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Ahmadi F, Lackner M. Recent findings in methanotrophs: genetics, molecular ecology, and biopotential. Appl Microbiol Biotechnol 2024; 108:60. [PMID: 38183483 DOI: 10.1007/s00253-023-12978-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/08/2023] [Accepted: 10/01/2023] [Indexed: 01/08/2024]
Abstract
The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.
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Affiliation(s)
- Fatemeh Ahmadi
- School of Agriculture and Environment, University of Western Australia, Crawley, 6009, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, 7001, Australia
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2
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Ou Y, Ren Z, Chen X, Jiang Z, Liu Q, Li X, Zheng Y, Liang X, Liu M, Hou L, Dong H. Global Atlas of Methane Metabolism Marker Genes in Soil. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9261-9271. [PMID: 38739716 DOI: 10.1021/acs.est.4c02827] [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: 05/16/2024]
Abstract
Methane, a greenhouse gas, plays a pivotal role in the global carbon cycle, influencing the Earth's climate. Only a limited number of microorganisms control the flux of biologically produced methane in nature, including methane-oxidizing bacteria, anaerobic methanotrophic archaea, and methanogenic archaea. Although previous studies have revealed the spatial and temporal distribution characteristics of methane-metabolizing microorganisms in local regions by using the marker genes pmoA or mcrA, their biogeographical patterns and environmental drivers remain largely unknown at a global scale. Here, we used 3419 metagenomes generated from georeferenced soil samples to examine the global patterns of methane metabolism marker gene abundances in soil, which generally represent the global distribution of methane-metabolizing microorganisms. The resulting maps revealed notable latitudinal trends in the abundances of methane-metabolizing microorganisms across global soils, with higher abundances in the sub-Arctic, sub-Antarctic, and tropical rainforest regions than in temperate regions. The variations in global abundances of methane-metabolizing microorganisms were primarily governed by vegetation cover. Our high-resolution global maps of methane-metabolizing microorganisms will provide valuable information for the prediction of biogenic methane emissions under current and future climate scenarios.
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Affiliation(s)
- Yafei Ou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Zhongda Ren
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Xi Chen
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Zhenran Jiang
- Department of Computer Science and Technology, East China Normal University, Shanghai 200062, China
| | - Qiancai Liu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Xiaofei Li
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Yanling Zheng
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Xia Liang
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Min Liu
- Key Laboratory of Geographic Information Science, Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Lijun Hou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
| | - Hongpo Dong
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai 200241, China
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3
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Islam MM, Jana SK, Sengupta S, Mandal S. Impact of Rhizospheric Microbiome on Rice Cultivation. Curr Microbiol 2024; 81:188. [PMID: 38780806 DOI: 10.1007/s00284-024-03703-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/13/2024] [Indexed: 05/25/2024]
Abstract
The rhizosphere niche is extremely important for the overall growth and development of plants. Evidently, it is necessary to understand the complete mechanism of plant microbe interactions of the rhizosphere for sustainable and low input productivity. To meet the increasing global food demand, rice (Oryza sativa L.) agriculture seeks optimal conditions. The unique oxic-anoxic interface of rice-growing soil has invited divergent microbes with dynamic biogeochemical cycles. This review provides the systematic analysis of microbes associated with the major biogeochemical cycles with the aim to generate better management strategies of rhizospheric microbiome in the field of rice agriculture. For instance, several methanogenic and methanotrophic bacteria in the rice rhizosphere make an equilibrium for methane concentration in the environment. The carbon sequestration in paddy soil is again done through many rhizospheric microorganisms that can directly assimilate CO2 with their photoautotrophic mode of nutrition. Also the phosphate solubilizing microbes remain to be the most important keys for the PGPR activity of the paddy ecosystem. In addition, rhizospheric microbiome remain crucial in degradation and solubilization of organo-sulfur and insoluble inorganic sulfides which can be taken by the plants. Further, this review elucidates on the advantages of using metagenomic and metaproteomic approaches as an alternative of traditional approaches to understand the overall metabolic pathways operational in paddy-field. These knowledges are expected to open new possibilities for designing the balanced microbiome used as inoculum for intensive farming and will eventually lead to exert positive impacts on rice cultivation.
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Affiliation(s)
- Md Majharul Islam
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Santosh Kumar Jana
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Subhadipa Sengupta
- Post Graduate Department of Botany, Bidhannagar College, EB -2, Sector 1, Salt Lake, Kolkata, 700064, India.
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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Goswami S, Singer SW, Simmons BA, Awasthi D. Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum. Front Bioeng Biotechnol 2024; 12:1412410. [PMID: 38812915 PMCID: PMC11133525 DOI: 10.3389/fbioe.2024.1412410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.
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Affiliation(s)
- Shubhasish Goswami
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Blake A. Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
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Corrêa PS, Fernandes MA, Jimenez CR, Mendes LW, Lima PDMT, Abdalla AL, Louvandini H. Interaction between methanotrophy and gastrointestinal nematodes infection on the rumen microbiome of lambs. FEMS Microbiol Ecol 2024; 100:fiae083. [PMID: 38821514 PMCID: PMC11165275 DOI: 10.1093/femsec/fiae083] [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: 07/28/2023] [Revised: 03/21/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Complex cross-talk occurs between gastrointestinal nematodes and gut symbiotic microbiota, with consequences for animal metabolism. To investigate the connection between methane production and endoparasites, this study evaluated the effect of mixed infection with Haemonchus contortus and Trichostrongylus colubriformis on methanogenic and methanotrophic community in rumen microbiota of lambs using shotgun metagenomic and real-time quantitative PCR (qPCR). The rumen content was collected from six Santa Inês lambs, (7 months old) before and after 42 days infection by esophageal tube. The metagenomic analysis showed that the infection affected the microbial community structure leading to decreased abundance of methanotrophs bacteria, i.e. α-proteobacteria and β-proteobacteria, anaerobic methanotrophic archaea (ANME), protozoa, sulfate-reducing bacteria, syntrophic bacteria with methanogens, geobacter, and genes related to pyruvate, fatty acid, nitrogen, and sulfur metabolisms, ribulose monophosphate cycle, and Entner-Doudoroff Pathway. Additionally, the abundance of methanogenic archaea and the mcrA gene did not change. The co-occurrence networks enabled us to identify the interactions between each taxon in microbial communities and to determine the reshaping of rumen microbiome associations by gastrointestinal nematode infection. Besides, the correlation between ANMEs was lower in the animal's postinfection. Our findings suggest that gastrointestinal parasites potentially lead to decreased methanotrophic metabolism-related microorganisms and genes.
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Affiliation(s)
- Patricia Spoto Corrêa
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Murilo Antonio Fernandes
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Carolina Rodriguez Jimenez
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Laboratory of Molecular Cell Biology, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Paulo de Mello Tavares Lima
- Department of Animal Science, University of Wyoming, 1000 East University Avenue, Laramie, WY 82071, United States
| | - Adibe Luiz Abdalla
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
| | - Helder Louvandini
- Laboratory of Animal Nutrition, Center for Nuclear Energy in Agriculture, University of São Paulo, 303 Centenario Avenue, Piracicaba, SP 13416-000, Brazil
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Wang Y, Wang Y, Zhou K, Zhang H, Cheng M, Wang B, Yan X. Isolation of a facultative methanotroph Methylocystis iwaonis SD4 from rice rhizosphere and establishment of rapid genetic tools for it. Biotechnol Lett 2024:10.1007/s10529-024-03495-y. [PMID: 38733438 DOI: 10.1007/s10529-024-03495-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: 03/17/2024] [Revised: 04/10/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice plants in Nanjing, China. This strain grew well on methane or methanol but was able to grow slowly using acetate or ethanol. Moreover, strain SD4 showed sustained growth at low concentrations of methane (100 and 500 ppmv). M. iwaonis SD4 could utilize diverse nitrogen sources, including nitrate, urea, ammonium as well as dinitrogen. Strain SD4 possessed genes encoding both the particulate methane monooxygenase and the soluble methane monooxygenase. Simple and rapid genetic manipulation methods were established for this strain, enabling vector transformation and unmarked genetic manipulation. Fast growth rate and efficient genetic tools make M. iwaonis SD4 an ideal model to study facultative methanotrophs, and the ability to grow on low concentration of methane implies its potential in methane removal.
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Affiliation(s)
- Yinghui Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Yuying Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Keyu Zhou
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Haili Zhang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Minggen Cheng
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Baozhan Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China
| | - Xin Yan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, People's Republic of China.
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Zheng Y, Wang H, Liu Y, Liu P, Zhu B, Zheng Y, Li J, Chistoserdova L, Ren ZJ, Zhao F. Electrochemically coupled CH 4 and CO 2 consumption driven by microbial processes. Nat Commun 2024; 15:3097. [PMID: 38600111 PMCID: PMC11006836 DOI: 10.1038/s41467-024-47445-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024] Open
Abstract
The chemical transformations of methane (CH4) and carbon dioxide (CO2) greenhouse gases typically have high energy barriers. Here we present an approach of strategic coupling of CH4 oxidation and CO2 reduction in a switched microbial process governed by redox cycling of iron minerals under temperate conditions. The presence of iron minerals leads to an obvious enhancement of carbon fixation, with the minerals acting as the electron acceptor for CH4 oxidation and the electron donor for CO2 reduction, facilitated by changes in the mineral structure. The electron flow between the two functionally active microbial consortia is tracked through electrochemistry, and the energy metabolism in these consortia is predicted at the genetic level. This study offers a promising strategy for the removal of CH4 and CO2 in the natural environment and proposes an engineering technique for the utilization of major greenhouse gases.
