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Karekar S, Stefanini R, Ahring B. Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens. Microorganisms 2022; 10:microorganisms10020397. [PMID: 35208852 PMCID: PMC8875654 DOI: 10.3390/microorganisms10020397] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/04/2022] Open
Abstract
Homo-acetogens are microbes that have the ability to grow on gaseous substrates such as H2/CO2/CO and produce acetic acid as the main product of their metabolism through a metabolic process called reductive acetogenesis. These acetogens are dispersed in nature and are found to grow in various biotopes on land, water and sediments. They are also commonly found in the gastro-intestinal track of herbivores that rely on a symbiotic relationship with microbes in order to breakdown lignocellulosic biomass to provide the animal with nutrients and energy. For this motive, the fermentation scheme that occurs in the rumen has been described equivalent to a consolidated bioprocessing fermentation for the production of bioproducts derived from livestock. This paper reviews current knowledge of homo-acetogenesis and its potential to improve efficiency in the rumen for production of bioproducts by replacing methanogens, the principal H2-scavengers in the rumen, thus serving as a form of carbon sink by deviating the formation of methane into bioproducts. In this review, we discuss the main strategies employed by the livestock industry to achieve methanogenesis inhibition, and also explore homo-acetogenic microorganisms and evaluate the members for potential traits and characteristics that may favor competitive advantage over methanogenesis, making them prospective candidates for competing with methanogens in ruminant animals.
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Affiliation(s)
- Supriya Karekar
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
| | - Renan Stefanini
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
| | - Birgitte Ahring
- Bioproducts Science and Engineering Laboratory, Washington State University Tri-Cities, 2720 Crimson Way, Richland, WA 99354, USA; (S.K.); (R.S.)
- Department of Biological Systems Engineering, Washington State University, Pullman, WA 99163, USA
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99163, USA
- Correspondence:
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Holmes DE, Zhou J, Ueki T, Woodard T, Lovley DR. Mechanisms for Electron Uptake by Methanosarcina acetivorans during Direct Interspecies Electron Transfer. mBio 2021; 12:e0234421. [PMID: 34607451 PMCID: PMC8546582 DOI: 10.1128/mbio.02344-21] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
Direct interspecies electron transfer (DIET) between bacteria and methanogenic archaea appears to be an important syntrophy in both natural and engineered methanogenic environments. However, the electrical connections on the outer surface of methanogens and the subsequent processing of electrons for carbon dioxide reduction to methane are poorly understood. Here, we report that the genetically tractable methanogen Methanosarcina acetivorans can grow via DIET in coculture with Geobacter metallireducens serving as the electron-donating partner. Comparison of gene expression patterns in M. acetivorans grown in coculture versus pure-culture growth on acetate revealed that transcripts for the outer-surface multiheme c-type cytochrome MmcA were higher during DIET-based growth. Deletion of mmcA inhibited DIET. The high aromatic amino acid content of M. acetivorans archaellins suggests that they might assemble into electrically conductive archaella. A mutant that could not express archaella was deficient in DIET. However, this mutant grew in DIET-based coculture as well as the archaellum-expressing parental strain in the presence of granular activated carbon, which was previously shown to serve as a substitute for electrically conductive pili as a conduit for long-range interspecies electron transfer in other DIET-based cocultures. Transcriptomic data suggesting that the membrane-bound Rnf, Fpo, and HdrED complexes also play a role in DIET were incorporated into a charge-balanced model illustrating how electrons entering the cell through MmcA can yield energy to support growth from carbon dioxide reduction. The results are the first genetics-based functional demonstration of likely outer-surface electrical contacts for DIET in a methanogen. IMPORTANCE The conversion of organic matter to methane plays an important role in the global carbon cycle and is an effective strategy for converting wastes to a useful biofuel. The reduction of carbon dioxide to methane accounts for approximately a third of the methane produced in anaerobic soils and sediments as well as waste digesters. Potential electron donors for carbon dioxide reduction are H2 or electrons derived from direct interspecies electron transfer (DIET) between bacteria and methanogens. Elucidating the relative importance of these electron donors has been difficult due to a lack of information on the electrical connections on the outer surfaces of methanogens and how they process the electrons received from DIET. Transcriptomic patterns and gene deletion phenotypes reported here provide insight into how a group of Methanosarcina organisms that play an important role in methane production in soils and sediments participate in DIET.
