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Ge M, Korrensalo A, Laiho R, Kohl L, Lohila A, Pihlatie M, Li X, Laine AM, Anttila J, Putkinen A, Wang W, Koskinen M. Plant-mediated CH 4 exchange in wetlands: A review of mechanisms and measurement methods with implications for modelling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169662. [PMID: 38159777 DOI: 10.1016/j.scitotenv.2023.169662] [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: 07/03/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Plant-mediated CH4 transport (PMT) is the dominant pathway through which soil-produced CH4 can escape into the atmosphere and thus plays an important role in controlling ecosystem CH4 emission. PMT is affected by abiotic and biotic factors simultaneously, and the effects of biotic factors, such as the dominant plant species and their traits, can override the effects of abiotic factors. Increasing evidence shows that plant-mediated CH4 fluxes include not only PMT, but also within-plant CH4 production and oxidation due to the detection of methanogens and methanotrophs attached to the shoots. Despite the inter-species and seasonal differences, and the probable contribution of within-plant microbes to total plant-mediated CH4 exchange (PME), current process-based ecosystem models only estimate PMT based on the bulk biomass or leaf area index of aerenchymatous plants. We highlight five knowledge gaps to which more research efforts should be devoted. First, large between-species variation, even within the same family, complicates general estimation of PMT, and calls for further work on the key dominant species in different types of wetlands. Second, the interface (rhizosphere-root, root-shoot, or leaf-atmosphere) and plant traits controlling PMT remain poorly documented, but would be required for generalizations from species to relevant functional groups. Third, the main environmental controls of PMT across species remain uncertain. Fourth, the role of within-plant CH4 production and oxidation is poorly quantified. Fifth, the simplistic description of PMT in current process models results in uncertainty and potentially high errors in predictions of the ecosystem CH4 flux. Our review suggest that flux measurements should be conducted over multiple growing seasons and be paired with trait assessment and microbial analysis, and that trait-based models should be developed. Only then we are capable to accurately estimate plant-mediated CH4 emissions, and eventually ecosystem total CH4 emissions at both regional and global scales.
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Affiliation(s)
- Mengyu Ge
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland.
| | - Aino Korrensalo
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, Kuopio 80101, Finland; Natural Resources Institute Finland, Latokartanonkaari 9, Helsinki 00790, Finland
| | - Raija Laiho
- Natural Resources Institute Finland, Latokartanonkaari 9, Helsinki 00790, Finland
| | - Lukas Kohl
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, Kuopio 80101, Finland
| | - Annalea Lohila
- Finnish Meteorological Institute, Erik Palménin aukio 1, Helsinki 00560, Finland
| | - Mari Pihlatie
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Department of Agricultural Sciences, Viikki Plant Science Centre (ViPS), University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | - Xuefei Li
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Anna M Laine
- Geological Survey of Finland, PO Box 1237, 70211 Kuopio, Finland
| | - Jani Anttila
- Natural Resources Institute Finland, Latokartanonkaari 9, Helsinki 00790, Finland
| | - Anuliina Putkinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Weifeng Wang
- College of Biology and the Environment, Nanjing Forestry University, 210037 Nanjing, China
| | - Markku Koskinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland; Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, PO Box 56, Helsinki 00014, Finland
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Putkinen A, Siljanen HMP, Laihonen A, Paasisalo I, Porkka K, Tiirola M, Haikarainen I, Tenhovirta S, Pihlatie M. New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing. THE NEW PHYTOLOGIST 2021; 231:524-536. [PMID: 33780002 DOI: 10.1111/nph.17365] [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: 12/21/2020] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
Methane (CH4 ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH4 cycle. Recent studies have focused on quantifying tree stems as sources of CH4 and understanding abiotic CH4 emissions in plant canopies, with the role of microbial in situ CH4 formation receiving less attention. Moreover, despite initial reports revealing CH4 consumption, studies have not adequately evaluated the potential of microbial CH4 oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH4 exchange of plants, and particularly in boreal trees. We detected CH4 -producing methanogens and novel monooxygenases, potentially involved in CH4 consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH4 emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH4 exchange. Our findings, together with the emerging diversity of novel CH4 -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH4 exchange.
