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Awala SI, Gwak JH, Kim Y, Jung MY, Dunfield PF, Wagner M, Rhee SK. Nitrous oxide respiration in acidophilic methanotrophs. Nat Commun 2024; 15:4226. [PMID: 38762502 PMCID: PMC11102522 DOI: 10.1038/s41467-024-48161-z] [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: 01/03/2024] [Accepted: 04/22/2024] [Indexed: 05/20/2024] Open
Abstract
Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.
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Affiliation(s)
- Samuel Imisi Awala
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
- Center for Ecology and Environmental Toxicology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, 28644, South Korea
| | - Joo-Han Gwak
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Yongman Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea
| | - Man-Young Jung
- Interdisciplinary Graduate Programme in Advance Convergence Technology and Science, Jeju National University, Jeju, Republic of Korea
- Department of Science Education, Jeju National University, Jeju, Republic of Korea
- Jeju Microbiome Center, Jeju National University, Jeju, Republic of Korea
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Althanstrasse 14, A-1090, Vienna, Austria
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark
| | - Sung-Keun Rhee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, 1 Chungdae-ro, Seowon-Gu, Cheongju, 28644, Republic of Korea.
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Ruff SE, Humez P, de Angelis IH, Diao M, Nightingale M, Cho S, Connors L, Kuloyo OO, Seltzer A, Bowman S, Wankel SD, McClain CN, Mayer B, Strous M. Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems. Nat Commun 2023; 14:3194. [PMID: 37311764 DOI: 10.1038/s41467-023-38523-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/05/2023] [Indexed: 06/15/2023] Open
Abstract
Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 107 mL-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.
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Affiliation(s)
- S Emil Ruff
- Department of Geoscience, University of Calgary, Calgary, Canada.
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA.
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, MA, USA.
| | - Pauline Humez
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Isabella Hrabe de Angelis
- Department of Geoscience, University of Calgary, Calgary, Canada
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Muhe Diao
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Sara Cho
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Liam Connors
- Department of Geoscience, University of Calgary, Calgary, Canada
| | | | - Alan Seltzer
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Samuel Bowman
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Cynthia N McClain
- Department of Geoscience, University of Calgary, Calgary, Canada
- Alberta Environment and Protected Areas, Calgary, Canada
- Alberta Biodiversity Monitoring Institute, Edmonton, Canada
| | - Bernhard Mayer
- Department of Geoscience, University of Calgary, Calgary, Canada
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, Canada
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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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Xu J, Wang J, Ma C, Wei Z, Zhai Y, Tian N, Zhu Z, Xue M, Li D. Embracing a low-carbon future by the production and marketing of C1 gas protein. Biotechnol Adv 2023; 63:108096. [PMID: 36621726 DOI: 10.1016/j.biotechadv.2023.108096] [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: 08/29/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023]
Abstract
Food scarcity and environmental deterioration are two major problems that human populations currently face. Fortunately, the disruptive innovation of raw food materials has been stimulated by the rapid evolution of biomanufacturing. Therefore, it is expected that the new trends in technology will not only alter the natural resource-dependent food production systems and the traditional way of life but also reduce and assimilate the greenhouse gases released into the atmosphere. This review article summarizes the metabolic pathways associated with C1 gas conversion and the production of single-cell protein for animal feed. Moreover, the protein function, worldwide authorization, market access, and methods to overcome challenges in C1 gas assimilation microbial cell factory construction are also provided. With widespread attention and increasing policy support, the production of C1 gas protein will bring more opportunities and make tremendous contributions to our sustainable future.
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Affiliation(s)
- Jian Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Jie Wang
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunling Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Haihe Laboratory of Synthetic Biology, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zuoxi Wei
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Yida Zhai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Na Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China
| | - Zhiguang Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China.
| | - Min Xue
- Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Demao Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Centre of Technology Innovation for Synthetic Biology, Tianjin, China; Tianjin Key Laboratory for Industrial Biological Systems and Bioprocessing Engineering, Tianjin, China.
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Singh AK, Nakhate SP, Gupta RK, Chavan AR, Poddar BJ, Prakash O, Shouche YS, Purohit HJ, Khardenavis AA. Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm. ENVIRONMENTAL RESEARCH 2022; 215:114199. [PMID: 36058281 DOI: 10.1016/j.envres.2022.114199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 05/21/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.
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Affiliation(s)
- Ashish Kumar Singh
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suraj Prabhakarrao Nakhate
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rakesh Kumar Gupta
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Atul Rajkumar Chavan
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhagyashri Jagdishprasad Poddar
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Om Prakash
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Yogesh S Shouche
- National Centre for Microbial Resource, National Centre for Cell Sciences, Pune, Maharashtra, 411007, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anshuman Arun Khardenavis
- Environmental Biotechnology and Genomics Division, CSIR-National Environmental Engineering Research Institute, Nehru Marg, Nagpur, 440020, Maharashtra, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Tentori EF, Fang S, Richardson RE. RNA Biomarker Trends across Type I and Type II Aerobic Methanotrophs in Response to Methane Oxidation Rates and Transcriptome Response to Short-Term Methane and Oxygen Limitation in Methylomicrobium album BG8. Microbiol Spectr 2022; 10:e0000322. [PMID: 35678574 PMCID: PMC9241951 DOI: 10.1128/spectrum.00003-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/21/2022] [Indexed: 11/26/2022] Open
Abstract
Methanotrophs, which help regulate atmospheric levels of methane, are active in diverse natural and man-made environments. This range of habitats and the feast-famine cycles seen by many environmental methanotrophs suggest that methanotrophs dynamically mediate rates of methane oxidation. Global methane budgets require ways to account for this variability in time and space. Functional gene biomarker transcripts are increasingly studied to inform the dynamics of diverse biogeochemical cycles. Previously, per-cell transcript levels of the methane oxidation biomarker pmoA were found to vary quantitatively with respect to methane oxidation rates in the model aerobic methanotroph Methylosinus trichosporium OB3b. In the present study, these trends were explored for two additional aerobic methanotroph pure cultures grown in membrane bioreactors, Methylocystis parvus OBBP and Methylomicrobium album BG8. At steady-state conditions, per-cell pmoA mRNA transcript levels strongly correlated with per-cell methane oxidation across the three methanotrophs across many orders of magnitude of activity (R2 = 0.91). The inclusion of both type I and type II aerobic methanotrophs suggests a universal trend between in situ activity level and pmoA RNA biomarker levels which can aid in improving estimates of both subsurface and atmospheric methane. Additionally, genome-wide expression data (obtained by transcriptome sequencing [RNA-seq]) were used to explore transcriptomic responses of steady-state M. album BG8 cultures to short-term CH4 and O2 limitation. These limitations induced regulation of genes involved in central carbon metabolism (including carbon storage), cell motility, and stress response. IMPORTANCE Methanotrophs are naturally occurring microorganisms capable of oxidizing methane, having an impact on global net methane emissions. Additionally, they have also gained interest for their biotechnological applications in single-cell protein production, biofuels, and bioplastics. Having better ways of measuring methanotroph activity and understanding how methanotrophs respond to changing conditions is imperative for both optimization in controlled-growth applications and understanding in situ methane oxidation rates. In this study, we explored the applicability of methane oxidation biomarkers as a universal indicator of methanotrophic activity and explored methanotroph transcriptomic response to short-term changes in substrate availability. Our results contribute to better understanding the activity of aerobic methanotrophs, their core metabolic pathways, and their stress responses.
