sponge reactors under 38 different environmental conditions with a wide range of methane (0.01–80%) and ammonium concentrations (0.001–2,000 mg N L–1) and pH 4–7. Enrichment results revealed that pH was a crucial factor influencing the MOB type enriched. Type II was dominantly enriched at low pH (4–5), whereas Type I was dominant around neutral pH (6–7). However, there were some unusual cultivated biomass samples. Even though high methane oxidation activity was observed, very few or zero conventional MOB were detected using common FISH probes and primer sets for the 16S rRNA gene and pmoA gene amplification. Mycobacterium mostly dominated the microbial community in the biomass cultivated at very high NH4+ concentrations, strongly implying that it exhibits methane oxidation activity. Collectively, the present results revealed the presence of many unknown phylogenetic groups with the capacity for methane oxidation other than the reported MOB.
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Affiliation(s)
- Hiromi Kambara
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | - Takahiro Shinno
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Hiroshima University
| | | | - Shuji Matsushita
- Agricultural Technology Research Center, Hiroshima Prefectural Technology Research Institute
| | - Yoshiteru Aoi
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University
| | - Tomonori Kindaichi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Noriatsu Ozaki
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
| | - Akiyoshi Ohashi
- Department of Civil and Environmental Engineering, Graduate School of Advanced Science and Engineering, Hiroshima University
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Yang Y, Chen J, Pratscher J, Xie S. DNA-SIP reveals an overlooked methanotroph, Crenothrix sp., involved in methane consumption in shallow lake sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152742. [PMID: 34974014 DOI: 10.1016/j.scitotenv.2021.152742] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 06/14/2023]
Abstract
Methanotrophs are the main consumers of methane produced in lake sediments. In shallow lakes suffering from eutrophication, methanogenesis is accelerated by the excess organic carbon input, and thus methanotrophs play a key role in regulating this methane flux as well as carbon cycling. Here, we applied nucleic acid stable isotope probing (SIP) to investigate the active methanotrophic microbial community in sediments of several shallow lakes affected by eutrophication. Our results showed that an active methanotrophic community dominated by gamma-proteobacterial methanotrophs, as well as abundant beta-proteobacterial methanol-utilizers, was involved in methane-derived carbon assimilation. Crenothrix, a filamentous methanotroph, was found to be a key methane consumer in all studied lakes. The ecological role of Crenothrix in lacustrine ecosystems is so far poorly understood, with only limited information on its existence in the water column of stratified lakes. Our results provide a novel ecological insight into this group by revealing a wide distribution of Crenothrix in lake sediments. The active methane assimilation by Crenothrix also suggested that it might represent a so far overlooked but crucial biological sink of methane in shallow lakes.
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Affiliation(s)
- Yuyin Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China; The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh EH14 4AP, UK
| | - Jianfei Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Jennifer Pratscher
- The Lyell Centre, School of Energy, Geoscience, Infrastructure and Society, Heriot-Watt University, Research Avenue South, Edinburgh EH14 4AP, UK
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
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Variable Inhibition of Nitrous Oxide Reduction in Denitrifying Bacteria by Different Forms of Methanobactin. Appl Environ Microbiol 2022; 88:e0234621. [PMID: 35285718 DOI: 10.1128/aem.02346-21] [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: 11/20/2022] Open
Abstract