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Affiliation(s)
- Yue Zheng
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- State Key Laboratory of Marine Environmental Science, and College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Huan Wang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
- State Key Laboratory of Marine Environmental Science, and College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Yan Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Peiyu Liu
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Baoli Zhu
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and Taoyuan Agro-ecosystem Research Station, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Yanning Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinhua Li
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | | | - Zhiyong Jason Ren
- Department of Civil and Environmental Engineering, and Andlinger Center for Energy and the Environment, Princeton University, 41 Olden St., Princeton, NJ, 08540, USA.
| | - Feng Zhao
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
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Furtak A, Szafranek-Nakonieczna A, Furtak K, Pytlak A. A review of organophosphonates, their natural and anthropogenic sources, environmental fate and impact on microbial greenhouse gases emissions - Identifying knowledge gaps. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 355:120453. [PMID: 38430886 DOI: 10.1016/j.jenvman.2024.120453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Organophosphonates (OPs) are a unique group of natural and synthetic compounds, characterised by the presence of a stable, hard-to-cleave bond between the carbon and phosphorus atoms. OPs exhibit high resistance to abiotic degradation, excellent chelating properties and high biological activity. Despite the huge and increasing scale of OP production and use worldwide, little is known about their transportation and fate in the environment. Available data are dominated by information concerning the most recognised organophosphonate - the herbicide glyphosate - while other OPs have received little attention. In this paper, a comprehensive review of the current state of knowledge about natural and artificial OPs is presented (including glyphosate). Based on the available literature, a number of knowledge gaps have been identified that need to be filled in order to understand the environmental effects of these abundant compounds. Special attention has been given to GHG-related processes, with a particular focus on CH4. This stems from the recent discovery of OP-dependent CH4 production in aqueous environments under aerobic conditions. The process has changed the perception of the biogeochemical cycle of CH4, since it was previously thought that biological methane formation was only possible under anaerobic conditions. However, there is a lack of knowledge on whether OP-associated methane is also formed in soils. Moreover, it remains unclear whether anthropogenic OPs affect the CH4 cycle, a concern of significant importance in the context of the increasing rate of global warming. The literature examined in this review also calls for additional research into the date of OPs in waste and sewage and in their impact on environmental microbiomes.
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Affiliation(s)
- Adam Furtak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland
| | - Anna Szafranek-Nakonieczna
- Department of Biology and Biotechnology of Microorganisms, Institute of Medical Sciences, The John Paul II Catholic University of Lublin, Konstantynów 1 I, 20-708, Lublin, Poland
| | - Karolina Furtak
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation - State Research Institute, Krańcowa 8, INCBR Centre, 24-100, Puławy, Poland
| | - Anna Pytlak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
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Lim J, Wehmeyer H, Heffner T, Aeppli M, Gu W, Kim PJ, Horn MA, Ho A. Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture. FEMS Microbiol Ecol 2024; 100:fiae008. [PMID: 38327184 PMCID: PMC10872700 DOI: 10.1093/femsec/fiae008] [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: 09/05/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024] Open
Abstract
Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.
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Affiliation(s)
- Jiyeon Lim
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Helena Wehmeyer
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
| | - Tanja Heffner
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Meret Aeppli
- Environmental Engineering Institute IIE-ENAC, Laboratory SOIL, Ecole Polytechnique Fédérale de Lausanne (EPFL), Valais Wallis, CH 1950 Sion, Switzerland
| | - Wenyu Gu
- Environmental Engineering Institute IIE-ENAC, Laboratory MICROBE, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH 1015 Lausanne, Switzerland
| | - Pil Joo Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany
| | - Adrian Ho
- Nestlè Research, Route du Jorat 57, CH 1000 Lausanne 26, Switzerland
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Ma JY, Yan Z, Sun XD, Jiang YQ, Duan JL, Feng LJ, Zhu FP, Liu XY, Xia PF, Yuan XZ. A hybrid photocatalytic system enables direct glucose utilization for methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2317058121. [PMID: 38232281 PMCID: PMC10823229 DOI: 10.1073/pnas.2317058121] [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: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
Integration of methanogenic archaea with photocatalysts presents a sustainable solution for solar-driven methanogenesis. However, maximizing CH4 conversion efficiency remains challenging due to the intrinsic energy conservation and strictly restricted substrates of methanogenic archaea. Here, we report a solar-driven biotic-abiotic hybrid (biohybrid) system by incorporating cadmium sulfide (CdS) nanoparticles with a rationally designed methanogenic archaeon Methanosarcina acetivorans C2A, in which the glucose synergist protein and glucose kinase, an energy-efficient route for glucose transport and phosphorylation from Zymomonas mobilis, were implemented to facilitate nonnative substrate glucose for methanogenesis. We demonstrate that the photo-excited electrons facilitate membrane-bound electron transport chain, thereby augmenting the Na+ and H+ ion gradients across membrane to enhance adenosine triphosphate (ATP) synthesis. Additionally, this biohybrid system promotes the metabolism of pyruvate to acetyl coenzyme A (AcCoA) and inhibits the flow of AcCoA to the tricarboxylic acid (TCA) cycle, resulting in a 1.26-fold augmentation in CH4 production from glucose-derived carbon. Our results provide a unique strategy for enhancing methanogenesis through rational biohybrid design and reprogramming, which gives a promising avenue for sustainably manufacturing value-added chemicals.
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Affiliation(s)
- Jing-Ya Ma
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Zhen Yan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xiao-Dong Sun
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Yu-Qian Jiang
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Jian-Lu Duan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Li-Juan Feng
- College of Geography and Environment, Shandong Normal University, Jinan250014, People’s Republic of China
| | - Fan-Ping Zhu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xiao-Yu Liu
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Peng-Fei Xia
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
| | - Xian-Zheng Yuan
- Shandong Key Laboratory of Environmental Processes and Health, School of Environmental Science and Engineering, Shandong University, Qingdao266237, People’s Republic of China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao266237, People’s Republic of China
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Ricci F, Greening C. Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry. Trends Microbiol 2024:S0966-842X(23)00332-3. [PMID: 38296716 DOI: 10.1016/j.tim.2023.11.013] [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: 07/26/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 02/02/2024]
Abstract
Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.
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Affiliation(s)
- Francesco Ricci
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia.
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Melbourne, Victoria, Australia.
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12
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Huang L, Tang R, Huang S, Tang J, Lin H, Yuan Y, Zhou S. Fate of carbon influenced by the in-situ growth of phototrophic biofilms at the soil-water interface of paddy soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168451. [PMID: 37956834 DOI: 10.1016/j.scitotenv.2023.168451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023]
Abstract
Phototrophic biofilms (PBs) are commonly found in the sediment/soil-water interface of paddy soils and have a significant impact on carbon cycles. However, the specific carbon fate influenced by the in-situ growth of PBs in paddy soil remains unclear. In this study, we investigated the effect of in situ PBs growth on methane and carbon dioxide emissions, as well as dissolved organic matter (DOM) transformation. Our findings demonstrated a negative correlation between PBs growth and methane and carbon dioxide emissions, while showing a positive correlation with DOM composition. The in-situ growth of PBs reduced methane emissions by approximately 79 % and carbon dioxide emissions by approximately 33 % in the daytime, and also slowed down the degradation rate of dissolved organic matter from over 30.4 % to <16 %. Microsensor measurements revealed that these changes were attributed to the increased concentration and penetration depth of oxygen, as well as variations in pH caused by the growth of in situ PBs. Co-occurrence analysis indicated a robust correlation between DOM transformation and the significantly suppressed methanogenesis by methanogens such as Methanosaeta, Methanomassiliicoccus and Methanosarcina, and also the notably enhanced methane oxidation by methanotrophs including Methylobacterium, Methyloversatilis and Methylomonas, in response to the growth of PBs. These findings shed light on the impact of in situ PBs on methane and carbon dioxide emissions and DOM transformation, providing new insights for understanding carbon cycling in paddy soils.
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Affiliation(s)
- Lingyan Huang
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, China; Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rong Tang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China
| | - Shaofu Huang
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiahuan Tang
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hao Lin
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecology and Resources Engineering, Wuyi University, Wuyishan, China; Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, China.
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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13
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Beals DG, Puri AW. Linking methanotroph phenotypes to genotypes using a simple spatially resolved model ecosystem. THE ISME JOURNAL 2024; 18:wrae060. [PMID: 38622932 PMCID: PMC11072679 DOI: 10.1093/ismejo/wrae060] [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: 11/14/2023] [Revised: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
Connecting genes to phenotypic traits in bacteria is often challenging because of a lack of environmental context in laboratory settings. Laboratory-based model ecosystems offer a means to better account for environmental conditions compared with standard planktonic cultures and can help link genotypes and phenotypes. Here, we present a simple, cost-effective, laboratory-based model ecosystem to study aerobic methane-oxidizing bacteria (methanotrophs) within the methane-oxygen counter gradient typically found in the natural environment of these organisms. Culturing the methanotroph Methylomonas sp. strain LW13 in this system resulted in the formation of a distinct horizontal band at the intersection of the counter gradient, which we discovered was not due to increased numbers of bacteria at this location but instead to an increased amount of polysaccharides. We also discovered that different methanotrophic taxa form polysaccharide bands with distinct locations and morphologies when grown in the methane-oxygen counter gradient. By comparing transcriptomic data from LW13 growing within and surrounding this band, we identified genes upregulated within the band and validated their involvement in growth and band formation within the model ecosystem using knockout strains. Notably, deletion of these genes did not negatively affect growth using standard planktonic culturing methods. This work highlights the use of a laboratory-based model ecosystem that more closely mimics the natural environment to uncover bacterial phenotypes missing from standard laboratory conditions, and to link these phenotypes with their genetic determinants.