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Affiliation(s)
- Egidio F. Tentori
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Shania Fang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
| | - Ruth E. Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, USA
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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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Wu C, Zhou L, Zhou C, Zhou Y, Xia S, Rittmann BE. Co-removal of 2,4-dichlorophenol and nitrate using a palladized biofilm: Denitrification-promoted microbial mineralization following catalytic dechlorination. JOURNAL OF HAZARDOUS MATERIALS 2022; 422:126916. [PMID: 34425432 DOI: 10.1016/j.jhazmat.2021.126916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/02/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
The effects of nitrate on 2,4-dichlorophenol (2,4-DCP) dechlorination and biodegradation in a hydrogen (H2)-based palladized membrane biofilm reactor (Pd-MBfR) were studied. The Pd-MBfR was created by synthesizing palladium nanoparticle (Pd0NPs) that spontaneously associated with the biofilm to form a Pd0-biofilm. Without input of nitrate, the Pd-MBfR had rapid and stable catalytic hydrodechlorination: 93% of the 100-μM influent 2,4-DCP was continuously converted to phenol, part of which was then fermented via acetogenesis and methanogenesis. Introduction of nitrate enabled phenol mineralization via denitrification with only a minor decrease in catalytic hydrodechlorination. Phenol-degrading bacteria capable of nitrate respiration were enriched in the Pd0-biofilm, which was dominated by the heterotrophic genera Thauera and Azospira. Because the heterotrophic denitrifiers had greater yields than autotrophic denitrifiers, phenol was a more favorable electron donor than H2 for denitrification. This feature facilitated phenol mineralization and ameliorated denitrification inhibition of catalytic dechlorination through competition for H2. Increased nitrite loading eventually led to deterioration of the dechlorination flux and selectivity toward phenol. This study documents simultaneous removal of 2,4-DCP and nitrate in the Pd-MBfR and interactions between the two reductions.
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Affiliation(s)
- Chengyang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Luman Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
| | - Yun Zhou
- Huazhong Agricultural University, Wuhan, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, USA
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Malyan SK, Bhatia A, Tomer R, Harit RC, Jain N, Bhowmik A, Kaushik R. Mitigation of yield-scaled greenhouse gas emissions from irrigated rice through Azolla, Blue-green algae, and plant growth-promoting bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:51425-51439. [PMID: 33987722 DOI: 10.1007/s11356-021-14210-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Irrigated transplanted flooded rice is a major source of methane (CH4) emission. We carried out experiments for 2 years in irrigated flooded rice to study if interventions like methane-utilizing bacteria, Blue-green algae (BGA), and Azolla could mitigate the emission of CH4 and nitrous oxide (N2O) and lower the yield-scaled global warming potential (GWP). The experiment included nine treatments: T1 (120 kg N ha-1 urea), T2 (90 kg N ha-1 urea + 30 kg N ha-1 fresh Azolla), T3 (90 kg N ha-1 urea + 30 kg N ha-1 Blue-green algae (BGA), T4 (60 kg N ha-1 urea + 30 kg N ha-1 BGA + 30 kg N ha-1 Azolla, T5 (120 kg N ha-1 urea + Hyphomicrobium facile MaAL69), T6 (120 kg N ha-1 by urea + Burkholderia vietnamiensis AAAr40), T7 (120 kg N ha-1 by urea + Methylobacteruim oryzae MNL7), T8 (120 kg N ha-1 urea + combination of Burkholderia AAAr40, Hyphomicrobium facile MaAL69, Methylobacteruim oryzae MNL7), and T9 (no N fertilizer). Maximum decrease in cumulative CH4 emission was observed with the application of Methylobacteruim oryzae MNL7 in T7 (19.9%), followed by Azolla + BGA in T4 (13.2%) as compared to T1 control. N2O emissions were not significantly affected by the application of CH4-oxidizing bacteria. However, significantly lower (P<0.01) cumulative N2O emissions was observed in T4 (40.7%) among the fertilized treatments. Highest yields were observed in Azolla treatment T2 with 25% less urea N application. The reduction in yield-scaled GWP was at par in T4 (Azolla and BGA) and T7 (Methylobacteruim oryzae MNL7) treatments and reduced by 27.4% and 15.2% in T4 and T7, respectively, as compared to the T1 (control). K-means clustering analysis showed that the application of Methylobacteruim oryzae MNL7, Azolla, and Azolla + BGA can be an effective mitigation option to reduce the global warming potential while increasing the yield.