Aerobic methanotrophic activity is highly dependent on copper availability, and methanotrophs have developed multiple strategies to collect copper. Specifically, when copper is limiting (ambient concentrations less than 1 μM), some methanotrophs produce and secret a small modified peptide (less than 1,300 Da) termed methanobactin (MB) that binds copper with high affinity. As MB is secreted into the environment, other microbes that require copper for their metabolism may be inhibited as MB may make copper unavailable; e.g., inhibition of denitrifiers as complete conversion nitrate to dinitrogen involves multiple enzymes, some of which are copper-dependent. Of key concern is inhibition of the copper-dependent nitrous oxide reductase (NosZ), the only known enzyme capable of converting nitrous oxide (N2O) to dinitrogen. Herein, we show that different forms of MB differentially affect copper uptake and N2O reduction by Pseudomonas stutzeri strain DCP-Ps1 (that expresses clade I NosZ) and Dechloromonas aromatica strain RCB (that expresses clade II NosZ). Specifically, in the presence of MB from Methylocystis sp. strain SB2 (SB2-MB), copper uptake and nosZ expression were more significantly reduced than in the presence of MB from Methylosinus trichosporium OB3b (OB3b-MB). Further, N2O accumulation increased more significantly for both P. stutzeri strain DCP-Ps1 and D. aromatica strain RCB in the presence of SB2-MB versus OB3b-MB. These data illustrate that copper competition between methanotrophs and denitrifying bacteria can be significant and that the extent of such competition is dependent on the form of MB that methanotrophs produce. IMPORTANCE Herein, it was demonstrated that the different forms of methanobactin differentially enhance N2O emissions from Pseudomonas stutzeri strain DCP-Ps1 (harboring clade I nitrous oxide reductase) and Dechloromonas aromatica strain RCB (harboring clade II nitrous oxide reductase). This work contributes to our understanding of how aerobic methanotrophs compete with denitrifiers for the copper uptake and also suggests how MBs prevent copper collection by denitrifiers, thus downregulating expression of nitrous oxide reductase. This study provides critical information for enhanced understanding of microbe-microbe interactions that are important for the development of better predictive models of net greenhouse gas emissions (i.e., methane and nitrous oxide) that are significantly controlled by microbial activity.
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Genome Sequence of a Thermoacidophilic Methanotroph Belonging to the Verrucomicrobiota Phylum from Geothermal Hot Springs in Yellowstone National Park: A Metagenomic Assembly and Reconstruction. Microorganisms 2022; 10:microorganisms10010142. [PMID: 35056591 PMCID: PMC8779874 DOI: 10.3390/microorganisms10010142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Verrucomicrobiotal methanotrophs are thermoacidophilic methane oxidizers that have been isolated from volcanic and geothermal regions of the world. We used a metagenomic approach that entailed obtaining the whole genome sequence of a verrucomicrobiotal methanotroph from a microbial consortium enriched from samples obtained from Nymph Lake (89.9 °C, pH 2.73) in Yellowstone National Park in the USA. To identify and reconstruct the verrucomicrobiotal genome from Illumina NovaSeq 6000 sequencing data, we constructed a bioinformatic pipeline with various combinations of de novo assembly, alignment, and binning algorithms. Based on the marker gene (pmoA), we identified and assembled the Candidatus Methylacidiphilum sp. YNP IV genome (2.47 Mbp, 2392 ORF, and 41.26% GC content). In a comparison of average nucleotide identity between Ca. Methylacidiphilum sp. YNP IV and Ca. Methylacidiphilum fumariolicum SolV, its closest 16S rRNA gene sequence relative, is lower than 95%, suggesting that Ca. Methylacidiphilum sp. YNP IV can be regarded as a different species. The Ca. Methylacidiphilum sp. YNP IV genome assembly showed most of the key genes for methane metabolism, the CBB pathway for CO2 fixation, nitrogen fixation and assimilation, hydrogenases, and rare earth elements transporter, as well as defense mechanisms. The assembly and reconstruction of a thermoacidophilic methanotroph belonging to the Verrucomicrobiota phylum from a geothermal environment adds further evidence and knowledge concerning the diversity of biological methane oxidation and on the adaptation of this geochemically relevant reaction in extreme environments.