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Affiliation(s)
- Delaney G Beals
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
| | - Aaron W Puri
- Department of Chemistry and the Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, United States
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14
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Verrone V, Gupta A, Laloo AE, Dubey RK, Hamid NAA, Swarup S. Organic matter stability and lability in terrestrial and aquatic ecosystems: A chemical and microbial perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167757. [PMID: 37852479 DOI: 10.1016/j.scitotenv.2023.167757] [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: 07/18/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
Terrestrial and aquatic ecosystems have specific carbon fingerprints and sequestration potential, due to the intrinsic properties of the organic matter (OM), mineral content, environmental conditions, and microbial community composition and functions. A small variation in the OM pool can imbalance the carbon dynamics that ultimately affect the climate and functionality of each ecosystem, at regional and global scales. Here, we review the factors that continuously contribute to carbon stability and lability, with particular attention to the OM formation and nature, as well as the microbial activities that drive OM aggregation, degradation and eventually greenhouse gas emissions. We identified that in both aquatic and terrestrial ecosystems, microbial attributes (i.e., carbon metabolism, carbon use efficiency, necromass, enzymatic activities) play a pivotal role in transforming the carbon stock and yet they are far from being completely characterised and not often included in carbon estimations. Therefore, future research must focus on the integration of microbial components into carbon mapping and models, as well as on translating molecular-scaled studies into practical approaches. These strategies will improve carbon management and restoration across ecosystems and contribute to overcome current climate challenges.
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Affiliation(s)
- Valeria Verrone
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Abhishek Gupta
- Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore.
| | - Andrew Elohim Laloo
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore
| | - Rama Kant Dubey
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore; Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281406, India
| | - Nur Ashikin Abdul Hamid
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore
| | - Sanjay Swarup
- National University of Singapore Environmental Research Institute, National University of Singapore,117411, Singapore; Singapore Centre of Environmental Engineering and Life Sciences, National University of Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
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15
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Kubaczyński A, Walkiewicz A, Pytlak A, Grządziel J, Gałązka A, Brzezińska M. Application of nitrogen-rich sunflower husks biochar promotes methane oxidation and increases abundance of Methylobacter in nitrogen-poor soil. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 348:119324. [PMID: 37857224 DOI: 10.1016/j.jenvman.2023.119324] [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: 07/05/2023] [Revised: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
The area of sunflower crops is steadily increasing. A beneficial way of managing sunflower waste biomass could be its use as a feedstock for biochar production. Biochar is currently being considered as an additive for improving soil parameters, including the ability to oxidise methane (CH4) - one of the key greenhouse gases (GHG). Despite the high production of sunflower husk, there is still insufficient information on the impact of sunflower husk biochar on the soil environment, especially on the methanotrophy process. To fill this knowledge gap, an experiment was designed to evaluate the effects of addition of sunflower husk biochar (produced at 450-550 °C) at a wide range of doses (1-100 Mg ha-1) to Haplic Luvisol. In the presented study, the CH4 oxidation potential of soil with and without sunflower husk biochar was investigated at 60 and 100% water holding capacity (WHC), and with the addition of 1% CH4 (v/v). The comprehensive study included GHG exchange (CH4 and CO2), physicochemical properties of soil (pH, soil organic carbon (SOC), dissolved organic carbon (DOC), nitrate nitrogen (NO3--N), WHC), and the structure of soil microbial communities. That study showed that even low biochar doses (5 and 10 Mg ha-1) were sufficient to enhance pH, SOC, DOC and NO3--N content. Importantly, sunflower husk biochar was significant source of NO3--N, which soil concentration increased from 9.40 ± 0.09 mg NO3--N kg-1 for the control to even 19.40 ± 0.26 mg NO3--N kg-1 (for 100 Mg ha-1). Significant improvement of WHC (by 11.0-12.4%) was observed after biochar addition at doses of 60 Mg ha-1 and higher. At 60% WHC, application of biochar at a dose of 40 Mg ha-1 brought significant improvements in CH4 oxidation rate, which was 4.89 ± 0.37 mg CH4-C kg-1 d-1. Higher biochar doses were correlated with further improvement of CH4 oxidation rates, which at 100 Mg ha-1 was seventeen-fold higher (8.36 ± 0.84 mg CH4-C kg-1 d-1) than in the biochar-free control (0.48 ± 0.28 mg CH4-C kg-1 d-1). CO2 emissions were not proportional to biochar doses and only grew circa (ca.) twofold from 3.16 to 6.90 mg CO2-C kg-1 d-1 at 100 Mg ha-1. Above 60 Mg ha-1, the diversity of methanotrophic communities increased, with Methylobacter becoming the most abundant genus, which was as high as 7.45%. This is the first, such advanced and multifaceted study of the wide range of sunflower husk biochar doses on Haplic Luvisol. The positive correlation between soil conditions, methanotroph abundance and CH4 oxidation confirmed the multifaceted, positive effect of sunflower husk biochar on Haplic Luvisol. Sunflower husk biochar can be successfully used for Haplic Luvisol supplementation. This additive facilitates soil protection against degradation and has the potential to mitigate GHG emissions.
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Affiliation(s)
- Adam Kubaczyński
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
| | - Anna Walkiewicz
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
| | - Anna Pytlak
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
| | - Jarosław Grządziel
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation-State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100, Puławy, Poland.
| | - Anna Gałązka
- Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation-State Research Institute (IUNG-PIB), Czartoryskich 8, 24-100, Puławy, Poland.
| | - Małgorzata Brzezińska
- Department of Natural Environment Biogeochemistry, Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290, Lublin, Poland.
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16
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Fenibo EO, Selvarajan R, Wang H, Wang Y, Abia ALK. Untapped talents: insight into the ecological significance of methanotrophs and its prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166145. [PMID: 37579801 DOI: 10.1016/j.scitotenv.2023.166145] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/06/2023] [Accepted: 08/06/2023] [Indexed: 08/16/2023]
Abstract
The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.
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Affiliation(s)
- Emmanuel Oliver Fenibo
- World Bank Africa Centre of Excellence, Centre for Oilfield Chemical Research, University of Port Harcourt, Port Harcourt 500272, Nigeria
| | - Ramganesh Selvarajan
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China; Department of Environmental Science, University of South Africa, Florida Campus, 1710, South Africa
| | - Huiqi Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Yue Wang
- Laboratory of Extraterrestrial Ocean Systems (LEOS), Institute of Deep-Sea Science and Engineering (IDSSE), Chinese Academy of Sciences (CAS), Sanya, China
| | - Akebe Luther King Abia
- Environmental Research Foundation, Westville 3630, South Africa; Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
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17
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Rumora A, Hopkins L, Yim K, Baykus MF, Martinez L, Jimenez L. Detection and Characterization of Electrogenic Bacteria from Soils. BIOTECH 2023; 12:65. [PMID: 38131677 PMCID: PMC10871078 DOI: 10.3390/biotech12040065] [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: 10/23/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
Soil microbial fuel cells (SMFCs) are bioelectrical devices powered by the oxidation of organic and inorganic compounds due to microbial activity. Seven soils were randomly selected from Bergen Community College or areas nearby, located in the state of New Jersey, USA, were used to screen for the presence of electrogenic bacteria. SMFCs were incubated at 35-37 °C. Electricity generation and electrogenic bacteria were determined using an application developed for cellular phones. Of the seven samples, five generated electricity and enriched electrogenic bacteria. Average electrical output for the seven SMFCs was 155 microwatts with the start-up time ranging from 1 to 11 days. The highest output and electrogenic bacterial numbers were found with SMFC-B1 with 143 microwatts and 2.99 × 109 electrogenic bacteria after 15 days. Optimal electrical output and electrogenic bacterial numbers ranged from 1 to 21 days. Microbial DNA was extracted from the top and bottom of the anode of SMFC-B1 using the ZR Soil Microbe DNA MiniPrep Protocol followed by PCR amplification of 16S rRNA V3-V4 region. Next-generation sequencing of 16S rRNA genes generated an average of 58 k sequences. BLAST analysis of the anode bacterial community in SMFC-B1 demonstrated that the predominant bacterial phylum was Bacillota of the class Clostridia (50%). However, bacteria belonging to the phylum Pseudomonadota (15%) such as Magnetospirillum sp. and Methylocaldum gracile were also part of the predominant electrogenic bacterial community in the anode. Unidentified uncultured bacteria accounted for 35% of the predominant bacterial community. Bioelectrical devices such as MFCs provide sustainable and clean alternatives to future applications for electricity generation, waste treatment, and biosensors.
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Affiliation(s)
| | | | | | | | | | - Luis Jimenez
- Biology and Horticulture Department, Bergen Community College, 400 Paramus Road, Paramus, NJ 07652, USA; (A.R.); (K.Y.); (L.M.)
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18
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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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19
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Pérez G, Krause SMB, Bodelier PLE, Meima-Franke M, Pitombo L, Irisarri P. Interactions between Cyanobacteria and Methane Processing Microbes Mitigate Methane Emissions from Rice Soils. Microorganisms 2023; 11:2830. [PMID: 38137974 PMCID: PMC10745823 DOI: 10.3390/microorganisms11122830] [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: 10/16/2023] [Revised: 11/16/2023] [Accepted: 11/18/2023] [Indexed: 12/24/2023] Open
Abstract
Cyanobacteria play a relevant role in rice soils due to their contribution to soil fertility through nitrogen (N2) fixation and as a promising strategy to mitigate methane (CH4) emissions from these systems. However, information is still limited regarding the mechanisms of cyanobacterial modulation of CH4 cycling in rice soils. Here, we focused on the response of methane cycling microbial communities to inoculation with cyanobacteria in rice soils. We performed a microcosm study comprising rice soil inoculated with either of two cyanobacterial isolates (Calothrix sp. and Nostoc sp.) obtained from a rice paddy. Our results demonstrate that cyanobacterial inoculation reduced CH4 emissions by 20 times. Yet, the effect on CH4 cycling microbes differed for the cyanobacterial strains. Type Ia methanotrophs were stimulated by Calothrix sp. in the surface layer, while Nostoc sp. had the opposite effect. The overall pmoA transcripts of Type Ib methanotrophs were stimulated by Nostoc. Methanogens were not affected in the surface layer, while their abundance was reduced in the sub surface layer by the presence of Nostoc sp. Our results indicate that mitigation of methane emission from rice soils based on cyanobacterial inoculants depends on the proper pairing of cyanobacteria-methanotrophs and their respective traits.
