1
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Zhang X, Zhang X, Yang Y. Update of gut gas metabolism in ulcerative colitis. Expert Rev Gastroenterol Hepatol 2024; 18:339-349. [PMID: 39031456 DOI: 10.1080/17474124.2024.2383635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 07/19/2024] [Indexed: 07/22/2024]
Abstract
INTRODUCTION Ulcerative colitis (UC) is a chronic, nonspecific inflammatory disease of the intestine. The intestinal microbiota is essential in the occurrence and development of UC. Gut gases are produced via bacterial fermentation or chemical interactions, which can reveal altered intestinal microbiota, abnormal cellular metabolism, and inflammation responses. Recent studies have demonstrated that UC patients have an altered gut gas metabolism. AREAS COVERED In this review, we integrate gut gas metabolism advances in UC and discuss intestinal gases' clinical values as new biomarkers or therapeutic targets for UC, providing the foundation for further research. Literature regarding gut gas metabolism and its significance in UC from inception to October 2023 was searched on the MEDLINE database and references from relevant articles were investigated. EXPERT OPINION Depending on their type, concentration, and volume, gut gases can induce or alleviate clinical symptoms and regulate intestinal motility, inflammatory responses, immune function, and oxidative stress, significantly impacting UC. Gut gases may function as new biomarkers and provide potential diagnostic or therapeutic targets for UC.
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Affiliation(s)
- Xiaohan Zhang
- Medical School, Nankai University, Tianjin, China
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiuli Zhang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yunsheng Yang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
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2
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Palacios PA, Philips J, Bentien A, Kofoed MVW. Relevance of extracellular electron uptake mechanisms for electromethanogenesis applications. Biotechnol Adv 2024; 73:108369. [PMID: 38685440 DOI: 10.1016/j.biotechadv.2024.108369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/21/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024]
Abstract
Electromethanogenesis has emerged as a biological branch of Power-to-X technologies that implements methanogenic microorganisms, as an alternative to chemical Power-to-X, to convert electrical power from renewable sources, and CO2 into methane. Unlike biomethanation processes where CO2 is converted via exogenously added hydrogen, electromethanogenesis occurs in a bioelectrochemical set-up that combines electrodes and microorganisms. Thereby, mixed, or pure methanogenic cultures catalyze the reduction of CO2 to methane via reducing equivalents supplied by a cathode. Recent advances in electromethanogenesis have been driven by interdisciplinary research at the intersection of microbiology, electrochemistry, and engineering. Integrating the knowledge acquired from these areas is essential to address the specific challenges presented by this relatively young biotechnology, which include electron transfer limitations, low energy and product efficiencies, and reactor design to enable upscaling. This review approaches electromethanogenesis from a multidisciplinary perspective, putting emphasis on the extracellular electron uptake mechanisms that methanogens use to obtain energy from cathodes, since understanding these mechanisms is key to optimize the electrochemical conditions for the development of these systems. This work summarizes the direct and indirect extracellular electron uptake mechanisms that have been elucidated to date in methanogens, along with the ones that remain unsolved. As the study of microbial corrosion, a similar bioelectrochemical process with Fe0 as electron source, has contributed to elucidate different mechanisms on how methanogens use solid electron donors, insights from both fields, biocorrosion and electromethanogenesis, are combined. Based on the repertoire of mechanisms and their potential to convert CO2 to methane, we conclude that for future applications, electromethanogenesis should focus on the indirect mechanism with H2 as intermediary. By summarizing and linking the general aspects and challenges of this process, we hope that this review serves as a guide for researchers working on electromethanogenesis in different areas of expertise to overcome the current limitations and continue with the optimization of this promising interdisciplinary technology.
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Affiliation(s)
- Paola Andrea Palacios
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark.
| | - Jo Philips
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark
| | - Anders Bentien
- Department of Biological and Chemical Engineering, Aarhus University, Aabogade 40, Aarhus N, 8200 Aarhus, Denmark
| | - Michael Vedel Wegener Kofoed
- Department of Biological and Chemical Engineering, Aarhus University, Gustav Wieds Vej 10C, 8200 Aarhus, Denmark
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3
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El Jeni R, Villot C, Koyun OY, Osorio-Doblado A, Baloyi JJ, Lourenco JM, Steele M, Callaway TR. Invited review: "Probiotic" approaches to improving dairy production: Reassessing "magic foo-foo dust". J Dairy Sci 2024; 107:1832-1856. [PMID: 37949397 DOI: 10.3168/jds.2023-23831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023]
Abstract
The gastrointestinal microbial consortium in dairy cattle is critical to determining the energetic status of the dairy cow from birth through her final lactation. The ruminant's microbial community can degrade a wide variety of feedstuffs, which can affect growth, as well as production rate and efficiency on the farm, but can also affect food safety, animal health, and environmental impacts of dairy production. Gut microbial diversity and density are powerful tools that can be harnessed to benefit both producers and consumers. The incentives in the United States to develop Alternatives to Antibiotics for use in food-animal production have been largely driven by the Veterinary Feed Directive and have led to an increased use of probiotic approaches to alter the gastrointestinal microbial community composition, resulting in improved heifer growth, milk production and efficiency, and animal health. However, the efficacy of direct-fed microbials or probiotics in dairy cattle has been highly variable due to specific microbial ecological factors within the host gut and its native microflora. Interactions (both synergistic and antagonistic) between the microbial ecosystem and the host animal physiology (including epithelial cells, immune system, hormones, enzyme activities, and epigenetics) are critical to understanding why some probiotics work but others do not. Increasing availability of next-generation sequencing approaches provides novel insights into how probiotic approaches change the microbial community composition in the gut that can potentially affect animal health (e.g., diarrhea or scours, gut integrity, foodborne pathogens), as well as animal performance (e.g., growth, reproduction, productivity) and fermentation parameters (e.g., pH, short-chain fatty acids, methane production, and microbial profiles) of cattle. However, it remains clear that all direct-fed microbials are not created equal and their efficacy remains highly variable and dependent on stage of production and farm environment. Collectively, data have demonstrated that probiotic effects are not limited to the simple mechanisms that have been traditionally hypothesized, but instead are part of a complex cascade of microbial ecological and host animal physiological effects that ultimately impact dairy production and profitability.
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Affiliation(s)
- R El Jeni
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - C Villot
- Lallemand SAS, Blagnac, France, 31069
| | - O Y Koyun
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - A Osorio-Doblado
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - J J Baloyi
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - J M Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602
| | - M Steele
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - T R Callaway
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602.
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4
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Hessler T, Harrison ST, Banfield JF, Huddy RJ. Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2830-2846. [PMID: 38301118 PMCID: PMC10867827 DOI: 10.1021/acs.est.3c04187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/28/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.
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Affiliation(s)
- Tomas Hessler
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- Environmental
Genomics and Systems Biology Division, Lawrence
Berkeley National Laboratory, Berkeley, California CA94720, United States
| | - Susan T.L. Harrison
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
| | - Jillian F. Banfield
- The
Innovative Genomics Institute at the University of California, Berkeley, California CA94720, United
States
- The
Department of Earth and Planetary Science, University of California, Berkeley, California CA94720, United States
- The
Department of Environmental Science, Policy and Management, University of California, Berkeley, California CA94720, United States
| | - Robert J. Huddy
- The
Center for Bioprocess Engineering Research, University of Cape Town, Cape Town 7700, South Africa
- Department
of Chemical Engineering, University of Cape
Town, Cape Town 7700, South Africa
- The Future
Water Institute, University of Cape Town, Cape Town 7700, South Africa
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5
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Sandfeld T, Grøn LV, Munoz L, Meyer RL, Koren K, Philips J. Considerations on the use of microsensors to profile dissolved H2 concentrations in microbial electrochemical reactors. PLoS One 2024; 19:e0293734. [PMID: 38241241 PMCID: PMC10798470 DOI: 10.1371/journal.pone.0293734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/18/2023] [Indexed: 01/21/2024] Open
Abstract
Measuring the distribution and dynamics of H2 in microbial electrochemical reactors is valuable to gain insights into the processes behind novel bioelectrochemical technologies, such as microbial electrosynthesis. Here, a microsensor method to measure and profile dissolved H2 concentrations in standard H-cell reactors is described. Graphite cathodes were oriented horizontally to enable the use of a motorized microprofiling system and a stereomicroscope was used to place the H2 microsensor precisely on the cathode surface. Profiling was performed towards the gas-liquid interface, while preserving the electric connections and flushing the headspace (to maintain anoxic conditions) and under strict temperature control (to overcome the temperature sensitivity of the microsensors). This method was tested by profiling six reactors, with and without inoculation of the acetogen Sporomusa ovata, at three different time points. H2 accumulated over time in the abiotic controls, while S. ovata maintained low H2 concentrations throughout the liquid phase (< 4 μM) during the whole experimental period. These results demonstrate that this setup generated insightful H2 profiles. However, various limitations of this microsensor method were identified, as headspace flushing lowered the dissolved H2 concentrations over time. Moreover, microsensors can likely not accurately measure H2 in the immediate vicinity of the solid cathode, because the solids cathode surface obstructs H2 diffusion into the microsensor. Finally, the reactors had to be discarded after microsensor profiling. Interested users should bear these considerations in mind when applying microsensors to characterize microbial electrochemical reactors.