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Peat-Inhabiting Verrucomicrobia of the Order Methylacidiphilales Do Not Possess Methanotrophic Capabilities. Microorganisms 2021; 9:microorganisms9122566. [PMID: 34946166 PMCID: PMC8706344 DOI: 10.3390/microorganisms9122566] [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: 11/18/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023] Open
Abstract
Methanotrophic verrucomicrobia of the order Methylacidiphilales are known as extremely acidophilic, thermophilic or mesophilic bacteria that inhabit acidic geothermal ecosystems. The occurrence of verrucomicrobial methanotrophs in other types of acidic environments remains an open question. Notably, Methylacidiphilales-affiliated 16S rRNA gene sequences are commonly retrieved from acidic (pH 3.5–5.5) peatlands. In this study, we compared the patterns of verrucomicrobial diversity in four acidic raised bogs and six neutral fens located in European North Russia. Methylacidiphilales-like 16S rRNA gene reads displaying 83–86% similarity to 16S rRNA gene sequences of currently described verrucomicrobial methanotrophs were recovered exclusively from raised bogs. Laboratory incubation of peat samples with 10% methane for 3 weeks resulted in the pronounced increase of a relative abundance of alphaproteobacterial methanotrophs, while no response was detected for Methylacidiphilales-affiliated bacteria. Three metagenome-assembled genomes (MAGs) of peat-inhabiting Methylacidiphilales bacteria were reconstructed and examined for the presence of genes encoding methane monooxygenase enzymes and autotrophic carbon fixation pathways. None of these genomic determinants were detected in assembled MAGs. Metabolic reconstructions predicted a heterotrophic metabolism, with a potential to hydrolyze several plant-derived polysaccharides. As suggested by our analysis, peat-inhabiting representatives of the Methylacidiphilales are acidophilic aerobic heterotrophs, which comprise a sister family of the methanotrophic Methylacidiphilaceae.
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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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Two TonB-dependent transporters in Methylosinus trichosporium OB3b are responsible for uptake of different forms of methanobactin and are involved in the canonical 'copper switch'. Appl Environ Microbiol 2021; 88:e0179321. [PMID: 34669437 DOI: 10.1128/aem.01793-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Copper is an important component of methanotrophic physiology as it controls the expression and activity of alternative forms of methane monooxygenase (MMO). To collect copper, some methanotrophs secrete a chalkophore or copper-binding compound called methanobactin (MB). MB is a ribosomally synthesized post-translationally modified polypeptide (RiPP) that, after binding copper, is collected by MbnT, a TonB-dependent transporter (TBDT). Structurally different forms of MB have been characterized, and here we show that different forms of MB are collected by specific TBDTs. Further, we report that in the model methanotroph, Methylosinus trichosporium OB3b, expression of the TBDT required for uptake of a different MB made by Methylocystis sp. strain SB2 (MB-SB2), is induced in the presence of MB-SB2, suggesting that methanotrophs have developed specific machinery and regulatory systems to actively take up MB from other methanotrophs for copper collection. Moreover, the canonical "copper-switch" in Ms. trichosporium OB3b that controls expression of alternative MMOs is apparent if one of the two TBDTs required for MB-OB3b and MB-SB2 uptake is knocked out, but is disrupted if both TBDTs are knocked out. These data indicate that MB uptake, including the uptake of exogenous MB, plays an important role in the copper switch in M. trichosporium OB3b and thus overall activity. Based on these data, we propose a revised model for the "copper-switch" in this methanotroph that involves MB uptake. IMPORTANCE In this study, we demonstrate that different TonB-dependent transporters (TBDTs) in the model methanotroph Methylosinus trichosporium OB3b are responsible for uptake of either endogenous MB or exogenous MB. Interestingly, the presence of exogenous MB induces expression of its specific TBDT in M. trichosporium OB3b, suggesting that this methanotroph is able to actively take up MB produced by others. This work contributes to our understanding of how microbes collect and compete for copper, and also helps inform how such uptake coordinates the expression of different forms of methane monooxygenase. Such studies are likely to be very important to develop a better understanding of methanotrophic interactions via synthesis and secretion of secondary metabolites such as methanobactin and thus provide additional means whereby these microbes can be manipulated for a variety of environmental and industrial purposes.