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Affiliation(s)
- Anuliina Putkinen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Henri M P Siljanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
- Department of Ecogenomics and Archaea Biology, University of Vienna, Vienna, A-1090, Austria
| | - Antti Laihonen
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Inga Paasisalo
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, 70200, Finland
| | - Kaija Porkka
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Natural Resources Institute Finland, Savonlinna, FI-57200, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, University of Jyväskylä, PO Box 35, Jyväskylä, FI-40014, Finland
| | - Iikka Haikarainen
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Salla Tenhovirta
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
| | - Mari Pihlatie
- Department of Agricultural Sciences, University of Helsinki, PO Box 56, Helsinki, 00014, Finland
- Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, 00560, Finland
- Department of Agricultural Sciences, Viikki Plant Science Centre (ViPS), University of Helsinki, Helsinki, 00014, Finland
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Kröber E, Wende S, Kanukollu S, Buchen-Tschiskale C, Besaury L, Keppler F, Vuilleumier S, Kolb S, Bringel F. 13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern. Environ Microbiol 2021; 23:4450-4465. [PMID: 34121306 DOI: 10.1111/1462-2920.15638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/20/2022]
Abstract
Chloromethane (CH3 Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH3 Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters. Mitigation of CH3 Cl to the atmosphere by methylotrophic bacteria, a global sink for this compound, is likely underestimated and remains poorly characterized. We identified and characterized CH3 Cl-degrading bacteria associated with intact and living tree fern plants of the species Cyathea australis by stable isotope probing (SIP) with 13 C-labelled CH3 Cl combined with metagenomics. Metagenome-assembled genomes (MAGs) related to Methylobacterium and Friedmanniella were identified as being involved in the degradation of CH3 Cl in the phyllosphere, i.e., the aerial parts of the tree fern, while a MAG related to Sorangium was linked to CH3 Cl degradation in the fern rhizosphere. The only known metabolic pathway for CH3 Cl degradation, via a methyltransferase system including the gene cmuA, was not detected in metagenomes or MAGs identified by SIP. Hence, a yet uncharacterized methylotrophic cmuA-independent pathway may drive CH3 Cl degradation in the investigated tree ferns.
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Affiliation(s)
- Eileen Kröber
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Sonja Wende
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Saranya Kanukollu
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Caroline Buchen-Tschiskale
- Isotope Biogeochemistry and Gas Fluxes, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany
| | - Ludovic Besaury
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Heidelberg, Germany
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
| | - Steffen Kolb
- Microbial Biogeochemistry, RA Landscape Functioning, ZALF Leibniz Centre for Agricultural Landscape Research, Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Françoise Bringel
- Génétique Moléculaire, Génomique, Microbiologie (GMGM), Université de Strasbourg, UMR 7156 CNRS, Strasbourg, France
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Jeffrey LC, Maher DT, Tait DR, Reading MJ, Chiri E, Greening C, Johnston SG. Isotopic evidence for axial tree stem methane oxidation within subtropical lowland forests. THE NEW PHYTOLOGIST 2021; 230:2200-2212. [PMID: 33715152 DOI: 10.1111/nph.17343] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Knowledge regarding mechanisms moderating methane (CH4 ) sink/source behaviour along the soil-tree stem-atmosphere continuum remains incomplete. Here, we applied stable isotope analysis (δ13 C-CH4 ) to gain insights into axial CH4 transport and oxidation in two globally distributed subtropical lowland species (Melaleuca quinquenervia and Casuarina glauca). We found consistent trends in CH4 flux (decreasing with height) and δ13 C-CH4 enrichment (increasing with height) in relation to stem height from ground. The average lower tree stem δ13 C-CH4 (0-40 cm) of Melaleuca and Casuarina (-53.96‰ and -65.89‰) were similar to adjacent flooded soil CH4 ebullition (-52.87‰ and -62.98‰), suggesting that stem CH4 is derived mainly by soil sources. Upper stems (81-200 cm) displayed distinct δ13 C-CH4 enrichment (Melaleuca -44.6‰ and Casuarina -46.5‰, respectively). Coupled 3D-photogrammetry with novel 3D-stem measurements revealed distinct hotspots of CH4 flux and isotopic fractionation on Melaleuca, which were likely due to bark anomalies in which preferential pathways of gas efflux were enhanced. Diel experiments revealed greater δ13 C-CH4 enrichment and higher oxidation rates in the afternoon, compared with the morning. Overall, we estimated that c. 33% of the methane was oxidised between lower and upper stems during axial transport, therefore potentially representing a globally significant, yet previously unaccounted for, methane sink.