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Affiliation(s)
- Sandeep K Malyan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Ritu Tomer
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ramesh Chand Harit
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niveta Jain
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arpan Bhowmik
- Division of Design of Experiments, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India
| | - Rajeev Kaushik
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Wang S, Liu Q, Li J, Wang Z. Methane in wastewater treatment plants: status, characteristics, and bioconversion feasibility by methane oxidizing bacteria for high value-added chemicals production and wastewater treatment. WATER RESEARCH 2021; 198:117122. [PMID: 33865027 DOI: 10.1016/j.watres.2021.117122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/23/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Methane is a type of renewable fuel that can generate many types of high value-added chemicals, however, besides heat and power production, there is little methane utilization in most of the wastewater treatment plants (WWTPs) all round the world currently. In this review, the status of methane production performance from WWTPs was firstly investigated. Subsequently, based on the identification and classification of methane oxidizing bacteria (MOB), the key enzymes and metabolic pathway of MOB were presented in depth. Then the production, extraction and purification process of high value-added chemicals, including methanol, ectoine, biofuel, bioplastic, methane protein and extracellular polysaccharides, were introduced in detail, which was conducive to understand the bioconversion process of methane. Finally, the use of methane in wastewater treatment process, including nitrogen removal, emerging contaminants removal as well as resource recovery was extensively explored. These findings could provide guidance in the development of sustainable economy and environment, and facilitate biological methane conversion by using MOB in further attempts.
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Affiliation(s)
- Shuo Wang
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China
| | - Qixin Liu
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Ji Li
- Jiangsu Key Laboratory of Anaerobic Biotechnology, School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China; Jiangsu College of Water Treatment Technology and Material Collaborative Innovation Center, Suzhou 215009, China.
| | - Zhiwu Wang
- Department of Civil and Environmental Engineering, Virginia Tech, Manassas, VA 20110, USA.
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11
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12
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Wang Z, Gao P, Ji Y, Zhang H, Wu X, Ma J, Li S. Effects of salinity on the simultaneous anammox and denitrification process: performance, sludge morphology and shifts in microbial communities. ROYAL SOCIETY OPEN SCIENCE 2021; 8:202099. [PMID: 34040787 PMCID: PMC8113906 DOI: 10.1098/rsos.202099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/14/2021] [Indexed: 05/07/2023]
Abstract
In this study, the long-term effects of different salinities on the performance, sludge morphology and shifts in microbial communities were studied in a simultaneous anammox and denitrification (SAD) process at a C/N ratio of 0.5. Stable nitrogen removal efficiencies of 86.96 and 84.58% and nitrogen removal rates of 0.95 and 0.93 kg (m3 d)-1 could be achieved under low (25 mmol l-1) and moderate (50 mmol l-1) salinity, respectively. However, the performance collapsed when the system was exposed to high salinity (100 mmol l-1). The content of extracellular polymeric substances increased as salinity increased, which resulted in larger sizes of granular sludge under low and moderate salinities. Nevertheless, high salinity shock disintegrated granular sludge, thereby decreasing the average granule size. The Illumina-Miseq sequencing results revealed that Candidatus Jettenia was the sole salinity-tolerant AnAOB genus during the entire operation, whereas the main denitrification bacterial genera shifted from Denitrisoma under low salinity to Denitrisoma, Thauera and Ignavibacterium under high salinity. The results of this study provide a comprehensive and practical evaluation of the SAD process for organic nitrogen-rich saline wastewater treatment.
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Affiliation(s)
- Zhaozhao Wang
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Peng Gao
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Ying Ji
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Huan Zhang
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Xinjuan Wu
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Jun Ma
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
| | - Simin Li
- College of Energy and Environmental Engineering, Hebei University of Engineering, Handan 056038, People's Republic of China
- Hebei Technology Innovation Center for Water Pollution Control and Water Ecological Remediation, Hebei University of Engineering, Handan 056038, People's Republic of China
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Nguyen DTN, Lee OK, Nguyen TT, Lee EY. Type II methanotrophs: A promising microbial cell-factory platform for bioconversion of methane to chemicals. Biotechnol Adv 2021; 47:107700. [PMID: 33548453 DOI: 10.1016/j.biotechadv.2021.107700] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Methane, the predominant element in natural gas and biogas, represents a promising alternative to carbon feedstocks in the biotechnological industry due to its low cost and high abundance. The bioconversion of methane to value-added products can enhance the value of gas and mitigate greenhouse gas emissions. Methanotrophs, methane-utilizing bacteria, can make a significant contribution to the production of various valuable biofuels and chemicals from methane. Type II methanotrophs in comparison with Type I methanotrophs have distinct advantages, including high acetyl-CoA flux and the co-incorporation of two important greenhouse gases (methane and CO2), making it a potential microbial cell-factory platform for methane-derived biomanufacturing. Herein, we review the most recent advances in Type II methanotrophs related to multi-omics studies and metabolic engineering. Representative examples and prospects of metabolic engineering strategies for the production of suitable products are also discussed.
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Affiliation(s)
- Diep Thi Ngoc Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Thu Thi Nguyen
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Gyeonggi-do 17104, Republic of Korea.
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Farhan Ul Haque M, Xu HJ, Murrell JC, Crombie A. Facultative methanotrophs - diversity, genetics, molecular ecology and biotechnological potential: a mini-review. MICROBIOLOGY (READING, ENGLAND) 2020; 166:894-908. [PMID: 33085587 PMCID: PMC7660913 DOI: 10.1099/mic.0.000977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 12/18/2022]
Abstract
Methane-oxidizing bacteria (methanotrophs) play a vital role in reducing atmospheric methane emissions, and hence mitigating their potent global warming effects. A significant proportion of the methane released is thermogenic natural gas, containing associated short-chain alkanes as well as methane. It was one hundred years following the description of methanotrophs that facultative strains were discovered and validly described. These can use some multi-carbon compounds in addition to methane, often small organic acids, such as acetate, or ethanol, although Methylocella strains can also use short-chain alkanes, presumably deriving a competitive advantage from this metabolic versatility. Here, we review the diversity and molecular ecology of facultative methanotrophs. We discuss the genetic potential of the known strains and outline the consequent benefits they may obtain. Finally, we review the biotechnological promise of these fascinating microbes.