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Affiliation(s)
| | - Louise Vinther Grøn
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Laura Munoz
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Klaus Koren
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Jo Philips
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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6
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Keller NS, Lüders K, Hornbruch G, Birnstengel S, Vogt C, Ebert M, Kallies R, Dahmke A, Richnow HH. Rapid Consumption of Dihydrogen Injected into a Shallow Aquifer by Ecophysiologically Different Microbes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:333-341. [PMID: 38117480 PMCID: PMC10785757 DOI: 10.1021/acs.est.3c04340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023]
Abstract
The envisaged future dihydrogen (H2) economy requires a H2 gas grid as well as large deep underground stores. However, the consequences of an unintended spread of H2 through leaky pipes, wells, or subterranean gas migrations on groundwater resources and their ecosystems are poorly understood. Therefore, we emulated a short-term leakage incident by injecting gaseous H2 into a shallow aquifer at the TestUM test site and monitored the subsequent biogeochemical processes in the groundwater system. At elevated H2 concentrations, an increase in acetate concentrations and a decrease in microbial α-diversity with a concomitant change in microbial β-diversity were observed. Additionally, microbial H2 oxidation was indicated by temporally higher abundances of taxa known for aerobic or anaerobic H2 oxidation. After H2 concentrations diminished below the detection limit, α- and β-diversity approached baseline values. In summary, the emulated H2 leakage resulted in a temporally limited change of the groundwater microbiome and associated geochemical conditions due to the intermediate growth of H2 consumers. The results confirm the general assumption that H2, being an excellent energy and electron source for many microorganisms, is quickly microbiologically consumed in the environment after a leakage.
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Affiliation(s)
- Nina S. Keller
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Klas Lüders
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Götz Hornbruch
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Susann Birnstengel
- Department
of Monitoring & Exploration Technologies, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Carsten Vogt
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Markus Ebert
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - René Kallies
- Department
of Environmental Microbiology, Helmholtz
Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Andreas Dahmke
- Department
of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy
(KGE), 24118 Kiel, Germany
| | - Hans H. Richnow
- Department
of Isotope Biogeochemistry, Helmholtz Centre
for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Isodetect
GmbH, Deutscher Platz
5b, 04103 Leipzig, Germany
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7
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Li Q, Ma Z, Huo J, Zhang X, Wang R, Zhang S, Jiao J, Dong X, Janssen PH, Ungerfeld EM, Greening C, Tan Z, Wang M. Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield. THE ISME JOURNAL 2024; 18:wrad016. [PMID: 38365243 PMCID: PMC10811737 DOI: 10.1093/ismejo/wrad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 02/18/2024]
Abstract
Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.
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Affiliation(s)
- Qiushuang Li
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Ma
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China
| | - Jiabin Huo
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiumin Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Rong Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Shizhe Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Jinzhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Xiyang Dong
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Peter H Janssen
- AgResearch Limited, Grasslands Research Centre, Palmerston North, Private Bag 11008, New Zealand
| | - Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias (INIA), Temuco, Vilcún 4880000, Chile
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Zhiliang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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8
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Chen G, Wang R, Sun M, Chen J, Iyobosa E, Zhao J. Carbon dioxide reduction to high-value chemicals in microbial electrosynthesis system: Biological conversion and regulation strategies. CHEMOSPHERE 2023; 344:140251. [PMID: 37769909 DOI: 10.1016/j.chemosphere.2023.140251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Large emissions of atmospheric carbon dioxide (CO2) are causing climatic and environmental problems. It is crucial to capture and utilize the excess CO2 through diverse methods, among which the microbial electrosynthesis (MES) system has become an attractive and promising technology to mitigate greenhouse effects while reducing CO2 to high-value chemicals. However, the biological conversion and metabolic pathways through microbial catalysis have not been clearly elucidated. This review first introduces the main acetogenic bacteria for CO2 reduction and extracellular electron transfer mechanisms in MES. It then intensively analyzes the CO2 bioconversion pathways and carbon chain elongation processes in MES, together with energy supply and utilization. The factors affecting MES performance, including physical, chemical, and biological aspects, are summarized, and the strategies to promote and regulate bioconversion in MES are explored. Finally, challenges and perspectives concerning microbial electrochemical carbon sequestration are proposed, and suggestions for future research are also provided. This review provides theoretical foundation and technical support for further development and industrial application of MES for CO2 reduction.
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Affiliation(s)
- Gaoxiang Chen
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Rongchang Wang
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China.
| | - Maoxin Sun
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Jie Chen
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Eheneden Iyobosa
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Jianfu Zhao
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
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9
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Laura M, Jo P. No acetogen is equal: Strongly different H 2 thresholds reflect diverse bioenergetics in acetogenic bacteria. Environ Microbiol 2023; 25:2032-2040. [PMID: 37209014 DOI: 10.1111/1462-2920.16429] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/09/2023] [Indexed: 05/21/2023]
Abstract
Acetogens share the capacity to convert H2 and CO2 into acetate for energy conservation (ATP synthesis). This reaction is attractive for applications, such as gas fermentation and microbial electrosynthesis. Different H2 partial pressures prevail in these distinctive applications (low concentrations during microbial electrosynthesis [<40 Pa] vs. high concentrations with gas fermentation [>9%]). Strain selection thus requires understanding of how different acetogens perform under different H2 partial pressures. Here, we determined the H2 threshold (H2 partial pressure at which acetogenesis halts) for eight different acetogenic strains under comparable conditions. We found a three orders of magnitude difference between the lowest and highest H2 threshold (6 ± 2 Pa for Sporomusa ovata vs. 1990 ± 67 Pa for Clostridium autoethanogenum), while Acetobacterium strains had intermediate H2 thresholds. We used these H2 thresholds to estimate ATP gains, which ranged from 0.16 to 1.01 mol ATP per mol acetate (S. ovata vs. C. autoethanogenum). The experimental H2 thresholds thus suggest strong differences in the bioenergetics of acetogenic strains and possibly also in their growth yields and kinetics. We conclude that no acetogen is equal and that a good understanding of their differences is essential to select the most optimal strain for different biotechnological applications.
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Affiliation(s)
- Munoz Laura
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Philips Jo
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
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10
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Li J, Zhao S, Meng Z, Gao Y, Miao J, Mao S, Jin W. Effects of Fumarate and Nitroglycerin on In Vitro Rumen Fermentation, Methane and Hydrogen Production, and on Microbiota. BIOLOGY 2023; 12:1011. [PMID: 37508440 PMCID: PMC10376899 DOI: 10.3390/biology12071011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
This study aimed to investigate the effects of fumarate and nitroglycerin on rumen fermentation, methane and hydrogen production, and microbiota. In vitro rumen fermentation was used in this study with four treatment groups: control (CON), fumarate (FA), nitroglycerin (NG) and fumarate plus nitroglycerin (FN). Real-time PCR and 16S rRNA gene sequencing were used to analyze microbiota. The results showed that nitroglycerin completely inhibited methane production and that this resulted in hydrogen accumulation. Fumarate decreased the hydrogen accumulation and improved the rumen fermentation parameters. Fumarate increased the concentration of propionate and microbial crude protein, and decreased the ratio of acetate to propionate in FN. Fumarate, nitroglycerin and their combination did not affect the abundance of bacteria, protozoa and anaerobic fungi, but altered archaea. The PCoA showed that the bacterial (Anosim, R = 0.747, p = 0.001) and archaeal communities (Anosim, R = 0.410, p = 0.005) were different among the four treatments. Compared with CON, fumarate restored Bacteroidetes, Firmicutes, Spirochaetae, Actinobacteria, Unclassified Ruminococcaceae, Streptococcus, Treponema and Bifidobacterium in relative abundance in FN, but did not affect Succinivibrio, Ruminobacter and archaeal taxa. The results indicated that fumarate alleviated the depressed rumen fermentation caused by the inhibition of methanogenesis by nitroglycerin. This may potentially provide an alternative way to use these chemicals to mitigate methane emission in ruminants.
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Affiliation(s)
- Jichao Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengwei Zhao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenxiang Meng
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlong Gao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jing Miao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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11
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Conrad R. Complexity of temperature dependence in methanogenic microbial environments. Front Microbiol 2023; 14:1232946. [PMID: 37485527 PMCID: PMC10359720 DOI: 10.3389/fmicb.2023.1232946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
There is virtually no environmental process that is not dependent on temperature. This includes the microbial processes that result in the production of CH4, an important greenhouse gas. Microbial CH4 production is the result of a combination of many different microorganisms and microbial processes, which together achieve the mineralization of organic matter to CO2 and CH4. Temperature dependence applies to each individual step and each individual microbe. This review will discuss the different aspects of temperature dependence including temperature affecting the kinetics and thermodynamics of the various microbial processes, affecting the pathways of organic matter degradation and CH4 production, and affecting the composition of the microbial communities involved. For example, it was found that increasing temperature results in a change of the methanogenic pathway with increasing contribution from mainly acetate to mainly H2/CO2 as immediate CH4 precursor, and with replacement of aceticlastic methanogenic archaea by thermophilic syntrophic acetate-oxidizing bacteria plus thermophilic hydrogenotrophic methanogenic archaea. This shift is consistent with reaction energetics, but it is not obligatory, since high temperature environments exist in which acetate is consumed by thermophilic aceticlastic archaea. Many studies have shown that CH4 production rates increase with temperature displaying a temperature optimum and a characteristic apparent activation energy (Ea). Interestingly, CH4 release from defined microbial cultures, from environmental samples and from wetland field sites all show similar Ea values around 100 kJ mol-1 indicating that CH4 production rates are limited by the methanogenic archaea rather than by hydrolysis of organic matter. Hence, the final rather than the initial step controls the methanogenic degradation of organic matter, which apparently is rarely in steady state.