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Affiliation(s)
- Luke C Jeffrey
- SCU Geoscience, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
- Faculty of Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Damien T Maher
- SCU Geoscience, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
- Faculty of Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Douglas R Tait
- SCU Geoscience, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
- Faculty of Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Michael J Reading
- SCU Geoscience, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
- Faculty of Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
| | - Eleonora Chiri
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Scott G Johnston
- SCU Geoscience, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
- Faculty of Science and Engineering, Southern Cross University, PO Box 157, Lismore, NSW, 2480, Australia
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Davamani V, Parameswari E, Arulmani S. Mitigation of methane gas emissions in flooded paddy soil through the utilization of methanotrophs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 726:138570. [PMID: 32305766 DOI: 10.1016/j.scitotenv.2020.138570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
The utilization of methanotrophs for reducing the global warming potential in a flooded paddy system is the progressive investigation in the recent. The field investigation was conducted in Tamil Nadu Rice Research Institute, Aduthurai. This study showed the effect of isolated methanotroph strain (MR15) on the reduction of methane emission and improvement in growth parameters and yield of paddy. The treatments included the diverse dosages of methanotroph consortium (0, 25, 50, 75 & 100%). The total seasonal methane emission varied between 1.96 and 5.04 kg ha-1 for the season of Kharif and 2.18 to 5.81 kg ha-1 for the season of Rabi owing to the footprint of methanotroph. Irrespective of treatments, the mean seasonal emission was more prominent during Rabi compared to the Kharif season. The dosage of methanotroph consortium significantly influenced not only seasonal methane emission but also the grain yield percentage, which increased over 100% Recommended Dose of Fertilizers (RDF). Application of 100% methanotroph consortium (i.e.6.25 kg ha-1) minimizes the methane emission by 60% with an increase in grain yield by 35% and lessens the usage of additional nutrients. Overall, this study showed a sign of atmospheric methane uptake with increase growth potential and yield of paddy cultivation using methanotroph consortium.
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Affiliation(s)
- Veeraswamy Davamani
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India.
| | - Ettiyagounder Parameswari
- Department of Environmental Sciences, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India
| | - Subramanian Arulmani
- Department of Chemistry, National Institute of Technology, Tiruchirapalli & Bannari Amman Institute of Technology, Sathyamangalam 638401, Tamil Nadu, India
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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Keppler F, Röhling AN, Jaeger N, Schroll M, Hartmann SC, Greule M. Sources and sinks of chloromethane in a salt marsh ecosystem: constraints from concentration and stable isotope measurements of laboratory incubation experiments. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2020; 22:627-641. [PMID: 32080692 DOI: 10.1039/c9em00540d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chloromethane (CH3Cl) is the most abundant long-lived chlorinated organic compound in the atmosphere and contributes significantly to natural stratospheric ozone depletion. Salt marsh ecosystems including halophyte plants are a known source of atmospheric CH3Cl but estimates of their total global source strength are highly uncertain and knowledge of the major production and consumption processes in the atmosphere-halophyte-soil system is yet incomplete. In this study we investigated the halophyte plant, Salicornia europaea, and soil samples from a coastal salt marsh site in Sardinia/Italy for their potential to emit and consume CH3Cl and using flux measurements, stable isotope techniques and Arrhenius plots differentiated between biotic and abiotic processes. Our laboratory approach clearly shows that at least 6 different production and consumption processes are active in controlling atmospheric CH3Cl fluxes of a salt marsh ecosystem. CH3Cl release by dried plant and soil material was substantially higher than that from the fresh material at temperatures ranging from 20 to 70 °C. Results of Arrhenius plots helped to distinguish between biotic and abiotic formation processes in plants and soils. Biotic CH3Cl consumption rates were highest at 30 °C for plants and 50 °C for soils, and microbial uptake was higher in soils with higher organic matter content. Stable isotope techniques helped to distinguish between formation and degradation processes and also provided a deeper insight into potential methyl moiety donor compounds, such as S-adenosyl-l-methionine, S-methylmethionine and pectin, that might be involved in the abiotic and biotic CH3Cl production processes. Our results clearly indicate that cycling of CH3Cl in salt marsh ecosystems is a result of several biotic and abiotic processes occurring simultaneously in the atmosphere-plant-soil system. Important precursor compounds for biotic and abiotic CH3Cl formation might be methionine derivatives and pectin. All formation and degradation processes are temperature dependent and thus environmental changes might affect the strength of each source and sink within salt marsh ecosystems and thus considerably alter total fluxes of CH3Cl from salt marsh ecosystems to the atmosphere.