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Rahalkar MC, Khatri K, Pandit P, Bahulikar RA, Mohite JA. Cultivation of Important Methanotrophs From Indian Rice Fields. Front Microbiol 2021; 12:669244. [PMID: 34539593 PMCID: PMC8447245 DOI: 10.3389/fmicb.2021.669244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/15/2022] Open
Abstract
Methanotrophs are aerobic to micro-aerophilic bacteria, which oxidize and utilize methane, the second most important greenhouse gas. The community structure of the methanotrophs in rice fields worldwide has been studied mainly using culture-independent methods. Very few studies have focused on culturing methanotrophs from rice fields. We developed a unique method for the cultivation of methanotrophs from rice field samples. Here, we used a modified dilute nitrate mineral salts (dNMS) medium, with two cycles of dilution till extinction series cultivation with prolonged incubation time, and used agarose in the solid medium. The cultivation approach resulted in the isolation of methanotrophs from seven genera from the three major groups: Type Ia (Methylomonas, Methylomicrobium, and Methylocucumis), Type Ib (Methylocaldum and Methylomagnum), and Type II (Methylocystis and Methylosinus). Growth was obtained till 10–6–10–8 dilutions in the first dilution series, indicating the culturing of dominant methanotrophs. Our study was supported by 16S rRNA gene-based next-generation sequencing (NGS) of three of the rice samples. Our analyses and comparison with the global scenario suggested that the cultured members represented the major detected taxa. Strain RS1, representing a putative novel species of Methylomicrobium, was cultured; and the draft genome sequence was obtained. Genome analysis indicated that RS1 represented a new putative Methylomicrobium species. Methylomicrobium has been detected globally in rice fields as a dominant genus, although no Methylomicrobium strains have been isolated from rice fields worldwide. Ours is one of the first extensive studies on cultured methanotrophs from Indian rice fields focusing on the tropical region, and a unique method was developed. A total of 29 strains were obtained, which could be used as models for studying methane mitigation from rice fields and for environmental and biotechnological applications.
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Affiliation(s)
- Monali C Rahalkar
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Kumal Khatri
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Pranitha Pandit
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | - Rahul A Bahulikar
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Jyoti A Mohite
- C2, Bioenergy Group, MACS Agharkar Research Institute, Pune, India.,Department of Microbiology, Savitribai Phule Pune University, Pune, India
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Dalcin Martins P, de Jong A, Lenstra WK, van Helmond NAGM, Slomp CP, Jetten MSM, Welte CU, Rasigraf O. Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments. Microbiologyopen 2021; 10:e1175. [PMID: 33650794 PMCID: PMC7914226 DOI: 10.1002/mbo3.1175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate, or oxygen can be used. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane‐ and iron‐rich sediments from the Bothnian Sea to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we investigated shifts in microbial community composition after approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were identified and used to infer putative microbial metabolism. Metagenome‐assembled genomes representing novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria were recovered and revealed a potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new hypotheses on the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that microorganisms potentially composing the methane biofilter in these sediments may be more diverse than previously appreciated.