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12
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Karadagli F, Marcus A, Rittmann BE. Microbiological hydrogen (H 2 ) thresholds in anaerobic continuous-flow systems: Effects of system characteristics. Biotechnol Bioeng 2023. [PMID: 37148477 DOI: 10.1002/bit.28415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
Hydrogen (H2 ) concentrations that were associated with microbiological respiratory processes (RPs) such as sulfate reduction and methanogenesis were quantified in continuous-flow systems (CFSs) (e.g., bioreactors, sediments). Gibbs free energy yield (ΔǴ ~ 0) of the relevant RP has been proposed to control the observed H2 concentrations, but most of the reported values do not align with the proposed energetic trends. Alternatively, we postulate that system characteristics of each experimental design influence all system components including H2 concentrations. To analyze this proposal, a Monod-based mathematical model was developed and used to design a gas-liquid bioreactor for hydrogenotrophic methanogenesis with Methanobacterium bryantii M.o.H. Gas-to-liquid H2 mass transfer, microbiological H2 consumption, biomass growth, methane formation, and Gibbs free energy yields were evaluated systematically. Combining model predictions and experimental results revealed that an initially large biomass concentration created transients during which biomass consumed [H2 ]L rapidly to the thermodynamic H2 -threshold (≤1 nM) that triggerred the microorganisms to stop H2 oxidation. With no H2 oxidation, continuous gas-to-liquid H2 transfer increased [H2 ]L to a level that signaled the methanogens to resume H2 oxidation. Thus, an oscillatory H2 -concentration profile developed between the thermodynamic H2 -threshold (≤1 nM) and a low [H2 ]L (~10 nM) that relied on the rate of gas-to-liquid H2 -transfer. The transient [H2 ]L values were too low to support biomass synthesis that could balance biomass losses through endogenous oxidation and advection; thus, biomass declined continuously and disappeared. A stable [H2 ]L (1807 nM) emerged as a result of abiotic H2 -balance between gas-to-liquid H2 transfer and H2 removal via advection of liquid-phase.
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Affiliation(s)
- Fatih Karadagli
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
| | - Andrew Marcus
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Skyology Inc., San Francisco, California, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
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13
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Chen K, Chen X, Stegen JC, Villa JA, Bohrer G, Song X, Chang KY, Kaufman M, Liang X, Guo Z, Roden EE, Zheng C. Vertical Hydrologic Exchange Flows Control Methane Emissions from Riverbed Sediments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:4014-4026. [PMID: 36811826 DOI: 10.1021/acs.est.2c07676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
CH4 emissions from inland waters are highly uncertain in the current global CH4 budget, especially for streams, rivers, and other lotic systems. Previous studies have attributed the strong spatiotemporal heterogeneity of riverine CH4 to environmental factors such as sediment type, water level, temperature, or particulate organic carbon abundance through correlation analysis. However, a mechanistic understanding of the basis for such heterogeneity is lacking. Here, we combine sediment CH4 data from the Hanford reach of the Columbia River with a biogeochemical-transport model to show that vertical hydrologic exchange flows (VHEFs), driven by the difference between river stage and groundwater level, determine CH4 flux at the sediment-water interface. CH4 fluxes show a nonlinear relationship with the magnitude of VHEFs, where high VHEFs introduce O2 into riverbed sediments, which inhibit CH4 production and induce CH4 oxidation, and low VHEFs cause transient reduction in CH4 flux (relative to production) due to reduced advective CH4 transport. In addition, VHEFs lead to the hysteresis of temperature rise and CH4 emissions because high river discharge caused by snowmelt in spring leads to strong downwelling flow that offsets increasing CH4 production with temperature rise. Our findings reveal how the interplay between in-stream hydrologic flux besides fluvial-wetland connectivity and microbial metabolic pathways that compete with methanogenic pathways can produce complex patterns in CH4 production and emission in riverbed alluvial sediments.
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Affiliation(s)
- Kewei Chen
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xingyuan Chen
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James C Stegen
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jorge A Villa
- School of Geosciences, University of Louisiana at Lafayette, Lafayette, Louisiana 70506, United States
| | - Gil Bohrer
- Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, Ohio 43210, United States
| | - Xuehang Song
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kuang-Yu Chang
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew Kaufman
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xiuyu Liang
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiling Guo
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Chunmiao Zheng
- School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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14
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de Smit S, Langedijk JJH, van Haalen LCA, Lin SH, Bitter JH, Strik DPBTB. Methodology for In Situ Microsensor Profiling of Hydrogen, pH, Oxidation-Reduction Potential, and Electric Potential throughout Three-Dimensional Porous Cathodes of (Bio)Electrochemical Systems. Anal Chem 2023; 95:2680-2689. [PMID: 36715453 PMCID: PMC9909735 DOI: 10.1021/acs.analchem.2c03121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/17/2023] [Indexed: 01/31/2023]
Abstract
We developed a technique based on the use of microsensors to measure pH and H2 gradients during microbial electrosynthesis. The use of 3D electrodes in (bio)electrochemical systems likely results in the occurrence of gradients from the bulk conditions into the electrode. Since these gradients, e.g., with respect to pH and reactant/product concentrations determine the performance of the electrode, it is essential to be able to accurately measure them. Apart from these parameters, also local oxidation-reduction potential and electric field potential were determined in the electrolyte and throughout the 3D porous electrodes. Key was the realization that the presence of an electric field disturbed the measurements obtained by the potentiometric type of microsensor. To overcome the interference on the pH measure, a method was validated where the signal was corrected for the local electric field measured with the electric potential microsensor. The developed method provides a useful tool for studies about electrode design, reactor engineering, measuring gradients in electroactive biofilms, and flow dynamics in and around 3D porous electrodes of (bio)electrochemical systems.
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Affiliation(s)
- Sanne
M. de Smit
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
- Biobased
Chemistry and Technology, Wageningen University
and Research, Wageningen 6708WG, The Netherlands
| | - Jelle J. H. Langedijk
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Lennert C. A. van Haalen
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Shih Hsuan Lin
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
| | - Johannes H. Bitter
- Biobased
Chemistry and Technology, Wageningen University
and Research, Wageningen 6708WG, The Netherlands
| | - David P. B. T. B. Strik
- Environmental
Technology, Wageningen University and Research, Wageningen 6708WG, The Netherlands
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15
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Karekar SC, Ahring BK. Reducing methane production from rumen cultures by bioaugmentation with homoacetogenic bacteria. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2022. [DOI: 10.1016/j.bcab.2022.102526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Li QS, Wang R, Ma ZY, Zhang XM, Jiao JZ, Zhang ZG, Ungerfeld EM, Yi KL, Zhang BZ, Long L, Long Y, Tao Y, Huang T, Greening C, Tan ZL, Wang M. Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants. THE ISME JOURNAL 2022; 16:2535-2546. [PMID: 35931768 PMCID: PMC9562222 DOI: 10.1038/s41396-022-01294-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/29/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022]
Abstract
Ruminants are important for global food security but emit the greenhouse gas methane. Rumen microorganisms break down complex carbohydrates to produce volatile fatty acids and molecular hydrogen. This hydrogen is mainly converted into methane by archaea, but can also be used by hydrogenotrophic acetogenic and respiratory bacteria to produce useful metabolites. A better mechanistic understanding is needed on how dietary carbohydrates influence hydrogen metabolism and methanogenesis. We profiled the composition, metabolic pathways, and activities of rumen microbiota in 24 beef cattle adapted to either fiber-rich or starch-rich diets. The fiber-rich diet selected for fibrolytic bacteria and methanogens resulting in increased fiber utilization, while the starch-rich diet selected for amylolytic bacteria and lactate utilizers, allowing the maintenance of a healthy rumen and decreasing methane production (p < 0.05). Furthermore, the fiber-rich diet enriched for hydrogenotrophic methanogens and acetogens leading to increased electron-bifurcating [FeFe]-hydrogenases, methanogenic [NiFe]- and [Fe]-hydrogenases and acetyl-CoA synthase, with lower dissolved hydrogen (42%, p < 0.001). In contrast, the starch-rich diet enriched for respiratory hydrogenotrophs with greater hydrogen-producing group B [FeFe]-hydrogenases and respiratory group 1d [NiFe]-hydrogenases. Parallel in vitro experiments showed that the fiber-rich selected microbiome enhanced acetate and butyrate production while decreasing methane production (p < 0.05), suggesting that the enriched hydrogenotrophic acetogens converted some hydrogen that would otherwise be used by methanogenesis. These insights into hydrogen metabolism and methanogenesis improve understanding of energy harvesting strategies, healthy rumen maintenance, and methane mitigation in ruminants.
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Affiliation(s)
- Qiu Shuang Li
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Zhi Yuan Ma
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiu Min Zhang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Jin Zhen Jiao
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China
| | - Zhi Gang Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, Yunnan, China
| | - Emilio M Ungerfeld
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias (INIA), Temuco, Chile
| | - Kang Le Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
| | - Bai Zhong Zhang
- Hunan Institute of Animal and Veterinary Science, Changsha, Hunan, China
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
| | - Liang Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
- Hunan De Nong Animal Husbandry Group Co. Ltd, Huayuan, Hunan, China
| | - Yun Long
- Xiangxi Cattle Engineering Technology Center of Hunan Province, Huayuan, Hunan, China
- Hunan De Nong Animal Husbandry Group Co. Ltd, Huayuan, Hunan, China
| | - Ye Tao
- Shanghai BIOZERON Biotechnology Company Ltd, Shanghai, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chris Greening
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Australia
| | - Zhi Liang Tan
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Min Wang
- Key Laboratory for Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, China.