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Affiliation(s)
- Germán Pérez
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
| | - Sascha M. B. Krause
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
- School of Ecology and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Paul L. E. Bodelier
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Marion Meima-Franke
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands or (G.P.); (S.M.B.K.); (M.M.-F.)
| | - Leonardo Pitombo
- Department of Environmental Sciences, Federal University of São Carlos (UFSCar), São Paulo 18052-780, Brazil;
| | - Pilar Irisarri
- Laboratory of Microbiology, Department of Plant Biology, Agronomy Faculty, University of the Republic, Montevideo 12900, Uruguay;
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20
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Aryee G, Luecke SM, Dahlen CR, Swanson KC, Amat S. Holistic View and Novel Perspective on Ruminal and Extra-Gastrointestinal Methanogens in Cattle. Microorganisms 2023; 11:2746. [PMID: 38004757 PMCID: PMC10673468 DOI: 10.3390/microorganisms11112746] [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: 10/23/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the extensive research conducted on ruminal methanogens and anti-methanogenic intervention strategies over the last 50 years, most of the currently researched enteric methane (CH4) abatement approaches have shown limited efficacy. This is largely because of the complex nature of animal production and the ruminal environment, host genetic variability of CH4 production, and an incomplete understanding of the role of the ruminal microbiome in enteric CH4 emissions. Recent sequencing-based studies suggest the presence of methanogenic archaea in extra-gastrointestinal tract tissues, including respiratory and reproductive tracts of cattle. While these sequencing data require further verification via culture-dependent methods, the consistent identification of methanogens with relatively greater frequency in the airway and urogenital tract of cattle, as well as increasing appreciation of the microbiome-gut-organ axis together highlight the potential interactions between ruminal and extra-gastrointestinal methanogenic communities. Thus, a traditional singular focus on ruminal methanogens may not be sufficient, and a holistic approach which takes into consideration of the transfer of methanogens between ruminal, extra-gastrointestinal, and environmental microbial communities is of necessity to develop more efficient and long-term ruminal CH4 mitigation strategies. In the present review, we provide a holistic survey of the methanogenic archaea present in different anatomical sites of cattle and discuss potential seeding sources of the ruminal methanogens.
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Affiliation(s)
- Godson Aryee
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Sarah M. Luecke
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
| | - Carl R. Dahlen
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Kendall C. Swanson
- Department of Animal Sciences, and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58102, USA; (C.R.D.); (K.C.S.)
| | - Samat Amat
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND 58108, USA; (G.A.); (S.M.L.)
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21
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Bachleitner S, Ata Ö, Mattanovich D. The potential of CO 2-based production cycles in biotechnology to fight the climate crisis. Nat Commun 2023; 14:6978. [PMID: 37914683 PMCID: PMC10620168 DOI: 10.1038/s41467-023-42790-6] [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: 08/01/2023] [Accepted: 10/21/2023] [Indexed: 11/03/2023] Open
Abstract
Rising CO2 emissions have pushed scientists to develop new technologies for a more sustainable bio-based economy. Microbial conversion of CO2 and CO2-derived carbon substrates into valuable compounds can contribute to carbon neutrality and sustainability. Here, we discuss the potential of C1 carbon sources as raw materials to produce energy, materials, and food and feed using microbial cell factories. We provide an overview of potential microbes, natural and synthetic C1 utilization pathways, and compare their metabolic driving forces. Finally, we sketch a future in which C1 substrates replace traditional feedstocks and we evaluate the costs associated with such an endeavor.
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Affiliation(s)
- Simone Bachleitner
- University of Natural Resources and Life Sciences, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Vienna, 1190, Austria
| | - Özge Ata
- University of Natural Resources and Life Sciences, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Vienna, 1190, Austria
- Austrian Centre of Industrial Biotechnology, Vienna, 1190, Austria
| | - Diethard Mattanovich
- University of Natural Resources and Life Sciences, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Vienna, 1190, Austria.
- Austrian Centre of Industrial Biotechnology, Vienna, 1190, Austria.
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22
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Bedekar AA, Deewan A, Jagtap SS, Parker DA, Liu P, Mackie RI, Rao CV. Transcriptional and metabolomic responses of Methylococcus capsulatus Bath to nitrogen source and temperature downshift. Front Microbiol 2023; 14:1259015. [PMID: 37928661 PMCID: PMC10623323 DOI: 10.3389/fmicb.2023.1259015] [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: 07/14/2023] [Accepted: 10/10/2023] [Indexed: 11/07/2023] Open
Abstract
Methanotrophs play a significant role in methane oxidation, because they are the only biological methane sink present in nature. The methane monooxygenase enzyme oxidizes methane or ammonia into methanol or hydroxylamine, respectively. While much is known about central carbon metabolism in methanotrophs, far less is known about nitrogen metabolism. In this study, we investigated how Methylococcus capsulatus Bath, a methane-oxidizing bacterium, responds to nitrogen source and temperature. Batch culture experiments were conducted using nitrate or ammonium as nitrogen sources at both 37°C and 42°C. While growth rates with nitrate and ammonium were comparable at 42°C, a significant growth advantage was observed with ammonium at 37°C. Utilization of nitrate was higher at 42°C than at 37°C, especially in the first 24 h. Use of ammonium remained constant between 42°C and 37°C; however, nitrite buildup and conversion to ammonia were found to be temperature-dependent processes. We performed RNA-seq to understand the underlying molecular mechanisms, and the results revealed complex transcriptional changes in response to varying conditions. Different gene expression patterns connected to respiration, nitrate and ammonia metabolism, methane oxidation, and amino acid biosynthesis were identified using gene ontology analysis. Notably, key pathways with variable expression profiles included oxidative phosphorylation and methane and methanol oxidation. Additionally, there were transcription levels that varied for genes related to nitrogen metabolism, particularly for ammonia oxidation, nitrate reduction, and transporters. Quantitative PCR was used to validate these transcriptional changes. Analyses of intracellular metabolites revealed changes in fatty acids, amino acids, central carbon intermediates, and nitrogen bases in response to various nitrogen sources and temperatures. Overall, our results offer improved understanding of the intricate interactions between nitrogen availability, temperature, and gene expression in M. capsulatus Bath. This study enhances our understanding of microbial adaptation strategies, offering potential applications in biotechnological and environmental contexts.
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Affiliation(s)
- Ashwini Ashok Bedekar
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Anshu Deewan
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Sujit S. Jagtap
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - David A. Parker
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Ping Liu
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Shell Exploration and Production Inc., Westhollow Technology Center, Houston, TX, United States
| | - Roderick I. Mackie
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Christopher V. Rao
- Energy and Biosciences Institute, Materials Research Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Champaign, IL, United States
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23
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Wei L, Wang J, Liu X, Lai Q, Li G, Fu X, Li G, Shao Z, Dong C. Galbibacter pacificus sp. nov., isolated from surface seawater of the western Pacific Ocean and transfer of Joostella marina to the genus Galbibacter as Galbibacter orientalis nom. nov. and emended description of the genus Galbibacter. Int J Syst Evol Microbiol 2023; 73. [PMID: 37801073 DOI: 10.1099/ijsem.0.006078] [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: 10/07/2023] Open
Abstract
Two Gram-stain-negative, non-motile, non-spore-forming, strictly aerobic and rod-shaped bacterial strains, CMA-7T and CAA-3, were isolated from surface seawater samples collected from the western Pacific Ocean. Phylogeny of 16S rRNA gene sequences indicated they were related to the genera Galbibacter and Joostella and shared 95.1, 90.9 and 90.8% sequence similarity with G. mesophilus Mok-17T, J. marina DSM 19592T and G. marinus ck-I2-15T, respectively. Phylogenomic analysis showed that the two strains, together with the members of the genera Galbibacter and Joostella, formed a monophyletic clade that could also be considered a monophyletic taxon. This distinctiveness was supported by amino acid identity and percentage of conserved proteins indices, phenotypic and chemotaxonomic characteristics and comparative genomics analysis. Digital DNA‒DNA hybridization values and average nucleotide identities between the two strains and their closest relatives were 18.0-20.8 % and 77.7-79.3 %, respectively. The principal fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, Summed Feature 3 (C16 : 1 ω7c/C16 : 1 ω6c or C16 : 1 ω6c/C16 : 1 ω7c), Summed Feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl), and C15 : 0 3-OH. The predominant respiratory quinone was MK-6. The polar lipids were phosphatidylethanolamine, aminolipid, aminophospholipid, phospholipid, phosphoglycolipid, glycolipid and unknown polar lipid. The genomic DNA G+C content of strains CMA-7T and CAA-3 was both 38.4 mol%. Genomic analysis indicated they have the potential to degrade cellulose and chitin. Based on the polyphasic evidence presented in this study, the two strains represent a novel species within the genus Galbibacter, for which the name Galbibacter pacificus sp. nov. is proposed. The type strain is CMA-7T (=MCCC M28999T = KCTC 92588T). Moreover, the transfer of Joostella marina to the genus Galbibacter as Galbibacter orientalis nom. nov. (type strain En5T = KCTC 12518T = DSM 19592T=CGMCC 1.6973T) is also proposed.
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Affiliation(s)
- Lin Wei
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Xiupian Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guizhen Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Guangyu Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
| | - Chunming Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of China; State Key Laboratory Breeding Base of Marine Genetic Resources; Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen 361005, PR China
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24
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Shinjo R, Oe F, Nakagawa K, Murase J, Asakawa S, Watanabe T. Type-specific quantification of particulate methane monooxygenase gene of methane-oxidizing bacteria at the oxic-anoxic interface of a surface paddy soil by digital PCR. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:392-403. [PMID: 37078408 PMCID: PMC10472520 DOI: 10.1111/1758-2229.13155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Aerobic methane-oxidizing bacteria (MOB) play an important role in mitigating methane emissions from paddy fields. In this study, we developed a differential quantification method for the copy number of pmoA genes of type Ia, Ib, and IIa MOB in paddy field soil using chip-based digital PCR. Three probes specific to the pmoA of type Ia, Ib, and IIa MOB worked well in digital PCR quantification when genomic DNA of MOB isolates and PCR-amplified DNA fragments of pmoA were examined as templates. When pmoA genes in the surface soil layer of a flooded paddy were quantified by digital PCR, the copy numbers of type Ia, Ib, and IIa MOB were 105 -106 , 105 -106 , and 107 copies g-1 dry soil, respectively, with the highest values in the top 0-2-mm soil layer. Especially, the copy numbers of type Ia and Ib MOB increased by 240% and 380% at the top layer after soil flooding, suggesting that the soil circumstances at the oxic-anoxic interfaces were more preferential for growth of type I MOB than type II MOB. Thus, type I MOB likely play an important role in the methane consumption at the surface paddy soil.