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Affiliation(s)
- Paula Dalcin Martins
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anniek de Jong
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Wytze K Lenstra
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Niels A G M van Helmond
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Caroline P Slomp
- Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Department of Earth Sciences, Utrecht University, Utrecht, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology (SIAM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Olivia Rasigraf
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.,Netherlands Earth System Science Centre (NESSC), Utrecht, The Netherlands.,Geomicrobiology, German Research Centre for Geosciences (GFZ), Potsdam, Germany
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Huang Y, Ji X, Ma Z, Łężyk M, Xue Y, Zhao H. Green chemical and biological synthesis of cadaverine: recent development and challenges. RSC Adv 2021; 11:23922-23942. [PMID: 35479032 PMCID: PMC9036910 DOI: 10.1039/d1ra02764f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/29/2021] [Indexed: 11/21/2022] Open
Abstract
Cadaverine has great potential to be used as an important monomer for the development of a series of high value-added products with market prospects. The most promising strategies for cadaverine synthesis involve using green chemical and bioconversion technologies. Herein, the review focuses on the progress and strategies towards the green chemical synthesis and biosynthesis of cadaverine. Specifically, we address the specific biosynthetic pathways of cadaverine from different substrates as well as extensively discussing the origination, structure and catalytic mechanism of the key lysine decarboxylases. The advanced strategies for process intensification, the separation and purification of cadaverine have been summarized. Furthermore, the challenging issues of the environmental, economic, and applicable impact for cadaverine production are also highlighted. This review concludes with the promising outlooks of state-of-the-art applications of cadaverine along with some insights toward their challenges and potential improvements.
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Affiliation(s)
- Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
- Zhongke Langfang Institute of Process Engineering Langfang 065001 China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Zhanling Ma
- Zhengzhou Institute of Emerging Industrial Technology Zhengzhou City Henan 450000 China
| | - Mateusz Łężyk
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology Berdychowo 4 60-965 Poznan Poland
| | - Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences Beijing 100190 China
| | - Hai Zhao
- Innovation Academy for Green Manufacture, Chinese Academy of Sciences Beijing 100190 China
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Liu D, Yang Y, Ai J, Li Y, Xing Y, Li J. Research on microbial structures, functions and metabolic pathways in an advanced denitrification system coupled with aerobic methane oxidation based on metagenomics. BIORESOURCE TECHNOLOGY 2021; 332:125047. [PMID: 33839509 DOI: 10.1016/j.biortech.2021.125047] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Methanotrophs can oxidize methane as the sole carbon and energy, and the resulting intermediate products can be simultaneously utilized by coexistent denitrifying bacteria to remove the nitrogen, which named Aerobic Methane Oxidation Coupled to Denitrification (AME-D). In this paper, an AME-D system was built in an improved denitrification bio-filter, to analyze the nitrogen removal efficiency and mechanism. The maximum TN removal rate reached 95.05%. As shown in Raman spectroscopy, in the effluent wave crests generated by the symmetric expansion and contraction of NO3- disappeared, and the distortion of olefin CH2 and C-OH stretching of alcohols appeared. Metagenomics revealed Methylotenera and Methylobacter were the dominated methanotrophs. There was a completed methane and nitrogen metabolism pathway with the synergism of nxrAB, narGHI, nasAB, pmo-amoABC and mmo genes. Dissimilatory reduction pathway was the primary nitrate removal pathway. Moreover, Bradyrhizobium could participate in methane and nitrogen metabolism simultaneously.
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Affiliation(s)
- Dengping Liu
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Yanan Yang
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Sinopec Great Wall Energy and Chemical (Guizhou) Co., LTD, Zhijin, Guizhou 552100, China
| | - Jia Ai
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China
| | - Yancheng Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, Guizhou 550025, China.