- University of Chinese Academy of Sciences, Beijing, China.
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17
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Laguillaumie L, Rafrafi Y, Moya-Leclair E, Delagnes D, Dubos S, Spérandio M, Paul E, Dumas C. Stability of ex situ biological methanation of H 2/CO 2 with a mixed microbial culture in a pilot scale bubble column reactor. BIORESOURCE TECHNOLOGY 2022; 354:127180. [PMID: 35439560 DOI: 10.1016/j.biortech.2022.127180] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Biological methanation is a promising technology for gas and carbon valorisation. Therefore, process stability is required to allow its scale up and development. A pilot scale bubble column reactor was used for ex situ biological methanation with Mixed Microbial Culture (MMC). A 16S rRNA high throughput sequencing analysis revealed the MMC reached a stable composition with 50-60% Methanobacterium in closed liquid mode, a robust genus adapted to large scale constraints. Class MBA03 was identified as an indicator of process stability. Methanogenic genera moved toward 50% of Methanothermobacter when intensifying the process, and proteolytic activity was identified while 94% of H2/CO2 was converted into methane at 4NL.L-1.d-1. This study gives clarifications on the origin of volatile fatty acids (VFA) apparitions. Acetate and propionate accumulated when methanogenic activity weakened due to nutritive deficiency, and when PH2 reached 0.7 bar. The MMC withstood a storage period of 34d at room temperature indicating its suitability for industrial constraints.
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Affiliation(s)
- Léa Laguillaumie
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Yan Rafrafi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | | | - Simon Dubos
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Etienne Paul
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Claire Dumas
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.
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18
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Greening C, Grinter R. Microbial oxidation of atmospheric trace gases. Nat Rev Microbiol 2022; 20:513-528. [PMID: 35414013 DOI: 10.1038/s41579-022-00724-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H2), carbon monoxide (CO) and methane (CH4). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H2 and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH4, H2 and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Securing Antarctica's Environmental Future, Monash University, Clayton, Victoria, Australia. .,Centre to Impact AMR, Monash University, Clayton, Victoria, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
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19
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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20
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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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21
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Krohn C, Zhang P, Wood JL, Hayden HL, Franks AE, Jin J, Tang C. Biochar reduced extractable dieldrin concentrations and promoted oligotrophic growth including microbial degraders of chlorinated pollutants. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127156. [PMID: 34544006 DOI: 10.1016/j.jhazmat.2021.127156] [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: 05/19/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
The role of organic amendments for natural degradation of aged persistent organic pollutants (POPs) in agricultural soils remains controversial. We hypothesised that organic amendments enhance bacterial activity and function at the community level, facilitating the degradation of aged POPs. An incubation study was conducted in a closed chamber over 12 months to assess the effects of selected organic amendments on extractable residues of aged dieldrin. The role of bacterial diversity and changes in community function was explored through sequenced marker genes. Linear mixed effect models indicated that, independent of amendment type, cumulative CO2 release was negatively associated with decreases in dieldrin concentration, by up to 7% per µmol CO2-C respired by microorganisms. The addition of poultry litter led to the highest daily carbon mineralisation, which was associated with low dieldrin dissipation after 9 months. In comparison, biochar resulted in significant decreases in extractable dieldrin residues over time, which coincided with shifts towards aerobic, oligotrophic, gram-negative bacteria, some with dehalogenation metabolism, and with increased potentials for biosynthesis of membrane components such as fatty acids and high redox quinones. The results supported an alternative theory that labile carbon promoted blooms of copiotrophic growth, which suppressed the required community-level traits and oligotrophic diversity to degrade chlorinated pollutants.
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Affiliation(s)
- Christian Krohn
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Pei Zhang
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Macleod, VIC 3085, Australia
| | - Jennifer L Wood
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia; Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Helen L Hayden
- Agriculture Victoria, Department of Jobs, Precincts and Regions, Centre for AgriBioscience Bundoora, VIC 3083, Australia
| | - Ashley E Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia; Centre for Future Landscapes, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia
| | - Jian Jin
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia.
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, Centre for AgriBioScience, La Trobe University, Melbourne Campus, Bundoora, VIC 3086, Australia.
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22
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Chatzipanagiotou KR, Jourdin L, Bitter H, Strik D. Concentration-dependent effects of nickel doping on activated carbon biocathodes. Catal Sci Technol 2022. [DOI: 10.1039/d1cy02151f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In microbial electrosynthesis (MES), microorganisms grow on a cathode electrode as biofilm, or in the catholyte as planktonic biomass, and utilize CO2 for their growth and metabolism. Modification of the...
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Hydrogen sulfide in ageing, longevity and disease. Biochem J 2021; 478:3485-3504. [PMID: 34613340 PMCID: PMC8589328 DOI: 10.1042/bcj20210517] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022]
Abstract
Hydrogen sulfide (H2S) modulates many biological processes, including ageing. Initially considered a hazardous toxic gas, it is now recognised that H2S is produced endogenously across taxa and is a key mediator of processes that promote longevity and improve late-life health. In this review, we consider the key developments in our understanding of this gaseous signalling molecule in the context of health and disease, discuss potential mechanisms through which H2S can influence processes central to ageing and highlight the emergence of novel H2S-based therapeutics. We also consider the major challenges that may potentially hinder the development of such therapies.
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Kremp F, Müller V. Methanol and methyl group conversion in acetogenic bacteria: biochemistry, physiology and application. FEMS Microbiol Rev 2021; 45:5903270. [PMID: 32901799 DOI: 10.1093/femsre/fuaa040] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/29/2020] [Indexed: 12/24/2022] Open
Abstract
The production of bulk chemicals mostly depends on exhausting petroleum sources and leads to emission of greenhouse gases. Within the last decades the urgent need for alternative sources has increased and the development of bio-based processes received new attention. To avoid the competition between the use of sugars as food or fuel, other feedstocks with high availability and low cost are needed, which brought acetogenic bacteria into focus. This group of anaerobic organisms uses mixtures of CO2, CO and H2 for the production of mostly acetate and ethanol. Also methanol, a cheap and abundant bulk chemical produced from methane, is a suitable substrate for acetogenic bacteria. In methylotrophic acetogens the methyl group is transferred to the Wood-Ljungdahl pathway, a pathway to reduce CO2 to acetate via a series of C1-intermediates bound to tetrahydrofolic acid. Here we describe the biochemistry and bioenergetics of methanol conversion in the biotechnologically interesting group of anaerobic, acetogenic bacteria. Further, the bioenergetics of biochemical production from methanol is discussed.
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Affiliation(s)
- Florian Kremp
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue Str. 9, D-60438 Frankfurt, Germany
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Robles A, Yellowman TL, Joshi S, Mohana Rangan S, Delgado AG. Microbial Chain Elongation and Subsequent Fermentation of Elongated Carboxylates as H 2-Producing Processes for Sustained Reductive Dechlorination of Chlorinated Ethenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10398-10410. [PMID: 34283573 DOI: 10.1021/acs.est.1c01319] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In situ anaerobic groundwater bioremediation of trichloroethene (TCE) to nontoxic ethene is contingent on organohalide-respiring Dehalococcoidia, the most common strictly hydrogenotrophic Dehalococcoides mccartyi (D. mccartyi). The H2 requirement for D. mccartyi is fulfilled by adding various organic substrates (e.g., lactate, emulsified vegetable oil, and glucose/molasses), which require fermenting microorganisms to convert them to H2. The net flux of H2 is a crucial controlling parameter in the efficacy of bioremediation. H2 consumption by competing microorganisms (e.g., methanogens and homoacetogens) can diminish the rates of reductive dechlorination or stall the process altogether. Furthermore, some fermentation pathways do not produce H2 or having H2 as a product is not always thermodynamically favorable under environmental conditions. Here, we report on a novel application of microbial chain elongation as a H2-producing process for reductive dechlorination. In soil microcosms bioaugmented with dechlorinating and chain-elongating enrichment cultures, near stoichiometric conversion of TCE (0.07 ± 0.01, 0.60 ± 0.03, and 1.50 ± 0.20 mmol L-1 added sequentially) to ethene was achieved when initially stimulated by chain elongation of acetate and ethanol. Chain elongation initiated reductive dechlorination by liberating H2 in the conversion of acetate and ethanol to butyrate and caproate. Syntrophic fermentation of butyrate, a chain-elongation product, to H2 and acetate further sustained the reductive dechlorination activity. Methanogenesis was limited during TCE dechlorination in soil microcosms and absent in transfer cultures fed with chain-elongation substrates. This study provides critical fundamental knowledge toward the feasibility of chlorinated solvent bioremediation based on microbial chain elongation.