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Affiliation(s)
| | - Hui-Juan Xu
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: Joint Institute for Environmental Research & Education, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, PR China
| | - J. Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andrew Crombie
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- Present address: School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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15
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Hakobyan A, Zhu J, Glatter T, Paczia N, Liesack W. Hydrogen utilization by Methylocystis sp. strain SC2 expands the known metabolic versatility of type IIa methanotrophs. Metab Eng 2020; 61:181-196. [PMID: 32479801 DOI: 10.1016/j.ymben.2020.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/20/2020] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
Methane, a non-expensive natural substrate, is used by Methylocystis spp. as a sole source of carbon and energy. Here, we assessed whether Methylocystis sp. strain SC2 is able to also utilize hydrogen as an energy source. The addition of 2% H2 to the culture headspace had the most significant positive effect on the growth yield under CH4 (6%) and O2 (3%) limited conditions. The SC2 biomass yield doubled from 6.41 (±0.52) to 13.82 (±0.69) mg cell dry weight per mmol CH4, while CH4 consumption was significantly reduced. Regardless of H2 addition, CH4 utilization was increasingly redirected from respiration to fermentation-based pathways with decreasing O2/CH4 mixing ratios. Theoretical thermodynamic calculations confirmed that hydrogen utilization under oxygen-limited conditions doubles the maximum biomass yield compared to fully aerobic conditions without H2 addition. Hydrogen utilization was linked to significant changes in the SC2 proteome. In addition to hydrogenase accessory proteins, the production of Group 1d and Group 2b hydrogenases was significantly increased in both short- and long-term incubations. Both long-term incubation with H2 (37 d) and treatments with chemical inhibitors revealed that SC2 growth under hydrogen-utilizing conditions does not require the activity of complex I. Apparently, strain SC2 has the metabolic capacity to channel hydrogen-derived electrons into the quinone pool, which provides a link between hydrogen oxidation and energy production. In summary, H2 may be a promising alternative energy source in biotechnologically oriented methanotroph projects that aim to maximize biomass yield from CH4, such as the production of high-quality feed protein.
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Affiliation(s)
- Anna Hakobyan
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jing Zhu
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Institute of Environmental Science and Technology, Zhejiang University, Hangzhou, China
| | - 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
- Research Group "Methanotrophic Bacteria and Environmental Genomics/Transcriptomics", Max Planck Institute for Terrestrial Microbiology, Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany.
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16
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The effect of combined cometabolism and gamma irradiation treatment on the biodegradability of diclofenac and sulfamethoxazole. Radiat Phys Chem Oxf Engl 1993 2020. [DOI: 10.1016/j.radphyschem.2019.108642] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Parsaeifard N, Sattler M, Nasirian B, Chen VCP. Enhancing anaerobic oxidation of methane in municipal solid waste landfill cover soil. WASTE MANAGEMENT (NEW YORK, N.Y.) 2020; 106:44-54. [PMID: 32182561 DOI: 10.1016/j.wasman.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/07/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Landfills are the third largest anthropogenic source of the greenhouse gas methane worldwide. In the upper portions of landfill covers, methane is oxidized aerobically by microorganisms to form the less-potent greenhouse gas carbon dioxide; however, because of the low permeability of oxygen, no aerobic oxidation occurs in deeper portions of the cover. Therefore, the goal of this study was to enhance anaerobic oxidation of methane (AOM) in the deeper parts of landfill covers, to increase overall methane removal, via addition of electron acceptors besides oxygen. In batch tests, landfill cover soil was amended using five alternate electron acceptors: iron(III), nitrate, nitrite, sulfate, and manganese. AOM was then measured via column tests, which included realistic conditions of gas flow, cover thickness, and compaction. In the batch tests, soils amended with nitrate, sulfate, and the combination of sulfate + hematite removed more methane compared to control soil. Methane generation inhibitor had no impact on net methane removal. Adding nutrients to the soil significantly enhanced methane removal only for the case of soil without electron acceptors. Greater methane removal was observed for reactors with higher initial methane concentration. Results of the column tests showed that soil amended with sulfate + iron had the highest (around 10%) removal of methane in the anoxic zone, followed by soil amended with sulfate. Hydrogen sulfide (H2S) gas was measured in the headspace of these two columns, which indicated that sulfate-reducing bacteria were likely responsible for methane removal.
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Affiliation(s)
- Niloofar Parsaeifard
- Department of Civil Engineering, University of Texas at Arlington, Box 19308, Arlington, TX 76019, United States.
| | - Melanie Sattler
- Department of Civil Engineering, University of Texas at Arlington, Box 19308, Arlington, TX 76019, United States
| | - Bahareh Nasirian
- Department of Industrial, Manufacturing, and Systems Engineering, University of Texas at Arlington, Box 19017, Arlington, TX 76019, United States
| | - Victoria C P Chen
- Department of Industrial, Manufacturing, and Systems Engineering, University of Texas at Arlington, Box 19017, Arlington, TX 76019, United States
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18
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Wang S, An Z, Wang ZW. Bioconversion of methane to chemicals and fuels by methane-oxidizing bacteria. ADVANCES IN BIOENERGY 2020. [DOI: 10.1016/bs.aibe.2020.04.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Bioproduction of Isoprenoids and Other Secondary Metabolites Using Methanotrophic Bacteria as an Alternative Microbial Cell Factory Option: Current Stage and Future Aspects. Catalysts 2019. [DOI: 10.3390/catal9110883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Methane is a promising carbon feedstock for industrial biomanufacturing because of its low price and high abundance. Recent advances in metabolic engineering and systems biology in methanotrophs have made it possible to produce a variety of value-added compounds from methane, including secondary metabolites. Isoprenoids are one of the largest family of secondary metabolites and have many useful industrial applications. In this review, we highlight the current efforts invested to methanotrophs for the production of isoprenoids and other secondary metabolites, including riboflavin and ectoine. The future outlook for improving secondary metabolites production (especially of isoprenoids) using metabolic engineering of methanotrophs is also discussed.
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20
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Khalifa AY, AlMalki M. Polyphasic characterization of Delftia acidovorans ESM-1, a facultative methylotrophic bacterium isolated from rhizosphere of Eruca sativa. Saudi J Biol Sci 2019; 26:1262-1267. [PMID: 31516356 PMCID: PMC6733694 DOI: 10.1016/j.sjbs.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 11/25/2022] Open
Abstract
In this study, one bacterial strain, ESM-1, was isolated from rhizosphere of Eruca sativa, growing in Al Hofouf, Saudia Arabia, after enrichment with methanol as a sole carbon and energy source in a batch culture. ESM-1 was characterized by a polyphasic approach. The strain was identified as Delftia acidovorans at similarity level of 99.9% of the 16S rRNA gene sequences. Results of the Biolog Gen III MicroPlate test system showed that strain ESM-1 reacted positively to 47 (50%) including the one-carbon compound formic acid, and partially positive to 6 (∼6.4%) out of the 94 different the traits examined. The total cellular fatty acids composition of the strain ESM-1 was (C16:1ω7c/C16:1ω6c) and C16:0) and matched that of Delftia acidovorans at a similarity index of 0.9, providing a robustness to the ESM-1 identification. Furthermore, ESM-1 displayed a complex polar lipid profile consisting of phosphatidylethanolamine, phosphatidylglycerol, glycolipid, aminolipid, in addition to uncharacterized lipids. The DNA G+C content of the strain was 66.6 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain ESM1-1 was clearly clustered within the Delftia clade and constructed a monophyletic subcluster with Delftia acidovorans NBRC14950. The results addressed that ESM-1 is a facultative methylotrophic bacterium indigenous to Al Hofouf region and opens the door for potential biotechnological applications (e.g., bioremediation) of this strain, in future. Additionally, these findings assure that the total cellular fatty acid analysis and 16S rRNA gene are reliable tool for bacterial characterization and identification.
