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Schmider T, Hestnes AG, Brzykcy J, Schmidt H, Schintlmeister A, Roller BRK, Teran EJ, Söllinger A, Schmidt O, Polz MF, Richter A, Svenning MM, Tveit AT. Physiological basis for atmospheric methane oxidation and methanotrophic growth on air. Nat Commun 2024; 15:4151. [PMID: 38755154 DOI: 10.1038/s41467-024-48197-1] [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: 02/13/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane. Still, the physiological basis allowing atmMOB to grow on air is not well understood. Here we assess the ability and strategies of seven methanotrophic species to grow with air as sole energy, carbon, and nitrogen source. Four species, including three outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, carbon monoxide, and hydrogen during 12 months of growth on air. These four species exhibited distinct substrate preferences implying the existence of multiple metabolic strategies to grow on air. The estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance in atmMOB and other aerobic microorganisms. Moreover, the atmMOB also covered their nitrogen requirements from air. During growth on air, the atmMOB decreased investments in biosynthesis while increasing investments in trace gas oxidation. Furthermore, we confirm that a high apparent specific affinity for methane is a key characteristic of atmMOB. Our work shows that atmMOB grow on the trace concentrations of methane, carbon monoxide, and hydrogen present in air and outlines the metabolic strategies that enable atmMOB to mitigate greenhouse gases.
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Affiliation(s)
- Tilman Schmider
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Julia Brzykcy
- Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096, Warsaw, Poland
| | - Hannes Schmidt
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Arno Schintlmeister
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Benjamin R K Roller
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Ezequiel Jesús Teran
- Centro de Investigaciones en Física e Ingeniería del Centro de la Provincia de Buenos Aires (CIFICEN-UNCPBA-CONICET-CICPBA), Pinto, 399, Tandil (7000), Argentina
- Universidad Nacional del Centro de la Provincia de Buenos Aires, Facultad de Ciencias Exactas, Instituto de Física Arroyo Seco (IFAS), Pinto, 399, Tandil (7000), Argentina
| | - Andrea Söllinger
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Oliver Schmidt
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Martin F Polz
- Department of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, 1030, Vienna, Austria
| | - Andreas Richter
- Department of Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem Research, University of Vienna, 1030, Vienna, Austria
| | - Mette M Svenning
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, 9037, Tromsø, Norway.
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Dai W, Du H, Zhou Q, Li S, Wang Y, Hou J, Guo C, Yang Q, Li C, Xie S, Li SC, Wu R. Metabolic profiles outperform the microbiota in assessing the response of vaginal microenvironments to the changed state of HPV infection. NPJ Biofilms Microbiomes 2024; 10:26. [PMID: 38509123 PMCID: PMC10954630 DOI: 10.1038/s41522-024-00500-0] [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: 07/30/2023] [Accepted: 03/11/2024] [Indexed: 03/22/2024] Open
Abstract
There is a deficiency in population-based studies investigating the impact of HPV infection on vaginal microenvironment, which influences the risk of persistent HPV infection. This prospective study aimed to unravel the dynamics of vaginal microbiota (VM) and vaginal metabolome in reaction to the changed state of HPV infection. Our results propose that the vaginal metabolome may be a superior indicator to VM when assessing the impact of altered HPV state on the vaginal microenvironment.
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Affiliation(s)
- Wenkui Dai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Hui Du
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Qian Zhou
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Sumei Li
- Department of Pharmacology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yinan Wang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Jun Hou
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Chunlei Guo
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Qing Yang
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Changzhong Li
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China
| | - Shouxia Xie
- Department of Pharmacology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
| | - Ruifang Wu
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China.
- Institute of Obstetrics and Gynecology, Shenzhen PKU-HKUST Medical Center, Shenzhen, China.
- Shenzhen Key Laboratory on Technology for Early Diagnosis of Major Gynecologic Diseases, Shenzhen, China.