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Affiliation(s)
- Aide Robles
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics, Arizona State University, Tempe, Arizona 85281, United States
| | - Theodora L Yellowman
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics, Arizona State University, Tempe, Arizona 85281, United States
| | - Sayalee Joshi
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics, Arizona State University, Tempe, Arizona 85281, United States
| | - Srivatsan Mohana Rangan
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics, Arizona State University, Tempe, Arizona 85281, United States
| | - Anca G Delgado
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, 1001 S. McAllister Ave., Tempe, Arizona 85287, United States
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona 85281, United States
- Engineering Research Center for Bio-mediated and Bio-inspired Geotechnics, Arizona State University, Tempe, Arizona 85281, United States
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Feldewert C, Lang K, Brune A. The hydrogen threshold of obligately methyl-reducing methanogens. FEMS Microbiol Lett 2021; 367:5895324. [PMID: 32821944 PMCID: PMC7485788 DOI: 10.1093/femsle/fnaa137] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
Methanogenesis is the final step in the anaerobic degradation of organic matter. The most important substrates of methanogens are hydrogen plus carbon dioxide and acetate, but also the use of methanol, methylated amines, and aromatic methoxy groups appears to be more widespread than originally thought. Except for most members of the family Methanosarcinaceae, all methylotrophic methanogens require external hydrogen as reductant and therefore compete with hydrogenotrophic methanogens for this common substrate. Since methanogenesis from carbon dioxide consumes four molecules of hydrogen per molecule of methane, whereas methanogenesis from methanol requires only one, methyl-reducing methanogens should have an energetic advantage over hydrogenotrophic methanogens at low hydrogen partial pressures. However, experimental data on their hydrogen threshold is scarce and suffers from relatively high detection limits. Here, we show that the methyl-reducing methanogens Methanosphaera stadtmanae (Methanobacteriales), Methanimicrococcus blatticola (Methanosarcinales), and Methanomassiliicoccus luminyensis (Methanomassiliicoccales) consume hydrogen to partial pressures < 0.1 Pa, which is almost one order of magnitude lower than the thresholds for M. stadtmanae and M. blatticola reported in the only previous study on this topic. We conclude that methylotrophic methanogens should outcompete hydrogenotrophic methanogens for hydrogen and that their activity is limited by the availability of methyl groups.
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Affiliation(s)
- Christopher Feldewert
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Kristina Lang
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Haluska AA, Finneran KT. Increasing electron donor concentration does not accelerate complete microbial reductive dechlorination in contaminated sediment with native organic carbon. Biodegradation 2021; 32:577-593. [PMID: 34081242 DOI: 10.1007/s10532-021-09953-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/22/2021] [Indexed: 11/26/2022]
Abstract
Experiments with Fe(III)-rich, chloroethene-contaminated sediment demonstrated that trichloroethylene (TCE) and vinyl chloride (VC) were completely reduced to ethene regardless of whether electron donor(s) were added at 1 × stoichiometry or 10 × stoichiometry relative to all-electron acceptors. Unamended controls uniformly reduced TCE to ethene with a mean time to complete dechlorination (operationally defined as the presence of stoichiometric ethene production) of 79 days. Adding 1 × and 10 × acetate hindered the rate and extent of TCE and VC reduction relative to unamended controls, with several only partially reduced when the experiments were terminated. Adding high molecular mass (soybean oil derivative) substrates did not increase microbial reductive dechlorination relative to unamended incubations, and in many cases, hindered microbial dechlorination in favor of methanogenesis. The mean time to complete dechlorination was comparable between low (× 1) and high (× 10) electron donor concentration for all lipid-based electron donors tested. Those tested included Newman Zone® Standard without sodium lactate (96 vs. 75 days, respectively), CAP 18 ME (85 vs. 94 days, respectively), EOS 598B42 (68 vs. 72 days, respectively), and acetate (134 vs. 125 days, respectively). These data suggest that the addition of an electron donor does not always increase the rate and extent of reductive dechlorination but will increase costs. In particular, increasing the concentration of electron donors higher than the stoichiometric demand only decreased complete microbial reductive dechlorination, which is the opposite of most standard "more time and more electrons" approaches. These data argue that site-specific electron donor demands must be evaluated, and in some cases, a monitored natural attenuation (MNA) approach is most favorable.
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Affiliation(s)
- Alexander Arthur Haluska
- Environmental Engineering and Earth Sciences, Clemson University, 312 Biosystems Research Complex, 105 Collings Street, Clemson, SC, 29634, USA
- Center for Applied Geoscience, Geological Institute, University of Tϋbingen, Hölderlinstrße 12, 72070, Tübingen, Germany
| | - Kevin T Finneran
- Environmental Engineering and Earth Sciences, Clemson University, 312 Biosystems Research Complex, 105 Collings Street, Clemson, SC, 29634, USA.
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Castilla-Archilla J, Heiberger J, Mills S, Hilbig J, Collins G, Lens PNL. Continuous Volatile Fatty Acid Production From Acid Brewery Spent Grain Leachate in Expanded Granular Sludge Bed Reactors. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.664944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The production of volatile fatty acids (VFAs) in expanded granular sludge bed (EGSB) reactors using leachate from thermal diluted acid hydrolysis of brewery spent grain was evaluated. Partial inhibition of the anaerobic digestion process to induce VFA accumulation was achieved by applying a high organic loading rate [from 15.3 to 46.0 gCOD/(L·day)], and using a feed with an inlet concentration of 15 g/L total carbohydrates. Two EGSB reactors were operated under identical conditions, both inoculated with the same granular sludge. However, granular sludge in one reactor (R1) was subsequently disaggregated to flocculent sludge by a pH shock, whereas granules remained intact in the other reactor (R2). The hydraulic retention time (HRT) of both reactors was decreased from 36 to 24, 18 and 12 h. The main fermented compounds were acetic acid, butyric acid, propionic acid and ethanol. Despite fluctuations between these products, their total concentration was quite stable throughout the trial at about 134.2 (±27.8) and 141.1 (±21.7) mmol/L, respectively, for R1 and R2. Methane was detected at the beginning of the trial, and following some periods of instability in the granular sludge reactor (R2). The hydrogen yield increased as the HRT decreased. The highest VFA production was achieved in the granular sludge reactor at a 24 h HRT, corresponding to 120.4 (±15.0) mmol/L of VFAs. This corresponded to an acidification level of 83.4 (±5.9) g COD of VFA per 100 gram of soluble COD.
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29
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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Pan X, Zhao L, Li C, Angelidaki I, Lv N, Ning J, Cai G, Zhu G. Deep insights into the network of acetate metabolism in anaerobic digestion: focusing on syntrophic acetate oxidation and homoacetogenesis. WATER RESEARCH 2021; 190:116774. [PMID: 33387947 DOI: 10.1016/j.watres.2020.116774] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 06/12/2023]
Abstract
Acetate is a pivotal intermediate product during anaerobic decomposition of organic matter. Its generation and consumption network is quite complex, which almost covers the most steps in anaerobic digestion (AD) process. Besides acidogenesis, acetogenesis and methanogenesis, syntrophic acetate oxidation (SAO) replaced acetoclastic methanogenesis to release the inhibition of AD at some special conditions, and the importance of considering homoacetogenesis had also been proved when analysing anaerobic fermentations. Syntrophic acetate-oxidizing bacteria (SAOB), with function of SAO, can survive under high temperature and ammonia/ volatile fatty acids (VFAs) concentrations, while, homoacetogens, performed homoacetogenesis, are more active under acidic, alkaline and low temperature (10°C-20°C) conditions, This review summarized the roles of SAO and homoacetogenesis in AD process, which contains the biochemical reactions, metabolism pathways, physiological characteristics and energy conservation of functional bacteria. The specific roles of these two processes in the subprocess of AD (i.e., acidogenesis, acetogenesis and methanogenesis) were also analyzed in detail. A two phases anaerobic digester is proposed for protein-rich waste(water) treatment by enhancing the functions of homoacetogens and SAOB compared to the traditional two-phases anaerobic digesters, in which the first phase is fermentation phase including acidogens and homoacetogens for acetate production, and second phase is a mixed culture coupling syntrophic fatty acids bacteria, SAOB and hydrogenotrophic methanogens for methane production. This review provides a new insight into the network on production and consumption of acetate in AD process.
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Affiliation(s)
- Xiaofang Pan
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Lixin Zhao
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agriculture Sciences, Beijing100081, China
| | - Chunxing Li
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Nan Lv
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Jing Ning
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Guanjing Cai
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China
| | - Gefu Zhu
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen361021, China.
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Meyer KM, Morris AH, Webster K, Klein AM, Kroeger ME, Meredith LK, Brændholt A, Nakamura F, Venturini A, Fonseca de Souza L, Shek KL, Danielson R, van Haren J, Barbosa de Camargo P, Tsai SM, Dini-Andreote F, de Mauro JMS, Barlow J, Berenguer E, Nüsslein K, Saleska S, Rodrigues JLM, Bohannan BJM. Belowground changes to community structure alter methane-cycling dynamics in Amazonia. ENVIRONMENT INTERNATIONAL 2020; 145:106131. [PMID: 32979812 DOI: 10.1016/j.envint.2020.106131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with increases in soil methane (CH4) emission. To better understand the drivers of this change, we measured soil CH4 flux, environmental conditions, and belowground microbial community structure across primary forests, cattle pastures, and secondary forests in two Amazonian regions. We show that pasture soils emit high levels of CH4 (mean: 3454.6 ± 9482.3 μg CH4 m-2 d-1), consistent with previous reports, while forest soils on average emit CH4 at modest rates (mean: 9.8 ± 120.5 μg CH4 m-2 d-1), but often act as CH4 sinks. We report that secondary forest soils tend to consume CH4 (mean: -10.2 ± 35.7 μg CH4 m-2 d-1), demonstrating that pasture CH4 emissions can be reversed. We apply a novel computational approach to identify microbial community attributes associated with flux independent of soil chemistry. While this revealed taxa known to produce or consume CH4 directly (i.e. methanogens and methanotrophs, respectively), the vast majority of identified taxa are not known to cycle CH4. Each land use type had a unique subset of taxa associated with CH4 flux, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, we show that microbial composition is crucial for understanding the observed CH4 dynamics and that microorganisms provide explanatory power that cannot be captured by environmental variables.