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Affiliation(s)
- Dawn E. Holmes
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Department of Physical and Biological Science, Western New England University, Springfield, Massachusetts, USA
| | - Jinjie Zhou
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Trevor Woodard
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts—Amherst, Amherst, Massachusetts, USA
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Walker DJF, Nevin KP, Holmes DE, Rotaru AE, Ward JE, Woodard TL, Zhu J, Ueki T, Nonnenmann SS, McInerney MJ, Lovley DR. Syntrophus conductive pili demonstrate that common hydrogen-donating syntrophs can have a direct electron transfer option. ISME JOURNAL 2020; 14:837-846. [PMID: 31896792 DOI: 10.1038/s41396-019-0575-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/02/2019] [Accepted: 12/16/2019] [Indexed: 11/09/2022]
Abstract
Syntrophic interspecies electron exchange is essential for the stable functioning of diverse anaerobic microbial communities. Hydrogen/formate interspecies electron transfer (HFIT), in which H2 and/or formate function as diffusible electron carriers, has been considered to be the primary mechanism for electron transfer because most common syntrophs were thought to lack biochemical components, such as electrically conductive pili (e-pili), necessary for direct interspecies electron transfer (DIET). Here we report that Syntrophus aciditrophicus, one of the most intensively studied microbial models for HFIT, produces e-pili and can grow via DIET. Heterologous expression of the putative S. aciditrophicus type IV pilin gene in Geobacter sulfurreducens yielded conductive pili of the same diameter (4 nm) and conductance of the native S. aciditrophicus pili and enabled long-range electron transport in G. sulfurreducens. S. aciditrophicus lacked abundant c-type cytochromes often associated with DIET. Pilin genes likely to yield e-pili were found in other genera of hydrogen/formate-producing syntrophs. The finding that DIET is a likely option for diverse syntrophs that are abundant in many anaerobic environments necessitates a reexamination of the paradigm that HFIT is the predominant mechanism for syntrophic electron exchange within anaerobic microbial communities of biogeochemical and practical significance.
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Affiliation(s)
- David J F Walker
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA.,Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Kelly P Nevin
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Dawn E Holmes
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA.,Department of Physical and Biological Science, Western New England University, Springfield, MA, USA
| | - Amelia-Elena Rotaru
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Joy E Ward
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Trevor L Woodard
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Jiaxin Zhu
- Department of Mechanical and Industrial Engineering, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Stephen S Nonnenmann
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, MA, USA.,Department of Mechanical and Industrial Engineering, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, MA, USA. .,Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, MA, USA.
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Zhang Y, Li Q, Dai Q, Kang Y. Microbial mechanism underlying high and stable methane oxidation rates during mudflat reclamation with long-term rice cultivation: Illumina high-throughput sequencing-based data analysis. JOURNAL OF HAZARDOUS MATERIALS 2019; 371:332-341. [PMID: 30856444 DOI: 10.1016/j.jhazmat.2019.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/10/2019] [Accepted: 03/06/2019] [Indexed: 06/09/2023]
Abstract
This study aimed to determine the methane oxidation rates (MOR), pmoA gene abundance and diversity, and microbial community composition using Illumina high-throughput sequencing. Mudflats located within Yancheng City, divided into different plots with 0-, 11-, and 20-year successive rice planting histories, were selected and sampled. The study found that the relative MOR (normalized with the 16S rRNA gene) increased dramatically after 11-year cultivation and remained stable in 20-year treatment, indicating that long-term rice cultivation in mudflats promoted MOR. The sequencing data analysis revealed that high MOR was related to the synergistic growth of methane-producing archaea (MPA) and aerobic and facultative methane-consuming bacteria (MCB) mainly belonging to Proteobacteria. Redundancy and correlation analyses showed that Methylophilaceae and Methylococcaceae affiliated within β- and γ-Proteobacterial methanotrophs were closely related to the relative MOR. Methane-oxidizing archaea (MOA) coupled to sulfate and nitrite reductions contributed more to the high and stable MOR compared with Proteobacterial MCB. Chloroflexi and Geobacter were the potential hydrogen donors for hydrogenotrophic MPA. The results showed that long-term rice cultivation in mudflats promoted the relative MOR. The unknown MOA coupled to sulfate and nitrite reductions, besides the necessary hydrogenotrophic MPA and their hydrogen donors (Chloroflexi and Geobacter) collectively contributed to methane cycling.
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Affiliation(s)
- Yang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Qing Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China
| | - Qigen Dai
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Research Institute of Rice Industry Engineering Technology, Yangzhou University, Yangzhou, 225009, PR China.
| | - Yijun Kang
- College of Marine and Bio-engineering, Yancheng Teachers University, Yancheng, Jiangsu, PR China.