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Affiliation(s)
- Rina Shinjo
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Fumika Oe
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Koki Nakagawa
- School of Agricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Jun Murase
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
| | - Takeshi Watanabe
- Graduate School of Bioagricultural SciencesNagoya University, ChikusaNagoya464‐8601Japan
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25
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Poma N, Bonini A, Vivaldi F, Biagini D, Di Luca M, Bottai D, Di Francesco F, Tavanti A. Biosensing systems for the detection and quantification of methane gas. Appl Microbiol Biotechnol 2023; 107:5627-5634. [PMID: 37486352 PMCID: PMC10439851 DOI: 10.1007/s00253-023-12629-7] [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: 03/02/2023] [Revised: 06/03/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023]
Abstract
Climate change due to the continuous increase in the release of green-house gasses associated with anthropogenic activity has made a significant impact on the sustainability of life on our planet. Methane (CH4) is a green-house gas whose concentrations in the atmosphere are on the rise. CH4 measurement is important for both the environment and the safety at the industrial and household level. Methanotrophs are distinguished for their unique characteristic of using CH4 as the sole source of carbon and energy, due to the presence of the methane monooxygenases that oxidize CH4 under ambient temperature conditions. This has attracted interest in the use of methanotrophs in biotechnological applications as well as in the development of biosensing systems for CH4 quantification and monitoring. Biosensing systems using methanotrophs rely on the use of whole microbial cells that oxidize CH4 in presence of O2, so that the CH4 concentration is determined in an indirect manner by measuring the decrease of O2 level in the system. Although several biological properties of methanotrophic microorganisms still need to be characterized, different studies have demonstrated the feasibility of the use of methanotrophs in CH4 measurement. This review summarizes the contributions in methane biosensing systems and presents a prospective of the valid use of methanotrophs in this field. KEY POINTS: • Methanotroph environmental relevance in methane oxidation • Methanotroph biotechnological application in the field of biosensing • Methane monooxygenase as a feasible biorecognition element in biosensors.
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Affiliation(s)
- Noemi Poma
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56127, Pisa, Italy
| | - Andrea Bonini
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56127, Pisa, Italy
- Groningen Biomolecular Sciences and Biotechnology, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Federico Vivaldi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
- Metitech S.R.L., Via Livornese 835, 56122, Pisa, Italy
| | - Denise Biagini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
| | - Mariagrazia Di Luca
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56127, Pisa, Italy
| | - Daria Bottai
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56127, Pisa, Italy
| | - Fabio Di Francesco
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, 56124, Pisa, Italy
- Metitech S.R.L., Via Livornese 835, 56122, Pisa, Italy
| | - Arianna Tavanti
- Department of Biology, University of Pisa, Via San Zeno 35-39, 56127, Pisa, Italy.
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26
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Chai F, Li L, Wang W, Xue S, Liu J. Electro-stimulated anaerobic oxidation of methane with synergistic denitrification by adding AQS: Electron transfer mode and mechanism. ENVIRONMENTAL RESEARCH 2023; 229:115997. [PMID: 37105293 DOI: 10.1016/j.envres.2023.115997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Denitrifying anaerobic methane-oxidizing (DAMO) processes, which link anaerobic methane oxidation (AMO) and denitrification, have a promising prospect in anaerobic wastewater treatment. In bioelectrochemical systems (BES), DAMO consortium presented potent metabolic activity. However, the extracellular electron transfer (EET) in BES was poorly understood. This study investigated the EET mechanisms and modes of electron transport in BES dominated by anaerobic methanotrophic bacteria. In the bioreactors with the auxiliary voltage of 0.5 and 1.1 V, named EMN-0.5 and EMN-1.1, respectively, biological voltages of 0.198 and 0.329 V were generated with power densities of 0.6 and 1.20 mW/m2, after removing the voltage. High throughput and metagenome analyses demonstrated that main methanotrophs were DAMO bacteria and Methylocystis sp. The electroactive bacteria detected were Pseudomonas sp., Hypomicrobium sp., Thiobacillus sp, and Rhodococcus sp. The pil, cytochrome c, hdr, and he/fp genes related to EET were present on the electrode surfaces. Carbon 13 isotope tracing and chemicals analysis by GC-MS exhibited that methanol was an intermediate product released to extracellular environment and acted as the electronic carrier to drive the EET in methane oxidation. Extracellular electron transfer was achieved through the collaboration of DAMO bacteria, Methylocystis sp., and Pseudomonas sp. Anthraquinone 2-sulfonic acid ester (AQS) could improve the rate of electron transfer to the extracellular space, especially in the EMN-0.5 reaction system. This study provides a new understanding of AMO consortium metabolism in BES and may provide a scientific basis for developing methane control technology.
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Affiliation(s)
- Fengguang Chai
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China
| | - Lin Li
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; National Engineering Laboratory for VOCs Pollution Control Material & Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Wenwen Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqing Road, Haidian District, Beijing, 100085, China; University of Chinese Academy of Sciences, 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, China
| | - Song Xue
- Environmental Simulation and Pollution Control State Key Joint Laboratory, State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Junxin Liu
- University of Chinese Academy of Sciences, 19(A) Yuquan Road, Shijingshan District, Beijing, 100049, 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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28
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Heffner T, Brami SA, Mendes LW, Kaupper T, Hannula ES, Poehlein A, Horn MA, Ho A. Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction. ISME COMMUNICATIONS 2023; 3:62. [PMID: 37355679 PMCID: PMC10290665 DOI: 10.1038/s43705-023-00271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/26/2023]
Abstract
Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.
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Affiliation(s)
- Tanja Heffner
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Semi A Brami
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- University of São Paulo CENA-USP, Center for Nuclear Energy in Agriculture, Avenida Centenario, 303, 13416-000, Piracicaba (SP), Brazil
| | - Thomas Kaupper
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Emilia S Hannula
- Leiden University, Department of Environmental Biology, Institute of Environmental Sciences, Einsteinweg 2, 2333CC, Leiden, the Netherlands
| | - Anja Poehlein
- Georg-August University Göttingen, Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstr. 8, D-37077, Göttingen, Germany
| | - Marcus A Horn
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Leibniz Universität Hannover, Institute for Microbiology, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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Vega MAP, Scholes RC, Brady AR, Daly RA, Narrowe AB, Vanzin GF, Wrighton KC, Sedlak DL, Sharp JO. Methane-Oxidizing Activity Enhances Sulfamethoxazole Biotransformation in a Benthic Constructed Wetland Biomat. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7240-7253. [PMID: 37099683 DOI: 10.1021/acs.est.2c09314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Ammonia monooxygenase and analogous oxygenase enzymes contribute to pharmaceutical biotransformation in activated sludge. In this study, we hypothesized that methane monooxygenase can enhance pharmaceutical biotransformation within the benthic, diffuse periphytic sediments (i.e., "biomat") of a shallow, open-water constructed wetland. To test this hypothesis, we combined field-scale metatranscriptomics, porewater geochemistry, and methane gas fluxes to inform microcosms targeting methane monooxygenase activity and its potential role in pharmaceutical biotransformation. In the field, sulfamethoxazole concentrations decreased within surficial biomat layers where genes encoding for the particulate methane monooxygenase (pMMO) were transcribed by a novel methanotroph classified as Methylotetracoccus. Inhibition microcosms provided independent confirmation that methane oxidation was mediated by the pMMO. In these same incubations, sulfamethoxazole biotransformation was stimulated proportional to aerobic methane-oxidizing activity and exhibited negligible removal in the absence of methane, in the presence of methane and pMMO inhibitors, and under anoxia. Nitrate reduction was similarly enhanced under aerobic methane-oxidizing conditions with rates several times faster than for canonical denitrification. Collectively, our results provide convergent in situ and laboratory evidence that methane-oxidizing activity can enhance sulfamethoxazole biotransformation, with possible implications for the combined removal of nitrogen and trace organic contaminants in wetland sediments.
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Affiliation(s)
- Michael A P Vega
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
| | - Rachel C Scholes
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Adam R Brady
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Gary F Vanzin
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Kelly C Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80523, United States
| | - David L Sedlak
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Jonathan O Sharp
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- NSF Engineering Research Center for Reinventing the Nation's Urban Water Infrastructure (ReNUWIt), Colorado School of Mines, Golden, Colorado 80401, United States
- Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
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Ali Eltayb W, Abdalla M, Ahmed EL-Arabey A, Boufissiou A, Azam M, Al-Resayes SI, Alam M. Exploring particulate methane monooxygenase (pMMO) proteins using experimentation and computational molecular docking. JOURNAL OF KING SAUD UNIVERSITY - SCIENCE 2023; 35:102634. [DOI: https:/doi.org/10.1016/j.jksus.2023.102634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Rafalska A, Walkiewicz A, Osborne B, Klumpp K, Bieganowski A. Variation in methane uptake by grassland soils in the context of climate change - A review of effects and mechanisms. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 871:162127. [PMID: 36764535 DOI: 10.1016/j.scitotenv.2023.162127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/19/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Grassland soils are climate-dependent ecosystems that have a significant greenhouse gas mitigating function through their ability to store large amounts of carbon (C). However, what is often not recognized is that they can also exhibit a high methane (CH4) uptake capacity that could be influenced by future increases in atmospheric carbon dioxide (CO2) concentration and variations in temperature and water availability. While there is a wealth of information on C sequestration in grasslands there is less consensus on how climate change impacts on CH4 uptake or the underlying mechanisms involved. To address this, we assessed existing knowledge on the impact of climate change components on CH4 uptake by grassland soils. Increases in precipitation associated with soils with a high background soil moisture content generally resulted in a reduction in CH4 uptake or even net emissions, while the effect was opposite in soils with a relatively low background moisture content. Initially wet grasslands subject to the combined effects of warming and water deficits may absorb more CH4, mainly due to increased gas diffusivity. However, in the longer-term heat and drought stress may reduce the activity of methanotrophs when the mean soil moisture content is below the optimum for their survival. Enhanced plant productivity and growth under elevated CO2, increased soil moisture and changed nutrient concentrations, can differentially affect methanotrophic activity, which is often reduced by increasing N deposition. Our estimations showed that CH4 uptake in grassland soils can change from -57.7 % to +6.1 % by increased precipitation, from -37.3 % to +85.3 % by elevated temperatures, from +0.87 % to +92.4 % by decreased precipitation, and from -66.7 % to +27.3 % by elevated CO2. In conclusion, the analysis suggests that grasslands under the influence of warming and drought may absorb even more CH4, mainly because of reduced soil water contents and increased gas diffusivity.