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Affiliation(s)
- Frank Keppler
- Institute of Earth Sciences, Heidelberg University, Im Neuenheimer Feld 234-236, D-69120 Heidelberg, Germany.
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Abstract
Aerobic methanotrophs have long been known to play a critical role in the global carbon cycle, being capable of converting methane to biomass and carbon dioxide. Interestingly, these microbes exhibit great sensitivity to copper and rare-earth elements, with the expression of key genes involved in the central pathway of methane oxidation controlled by the availability of these metals. That is, these microbes have a "copper switch" that controls the expression of alternative methane monooxygenases and a "rare-earth element switch" that controls the expression of alternative methanol dehydrogenases. Further, it has been recently shown that some methanotrophs can detoxify inorganic mercury and demethylate methylmercury; this finding is remarkable, as the canonical organomercurial lyase does not exist in these methanotrophs, indicating that a novel mechanism is involved in methylmercury demethylation. Here, we review recent findings on methanotrophic interactions with metals, with a particular focus on these metal switches and the mechanisms used by methanotrophs to bind and sequester metals.
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Kaparullina EN, Doronina NV, Mustakhimov II, Agafonova NV, Trotsenko YA. Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow region. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717010076] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Gar’kusha DN, Fedorov YA. Effect of plants on processes of methane cycle in bottom deposits and soil rhizosphere. CONTEMP PROBL ECOL+ 2017. [DOI: 10.1134/s1995425516060032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Farhan Ul Haque M, Gu W, Baral BS, DiSpirito AA, Semrau JD. Carbon source regulation of gene expression in Methylosinus trichosporium OB3b. Appl Microbiol Biotechnol 2017; 101:3871-3879. [PMID: 28108763 DOI: 10.1007/s00253-017-8121-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 01/06/2023]
Abstract
Gene expression in methanotrophs has been shown to be affected by the availability of a variety of metals, most notably copper regulating expression of alternative forms of methane monooxygenase. Here, we show that growth substrate also affects expression of genes encoding for enzymes responsible for the oxidation of methane to formaldehyde and the assimilation of carbon. Specifically, in Methylosinus trichosporium OB3b, expression of genes involved in the conversion of methane to methanol (pmoA and mmoX) and methanol to formaldehyde (mxaF, xoxF1, and xoxF2) as well as in carbon assimilation (fae1, fae2, metF, and sga) decreased when this strain was grown on methanol vs. methane, indicating that methanotrophs manipulate gene expression in response to growth substrate as well as the availability of copper. Interestingly, growth of M. trichosporium OB3b on methane vs. methanol was similar despite such large changes in gene expression. Finally, methanol-grown cultures of M. trichosporium OB3b also exhibited the "copper-switch." That is, expression of pmoA increased and mmoX decreased in the presence of copper, indicating that copper still controlled the expression of alternative forms of methane monooxygenase in M. trichosporium OB3b even though methane was not provided. Such findings indicate that methanotrophs can sense and respond to multiple environmental parameters simultaneously.
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Affiliation(s)
- Muhammad Farhan Ul Haque
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Wenyu Gu
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA
| | - Bipin S Baral
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-3260, USA
| | - Alan A DiSpirito
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011-3260, USA
| | - Jeremy D Semrau
- Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, MI, 48109-2125, USA.