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Affiliation(s)
- Ashraf Y.Z. Khalifa
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, University of Beni-Suef, Beni-Suef, Egypt
| | - M. AlMalki
- Biological Sciences Department, College of Science, King Faisal University, Saudi Arabia
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21
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Christiansen NA, Fryirs KA, Green TJ, Hose GC. The impact of urbanisation on community structure, gene abundance and transcription rates of microbes in upland swamps of Eastern Australia. PLoS One 2019; 14:e0213275. [PMID: 30830948 PMCID: PMC6398846 DOI: 10.1371/journal.pone.0213275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 02/18/2019] [Indexed: 11/18/2022] Open
Abstract
The Temperate Highland Peat Swamps on Sandstone of the Sydney Basin occur in the headwaters of Sydney's drinking water catchments and are listed as endangered ecosystems, yet they have suffered habitat losses and degradation due to human impacts such as urbanisation. Despite ongoing efforts to restore and better protect upland swamps, they remain poorly understood, potentially hindering the effectiveness of management efforts. Essential to overall ecosystem function and the provision of services for human and environmental benefit are the microbial component of wetland ecosystems. In the case of these swamps, the microbes, have not yet been studied. Here, we investigated differences in the microbial community of upland swamps in urbanised catchments compared to swamps from natural catchments in the Blue Mountains. A total of twelve swamps were sampled, six from within urbanised catchments and six with intact vegetation catchments, to compare sediment conditions and microbial community and genes expression and abundances. Catchment impervious area and number of stormwater drains entering a swamp, indicators for urbanisation, positively correlated with the pH and ammonium concentration of swamp sediment. Community analysis of the 16S rRNA gene (T-RFLP, qPCR) revealed the elevated pH of urbanised swamps coincided with changes to the abundance of bacteria and archaea. Furthermore, RT-qPCR revealed genes involved in carbon cycling (mcrA & pmoA) were more likely to be found in urbanised swamps. Taken together, our results indicate that urbanisation of the Blue Mountains is impacting the environmental services provided by the microbial community of upland swamps in the Sydney Basin.
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Affiliation(s)
- Nicole A. Christiansen
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
- * E-mail:
| | - Kirstie A. Fryirs
- Department of Environmental Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Timothy J. Green
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Grant C. Hose
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, Australia
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He R, Su Y, Ma RC, Zhuang S. Characterization of toluene metabolism by methanotroph and its effect on methane oxidation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:16816-16824. [PMID: 29616477 DOI: 10.1007/s11356-018-1863-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/26/2018] [Indexed: 06/08/2023]
Abstract
Methanotrophs not only oxidize CH4, but also can oxidize a relatively broad range of other substrates, including trichloroethylene, alkanes, alkenes, and aromatic compounds. In this study, Methylosinus sporium was used as a model organism to characterize toluene metabolism by methanotrophs. Reverse transcription quantitative PCR analysis showed that toluene enhanced the mmoX expression of M. sporium. When the toluene concentration was below 2000 mg m-3, the kinetics of toluene metabolism by M. sporium conformed to the Michaelis-Menten equation (Vmax = 0.238 g gdry weight-1 h-1, K m = 545.2 mg m-3). The use of a solid-phase extraction technique followed by a gas chromatography-mass spectrometry analysis and molecular docking calculation showed that toluene was likely to primarily bind the di-iron center structural region of soluble methane monooxygenase (sMMO) hydroxylase and then be oxidized to o-cresol. Although M. sporium oxidized toluene, it did not incorporate toluene into its biomass. The coexistence of toluene and CH4 could influence CH4 oxidation, the growth of methanotrophs, and the distribution of CH4-derived carbon, which were related to the ratio of the toluene concentration to biomass. These results would be helpful to understand the metabolism of CH4 and non-methane volatile organic compounds in the environment.
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Affiliation(s)
- Ruo He
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China.
| | - Yao Su
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
- Institute of Environment, Resource, Soil and Fertilizer, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Ruo-Chan Ma
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Shulin Zhuang
- Institute of Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
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Chidambarampadmavathy K, Karthikeyan OP, Huerlimann R, Maes GE, Heimann K. Responses of mixed methanotrophic consortia to variable Cu 2+/Fe 2+ ratios. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2017; 197:159-166. [PMID: 28365562 DOI: 10.1016/j.jenvman.2017.03.063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 05/22/2023]
Abstract
Methane mitigation in landfill top cover soils is mediated by methanotrophs whose optimal methane (CH4) oxidation capacity is governed by environmental and complex microbial community interactions. Optimization of CH4 remediating bio-filters need to take microbial responses into account. Divalent copper (Cu2+) and iron (Fe2+) are present in landfills at variable ratios and play a vital role in methane oxidation capacity and growth of methanotrophs. This study, as a first of its kind, therefore quantified effects of variable Cu2+ and Fe2+ (5:5, 5:25 and 5:50 μM) ratios on mixed methanotrophic communities enriched from landfill top cover (LB) and compost soils (CB). CH4 oxidation capacity, CH4 removal efficiencies, fatty acids content/profiles and polyhydroxybutyrate (PHB; a biopolymer) contents were also analysed to quantify performance and potential co-product development. Mixed methanotroph cultures were raised in 10 L continuous stirred tank reactors (CSTRs, Bioflo® & Celligen® 310 Fermentor/Bioreactor; John Morris Scientific, Chatswood, NSW, Australia). Community structure was determined by amplifying the V3-V4 region of 16s rRNA gene. Community structure and, consequently, fatty acid-profiles changed significantly with increasing Cu2+/Fe2+ ratios, and responses were different for LB and CB. Effects on methane oxidation capacities and PHB content were similar in the LB- and CB-CSTR, decreasing with increasing Cu2+/Fe2+ ratios, while biomass growth was unaffected. In general, high Fe2+ concentration favored growth of the type -II methanotroph Methylosinus in the CB-CSTR, but methanotroph abundances decreased in the LB-CSTR. Increase in Cu2+/Fe2+ ratio increased the growth of Sphingopyxis in both systems, while Azospirllum was co-dominant in the LB- but absent in the CB-CSTR. After 13 days, methane oxidation capacities and PHB content decreased by ∼50% and more in response to increasing Fe2+ concentrations. Although methanotroph abundance was ∼2% in the LB- (compared to >50% in CB-CSTR), methane oxidation capacities were comparable in the two systems, suggesting that methane oxidation capacity was maintained by the dominant Azospirllum and Sphingopyxis in the LB-CSTR. Despite similar methanotroph inoculum community composition and controlled environmental variables, increasing Cu2+/Fe2+ ratios resulted in significantly different microbial community structures in the LB- and CB-CSTR, indicative of complex microbial interactions. In summary, our results suggest that a detailed understanding of allelopathic interactions in mixed methanotrophic consortia is vital for constructing robust bio-filters for CH4 emission abatement.