| | - Yi Xing
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; School of Energy and Environmental Engineering, University of Science & Technology Beijing, Beijing 100083, China
| | - Jiang Li
- College of Resources and Environmental Engineering, Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang 500025, China; Guizhou Karst Environmental Ecosystems Observation and Research Station, Ministry of Education, Guiyang, Guizhou 550025, China
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Horizontal Gene Transfer of Genes Encoding Copper-Containing Membrane-Bound Monooxygenase (CuMMO) and Soluble Di-iron Monooxygenase (SDIMO) in Ethane- and Propane-Oxidizing Rhodococcus Bacteria. Appl Environ Microbiol 2021; 87:e0022721. [PMID: 33962978 DOI: 10.1128/aem.00227-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The families of copper-containing membrane-bound monooxygenases (CuMMOs) and soluble di-iron monooxygenases (SDIMOs) are involved not only in methane oxidation but also in short-chain alkane oxidation. Here, we describe Rhodococcus sp. strain ZPP, a bacterium able to grow with ethane or propane as the sole carbon and energy source, and report on the horizontal gene transfer (HGT) of actinobacterial hydrocarbon monooxygenases (HMOs) of the CuMMO family and the sMMO (soluble methane monooxygenase)-like SDIMO in the genus Rhodococcus. The key function of HMO in strain ZPP for propane oxidation was verified by allylthiourea inhibition. The HMO genes (designated hmoCAB) and those encoding sMMO-like SDIMO (designated smoXYB1C1Z) are located on a linear megaplasmid (pRZP1) of strain ZPP. Comparative genomic analysis of similar plasmids indicated the mobility of these plasmids within the genus Rhodococcus. The plasmid pRZP1 in strain ZPP could be conjugatively transferred to a recipient Rhodococcus erythropolis strain in a mating experiment and showed similar ethane- and propane-consuming activities. Finally, our findings demonstrate that the horizontal transfer of plasmid-based CuMMO and SDIMO genes confers the ability to use ethane and propane on the recipient. IMPORTANCE CuMMOs and SDIMOs initiate the aerobic oxidation of alkanes in bacteria. Here, the supposition that horizontally transferred plasmid-based CuMMO and SDIMO genes confer on the recipient similar abilities to use ethane and propane was proposed and confirmed in Rhodococcus. This study is a living example of HGT of CuMMOs and SDIMOs and outlines the plasmid-borne properties responsible for gaseous alkane degradation. Our results indicate that plasmids can support the rapid evolution of enzyme-mediated biogeochemical processes.
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Awala SI, Gwak JH, Kim YM, Kim SJ, Strazzulli A, Dunfield PF, Yoon H, Kim GJ, Rhee SK. Verrucomicrobial methanotrophs grow on diverse C3 compounds and use a homolog of particulate methane monooxygenase to oxidize acetone. ISME JOURNAL 2021; 15:3636-3647. [PMID: 34158629 PMCID: PMC8630023 DOI: 10.1038/s41396-021-01037-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 11/26/2022]
Abstract
Short-chain alkanes (SCA; C2-C4) emitted from geological sources contribute to photochemical pollution and ozone production in the atmosphere. Microorganisms that oxidize SCA and thereby mitigate their release from geothermal environments have rarely been studied. In this study, propane-oxidizing cultures could not be grown from acidic geothermal samples by enrichment on propane alone, but instead required methane addition, indicating that propane was co-oxidized by methanotrophs. “Methylacidiphilum” isolates from these enrichments did not grow on propane as a sole energy source but unexpectedly did grow on C3 compounds such as 2-propanol, acetone, and acetol. A gene cluster encoding the pathway of 2-propanol oxidation to pyruvate via acetol was upregulated during growth on 2-propanol. Surprisingly, this cluster included one of three genomic operons (pmoCAB3) encoding particulate methane monooxygenase (PMO), and several physiological tests indicated that the encoded PMO3 enzyme mediates the oxidation of acetone to acetol. Acetone-grown resting cells oxidized acetone and butanone but not methane or propane, implicating a strict substrate specificity of PMO3 to ketones instead of alkanes. Another PMO-encoding operon, pmoCAB2, was induced only in methane-grown cells, and the encoded PMO2 could be responsible for co-metabolic oxidation of propane to 2-propanol. In nature, propane probably serves primarily as a supplemental growth substrate for these bacteria when growing on methane.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yong-Man Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - So-Jeong Kim
- Geologic Environment Research Division, Korea Institute of Geoscience and Mineral Resources, Daejeon, 34132, Republic of Korea
| | - Andrea Strazzulli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Di Monte S. Angelo, Via Cupa Nuova Cinthia 21, 80126, Naples, Italy