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Iguchi H, Yurimoto H, Sakai Y. Interactions of Methylotrophs with Plants and Other Heterotrophic Bacteria. Microorganisms 2015; 3:137-51. [PMID: 27682083 PMCID: PMC5023238 DOI: 10.3390/microorganisms3020137] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/18/2015] [Accepted: 03/27/2015] [Indexed: 01/19/2023] Open
Abstract
Methylotrophs, which can utilize methane and/or methanol as sole carbon and energy sources, are key players in the carbon cycle between methane and CO2, the two most important greenhouse gases. This review describes the relationships between methylotrophs and plants, and between methanotrophs (methane-utilizers, a subset of methylotrophs) and heterotrophic bacteria. Some plants emit methane and methanol from their leaves, and provide methylotrophs with habitats. Methanol-utilizing methylotrophs in the genus Methylobacterium are abundant in the phyllosphere and have the ability to promote the growth of some plants. Methanotrophs also inhabit the phyllosphere, and methanotrophs with high methane oxidation activities have been found on aquatic plants. Both plant and environmental factors are involved in shaping the methylotroph community on plants. Methanotrophic activity can be enhanced by heterotrophic bacteria that provide growth factors (e.g., cobalamin). Information regarding the biological interaction of methylotrophs with other organisms will facilitate a better understanding of the carbon cycle that is driven by methylotrophs.
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Affiliation(s)
- Hiroyuki Iguchi
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan.
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Zlotnikov KM, Zlotnikov AK, Kaparullina EN, Doronina NV. Phylogenetic position and phosphate solubilization activity of lactic acid bacteria associated with different plants. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713030144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Wellner S, Lodders N, Kämpfer P. Diversity and biogeography of selected phyllosphere bacteria with special emphasis on Methylobacterium spp. Syst Appl Microbiol 2011; 34:621-30. [PMID: 22000032 DOI: 10.1016/j.syapm.2011.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 08/17/2011] [Accepted: 08/23/2011] [Indexed: 11/26/2022]
Abstract
On the basis of cultivation-dependent (isolation on mineral salt medium supplemented with 0.5% methanol) and -independent (DGGE analysis) methods, we investigated the influence of the host plant species Trifolium repens and Cerastium holosteoides, three geographic locations and the land-use types meadow, mown pasture and pasture on the abundance and community composition of selected phyllosphere bacteria with emphasis on Methylobacterium species. Methylobacterium abundance was significantly higher on leaves of T. repens (mean value 2.0×10(7) CFU PPFM per g leaf) than on leaves of C. holosteoides (mean value 2.0×10(6) CFU per g leaf). Leaves from the sampling site Schorfheide-Chorin showed slightly lower Methylobacterium numbers than leaves of the other sampling sites. Land-use and sampling period had no consistent influence on Methylobacterium community size. Methylobacterium community composition was very similar over both sampling periods, all three sampling sites, all land-use types and both plant species. Moreover, no relationship between geographic and genetic distance was observed. Community composition of selected Proteobacteria was influenced by plant species, geographic location and land-use. Often, differences in community composition could be observed between meadows, mown pastures and pastures but not between different kinds of meadows (cutted once versus three times) and mown pastures (fertilized versus non-fertilized). The results also indicate, that whether there are differences between land-use types or not strongly depends on the investigated host plant species and ecosystem. Besides Methylobacterium, representatives of Methylophilus were detected. The results indicate that Methylobacterium species are generally abundant and stable members of the phyllosphere community whereas other genera occur more occasionally, and that Methylobacterium clearly dominates the methylotrophic phyllosphere community.
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Affiliation(s)
- S Wellner
- Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
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16
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Oikawa PY, Giebel BM, da Silveira Lobo O'Reilly Sternberg L, Li L, Timko MP, Swart PK, Riemer DD, Mak JE, Lerdau MT. Leaf and root pectin methylesterase activity and 13C/12C stable isotopic ratio measurements of methanol emissions give insight into methanol production in Lycopersicon esculentum. THE NEW PHYTOLOGIST 2011; 191:1031-1040. [PMID: 21592134 DOI: 10.1111/j.1469-8137.2011.03770.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Plant production of methanol (MeOH) is a poorly understood aspect of metabolism, and understanding MeOH production in plants is crucial for modeling MeOH emissions. Here, we have examined the source of MeOH emissions from mature and immature leaves and whether pectin methylesterase (PME) activity is a good predictor of MeOH emission. We also investigated the significance of below-ground MeOH production for mature leaf emissions. We present measurements of MeOH emission, PME activity, and MeOH concentration in mature and immature tissues of tomato (Lycopersicon esculentum). We also present stable carbon isotopic signatures of MeOH emission and the pectin methoxyl pool. Our results suggest that below-ground MeOH production was not the dominant contributor to daytime MeOH emissions from mature and immature leaves. Stable carbon isotopic signatures of mature and immature leaf MeOH were similar, suggesting that they were derived from the same pathway. Foliar PME activity was related to MeOH flux, but unexplained variance suggested PME activity could not predict emissions. The data show that MeOH production and emission are complex and cannot be predicted using PME activity alone. We hypothesize that substrate limitation of MeOH synthesis and MeOH catabolism may be important regulators of MeOH emission.