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Affiliation(s)
- Adrianna Rafalska
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
| | - Anna Walkiewicz
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Bruce Osborne
- UCD School of Agriculture and Food Science and UCD Earth Institute, University College Dublin, Belfield, 4 Dublin, Ireland
| | - Katja Klumpp
- INRAE, University of Clermont Auvergne, VetAgro Sup, UREP Unité de Recherche sur l'Ecosystème Prairial, 63000 Clermont-Ferrand, France
| | - Andrzej Bieganowski
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
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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: 2] [Impact Index Per Article: 2.0] [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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Obregon Alvarez D, Fonseca de Souza L, Mendes LW, de Moraes MT, Tosi M, Venturini AM, Meyer KM, Barbosa de Camargo P, Bohannan BJM, Mazza Rodrigues JL, Dunfield KE, Tsai SM. Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin. Mol Ecol 2023. [PMID: 36896778 DOI: 10.1111/mec.16912] [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: 09/15/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4 ) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.
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Affiliation(s)
- Dasiel Obregon Alvarez
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Lucas William Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | | | - Micaela Tosi
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | | | - Kyle M Meyer
- Department of Integrative Biology, University of California-Berkeley, Berkeley, California, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | | | | | - Jorge L Mazza Rodrigues
- Department of Land, Air, and Water Resources, University of California-Davis, Davis, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kari E Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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Liu Z, Wang J, Xie J, Yao D, Yang S, Ge J. Interactions among heavy metals and methane-metabolizing microorganisms and their effects on methane emissions in Dajiuhu peatland. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:37415-37426. [PMID: 36572772 DOI: 10.1007/s11356-022-24868-8] [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: 06/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Peatlands play a crucial role in mediating the emissions of methane through active biogeochemical cycling of accumulated carbon driven by methane-metabolizing microorganisms; meanwhile, they serve as vital archives of atmospheric heavy metal deposition. Despite many edaphic factors confirmed as determinants to modulate the structure of methanotrophic and methanogenic communities, recognition of interactions among them is limited. In this study, peat soils were collected from Dajiuhu peatland to assess the presence of heavy metals, and methanotrophs and methanogens were investigated via high-throughput sequencing for functional genes mcrA and pmoA. Further analyses of the correlations between methane-related functional groups were conducted. The results demonstrated that both methane-metabolizing microorganisms and heavy metals have prominent vertical heterogeneity upward and downward along the depth of 20 cm. Pb, Cd, and Hg strongly correlated with methanotrophs and methanogens across all seasons and depths, serving as forceful factors in structural variations of methanogenic and methanotrophic communities. Particularly, Pb, Cd, and Hg were identified as excessive elements in Dajiuhu peatland. Furthermore, seasonal variations of networks among methane-related functional groups and environmental factors significantly affected the changes of methane fluxes across different seasons. Concretely, the complicated interactions were detrimental to methane emissions in the Dajiuhu peatland, leading to the minimum methane emissions in winter. Our study identified the key heavy metals affecting the composition of methane-metabolizing microorganisms and linkages between seasonal variations of methane emissions and interaction among heavy metals and methane-metabolizing microorganisms, which provided much new reference and theoretical basis for integrated management of natural peatlands.
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Affiliation(s)
- Ziwei Liu
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jiumei Wang
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jinlin Xie
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Dong Yao
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Shiyu Yang
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China
| | - Jiwen Ge
- School of Environmental Studies, China University of Geosciences (Wuhan), 68 Jincheng Street, Hongshan District, Wuhan, 430078, Hubei Province, China.
- Laboratory of Basin Hydrology and Wetland Eco-Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China.
- Hubei Key Laboratory of Wetland Evolution and Ecological Restoration, China University of Geosciences (Wuhan), Wuhan, 430078, China.
- Institution of Ecology and Environmental Sciences, China University of Geosciences (Wuhan), Wuhan, 430078, China.
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Lee J, Yun J, Yang Y, Jung JY, Lee YK, Yuan J, Ding W, Freeman C, Kang H. Attenuation of Methane Oxidation by Nitrogen Availability in Arctic Tundra Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2647-2659. [PMID: 36719133 DOI: 10.1021/acs.est.2c05228] [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
CH4 emission in the Arctic has large uncertainty due to the lack of mechanistic understanding of the processes. CH4 oxidation in Arctic soil plays a critical role in the process, whereby removal of up to 90% of CH4 produced in soils by methanotrophs can occur before it reaches the atmosphere. Previous studies have reported on the importance of rising temperatures in CH4 oxidation, but because the Arctic is typically an N-limited system, fewer studies on the effects of inorganic nitrogen (N) have been reported. However, climate change and an increase of available N caused by anthropogenic activities have recently been reported, which may cause a drastic change in CH4 oxidation in Arctic soils. In this study, we demonstrate that excessive levels of available N in soil cause an increase in net CH4 emissions via the reduction of CH4 oxidation in surface soil in the Arctic tundra. In vitro experiments suggested that N in the form of NO3- is responsible for the decrease in CH4 oxidation via influencing soil bacterial and methanotrophic communities. The findings of our meta-analysis suggest that CH4 oxidation in the boreal biome is more susceptible to the addition of N than in other biomes. We provide evidence that CH4 emissions in Arctic tundra can be enhanced by an increase of available N, with profound implications for modeling CH4 dynamics in Arctic regions.
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Affiliation(s)
- Jaehyun Lee
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Jeongeun Yun
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Yerang Yang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
| | - Ji Young Jung
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon21990, South Korea
| | - Junji Yuan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Weixin Ding
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing210008, China
| | - Chris Freeman
- School of Natural Sciences, Bangor University, BangorLL57 2UW, U.K
| | - Hojeong Kang
- School of Civil and Environmental Engineering, Yonsei University, Seoul03722, South Korea
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Yu G, Chen J, Wang G, Chen H, Huang J, Li Y, Wang W, Song F, Ma Y, Wang Q, Wang M, Ling T, Shu Z, Sun J, Yu Z. Recent advances in constructed wetlands methane reduction: Mechanisms and methods. Front Microbiol 2023; 14:1106332. [PMID: 36819020 PMCID: PMC9936987 DOI: 10.3389/fmicb.2023.1106332] [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: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Constructed wetlands (CWs) are artificial systems that use natural processes to treat wastewater containing organic pollutants. This approach has been widely applied in both developing and developed countries worldwide, providing a cost-effective method for industrial wastewater treatment and the improvement of environmental water quality. However, due to the large organic carbon inputs, CWs is produced in varying amounts of CH4 and have the potential to become an important contributor to global climate change. Subsequently, research on the mitigation of CH4 emissions by CWs is key to achieving sustainable, low-carbon dependency wastewater treatment systems. This review evaluates the current research on CH4 emissions from CWs through bibliometric analysis, summarizing the reported mechanisms of CH4 generation, transfer and oxidation in CWs. Furthermore, the important environmental factors driving CH4 generation in CW systems are summarized, including: temperature, water table position, oxidation reduction potential, and the effects of CW characteristics such as wetland type, plant species composition, substrate type, CW-coupled microbial fuel cell, oxygen supply, available carbon source, and salinity. This review provides guidance and novel perspectives for sustainable and effective CW management, as well as for future studies on CH4 reduction in CWs.
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Affiliation(s)
- Guanlong Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jundan Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Guoliang Wang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Huifang Chen
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Jiajun Huang
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Yifu Li
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Wenming Wang
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China,*Correspondence: Wenming Wang,
| | - Fengming Song
- Technology Center, Hunan Pilot Yanghu Reclaimed Water Co., Ltd., Changsha, China
| | - Yuanjun Ma
- Technology Department, Hunan Rongantai Ecological Technology Co., Ltd., Changsha, China
| | - Qi Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Miaomiao Wang
- Technology and Information Department, CCCC-TDC Environmental Engineering Co., Ltd., Tianjin, China
| | - Tao Ling
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Zhilai Shu
- Engineering Department, China Railway Wuju Group the First Engineering Co., Ltd., Changsha, China
| | - Julong Sun
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
| | - Zhi Yu
- School of Hydraulic and Environmental Engineering, Changsha University of Science & Technology, Changsha, China,Key Laboratory of Dongting Lake Aquatic Eco-Environmental Control and Restoration of Hunan Province, Changsha University of Science and Technology, Changsha, China
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Blumberg K, Miller M, Ponsero A, Hurwitz B. Ontology-driven analysis of marine metagenomics: what more can we learn from our data? Gigascience 2022; 12:giad088. [PMID: 37941395 PMCID: PMC10632069 DOI: 10.1093/gigascience/giad088] [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: 03/01/2023] [Revised: 06/30/2023] [Accepted: 09/28/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. RESULTS Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. CONCLUSIONS In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.