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Laskar F, Das Purkayastha S, Sen A, Bhattacharya MK, Misra BB. Diversity of methanogenic archaea in freshwater sediments of lacustrine ecosystems. J Basic Microbiol 2017; 58:101-119. [PMID: 29083035 DOI: 10.1002/jobm.201700341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/15/2022]
Abstract
About half of the global methane (CH4 ) emission is contributed by the methanogenic archaeal communities leading to a significant increase in global warming. This unprecedented situation has increased the ever growing necessity of evaluating the control measures for limiting CH4 emission to the atmosphere. Unfortunately, research endeavors on the diversity and functional interactions of methanogens are not extensive till date. We anticipate that the study of the diversity of methanogenic community is paramount for understanding the metabolic processes in freshwater lake ecosystems. Although there are several disadvantages of conventional culture-based methods for determining the diversity of methanogenic archaeal communities, in order to understand their ecological roles in natural environments it is required to culture the microbes. Recently different molecular techniques have been developed for determining the structure of methanogenic archaeal communities thriving in freshwater lake ecosystem. The two gene based cloning techniques required for this purpose are 16S rRNA and methyl coenzyme M reductase (mcrA) in addition to the recently developed metagenomics approaches and high throughput next generation sequencing efforts. This review discusses the various methods of culture-dependent and -independent measures of determining the diversity of methanogen communities in lake sediments in lieu of the different molecular approaches and inter-relationships of diversity of methanogenic archaea.
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Affiliation(s)
- Folguni Laskar
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Aniruddha Sen
- Advance Institutional Biotech Hub, Karimganj College, Karimganj, Assam, India
| | | | - Biswapriya B Misra
- Department of Genetics, Texas Biomedical Research Institute, San Antonio 78227, Texas, USA
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Thebrath B, Mayer HP, Conrad R. Bicarbonate-dependent production and methanogenic consumption of acetate in anoxic paddy soil. FEMS Microbiol Ecol 2011. [DOI: 10.1111/j.1574-6941.1992.tb01764.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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O’Reilly J, Chinalia F, Mahony T, Collins G, Wu J, O’Flaherty V. Cultivation of low-temperature (15°C), anaerobic, wastewater treatment granules. Lett Appl Microbiol 2009; 49:421-6. [DOI: 10.1111/j.1472-765x.2009.02682.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Thebrath B, Mayer HP, Conrad R. Bicarbonate-dependent production and methanogenic consumption of acetate in anoxic paddy soil. FEMS Microbiol Lett 2006. [DOI: 10.1111/j.1574-6968.1992.tb04821.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chin KJ, Janssen PH. Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil. Appl Environ Microbiol 2002; 68:2089-92. [PMID: 11916740 PMCID: PMC123890 DOI: 10.1128/aem.68.4.2089-2092.2002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2001] [Accepted: 01/11/2002] [Indexed: 11/20/2022] Open
Abstract
Propionate-forming bacteria seem to be abundant in anoxic rice paddy soil, but biogeochemical investigations show that propionate is not a correspondingly important intermediate in carbon flux in this system. Mixed cultures of Opitutus terrae strain PB90-1, a representative propionate-producing bacterium from rice paddy soil, and the hydrogenotrophic Methanospirillum hungatei strain SK maintained hydrogen partial pressures similar to those in the soil. The associated shift away from propionate formation observed in these cultures helps to reconcile the disparity between microbiological and biogeochemical studies.
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Affiliation(s)
- Kuk-Jeong Chin
- Max-Planck-Institut für Terrestrische Mikrobiologie, D-35043 Marburg, Germany
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SUGIMOTO ATSUKO, INOUE TETSUSHI, TAYASU ICHIRO, MILLER LEIGH, TAKEICHI SATOKI, ABE TAKUYA. Methane and hydrogen production in a termite-symbiont system. Ecol Res 2002. [DOI: 10.1046/j.1440-1703.1998.00262.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Conrad R, Klose M. How specific is the inhibition by methyl fluoride of acetoclastic methanogenesis in anoxic rice field soil? FEMS Microbiol Ecol 1999. [DOI: 10.1111/j.1574-6941.1999.tb00634.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Chin KJ, Conrad R. Intermediary metabolism in methanogenic paddy soil and the influence of temperature. FEMS Microbiol Ecol 1995. [DOI: 10.1111/j.1574-6941.1995.tb00166.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Krämer H, Conrad R. Measurement of dissolved H2 concentrations in methanogenic environments with a gas diffusion probe. FEMS Microbiol Ecol 1993. [DOI: 10.1111/j.1574-6941.1993.tb00027.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Peter Mayer H, Conrad R. Factors influencing the population of methanogenic bacteria and the initiation of methane production upon flooding of paddy soil. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb03930.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Conrad R, Bak F, Seitz H, Thebrath B, Mayer H, Schütz H. Hydrogen turnover by psychrotrophic homoacetogenic and mesophilic methanogenic bacteria in anoxic paddy soil and lake sediment. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03382.x] [Citation(s) in RCA: 150] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Conrad R, Mayer HP, Wüst M. Temporal change of gas metabolism by hydrogen-syntrophic methanogenic bacterial associations in anoxic paddy soil. FEMS Microbiol Lett 1989. [DOI: 10.1111/j.1574-6968.1989.tb03701.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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