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Affiliation(s)
| | - Brian M Giebel
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149-1098, USA
| | | | - Lei Li
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Peter K Swart
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149-1098, USA
| | - Daniel D Riemer
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149-1098, USA
| | - John E Mak
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
| | - Manuel T Lerdau
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA 22904-4123, USA
- Xishuangbanna Tropical Botanic Garden, Melung, Xishuangbanna, Yunnan, China
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17
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Production of an insecticidal crystal protein from Bacillus thuringiensis by the methylotroph Methylobacterium extorquens. Appl Environ Microbiol 2008; 74:5178-82. [PMID: 18552184 DOI: 10.1128/aem.00598-08] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Cry1Aa protein from Bacillus thuringiensis is an insecticidal protein that is highly active against several species of Lepidoptera. We cloned and expressed the cry1Aa gene in a plant-colonizing methylotroph, Methylobacterium extorquens, under the control of the strong M. extorquens AM1 methanol dehydrogenase promoter, P(mxaF). Transmission electron microscopy revealed characteristic bipyramidal intracellular delta-endotoxin crystals similar to the crystalline inclusions formed by B. thuringiensis. Both the protoxin protein and the activated toxin were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western analysis. In single-dose assays of the recombinant against the silkworm, Bombyx mori, both whole cells and cell lysates caused rapid feeding inhibition followed by mortality. The biomass and growth rate of recombinant cells in shake flask culture were similar to those of the wild-type strain, indicating a lack of fitness cost to the recombinant under controlled culture conditions. Recombinant Cry1Aa was expressed at a level of 4.5% of total M. extorquens cell protein. The potential benefits of modifying M. extorquens to deliver insecticidal Cry proteins for crop and forest protection are discussed.
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18
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Ghosh A, Goyal A, Jain RK. Study of methanol-induced phenotypic changes in a novel strain of Acinetobacter lwoffii. Arch Microbiol 2007; 188:533-9. [PMID: 17572881 DOI: 10.1007/s00203-007-0268-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2007] [Revised: 04/20/2007] [Accepted: 05/24/2007] [Indexed: 10/23/2022]
Abstract
A Gram-negative bacterial strain designated LS2 isolated from Lahaul-Spiti valley of North India was shown to produce pink pigment while utilizing methanol as sole source of carbon and energy. Interestingly, pigment production was inducible in nature since the organism did not produce any pigment when grown on other carbon sources. Based on phenotypic and phylogenetic characterization the non-pigmented methylotroph was identified as a novel strain of Acinetobacter lwoffii MTCC 8288 (DQ144736). By means of spectral and mass analyses the pigment was characterized as bacterioruberin-like carotenoid molecule. Here, the carotenoid pigment may form an important part of the antioxidant defense mechanism against oxidative stress imparted by methanol. The methanol utilization pathway in strain LS2 was deciphered by showing the presence of functional methanol dehydrogenase and formaldehyde dehydrogenase genes. In addition, to investigate methanol induced physiological changes, comparative fatty acid profile was analysed and distinctive qualitative as well as quantitative differences in fatty acid content were observed. Therefore, we suggest that strain LS2 exhibiting such unique phenotypic property should be assigned a taxonomic position other than the pigmented and non-pigmented methylotrophs.
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Affiliation(s)
- Anuradha Ghosh
- Institute of Microbial Technology, Sector-39A, Chandigarh, 160036, India
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