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Guo K, Glatter T, Paczia N, Liesack W. Asparagine Uptake: a Cellular Strategy of Methylocystis to Combat Severe Salt Stress. Appl Environ Microbiol 2023; 89:e0011323. [PMID: 37184406 PMCID: PMC10305061 DOI: 10.1128/aem.00113-23] [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: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
Methylocystis spp. are known to have a low salt tolerance (≤1.0% NaCl). Therefore, we tested various amino acids and other well-known osmolytes for their potential to act as an osmoprotectant under otherwise growth-inhibiting NaCl conditions. Adjustment of the medium to 10 mM asparagine had the greatest osmoprotective effect under severe salinity (1.50% NaCl), leading to partial growth recovery of strain SC2. The intracellular concentration of asparagine increased to 264 ± 57 mM, with a certain portion hydrolyzed to aspartate (4.20 ± 1.41 mM). In addition to general and oxidative stress responses, the uptake of asparagine specifically induced major proteome rearrangements related to the KEGG level 3 categories of "methane metabolism," "pyruvate metabolism," "amino acid turnover," and "cell division." In particular, various proteins involved in cell division (e.g., ChpT, CtrA, PleC, FtsA, FtsH1) and peptidoglycan synthesis showed a positive expression response. Asparagine-derived 13C-carbon was incorporated into nearly all amino acids. Both the exometabolome and the 13C-labeling pattern suggest that in addition to aspartate, the amino acids glutamate, glycine, serine, and alanine, but also pyruvate and malate, were most crucially involved in the osmoprotective effect of asparagine, with glutamate being a major hub between the central carbon and amino acid pathways. In summary, asparagine induced significant proteome rearrangements, leading to major changes in central metabolic pathway activity and the sizes of free amino acid pools. In consequence, asparagine acted, in part, as a carbon source for the growth recovery of strain SC2 under severe salinity. IMPORTANCE Methylocystis spp. play a major role in reducing methane emissions into the atmosphere from methanogenic wetlands. In addition, they contribute to atmospheric methane oxidation in upland soils. Although these bacteria are typical soil inhabitants, Methylocystis spp. are thought to have limited capacity to acclimate to salt stress. This called for a thorough study into potential osmoprotectants, which revealed asparagine as the most promising candidate. Intriguingly, asparagine was taken up quantitatively and acted, at least in part, as an intracellular carbon source under severe salt stress. The effect of asparagine as an osmoprotectant for Methylocystis spp. is an unexpected finding. It may provide Methylocystis spp. with an ecological advantage in wetlands, where these methanotrophs colonize the roots of submerged vascular plants. Collectively, our study offers a new avenue into research on compounds that may increase the resilience of Methylocystis spp. to environmental change.
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Affiliation(s)
- Kangli Guo
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Werner Liesack
- Methanotrophic Bacteria and Environmental Genomics/Transcriptomics Research Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
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Marshall AJ, Phillips L, Longmore A, Hayden HL, Tang C, Heidelberg KB, Mele P. Using metatranscriptomics to better understand the role of microbial nitrogen cycling in coastal sediment benthic flux denitrification efficiency. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023. [PMID: 36992633 DOI: 10.1111/1758-2229.13148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 06/19/2023]
Abstract
Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community-level nitrification-denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site- and season-specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling.
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Affiliation(s)
- Alexis J Marshall
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Lori Phillips
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
| | - Andrew Longmore
- Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, Australia
| | - Helen L Hayden
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
- School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Caixian Tang
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
| | - Karla B Heidelberg
- Department of Biology, The University of Southern California, Los Angeles, California, USA
| | - Pauline Mele
- La Trobe University, AgriBio Centre for AgriBiosciences, Bundoora, Australia
- Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Bundoora, Australia
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Wang H, Jurasinski G, Täumer J, Kuß AW, Groß V, Köhn D, Günther A, Urich T. Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5089-5101. [PMID: 36926875 DOI: 10.1021/acs.est.2c07461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Rewetted peatlands are reestablished hot spots for CH4 emissions, which are subject to increased drought events in the course of climate change. However, the dynamics of soil methane-cycling microbiomes in rewetted peatlands during summer drought are still poorly characterized. Using a quantitative metatranscriptomic approach, we investigated the changes in the transcript abundances of methanogen and methanotroph rRNA, as well as mcrA and pmoA mRNA before, during, and after the 2018 summer drought in a coastal and a percolation fen in northern Germany. Drought changed the community structure of methane-cycling microbiomes and decreased the CH4 fluxes as well as the rRNA and mRNA transcript abundances of methanogens and methanotrophs, but they showed no recovery or increase after the drought ended. The rRNA transcript abundance of methanogens was not correlated with CH4 fluxes in both fens. In the percolation fen, however, the mcrA transcript abundance showed a positive and significant correlation with CH4 fluxes. Importantly, when integrating pmoA abundance, a stronger correlation was observed between CH4 fluxes and mcrA/pmoA, suggesting that relationships between methanogens and methanotrophs are the key determinant of CH4 turnover. Our study provides a comprehensive understanding of the methane-cycling microbiome feedbacks to drought events in rewetted peatlands.