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Affiliation(s)
- Kai Blumberg
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Matthew Miller
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Alise Ponsero
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Bonnie Hurwitz
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem. Nat Microbiol 2022; 7:2089-2100. [PMID: 36329197 DOI: 10.1038/s41564-022-01252-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using 13C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.
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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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Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments. Microorganisms 2022; 10:microorganisms10091747. [PMID: 36144349 PMCID: PMC9506196 DOI: 10.3390/microorganisms10091747] [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: 05/30/2022] [Revised: 07/23/2022] [Accepted: 08/02/2022] [Indexed: 11/26/2022] Open
Abstract
Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.
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Zhang Z, Huang B, Wang Y, Zhan Y, Zhu M, Wang C. Dynamic alterations in the donkey fecal bacteria community and metabolome characteristics during gestation. Front Microbiol 2022; 13:927561. [PMID: 36060774 PMCID: PMC9434018 DOI: 10.3389/fmicb.2022.927561] [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: 05/26/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
In donkeys, the gestation period is a dynamic and precisely coordinated process involving systemic and local alterations. Both the gut microbiota and its link with blood metabolites are thought to play significant roles in maintaining maternal health and supporting fetal development during the gestation period. This study was conducted to evaluate gut microbiota changes and the correlation with plasma metabolites in Dezhou donkeys during the gestation period. The donkeys were divided into the four following groups according to their pregnancy stages: the non-pregnant (NP), early stage of pregnancy (P1), middle stage of pregnancy (P2), and late stage of pregnancy (P3) groups. A total of 24 (n = 6 per group) samples of donkey feces and plasma were collected. The results showed that the diversity (Shannon index) of fecal bacteria significantly increased throughout the gestation period. The phyla Spirochaetota and Fibrobacterota varied significantly according to the stages of pregnancy (p < 0.05). At the genus level, the abundance of Treponema in pregnant donkeys was greater than that in non-pregnant donkeys (p < 0.05), and the genus Streptococcus reached its maximum abundance in the P2 period (p < 0.05). The abundance of Ruminococcaceae_NK4A214_group and norank_f_norank_o_WCHB1-41 linearly increased with the progression of pregnancy (p < 0.05). In addition, the host plasma metabolome was altered significantly during the gestation period. Testolic acid, estradiol-17beta 3-sulfate, equol 7’-o-glucuronide, equol 4’-o-glucuronide, estrone, estrone 3-glucuronide, and estradiol were the most significant differential enriched metabolites, and they increased gradually as gestation progressed. The altered metabolites were mainly enriched in pathways matched to bile secretion, ABC transporters, amino acid metabolism, protein digestion and absorption, mineral absorption, fatty acid degradation, glycerophospholipid metabolism, and steroid hormone biosynthesis. We also found a significant correlation between the shifts in donkey fecal bacteria and changes in the host metabolism. In summary, this study provided systematic data on the fecal bacterial changes and host plasma metabolism of donkeys throughout pregnancy. The results indicated that host–bacteria interactions during the gestation period influence the host metabolism. These interactions benefit the pregnant donkeys by providing a sufficient supply of nutrients and energy for fetal growth and maternal health.
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Zhao Y, Jiang H, Wang X, Liu C, Yang Y. Quinolone antibiotics enhance denitrifying anaerobic methane oxidation in Wetland sediments: Counterintuitive results. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 305:119300. [PMID: 35427678 DOI: 10.1016/j.envpol.2022.119300] [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: 11/13/2021] [Revised: 03/25/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Denitrifying anaerobic methane oxidation (DAMO) plays an important role in the element cycle of wetlands. In recent years, the content of antibiotics in wetlands has gradually increased due to human activities. However, the impact of antibiotics on the ecological function of DAMO remains unclear. Here we studied the influence of three high-content quinolone antibiotics (QNs) on DAMO in the sediments of the Baiyangdian Wetland. The results show that QNs can significantly promote the potential DAMO rates. Moreover, the enhancement of potential DAMO rates is positively correlated with the dosage of QNs. This promotion effect of QNs on nitrate-DAMO can be attributed to the hormesis phenomenon or their inhibition of substrate competitors. As antibacterial agents, QNs inhibit nitrite-DAMO conducted by bacteria, but greatly promote nitrate-DAMO conducted by archaea. These results suggest that the short-term effect of QNs on DAMO in wetlands is promotion rather than inhibition.
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Affiliation(s)
- Yuewen Zhao
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen, 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China; Key Laboratory of Groundwater Sciences and Engineering, Ministry of Natural Resources, Shijiazhuang, 050800, China
| | - Hongchen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China.
| | - Xiuyan Wang
- Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China; Key Laboratory of Groundwater Sciences and Engineering, Ministry of Natural Resources, Shijiazhuang, 050800, China
| | - Changli Liu
- Fujian Provincial Key Laboratory of Water Cycling and Eco-Geological Processes, Xiamen, 361021, China; Institute of Hydrogeology and Environmental Geology, Chinese Academy of Geological Sciences, Shijiazhuang, 050061, China
| | - Yuqi Yang
- School of Water Resources and Environment, China University of Geosciences, Beijing, 100083, China
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Changes in Soil Microbial Community and Carbon Flux Regime across a Subtropical Montane Peatland-to-Forest Successional Series in Taiwan. FORESTS 2022. [DOI: 10.3390/f13060958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Subtropical montane peatland is among several rare ecosystems that continue to receive insufficient scientific exploration. We analyzed the vegetation types and soil bacterial composition, as well as surface carbon dioxide and methane fluxes along a successional peatland-to-upland-forest series in one such ecosystem in Taiwan. The Yuanyang Lake (YYL) study site is characterized by low temperature, high precipitation, prevailing fog, and acidic soil, which are typical conditions for the surrounding dominant Chamaecyparis obtusa var. formosana forest. Bacterial communities were dominated by Acidobacteriota and Proteobacteria. Along the bog-to-forest gradient, Proteobacteria decreased and Acidobacteriota increased while CO2 fluxes increased and CH4 fluxes decreased. Principal coordinate analysis allowed separating samples into four clusters, which correspond to samples from the bog, marsh, forest, and forest outside of the watershed. The majority of bacterial genera were found in all plots, suggesting that these communities can easily switch to other types. Variation among samples from the same vegetation type suggests influence of habitat heterogeneity on bacterial community composition. Variations of soil water content and season caused the variations of carbon fluxes. While CO2 flux decreased exponentially with increasing soil water content, the CH4 fluxes exhibited an exponential increase together with soil water content. Because YYL is in a process of gradual terrestrialization, especially under the warming climate, we expect changes in microbial composition and the greenhouse gas budget at the landscape scale within the next decades.
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Khanongnuch R, Mangayil R, Santala V, Hestnes AG, Svenning MM, Rissanen AJ. Batch Experiments Demonstrating a Two-Stage Bacterial Process Coupling Methanotrophic and Heterotrophic Bacteria for 1-Alkene Production From Methane. Front Microbiol 2022; 13:874627. [PMID: 35663866 PMCID: PMC9162803 DOI: 10.3389/fmicb.2022.874627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Methane (CH4) is a sustainable carbon feedstock for value-added chemical production in aerobic CH4-oxidizing bacteria (methanotrophs). Under substrate-limited (e.g., oxygen and nitrogen) conditions, CH4 oxidation results in the production of various short-chain organic acids and platform chemicals. These CH4-derived products could be broadened by utilizing them as feedstocks for heterotrophic bacteria. As a proof of concept, a two-stage system for CH4 abatement and 1-alkene production was developed in this study. Type I and Type II methanotrophs, Methylobacter tundripaludum SV96 and Methylocystis rosea SV97, respectively, were investigated in batch tests under different CH4 and air supplementation schemes. CH4 oxidation under either microaerobic or aerobic conditions induced the production of formate, acetate, succinate, and malate in M. tundripaludum SV96, accounting for 4.8–7.0% of consumed carbon from CH4 (C-CH4), while M. rosea SV97 produced the same compounds except for malate, and with lower efficiency than M. tundripaludum SV96, accounting for 0.7–1.8% of consumed C-CH4. For the first time, this study demonstrated the use of organic acid-rich spent media of methanotrophs cultivating engineered Acinetobacter baylyi ADP1 ‘tesA-undA cells for 1-alkene production. The highest yield of 1-undecene was obtained from the spent medium of M. tundripaludum SV96 at 68.9 ± 11.6 μmol mol Csubstrate–1. However, further large-scale studies on fermenters and their optimization are required to increase the production yields of organic acids in methanotrophs.
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Affiliation(s)
- Ramita Khanongnuch
- Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Rahul Mangayil
- Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Ville Santala
- Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Anne Grethe Hestnes
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Mette Marianne Svenning
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Antti J Rissanen
- Materials Science and Environmental Engineering, Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
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Chetri JK, Reddy KR, Green SJ. Use of methanotrophically activated biochar in novel biogeochemical cover system for carbon sequestration: Microbial characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153429. [PMID: 35101512 DOI: 10.1016/j.scitotenv.2022.153429] [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: 11/11/2021] [Revised: 01/05/2022] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Biochar-amended soils have been explored to enhance microbial methane (CH4) oxidation in landfill cover systems. Recently, research priorities have expanded to include the mitigation of other components of landfill gas such as carbon dioxide (CO2) and hydrogen sulfide (H2S) along with CH4. In this study, column tests were performed to simulate the newly proposed biogeochemical cover systems, which incorporate biochar-amended soil for CH4 oxidation and basic oxygen furnace (BOF) slag for CO2 and H2S mitigation, to evaluate the effect of cover configuration on microbial CH4 oxidation and community composition. Biogeochemical covers included a biochar-amended soil (10% w/w), and methanotroph-enriched activated biochar amended soil (5% or 10% w/w) as a biocover layer or CH4 oxidation layer. The primary outcome measures of interest were CH4 oxidation rates and the structure and abundance of methane-oxidation bacteria in the covers. All column reactors were active in CH4 oxidation, but columns containing activated biochar-amended soils had higher CH4 oxidation rates (133 to 143 μg CH4 g-1 day-1) than those containing non-activated biochar-amended soil (50 μg CH4 g-1 day-1) and no-biochar soil or control soil (43 μg CH4 g-1 day-1). All treatments showed significant increases in the relative abundance of methanotrophs from an average relative abundance of 5.6% before incubation to a maximum of 45% following incubation. In activated biochar, the abundance of Type II methanotrophs, primarily Methylocystis and Methylosinus, was greater than that of Type I methanotrophs (Methylobacter) due to which activated biochar-amended soils also showed higher abundance of Type II methanotrophs. Overall, biogeochemical cover profiles showed promising potential for CH4 oxidation without any adverse effect on microbial community composition and methane oxidation. Biochar activation led to an alteration of the dominant methanotrophic communities and increased CH4 oxidation.