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Hyeokjun Yoon
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, 42 Hwangyeong-ro, Seo-gu, Incheon, 22689, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, College of Natural Sciences, Chonnam National University, Yongbong-ro, Buk-gu, Gwangju, 61186, Republic of Korea
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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Xu H, Zhao P, Ran Q, Li W, Wang P, Luo Y, Huang C, Yang X, Yin J, Zhang R. Enhanced electrokinetic remediation for Cd-contaminated clay soil by addition of nitric acid, acetic acid, and EDTA: Effects on soil micro-ecology. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 772:145029. [PMID: 33770863 DOI: 10.1016/j.scitotenv.2021.145029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/15/2020] [Accepted: 01/04/2021] [Indexed: 05/09/2023]
Abstract
Enhanced electrokinetic remediation (EKR) allows the rapid remediation of heavy metal-contaminated clay, but the impacts of this process on soil micro-ecology have rarely been evaluated. In this study, nitric acid, acetic acid, and EDTA were applied for enhancement of EKR and the effects on Cd removal, soil enzyme activity, and soil bacterial communities (SBCs) were determined. Nitric acid and acetic acid allowed 93.2% and 91.8% Cd removal, respectively, and EDTA treatment resulted in 40.4% removal due to the formation of negatively charged EDTA-Cd complexes, resulting in opposing directions of Cd electromigration and electroosmosis flow and slow electromigration rate caused by low voltage drop. Activities of soil beta-glucosidase, acid phosphatase, and urease, were all reduced by enhanced EKR treatment, especially nitric acid treatment, by 46.2%, 58.8% and 57.7%, respectively. The SBCs were analyzed by high-throughput sequencing and revealed significantly increased diversity for acetic acid treatment, no effect for EDTA treatment, and reduced diversity for nitric acid treatment. Compared with nitric acid and EDTA, acetic acid treatment enhanced EKR for higher Cd removal and improved biodiversity.
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Affiliation(s)
- Haiyin Xu
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Peiling Zhao
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Qiyang Ran
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; Hunan Hengkai Environmental Protection Science & Technology Investment Co. Ltd, Changsha 410205, China
| | - Wenjuan Li
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ping Wang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China.
| | - Yuanling Luo
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China; Changsha Environmental Protection College, Changsha 410004, China.
| | - Chao Huang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiong Yang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Jingxuan Yin
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ruiqi Zhang
- College of Environmental Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, China
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Picone N, Blom P, Hogendoorn C, Frank J, van Alen T, Pol A, Gagliano AL, Jetten MSM, D'Alessandro W, Quatrini P, Op den Camp HJM. Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island. Front Microbiol 2021; 12:666929. [PMID: 34093485 PMCID: PMC8170126 DOI: 10.3389/fmicb.2021.666929] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/20/2021] [Indexed: 01/10/2023] Open
Abstract
Verrucomicrobial methanotrophs are a group of aerobic bacteria isolated from volcanic environments. They are acidophiles, characterized by the presence of a particulate methane monooxygenase (pMMO) and a XoxF-type methanol dehydrogenase (MDH). Metagenomic analysis of DNA extracted from the soil of Favara Grande, a geothermal area on Pantelleria Island, Italy, revealed the presence of two verrucomicrobial Metagenome Assembled Genomes (MAGs). One of these MAGs did not phylogenetically classify within any existing genus. After extensive analysis of the MAG, we propose the name of "Candidatus Methylacidithermus pantelleriae" PQ17 gen. nov. sp. nov. The MAG consisted of 2,466,655 bp, 71 contigs and 3,127 predicted coding sequences. Completeness was found at 98.6% and contamination at 1.3%. Genes encoding the pMMO and XoxF-MDH were identified. Inorganic carbon fixation might use the Calvin-Benson-Bassham cycle since all genes were identified. The serine and ribulose monophosphate pathways were incomplete. The detoxification of formaldehyde could follow the tetrahydrofolate pathway. Furthermore, "Ca. Methylacidithermus pantelleriae" might be capable of nitric oxide reduction but genes for dissimilatory nitrate reduction and nitrogen fixation were not identified. Unlike other verrucomicrobial methanotrophs, genes encoding for enzymes involved in hydrogen oxidation could not be found. In conclusion, the discovery of this new MAG expands the diversity and metabolism of verrucomicrobial methanotrophs.