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Affiliation(s)
- Kyle M Meyer
- Department of Integrative Biology, University of California - Berkeley, Berkeley, CA, USA; Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
| | - Andrew H Morris
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Ann M Klein
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA; College of the Siskiyous, Weed, CA, USA
| | - Marie E Kroeger
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Laura K Meredith
- School of Natural Resources and the Environment, Tucson, AZ, USA; Biosphere 2, University of Arizona, Tucson, AZ, USA
| | - Andreas Brændholt
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Fernanda Nakamura
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Andressa Venturini
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Leandro Fonseca de Souza
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Katherine L Shek
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Rachel Danielson
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, USA
| | - Joost van Haren
- Biosphere 2, University of Arizona, Tucson, AZ, USA; Honors College, University of Arizona, Tucson, AZ, USA
| | | | - Siu Mui Tsai
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Fernando Dini-Andreote
- Department of Soil Science, 'Luiz de Queiroz' College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - José M S de Mauro
- Universidade Federal do Oeste do Pará, Santarém-Tapajós, Pará, Brazil
| | - Jos Barlow
- Lancaster Environmental Centre, Lancaster University, Lancaster, UK
| | - Erika Berenguer
- Lancaster Environmental Centre, Lancaster University, Lancaster, UK; Environmental Change Institute, University of Oxford, Oxford, UK
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
| | - Scott Saleska
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Jorge L M Rodrigues
- Department of Land, Air, and Water Resources, University of California - Davis, Davis, CA, USA
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32
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Wang X, Xin J, Yuan M, Zhao F. Electron competition and electron selectivity in abiotic, biotic, and coupled systems for dechlorinating chlorinated aliphatic hydrocarbons in groundwater: A review. WATER RESEARCH 2020; 183:116060. [PMID: 32750534 DOI: 10.1016/j.watres.2020.116060] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/01/2020] [Accepted: 06/13/2020] [Indexed: 06/11/2023]
Abstract
Chlorinated aliphatic hydrocarbons (CAHs) have been frequently detected in aquifers in recent years. Owing to the bioaccumulation and toxicity of CAHs, it is essential to explore high-efficiency technologies for their complete dechlorination in groundwater. At present, the most widely used abiotic and biotic remediation technologies are based on zero-valent iron (ZVI) and functional anaerobic bacteria (FAB), respectively. However, the main obstacles to the full potential of both technologies in the field include their lowered efficiencies and increased economic costs due to the co-existence of a variety of natural electron acceptors in the environment, such as dissolved oxygen (DO), nitrate (NO3-), sulfate (SO42-), ferric iron (Fe (III)), bicarbonate (HCO3-), and even water, which compete for electrons with the target contaminants. Therefore, a clear understanding of the mechanisms governing electron competition and electron selectivity is significant for the accurate evaluation of the effectiveness of both technologies under natural hydrochemical conditions. We collected data from both abiotic and biotic CAH-remediation systems, summarized the dechlorination and undesired reactions in groundwater, discussed the characterization methods and general principles of electron competition, and described strategies to improve electron selectivity in both systems. Furthermore, we reviewed the emerging ZVI-FAB coupled system, which integrates abiotic and biotic processes to enhance dechlorination performance and electron utilization efficiency. Lastly, we propose future research needs to quantitatively understand the electron competition in abiotic, biotic, and coupled systems in more detail and to promote improved electron selectivity in groundwater remediation.
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Affiliation(s)
- Xiaohui Wang
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Jia Xin
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.
| | - Mengjiao Yuan
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
| | - Fang Zhao
- Key Lab of Marine Environmental Science and Ecology, Ministry of Education Shandong Provincial Key Laboratory of Marine Environment and Geological Engineering College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China
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Ntagia E, Chatzigiannidou I, Williamson AJ, Arends JBA, Rabaey K. Homoacetogenesis and microbial community composition are shaped by pH and total sulfide concentration. Microb Biotechnol 2020; 13:1026-1038. [PMID: 32126162 PMCID: PMC7264883 DOI: 10.1111/1751-7915.13546] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022] Open
Abstract
Biological CO2 sequestration through acetogenesis with H2 as electron donor is a promising technology to reduce greenhouse gas emissions. Today, a major issue is the presence of impurities such as hydrogen sulfide (H2 S) in CO2 containing gases, as they are known to inhibit acetogenesis in CO2 -based fermentations. However, exact values of toxicity and inhibition are not well-defined. To tackle this uncertainty, a series of toxicity experiments were conducted, with a mixed homoacetogenic culture, total dissolved sulfide concentrations ([TDS]) varied between 0 and 5 mM and pH between 5 and 7. The extent of inhibition was evaluated based on acetate production rates and microbial growth. Maximum acetate production rates of 0.12, 0.09 and 0.04 mM h-1 were achieved in the controls without sulfide at pH 7, pH 6 and pH 5. The half-maximal inhibitory concentration (IC50 qAc ) was 0.86, 1.16 and 1.36 mM [TDS] for pH 7, pH 6 and pH 5. At [TDS] above 3.33 mM, acetate production and microbial growth were completely inhibited at all pHs. 16S rRNA gene amplicon sequencing revealed major community composition transitions that could be attributed to both pH and [TDS]. Based on the observed toxicity levels, treatment approaches for incoming industrial CO2 streams can be determined.
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Affiliation(s)
- Eleftheria Ntagia
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Ioanna Chatzigiannidou
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Adam J. Williamson
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Jan B. A. Arends
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
| | - Korneel Rabaey
- Center for Microbial Ecology and Technology (CMET)Ghent UniversityCoupure Links 653Ghent9000Belgium
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Li Z, Wang X, Alberdi A, Deng J, Zhong Z, Si H, Zheng C, Zhou H, Wang J, Yang Y, Wright ADG, Mao S, Zhang Z, Guan L, Li G. Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts. Front Microbiol 2020; 11:1311. [PMID: 32714292 PMCID: PMC7344211 DOI: 10.3389/fmicb.2020.01311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 05/25/2020] [Indexed: 01/08/2023] Open
Abstract
Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.
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Affiliation(s)
- Zhipeng Li
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.,College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxu Wang
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jiabo Deng
- Chengdu Zoological Garden, Chengdu, China
| | - Zhenyu Zhong
- Beijing Milu Ecological Research Center, Beijing, China
| | - Huazhe Si
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Chengli Zheng
- Sichuan Institute of Musk Deer Breeding, Chengdu, China
| | - Hanlin Zhou
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, China
| | - Jianming Wang
- Sichuan Institute of Musk Deer Breeding, Chengdu, China
| | - Yifeng Yang
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - André-Denis G Wright
- College of Agricultural, Human, and Natural Resource Sciences, Washington State University, Pullman, WA, United States
| | - Shengyong Mao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhigang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guangyu Li
- Department of Special Economic Animal Nutrition and Feed Science, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
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Methane Production in Soil Environments-Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation. Microorganisms 2020; 8:microorganisms8060881. [PMID: 32545191 PMCID: PMC7357154 DOI: 10.3390/microorganisms8060881] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 11/17/2022] Open
Abstract
Flooding and desiccation of soil environments mainly affect the availability of water and oxygen. While water is necessary for all life, oxygen is required for aerobic microorganisms. In the absence of O2, anaerobic processes such as CH4 production prevail. There is a substantial theoretical knowledge of the biogeochemistry and microbiology of processes in the absence of O2. Noteworthy are processes involved in the sequential degradation of organic matter coupled with the sequential reduction of electron acceptors, and, finally, the formation of CH4. These processes follow basic thermodynamic and kinetic principles, but also require the presence of microorganisms as catalysts. Meanwhile, there is a lot of empirical data that combines the observation of process function with the structure of microbial communities. While most of these observations confirmed existing theoretical knowledge, some resulted in new information. One important example was the observation that methanogens, which have been believed to be strictly anaerobic, can tolerate O2 to quite some extent and thus survive desiccation of flooded soil environments amazingly well. Another example is the strong indication of the importance of redox-active soil organic carbon compounds, which may affect the rates and pathways of CH4 production. It is noteworthy that drainage and aeration turns flooded soils, not generally, into sinks for atmospheric CH4, probably due to the peculiarities of the resident methanotrophic bacteria.