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Affiliation(s)
- Jyoti K Chetri
- University of Illinois at Chicago, Department of Civil, Materials, and Environmental Engineering, 842 West Taylor Street, Chicago, IL 60607, USA.
| | - Krishna R Reddy
- University of Illinois at Chicago, Department of Civil, Materials, and Environmental Engineering, 842 West Taylor Street, Chicago, IL 60607, USA.
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, 1653 W. Congress Parkway, Jelke Building, Room 444, Chicago, IL 60612, USA.
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Recycling carbon for sustainable protein production using gas fermentation. Curr Opin Biotechnol 2022; 76:102723. [PMID: 35487158 DOI: 10.1016/j.copbio.2022.102723] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/23/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
Abstract
Current food production practices contribute significantly to climate change. To transition into a sustainable future, a combination of new food habits and a radical food production innovation must occur. Single-cell protein from microbial fermentation can profoundly impact sustainability. This review paper explores opportunities offered by gas fermentation to completely replace our reliance on fossil fuels for the production of food. Together with synthetic biology, designed microbial proteins from gas fermentation have the potential to reduce our dependence on fossil fuels and make food production more sustainable.
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Steinsdóttir HGR, Gómez Ramírez E, Mhatre S, Schauberger C, Bertagnolli AD, Pratte ZA, Stewart FJ, Thamdrup B, Bristow LA. Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics. Environ Microbiol 2022; 24:2361-2379. [PMID: 35415879 PMCID: PMC9323439 DOI: 10.1111/1462-2920.16003] [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: 10/19/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations, and 16S rRNA gene sequencing over three consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 μmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water, respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Eddy Gómez Ramírez
- CIMAR, Universidad de Costa Rica, San Pedro de Montes de Oca, Costa Rica
| | - Snehit Mhatre
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | | | - Anthony D Bertagnolli
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Zoe A Pratte
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana
| | - Frank J Stewart
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana.,School of Biological Sciences, Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA
| | - Bo Thamdrup
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Laura A Bristow
- Department of Biology, University of Southern Denmark, Odense, Denmark
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Xing T, Liu P, Ji M, Deng Y, Liu K, Wang W, Liu Y. Sink or Source: Alternative Roles of Glacier Foreland Meadow Soils in Methane Emission Is Regulated by Glacier Melting on the Tibetan Plateau. Front Microbiol 2022; 13:862242. [PMID: 35387086 PMCID: PMC8977769 DOI: 10.3389/fmicb.2022.862242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Glacier foreland soils have long been considered as methane (CH4) sinks. However, they are flooded by glacial meltwater annually during the glacier melting season, altering their redox potential. The impacts of this annual flooding on CH4 emission dynamics and methane-cycling microorganisms are not well understood. Herein, we measured in situ methane flux in glacier foreland soils during the pre-melting and melting seasons on the Tibetan Plateau. In addition, high-throughput sequencing and qPCR were used to investigate the diversity, taxonomic composition, and the abundance of methanogenic archaea and methanotrophic bacteria. Our results showed that the methane flux ranged from -10.11 to 4.81 μg·m-2·h-1 in the pre-melting season, and increased to 7.48-22.57 μg·m-2·h-1 in the melting season. This indicates that glacier foreland soils change from a methane sink to a methane source under the impact of glacial meltwater. The extent of methane flux depends on methane production and oxidation conducted by methanogens and methanotrophs. Among all the environmental factors, pH (but not moisture) is dominant for methanogens, while both pH and moisture are not that strong for methanotrophs. The dominant methanotrophs were Methylobacter and Methylocystis, whereas the methanogens were dominated by methylotrophic Methanomassiliicoccales and hydrogenotrophic Methanomicrobiales. Their distributions were also affected by microtopography and environmental factor differences. This study reveals an alternative role of glacier foreland meadow soils as both methane sink and source, which is regulated by the annual glacial melt. This suggests enhanced glacial retreat may positively feedback global warming by increasing methane emission in glacier foreland soils in the context of climate change.
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Affiliation(s)
- Tingting Xing
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing, China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Wenqiang Wang
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China.,Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
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Kaupper T, Mendes LW, Poehlein A, Frohloff D, Rohrbach S, Horn MA, Ho A. The methane-driven interaction network in terrestrial methane hotspots. ENVIRONMENTAL MICROBIOME 2022; 17:15. [PMID: 35382875 PMCID: PMC8981696 DOI: 10.1186/s40793-022-00409-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Biological interaction affects diverse facets of microbial life by modulating the activity, diversity, abundance, and composition of microbial communities. Aerobic methane oxidation is a community function, with emergent community traits arising from the interaction of the methane-oxidizers (methanotrophs) and non-methanotrophs. Yet little is known of the spatial and temporal organization of these interaction networks in naturally-occurring complex communities. We hypothesized that the assembled bacterial community of the interaction network in methane hotspots would converge, driven by high substrate availability that favors specific methanotrophs, and in turn influences the recruitment of non-methanotrophs. These environments would also share more co-occurring than site-specific taxa. RESULTS We applied stable isotope probing (SIP) using 13C-CH4 coupled to a co-occurrence network analysis to probe trophic interactions in widespread methane-emitting environments, and over time. Network analysis revealed predominantly unique co-occurring taxa from different environments, indicating distinctly co-evolved communities more strongly influenced by other parameters than high methane availability. Also, results showed a narrower network topology range over time than between environments. Co-occurrence pattern points to Chthoniobacter as a relevant yet-unrecognized interacting partner particularly of the gammaproteobacterial methanotrophs, deserving future attention. In almost all instances, the networks derived from the 13C-CH4 incubation exhibited a less connected and complex topology than the networks derived from the unlabelledC-CH4 incubations, likely attributable to the exclusion of the inactive microbial population and spurious connections; DNA-based networks (without SIP) may thus overestimate the methane-dependent network complexity. CONCLUSION We demonstrated that site-specific environmental parameters more strongly shaped the co-occurrence of bacterial taxa than substrate availability. Given that members of the interactome without the capacity to oxidize methane can exert interaction-induced effects on community function, understanding the co-occurrence pattern of the methane-driven interaction network is key to elucidating community function, which goes beyond relating activity to community composition, abundances, and diversity. More generally, we provide a methodological strategy that substantiates the ecological linkages between potentially interacting microorganisms with broad applications to elucidate the role of microbial interaction in community function.
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Affiliation(s)
- Thomas Kaupper
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Lucas W Mendes
- Center for Nuclear Energy in Agriculture, University of São Paulo CENA-USP, Piracicaba, SP, Brazil
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, George-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
| | - Daria Frohloff
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Stephan Rohrbach
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany
| | - Marcus A Horn
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
| | - Adrian Ho
- Institute for Microbiology, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419, Hannover, Germany.
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50
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Canatoy RC, Jeong ST, Galgo SJC, Kim PJ, Cho SR. Biochar as soil amendment: Syngas recycling system is essential to create positive carbon credit. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151140. [PMID: 34695470 DOI: 10.1016/j.scitotenv.2021.151140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Biochar utilization is accepted as the most cost-effective practice to mitigate global warming via increase in soil C stock. However, its utilization effect on greenhouse gas (GHG) fluxes was evaluated only within land application without considering industrial processes. To evaluate the net effect of biochar utilization on global warming within whole system boundary, swine manure-saw dust mixture was pyrolyzed under four different temperatures, and GHG fluxes were characterized under with/without syngas recycling systems. To determine GHG fluxes from biochar amended soil, 40 Mg ha-1 of biochar was mixed with soil and incubated under flooded and dried soil conditions. Finally, the effect of biochar utilization was generalized using net global warming potential (GWP) from industrial process to land application. Under without syngas recycling system, huge amounts of GHGs were emitted during pyrolysis, and GHG fluxes highly increased with increasing pyrolysis temperature, due to direct and indirect GHG emissions from feedstock combustion and electricity, respectively. However, syngas recycling system removed most of GHGs, except for direct N2O and indirect GHG emissions from electricity. Biochar application was very effective to mitigate GHG emissions within soil system boundary, and biochar produced at higher pyrolysis temperature showed higher effectivity in decreasing GHG fluxes. Within the whole system boundary from pyrolysis to soil application, without the installation of syngas recycling system, fresh manure application was more effective than biochar to reduce GHG emissions, regardless of soil water conditions. However, with the installation of syngas recycling system, biochar application was much more effective than fresh manure to decrease GHG fluxes. Biochar produced at higher temperature had higher effectivity to mitigate global warming impacts. In conclusion, to functionally mitigate global warming in soils, biochar should be produced in pyrolysis reactors equipped with syngas recycling system under higher temperature.
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Affiliation(s)
- Ronley C Canatoy
- Division of Agricultural Chemistry, Gyeongsang National University, Jinju 52828, South Korea
| | - Seung Tak Jeong
- Division of Agricultural Chemistry, Gyeongsang National University, Jinju 52828, South Korea
| | - Snowie Jane C Galgo
- Division of Agricultural Chemistry, Gyeongsang National University, Jinju 52828, South Korea
| | - Pil Joo Kim
- Division of Agricultural Chemistry, Gyeongsang National University, Jinju 52828, South Korea; Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, South Korea.
| | - Song Rae Cho
- Division of Agricultural Chemistry, Gyeongsang National University, Jinju 52828, South Korea.
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