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Affiliation(s)
- Karthigeyan Chidambarampadmavathy
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Obulisamy Parthiba Karthikeyan
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Sino-Forest Applied Research Centre for Pearl River Delta Environment (ARCPE), Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Roger Huerlimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Gregory E Maes
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Kirsten Heimann
- College of Science and Engineering, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
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Kim K, Kwon T, Sung BJ, Kim C. Effect of methane-sugar interaction on the solubility of methane in an aqueous solution. J Colloid Interface Sci 2017; 500:113-118. [PMID: 28402843 DOI: 10.1016/j.jcis.2017.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/27/2017] [Accepted: 04/02/2017] [Indexed: 10/19/2022]
Abstract
In this study, the effect of methane-sugar interaction on the solubility of methane in an aqueous solution at ambient pressure was investigated. Various sugars, such as fructose, glucose, sucrose, maltose, and raffinose, were used, and depending on the type and concentration of sugar, the methane solubility increased from 21.72mg/L (in pure water) to 24.86mg/L. Sugars with a low hydrogen-bonding number between the water and sugar molecules exhibited a large enhancement in methane solubility. The solute partitioning model and molecular dynamics simulations were employed to verify the results obtained for the experimental solubility of methane in aqueous sugar solutions.
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Affiliation(s)
- Kwangmin Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Taejin Kwon
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Choongik Kim
- Department of Chemical and Biomolecular Engineering, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea.
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Ross MO, Rosenzweig AC. A tale of two methane monooxygenases. J Biol Inorg Chem 2017; 22:307-319. [PMID: 27878395 PMCID: PMC5352483 DOI: 10.1007/s00775-016-1419-y] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Methane monooxygenase (MMO) enzymes activate O2 for oxidation of methane. Two distinct MMOs exist in nature, a soluble form that uses a diiron active site (sMMO) and a membrane-bound form with a catalytic copper center (pMMO). Understanding the reaction mechanisms of these enzymes is of fundamental importance to biologists and chemists, and is also relevant to the development of new biocatalysts. The sMMO catalytic cycle has been elucidated in detail, including O2 activation intermediates and the nature of the methane-oxidizing species. By contrast, many aspects of pMMO catalysis remain unclear, most notably the nuclearity and molecular details of the copper active site. Here, we review the current state of knowledge for both enzymes, and consider pMMO O2 activation intermediates suggested by computational and synthetic studies in the context of existing biochemical data. Further work is needed on all fronts, with the ultimate goal of understanding how these two remarkable enzymes catalyze a reaction not readily achieved by any other metalloenzyme or biomimetic compound.
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Affiliation(s)
- Matthew O Ross
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Amy C Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL, 60208, USA.
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Kim K, Kim Y, Yang J, Ha KS, Usta H, Lee J, Kim C. Enhanced mass transfer rate and solubility of methane via addition of alcohols for Methylosinus trichosporium OB3b fermentation. J IND ENG CHEM 2017. [DOI: 10.1016/j.jiec.2016.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Malyan SK, Bhatia A, Kumar A, Gupta DK, Singh R, Kumar SS, Tomer R, Kumar O, Jain N. Methane production, oxidation and mitigation: A mechanistic understanding and comprehensive evaluation of influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 572:874-896. [PMID: 27575427 DOI: 10.1016/j.scitotenv.2016.07.182] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/02/2016] [Accepted: 07/25/2016] [Indexed: 06/06/2023]
Abstract
Methane is one of the critical greenhouse gases, which absorb long wavelength radiation, affects the chemistry of atmosphere and contributes to global climate change. Rice ecosystem is one of the major anthropogenic sources of methane. The anaerobic waterlogged soil in rice field provides an ideal environment to methanogens for methanogenesis. However, the rate of methanogenesis differs according to rice cultivation regions due to a number of biological, environmental and physical factors like carbon sources, pH, Eh, temperature etc. The interplay between the different conditions and factors may also convert the rice fields into sink from source temporarily. Mechanistic understanding and comprehensive evaluation of these variations and responsible factors are urgently required for designing new mitigation options and evaluation of reported option in different climatic conditions. The objective of this review paper is to develop conclusive understanding on the methane production, oxidation, and emission and methane measurement techniques from rice field along with its mitigation/abatement mechanism to explore the possible reduction techniques from rice ecosystem.