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Ungerfeld EM. Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions. Front Microbiol 2020; 11:589. [PMID: 32351469 PMCID: PMC7174568 DOI: 10.3389/fmicb.2020.00589] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/18/2020] [Indexed: 01/10/2023] Open
Abstract
Rumen fermentation affects ruminants productivity and the environmental impact of ruminant production. The release to the atmosphere of methane produced in the rumen is a loss of energy and a cause of climate change, and the profile of volatile fatty acids produced in the rumen affects the post-absorptive metabolism of the host animal. Rumen fermentation is shaped by intracellular and intercellular flows of metabolic hydrogen centered on the production, interspecies transfer, and incorporation of dihydrogen into competing pathways. Factors that affect the growth of methanogens and the rate of feed fermentation impact dihydrogen concentration in the rumen, which in turn controls the balance between pathways that produce and incorporate metabolic hydrogen, determining methane production and the profile of volatile fatty acids. A basic kinetic model of competition for dihydrogen is presented, and possibilities for intervention to redirect metabolic hydrogen from methanogenesis toward alternative useful electron sinks are discussed. The flows of metabolic hydrogen toward nutritionally beneficial sinks could be enhanced by adding to the rumen fermentation electron acceptors or direct fed microbials. It is proposed to screen hydrogenotrophs for dihydrogen thresholds and affinities, as well as identifying and studying microorganisms that produce and utilize intercellular electron carriers other than dihydrogen. These approaches can allow identifying potential microbial additives to compete with methanogens for metabolic hydrogen. The combination of adequate microbial additives or electron acceptors with inhibitors of methanogenesis can be effective approaches to decrease methane production and simultaneously redirect metabolic hydrogen toward end products of fermentation with a nutritional value for the host animal. The design of strategies to redirect metabolic hydrogen from methane to other sinks should be based on knowledge of the physicochemical control of rumen fermentation pathways. The application of new –omics techniques together with classical biochemistry methods and mechanistic modeling can lead to exciting developments in the understanding and manipulation of the flows of metabolic hydrogen in rumen fermentation.
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Affiliation(s)
- Emilio M Ungerfeld
- Laboratorio de Fermentación Ruminal, Instituto de Investigaciones Agropecuarias (INIA), Centro Regional Carillanca, Temuco, Chile
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Philips J. Extracellular Electron Uptake by Acetogenic Bacteria: Does H 2 Consumption Favor the H 2 Evolution Reaction on a Cathode or Metallic Iron? Front Microbiol 2020; 10:2997. [PMID: 31998274 PMCID: PMC6966493 DOI: 10.3389/fmicb.2019.02997] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/11/2019] [Indexed: 12/30/2022] Open
Abstract
Some acetogenic bacteria are capable of using solid electron donors, such as a cathode or metallic iron [Fe(0)]. Acetogens using a cathode as electron donor are of interest for novel applications such as microbial electrosynthesis, while microorganisms using Fe(0) as electron donor cause detrimental microbial induced corrosion. The capacity to use solid electron donors strongly differs between acetogenic strains, which likely relates to their extracellular electron transfer (EET) mechanism. Different EET mechanisms have been proposed for acetogenic bacteria, including a direct mechanism and a H2 dependent indirect mechanism combined with extracellular hydrogenases catalyzing the H2 evolution reaction on the cathode or Fe(0) surface. Interestingly, low H2 partial pressures often prevail during acetogenesis with solid electron donors. Hence, an additional mechanism is here proposed: the maintenance of low H2 partial pressures by microbial H2 consumption, which thermodynamically favors the H2 evolution reaction on the cathode or Fe(0) surface. This work elaborates how the H2 partial pressure affects the H2 evolution onset potential and the H2 evolution rate on a cathode, as well as the free energy change of the anoxic corrosion reaction. In addition, the H2 consumption characteristics, i.e., H2 threshold (thermodynamic limit for H2 consumption) and H2 consumption kinetic parameters, of acetogenic bacteria are reviewed and evidence is discussed for strongly different H2 consumption characteristics. Different acetogenic strains are thus expected to maintain different H2 partial pressures on a cathode or Fe(0) surface, while those that maintain lower H2 partial pressures (lower H2 threshold, higher H2 affinity) more strongly increase the H2 evolution reaction. Consequently, I hypothesize that the different capacities of acetogenic bacteria to use solid electron donors are related to differences in their H2 consumption characteristics. The focus of this work is on acetogenic bacteria, but similar considerations are likely also relevant for other hydrogenotrophic microorganisms.
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Affiliation(s)
- Jo Philips
- Department of Engineering, Aarhus University, Aarhus, Denmark
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38
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Fazi S, Ungaro F, Venturi S, Vimercati L, Cruz Viggi C, Baronti S, Ugolini F, Calzolari C, Tassi F, Vaselli O, Raschi A, Aulenta F. Microbiomes in Soils Exposed to Naturally High Concentrations of CO 2 (Bossoleto Mofette Tuscany, Italy). Front Microbiol 2019; 10:2238. [PMID: 31681186 PMCID: PMC6797827 DOI: 10.3389/fmicb.2019.02238] [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: 03/22/2019] [Accepted: 09/12/2019] [Indexed: 01/05/2023] Open
Abstract
Direct and indirect effects of extremely high geogenic CO2 levels, commonly occurring in volcanic and hydrothermal environments, on biogeochemical processes in soil are poorly understood. This study investigated a sinkhole in Italy where long-term emissions of thermometamorphic-derived CO2 are associated with accumulation of carbon in the topsoil and removal of inorganic carbon in low pH environments at the bottom of the sinkhole. The comparison between interstitial soil gasses and those collected in an adjacent bubbling pool and the analysis of the carbon isotopic composition of CO2 and CH4 clearly indicated the occurrence of CH4 oxidation and negligible methanogenesis in soils at the bottom of the sinkhole. Extremely high CO2 concentrations resulted in higher microbial abundance (up to 4 × 109 cell g-1 DW) and a lower microbial diversity by favoring bacteria already reported to be involved in acetogenesis in mofette soils (i.e., Firmicutes, Chloroflexi, and Acidobacteria). Laboratory incubations to test the acetogenic and methanogenic potential clearly showed that all the mofette soil supplied with hydrogen gas displayed a remarkable CO2 fixation potential, primarily due to the activity of acetogenic microorganisms. By contrast, negligible production of acetate occurred in control tests incubated with the same soils, under identical conditions, without the addition of hydrogen. In this study, we report how changes in diversity and functions of the soil microbial community - induced by high CO2 concentration - create peculiar biogeochemical profile. CO2 emission affects carbon cycling through: (i) inhibition of the decomposition of the organic carbon and (ii) promotion of CO2-fixation via the acetyl-CoA pathway. Sites naturally exposed to extremely high CO2 levels could potentially represent an untapped source of microorganisms with unique capabilities to catalytically convert CO2 into valuable organic chemicals and fuels.
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Affiliation(s)
- Stefano Fazi
- Water Research Institute, National Research Council (IRSA-CNR), Rome, Italy
| | - Fabrizio Ungaro
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Stefania Venturi
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | | | - Silvia Baronti
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Francesca Ugolini
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Costanza Calzolari
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Franco Tassi
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Orlando Vaselli
- Institute of Geosciences and Earth Resources, National Research Council (IGG-CNR), Florence, Italy.,Department of Earth Sciences, University of Florence, Florence, Italy
| | - Antonio Raschi
- Institute of BioEconomy - National Research Council (IBE-CNR), Florence, Italy
| | - Federico Aulenta
- Water Research Institute, National Research Council (IRSA-CNR), Rome, Italy
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39
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Rira M, Morgavi DP, Genestoux L, Djibiri S, Sekhri I, Doreau M. Methanogenic potential of tropical feeds rich in hydrolyzable tannins1,2. J Anim Sci 2019; 97:2700-2710. [PMID: 31192352 DOI: 10.1093/jas/skz199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/20/2019] [Indexed: 11/14/2022] Open
Abstract
The present study was carried out to determine the effect of Acacia nilotica, a tropical plant rich in hydrolyzable tannins (HT), on rumen fermentation and methane (CH4) production in vitro. We used leaves and pods from A. nilotica alone and combined. The combination of HT from A. nilotica leaves and pods and condensed tannins (CT) from Calliandra calothyrsus and Leucaena leucocephala were also evaluated to assess potential differences in biological activity between HT and CT. Four series of 24-h incubations were performed using rumen contents of 4 sheep fed a tropical grass (natural grassland based on Dichanthium spp.). A first experiment tested different levels of replacement of this tropical forage (control [CTL] without tannins) by A. nilotica leaves or pods: 0:100, 25:75, 50:50, 75:25 and 100:0. A second experiment tested the mixture of A. nilotica leaves and pods in different proportions: 100:0, 75:25, 50:50, 25:75, and 0:100. A third experiment tested the 50:50 combination of A. nilotica leaves or pods with C. calothyrsus and L. leucocephala. Acacia nilotica pods and leaves had a high content of HT (350 and 178 g/kg DM, respectively), whereas C. calothyrsus and L. leucocephala had a high content of CT (361 and 180 g/kg DM, respectively). The inclusion of HT from A. nilotica leaves and pods decreased CH4 production dose-dependently (P < 0.01). Total replacement of the CTL by A. nilotica decreased CH4 production by 64 and 55% with leaves and pods, respectively. Pods were richer in HT than leaves, but their antimethanogenic effect did not differ (P > 0.05). Although A. nilotica leaves and pods inhibited fermentation, as indicated by the lower gas production and VFA production (P < 0.01), this effect was less pronounced than for CH4. Volatile fatty acid production decreased by 12% in leaves and by 30% in pods when compared with the CTL alone. Positive associative effect was reported for VFA, when HT-rich sources and CT-rich sources were mixed. Combining the 2 sources of HT did not show associative effects on fermentation or CH4 production (P > 0.05). Hydrolyzable tannin-rich sources were more effective in suppressing methanogenesis than CT-rich sources. Our results show that HT-rich A. nilotica leaves and pods have the potential to reduce ruminal CH4 production.