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Affiliation(s)
- Haitao Wang
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Gerald Jurasinski
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
- Interdisciplinary Faculty, University of Rostock, 18059 Rostock, Germany
- Peatland Science, University of Greifswald, 17489 Greifswald, Germany
| | - Jana Täumer
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Andreas W Kuß
- Human Molecular Genetics Group, Department of Functional Genomics, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Verena Groß
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
| | - Daniel Köhn
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
| | - Anke Günther
- Landscape Ecology, University of Rostock, 18059 Rostock, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
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Yan Z, Kang E, Zhang K, Hao Y, Wang X, Li Y, Li M, Wu H, Zhang X, Yan L, Zhang W, Li J, Yang A, Niu Y, Kang X. Asynchronous responses of microbial CAZymes genes and the net CO 2 exchange in alpine peatland following 5 years of continuous extreme drought events. ISME COMMUNICATIONS 2022; 2:115. [PMID: 37938678 PMCID: PMC9723601 DOI: 10.1038/s43705-022-00200-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/26/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2023]
Abstract
Peatlands act as an important sink of carbon dioxide (CO2). Yet, they are highly sensitive to climate change, especially to extreme drought. The changes in the net ecosystem CO2 exchange (NEE) under extreme drought events, and the driving function of microbial enzymatic genes involved in soil organic matter (SOM) decomposition, are still unclear. Herein we investigated the effects of extreme drought events in different periods of plant growth season at Zoige peatland on NEE and microbial enzymatic genes of SOM decomposition after 5 years. The results showed that the NEE of peatland decreased significantly by 48% and 26% on average (n = 12, P < 0.05) under the early and midterm extreme drought, respectively. The microbial enzymatic genes abundance of SOM decomposition showed the same decreasing trend under early and midterm extreme drought, but an increasing trend under late extreme drought. The microbial community that contributes to these degradation genes mainly derives from Proteobacteria and Actinobacteria. NEE was mainly affected by soil hydrothermal factors and gross primary productivity but weakly correlated with SOM enzymatic decomposition genes. Soil microbial respiration showed a positive correlation with microbial enzymatic genes involved in the decomposition of labile carbon (n = 18, P < 0.05). This study provided new insights into the responses of the microbial decomposition potential of SOM and ecosystem CO2 sink function to extreme drought events in the alpine peatland.
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Affiliation(s)
- Zhongqing Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Enze Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Kerou Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaodong Wang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yong Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Meng Li
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Haidong Wu
- Information Center of Ministry of Ecology and Environment, 100029, Beijing, China
| | - Xiaodong Zhang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Liang Yan
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Wantong Zhang
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ao Yang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China
| | - Yuechuan Niu
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xiaoming Kang
- Wetland Research Center, Institute of Ecological Conservation and Restoration, Chinese Academy of Forestry, 100091, Beijing, China.
- Sichuan Zoige Wetland Ecosystem Research Station, Tibetan Autonomous Prefecture of Aba, Ngawa, 624500, China.
- Beijing Key Laboratory of Wetland Services and Restoration, 100091, Beijing, China.
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Methylocystis sp. Strain SC2 Acclimatizes to Increasing NH 4+ Levels by a Precise Rebalancing of Enzymes and Osmolyte Composition. mSystems 2022; 7:e0040322. [PMID: 36154142 PMCID: PMC9600857 DOI: 10.1128/msystems.00403-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A high NH4+ load is known to inhibit bacterial methane oxidation. This is due to a competition between CH4 and NH3 for the active site of particulate methane monooxygenase (pMMO), which converts CH4 to CH3OH. Here, we combined global proteomics with amino acid profiling and nitrogen oxides measurements to elucidate the cellular acclimatization response of Methylocystis sp. strain SC2 to high NH4+ levels. Relative to 1 mM NH4+, a high (50 mM and 75 mM) NH4+ load under CH4-replete conditions significantly increased the lag phase duration required for proteome adjustment. The number of differentially regulated proteins was highly significantly correlated with an increasing NH4+ load. The cellular responses to increasing ionic and osmotic stress involved a significant upregulation of stress-responsive proteins, the K+ "salt-in" strategy, the synthesis of compatible solutes (glutamate and proline), and the induction of the glutathione metabolism pathway. A significant increase in the apparent Km value for CH4 oxidation during the growth phase was indicative of increased pMMO-based oxidation of NH3 to toxic hydroxylamine. The detoxifying activity of hydroxlyamine oxidoreductase (HAO) led to a significant accumulation of NO2- and, upon decreasing O2 tension, N2O. Nitric oxide reductase and hybrid cluster proteins (Hcps) were the candidate enzymes for the production of N2O. In summary, strain SC2 has the capacity to precisely rebalance enzymes and osmolyte composition in response to increasing NH4+ exposure, but the need to simultaneously combat both ionic-osmotic stress and the toxic effects of hydroxylamine may be the reason why its acclimatization capacity is limited to 75 mM NH4+. IMPORTANCE In addition to reducing CH4 emissions from wetlands and landfills, the activity of alphaproteobacterial methane oxidizers of the genus Methylocystis contributes to the sink capacity of forest and grassland soils for atmospheric methane. The methane-oxidizing activity of Methylocystis spp. is, however, sensitive to high NH4+ concentrations. This is due to the competition of CH4 and NH3 for the active site of particulate methane monooxygenase, thereby resulting in the production of toxic hydroxylamine with an increasing NH4+ load. An understanding of the physiological and molecular response mechanisms of Methylocystis spp. is therefore of great importance. Here, we combined global proteomics with amino acid profiling and NOx measurements to disentangle the cellular mechanisms underlying the acclimatization of Methylocystis sp. strain SC2 to an increasing NH4+ load.
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