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Affiliation(s)
- Sandeep K Malyan
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Arti Bhatia
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Amit Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Dipak Kumar Gupta
- ICAR-Central Arid Zone Research Institute, Regional Research Station, Pali-Marwar, Rajasthan 342003, India
| | - Renu Singh
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Smita S Kumar
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana 125001, India
| | - Ritu Tomer
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Om Kumar
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Niveta Jain
- Centre for Environment Science and Climate Resilient Agriculture, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Jílková V, Picek T, Šestauberová M, Krištůfek V, Cajthaml T, Frouz J. Methane and carbon dioxide flux in the profile of wood ant (Formica aquilonia) nests and the surrounding forest floor during a laboratory incubation. FEMS Microbiol Ecol 2016; 92:fiw141. [DOI: 10.1093/femsec/fiw141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2016] [Indexed: 11/14/2022] Open
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29
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Myung J, Flanagan JC, Waymouth RM, Criddle CS. Methane or methanol-oxidation dependent synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by obligate type II methanotrophs. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Alpha- and Gammaproteobacterial Methanotrophs Codominate the Active Methane-Oxidizing Communities in an Acidic Boreal Peat Bog. Appl Environ Microbiol 2016; 82:2363-2371. [PMID: 26873322 DOI: 10.1128/aem.03640-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/03/2016] [Indexed: 11/20/2022] Open
Abstract
The objective of this study was to characterize metabolically active, aerobic methanotrophs in an ombrotrophic peatland in the Marcell Experimental Forest, in Minnesota. Methanotrophs were investigated in the field and in laboratory incubations using DNA-stable isotope probing (SIP), expression studies on particulate methane monooxygenase (pmoA) genes, and amplicon sequencing of 16S rRNA genes. Potential rates of oxidation ranged from 14 to 17 μmol of CH4g dry weight soil(-1)day(-1) Within DNA-SIP incubations, the relative abundance of methanotrophs increased from 4% in situ to 25 to 36% after 8 to 14 days. Phylogenetic analysis of the(13)C-enriched DNA fractions revealed that the active methanotrophs were dominated by the genera Methylocystis(type II;Alphaproteobacteria),Methylomonas, and Methylovulum(both, type I;Gammaproteobacteria). In field samples, a transcript-to-gene ratio of 1 to 2 was observed for pmoA in surface peat layers, which attenuated rapidly with depth, indicating that the highest methane consumption was associated with a depth of 0 to 10 cm. Metagenomes and sequencing of cDNA pmoA amplicons from field samples confirmed that the dominant active methanotrophs were Methylocystis and Methylomonas Although type II methanotrophs have long been shown to mediate methane consumption in peatlands, our results indicate that members of the genera Methylomonas and Methylovulum(type I) can significantly contribute to aerobic methane oxidation in these ecosystems.
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Karthikeyan OP, Chidambarampadmavathy K, Nadarajan S, Lee PKH, Heimann K. Effect of CH4/O2 ratio on fatty acid profile and polyhydroxybutyrate content in a heterotrophic-methanotrophic consortium. CHEMOSPHERE 2015; 141:235-42. [PMID: 26247542 DOI: 10.1016/j.chemosphere.2015.07.054] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 06/14/2015] [Accepted: 07/19/2015] [Indexed: 05/22/2023]
Abstract
Understanding the role of heterotrophic-methanotrophic (H-Meth) communities is important for improvement of methane (CH4) oxidation capacities (MOC) particularly in conjunction with bio-product development in industrial bio-filters. Initially, a H-Meth consortium was established and enriched from marine sediments and characterized by next generation sequencing of the 16s rDNA gene. The enriched consortium was subjected to 10-50% CH4 (i.e., 0.20-1.6 CH4/O2 ratios) to study the effects on MOCs, biomass growth, fatty acid profiles and biopolymer (e.g. polyhydroxybutyrate; PHB) content. Methylocystis, Methylophaga and Pseudoxanthomonas dominated the H-Meth consortium. Culture enrichment of the H-Meth consortium resulted in 15-20-folds higher MOC compared to seed sediments. Increasing CH4 concentration (and decreased O2 levels) yielded higher MOCs, but did not improve total fatty acid contents. PHB contents varied between 2.5% and 8.5% independently of CH4/O2 ratios. The results suggest that H-Meth consortia could potentially be used in industrial bio-filters for production of biopolymer/biofuel precursors from CH4.
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Affiliation(s)
- Obulisamy P Karthikeyan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia
| | - Karthigeyan Chidambarampadmavathy
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Saravanan Nadarajan
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong
| | - Kirsten Heimann
- College of Marine and Environmental Sciences, James Cook University, Townsville 4811, Queensland, Australia; Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville 4811, Queensland, Australia; Comparative Genomics Centre, James Cook University, Townsville 4811, Queensland, Australia; Centre for Bio-discovery and Molecular Development of Therapeutics, James Cook University, Townsville 4811, Queensland, Australia.
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32
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Myung J, Galega WM, Van Nostrand JD, Yuan T, Zhou J, Criddle CS. Long-term cultivation of a stable Methylocystis-dominated methanotrophic enrichment enabling tailored production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate). BIORESOURCE TECHNOLOGY 2015; 198:811-818. [PMID: 26454368 DOI: 10.1016/j.biortech.2015.09.094] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/21/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
Methane (CH4) is a readily available feedstock for production of polyhydroxyalkanoates (PHAs). The structure and PHA production capacity of a Methylocystis-dominated methanotrophic enrichment was stable in long-term operation (>175 days) when grown exponentially under non-aseptic conditions in fill-and-draw batch cultures with ammonium as nitrogen source. Cells harvested in the draw step were incubated in the absence of nitrogen with various combinations of CH4 and valerate to assess capacity for synthesis of poly(3-hydroxybutyrate) (P3HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV). When fed CH4 alone, only P3HB was produced. When fed CH4 plus valerate, PHBV was synthesized. The mol% of 3-hydroxyvalerate (3HV) increased with added valerate. Oxidation of CH4 was required for valerate assimilation, and the fraction of CH4 oxidized increased with increased mol% 3 HV. By separating PHA accumulation from cell replication, tailored PHA-rich biomass can be generated by addition of co-substrate, while retaining a large inoculum for the next cycle of cell division.
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Affiliation(s)
- Jaewook Myung
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Wakuna M Galega
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA.
| | - Joy D Van Nostrand
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma, Norman, OK 73019, USA.
| | - Tong Yuan
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma, Norman, OK 73019, USA.
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Science, University of Oklahoma, Norman, OK 73019, USA.
| | - Craig S Criddle
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA; Woods Institute for the Environment, Stanford, CA 94305, USA; William and Cloy Codiga Resource Recovery Center, Stanford, CA 94305, USA.