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Affiliation(s)
- Nunzia Picone
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Pieter Blom
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Theo van Alen
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Antonina L Gagliano
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo, Palermo, Italy
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
| | - Walter D'Alessandro
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Palermo, Palermo, Italy
| | - Paola Quatrini
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Palermo, Italy
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research (IWWR), Radboud University, Nijmegen, Netherlands
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Murphy CL, Sheremet A, Dunfield PF, Spear JR, Stepanauskas R, Woyke T, Elshahed MS, Youssef NH. Genomic Analysis of the Yet-Uncultured Binatota Reveals Broad Methylotrophic, Alkane-Degradation, and Pigment Production Capacities. mBio 2021; 12:e00985-21. [PMID: 34006650 PMCID: PMC8262859 DOI: 10.1128/mbio.00985-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/18/2023] Open
Abstract
The recent leveraging of genome-resolved metagenomics has generated an enormous number of genomes from novel uncultured microbial lineages yet left many clades undescribed. Here, we present a global analysis of genomes belonging to Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. All orders in Binatota encoded the capacity for aerobic methylotrophy using methanol, methylamine, sulfomethanes, and chloromethanes as the substrates. Methylotrophy in Binatota was characterized by order-specific substrate degradation preferences, as well as extensive metabolic versatility, i.e., the utilization of diverse sets of genes, pathways, and combinations to achieve a specific metabolic goal. The genomes also encoded multiple alkane hydroxylases and monooxygenases, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids (lycopene, β- and γ-carotenes, xanthins, chlorobactenes, and spheroidenes) production. Further, the majority of genes involved in bacteriochlorophyll a, c, and d biosynthesis were identified, although absence of key genes and failure to identify a photosynthetic reaction center preclude proposing phototrophic capacities. Analysis of 16S rRNA databases showed the preferences of Binatota to terrestrial and freshwater ecosystems, hydrocarbon-rich habitats, and sponges, supporting their potential role in mitigating methanol and methane emissions, breakdown of alkanes, and their association with sponges. Our results expand the lists of methylotrophic, aerobic alkane-degrading, and pigment-producing lineages. We also highlight the consistent encountering of incomplete biosynthetic pathways in microbial genomes, a phenomenon necessitating careful assessment when assigning putative functions based on a set-threshold of pathway completion.IMPORTANCE A wide range of microbial lineages remain uncultured, yet little is known regarding their metabolic capacities, physiological preferences, and ecological roles in various ecosystems. We conducted a thorough comparative genomic analysis of 108 genomes belonging to the Binatota (UBP10), a globally distributed, yet-uncharacterized bacterial phylum. We present evidence that members of the order Binatota specialize in methylotrophy and identify an extensive repertoire of genes and pathways mediating the oxidation of multiple one-carbon (C1) compounds in Binatota genomes. The occurrence of multiple alkane hydroxylases and monooxygenases in these genomes was also identified, potentially enabling growth on a wide range of alkanes and fatty acids. Pigmentation is inferred from a complete pathway for carotenoids production. We also report on the presence of incomplete chlorophyll biosynthetic pathways in all genomes and propose several evolutionary-grounded scenarios that could explain such a pattern. Assessment of the ecological distribution patterns of the Binatota indicates preference of its members to terrestrial and freshwater ecosystems characterized by high methane and methanol emissions, as well as multiple hydrocarbon-rich habitats and marine sponges.
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Affiliation(s)
- Chelsea L Murphy
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Andriy Sheremet
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | | | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkley, California, USA
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
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