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Kalyuzhnaya MG, Puri AW, Lidstrom ME. Metabolic engineering in methanotrophic bacteria. Metab Eng 2015; 29:142-152. [PMID: 25825038 DOI: 10.1016/j.ymben.2015.03.010] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 02/26/2015] [Accepted: 03/17/2015] [Indexed: 12/19/2022]
Abstract
Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems.
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Affiliation(s)
- Marina G Kalyuzhnaya
- Biology Department, San Diego State University, San Diego, CA 92182-4614, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States
| | - Aaron W Puri
- Department of Chemical Engineering, Seattle, WA 98195, United States
| | - Mary E Lidstrom
- Department of Chemical Engineering, Seattle, WA 98195, United States; Department of Microbiology, University of Washington, Seattle, WA 98195, United States.
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34
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Biological conversion of methane to liquid fuels: status and opportunities. Biotechnol Adv 2014; 32:1460-75. [PMID: 25281583 DOI: 10.1016/j.biotechadv.2014.09.004] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 09/01/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Methane is the main component of natural gas and biogas. As an abundant energy source, methane is crucial not only to meet current energy needs but also to achieve a sustainable energy future. Conversion of methane to liquid fuels provides energy-dense products and therefore reduces costs for storage, transportation, and distribution. Compared to thermochemical processes, biological conversion has advantages such as high conversion efficiency and using environmentally friendly processes. This paper is a comprehensive review of studies on three promising groups of microorganisms (methanotrophs, ammonia-oxidizing bacteria, and acetogens) that hold potential in converting methane to liquid fuels; their habitats, biochemical conversion mechanisms, performance in liquid fuels production, and genetic modification to enhance the conversion are also discussed. To date, methane-to-methanol conversion efficiencies (moles of methanol produced per mole methane consumed) of up to 80% have been reported. A number of issues that impede scale-up of this technology, such as mass transfer limitations of methane, inhibitory effects of H2S in biogas, usage of expensive chemicals as electron donors, and lack of native strains capable of converting methane to liquid fuels other than methanol, are discussed. Future perspectives and strategies in addressing these challenges are also discussed.
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Sullivan BW, Selmants PC, Hart SC. What is the relationship between soil methane oxidation and other C compounds? GLOBAL CHANGE BIOLOGY 2014; 20:2381-2382. [PMID: 24446071 DOI: 10.1111/gcb.12533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Affiliation(s)
- Benjamin W Sullivan
- School of Forestry, Northern Arizona University, 200 E. Pine Knoll Drive, Flagstaff, AZ, 86011, USA
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Genomic and transcriptomic analyses of the facultative methanotroph Methylocystis sp. strain SB2 grown on methane or ethanol. Appl Environ Microbiol 2014; 80:3044-52. [PMID: 24610846 DOI: 10.1128/aem.00218-14] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A minority of methanotrophs are able to utilize multicarbon compounds as growth substrates in addition to methane. The pathways utilized by these microorganisms for assimilation of multicarbon compounds, however, have not been explicitly examined. Here, we report the draft genome of the facultative methanotroph Methylocystis sp. strain SB2 and perform a detailed transcriptomic analysis of cultures grown with either methane or ethanol. Evidence for use of the canonical methane oxidation pathway and the serine cycle for carbon assimilation from methane was obtained, as well as for operation of the complete tricarboxylic acid (TCA) cycle and the ethylmalonyl-coenzyme A (EMC) pathway. Experiments with Methylocystis sp. strain SB2 grown on methane revealed that genes responsible for the first step of methane oxidation, the conversion of methane to methanol, were expressed at a significantly higher level than those for downstream oxidative transformations, suggesting that this step may be rate limiting for growth of this strain with methane. Further, transcriptomic analyses of Methylocystis sp. strain SB2 grown with ethanol compared to methane revealed that on ethanol (i) expression of the pathway of methane oxidation and the serine cycle was significantly reduced, (ii) expression of the TCA cycle dramatically increased, and (iii) expression of the EMC pathway was similar. Based on these data, it appears that Methylocystis sp. strain SB2 converts ethanol to acetyl-coenzyme A, which is then funneled into the TCA cycle for energy generation or incorporated into biomass via the EMC pathway. This suggests that some methanotrophs have greater metabolic flexibility than previously thought and that operation of multiple pathways in these microorganisms is highly controlled and integrated.
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Abstract
Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria, organisms that live on methane gas as their sole carbon source. Understanding pMMO function has important implications for bioremediation applications and for the development of new, environmentally friendly catalysts for the direct conversion of methane to methanol. Crystal structures of pMMOs from three different methanotrophs reveal a trimeric architecture, consisting of three copies each of the pmoB, pmoA, and pmoC subunits. There are three distinct metal centers in each protomer of the trimer, mononuclear and dinuclear copper sites in the periplasmic regions of pmoB and a mononuclear site within the membrane that can be occupied by copper or zinc. Various models for the pMMO active site have been proposed within these structural constraints, including dicopper, tricopper, and diiron centers. Biochemical and spectroscopic data on pMMO and recombinant soluble fragments, denoted spmoB proteins, indicate that the active site involves copper and is located at the site of the dicopper center in the pmoB subunit. Initial spectroscopic evidence for O(2) binding at this site has been obtained. Despite these findings, questions remain about the active site identity and nuclearity and will be the focus of future studies.
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Affiliation(s)
- Megen A. Culpepper
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, IL 60208, USA
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38
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Stimulation of methanotrophic growth in cocultures by cobalamin excreted by rhizobia. Appl Environ Microbiol 2011; 77:8509-15. [PMID: 21984248 DOI: 10.1128/aem.05834-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophs play a key role in the global carbon cycle, in which they affect methane emissions and help to sustain diverse microbial communities through the conversion of methane to organic compounds. To investigate the microbial interactions that cause positive effects on methanotrophs, cocultures were constructed using Methylovulum miyakonense HT12 and each of nine nonmethanotrophic bacteria, which were isolated from a methane-utilizing microbial consortium culture established from forest soil. Three rhizobial strains were found to strongly stimulate the growth and methane oxidation of M. miyakonense HT12 in cocultures. We purified the stimulating factor produced by Rhizobium sp. Rb122 and identified it as cobalamin. Growth stimulation by cobalamin was also observed for three other gammaproteobacterial methanotrophs. These results suggest that microbial interactions through cobalamin play an important role in methane oxidation in various ecosystems.
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