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Affiliation(s)
- Moufida Rira
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria.,†INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Lucette Genestoux
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
| | - Sihem Djibiri
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria
| | - Ines Sekhri
- Ecole Nationale Supérieure de Biotechnologie, Ali Mendjli, Constantine, Algeria
| | - Michel Doreau
- †INRA, VetAgro Sup, UMR1213 Herbivores, Saint-Genès-Champanelle, France
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40
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Laskar M, Awata T, Kasai T, Katayama A. Anaerobic Dechlorination by a Humin-Dependent Pentachlorophenol-Dechlorinating Consortium under Autotrophic Conditions Induced by Homoacetogenesis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E2873. [PMID: 31405258 PMCID: PMC6720667 DOI: 10.3390/ijerph16162873] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/03/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
Anoxic aquifers suffer from energy limitations due to the unavailability of organic substrates, as dictated by hydrogen (H2) for various electron-accepting processes. This deficiency often results in the accumulation of persistent organic pollutants, where bioremediation using organic compounds often leads to secondary contamination. This study involves the reductive dechlorination of pentachlorophenol (PCP) by dechlorinators that do not use H2 directly, but rather through a reduced state of humin-a solid-phase humic substance-as the extracellular electron donor, which requires an organic donor such as formate, lactate, etc. This shortcoming was addressed by the development of an anaerobic mixed culture that was capable of reductively dechlorinating PCP using humin under autotrophic conditions induced by homoacetogenesis. Here, H2 was used for carbon-dioxide fixation to acetate; the acetate produced was used for the reduction of humin; and consequently used for dechlorination through reduced humin. The 16SrRNA gene sequencing analysis showed Dehalobacter and Dehalobacterium as the possible dechlorinators, while Clostridium and Oxobacter were identified as the homoacetogens. Thus, this work contributes to the development of an anaerobic consortium that balanced H2 dependency, where efficiency of humin reduction extends the applicability of anaerobic microbial remediation in aquifers through autotrophy, syntrophy, and reductive dechlorination.
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Affiliation(s)
- Mahasweta Laskar
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Takanori Awata
- National Institute for Land and Infrastructure Management, Tsukuba 305-0804, Japan
| | - Takuya Kasai
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan
| | - Arata Katayama
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan.
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41
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Schmidt HP, Hagemann N, Draper K, Kammann C. The use of biochar in animal feeding. PeerJ 2019; 7:e7373. [PMID: 31396445 PMCID: PMC6679646 DOI: 10.7717/peerj.7373] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/28/2019] [Indexed: 12/24/2022] Open
Abstract
Biochar, that is, carbonized biomass similar to charcoal, has been used in acute medical treatment of animals for many centuries. Since 2010, livestock farmers increasingly use biochar as a regular feed supplement to improve animal health, increase nutrient intake efficiency and thus productivity. As biochar gets enriched with nitrogen-rich organic compounds during the digestion process, the excreted biochar-manure becomes a more valuable organic fertilizer causing lower nutrient losses and greenhouse gas emissions during storage and soil application. Scientists only recently started to investigate the mechanisms of biochar in the different stages of animal digestion and thus most published results on biochar feeding are based so far on empirical studies. This review summarizes the state of knowledge up to the year 2019 by evaluating 112 relevant scientific publications on the topic to derive initial insights, discuss potential mechanisms behind observations and identify important knowledge gaps and future research needs. The literature analysis shows that in most studies and for all investigated farm animal species, positive effects on different parameters such as toxin adsorption, digestion, blood values, feed efficiency, meat quality and/or greenhouse gas emissions could be found when biochar was added to feed. A considerable number of studies provided statistically non-significant results, though tendencies were mostly positive. Rare negative effects were identified in regard to the immobilization of liposoluble feed ingredients (e.g., vitamin E or Carotenoids) which may limit long-term biochar feeding. We found that most of the studies did not systematically investigate biochar properties (which may vastly differ) and dosage, which is a major drawback for generalizing results. Our review demonstrates that the use of biochar as a feed additive has the potential to improve animal health, feed efficiency and livestock housing climate, to reduce nutrient losses and greenhouse gas emissions, and to increase the soil organic matter content and thus soil fertility when eventually applied to soil. In combination with other good practices, co-feeding of biochar may thus have the potential to improve the sustainability of animal husbandry. However, more systematic multi-disciplinary research is definitely needed to arrive at generalizable recommendations.
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Affiliation(s)
| | - Nikolas Hagemann
- Ithaka Institute for Carbon Strategies, Arbaz, Valais, Switzerland
- Environmental Analytics, Agroscope, Zurich, Switzerland
| | | | - Claudia Kammann
- Department of Applied Ecology, Hochschule Geisenheim University, Geisenheim, Germany
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42
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Greening C, Geier R, Wang C, Woods LC, Morales SE, McDonald MJ, Rushton-Green R, Morgan XC, Koike S, Leahy SC, Kelly WJ, Cann I, Attwood GT, Cook GM, Mackie RI. Diverse hydrogen production and consumption pathways influence methane production in ruminants. ISME JOURNAL 2019; 13:2617-2632. [PMID: 31243332 PMCID: PMC6776011 DOI: 10.1038/s41396-019-0464-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 01/17/2023]
Abstract
Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two-thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyse H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g., Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate and nitrite reduction (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis-related transcripts predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared with pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognised. There is evidence that alternative hydrogenotrophs, including acetogenic and respiratory bacteria, can prosper in the rumen and effectively compete with methanogens for H2. These findings may help to inform ongoing strategies to mitigate methane emissions by increasing flux through alternative H2 uptake pathways, including through animal selection, dietary supplementation and methanogenesis inhibitors.
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Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia.
| | - Renae Geier
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Cecilia Wang
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura C Woods
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Michael J McDonald
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Rowena Rushton-Green
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Xochitl C Morgan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Satoshi Koike
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sinead C Leahy
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | | | - Isaac Cann
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Graeme T Attwood
- Grasslands Research Centre, AgResearch Ltd., Palmerston North, 4410, New Zealand
| | - Gregory M Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Roderick I Mackie
- Department of Animal Sciences and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Lynch TA, Wang Y, van Brunt B, Pacheco D, Janssen PH. Modelling thermodynamic feedback on the metabolism of hydrogenotrophic methanogens. J Theor Biol 2019; 477:14-23. [PMID: 31150665 DOI: 10.1016/j.jtbi.2019.05.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 11/25/2022]
Abstract
The magnitude of the Gibbs free energy change of the substrate transformation that supports the growth of a microbe is decreased when the concentrations of the substrates are decreased and when the concentrations of the products of metabolism are increased. Microbes require a supply of ATP for cell maintenance and growth, and coupling the transformation of substrates to products with the formation of ATP also decreases the magnitude of the Gibbs free energy change. Here we include these three thermodynamic controllers (substrate and product concentration, and ATP formation) in a model of substrate transformation by hydrogenotrophic methanogens that results in a number of realistic behaviours. First, a threshold for substrate use emerges, below which the methanogen cannot metabolise its substrate. Under this model, microbes that capture more of the Gibbs free energy change from substrate transformation in the form of ATP have greater thresholds for their substrate, in line with observations of actual microbes. Second, an apparent saturation constant emerges that is controlled by the thermodynamics of the reaction. This increases with increasing ATP synthesis per substrate, so that methanogens that conserve more ATP grow faster at higher substrate concentrations, but are less competitive at low substrate concentrations. As a result, simply changing the ATP yield (moles of ATP per mole of substrate) results in methanogens with differing ecological strategies through thermodynamic impacts on their metabolism. Third, end-product inhibition through thermodynamic feedback can limit the growth of microbes, and those that capture more ATP per substrate are limited by smaller product concentrations than those that capture less ATP.
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Affiliation(s)
- T A Lynch
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Y Wang
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand; AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - B van Brunt
- Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - D Pacheco
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand
| | - P H Janssen
- AgResearch, Grasslands Research Centre, Palmerston North 4442, New Zealand.
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Zhou GW, Yang XR, Sun AQ, Li H, Lassen SB, Zheng BX, Zhu YG. Mobile Incubator for Iron(III) Reduction in the Gut of the Soil-Feeding Earthworm Pheretima guillelmi and Interaction with Denitrification. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:4215-4223. [PMID: 30882209 DOI: 10.1021/acs.est.8b06187] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Diets of soil-feeding earthworms contain abundant nitrate and iron(III) oxides, which are potential electron acceptors for mineralization of organic compounds. The earthworm gut provides an ideal habitat for ingested iron(III)-reducing microorganisms. However, little is known about iron(III) reduction and its interaction with other processes in the guts of earthworms. Here, we determined the dynamics of iron(III) and revealed its interaction with the turnover of organic acids and nitrate in the gut of the earthworm Pheretima guillelmi. Samples from gut contents combined with anoxic incubation were used for chemical analysis and 16S rRNA based Illumina sequencing. Chemical analysis showed that higher ratios of iron(II)/iron(III), nitrite/nitrate, and more abundant organic acids were contained in the in vivo gut of the earthworm P. guillelmi than those in the in situ soil. A higher rate of iron(III) reduction was detected in treatments of microcosmic incubation with gut contents (IG gut) than that with soil (IG soil), and nitrate reduction occurred earlier than iron(III) reduction in both treatments. Potential iron(III) reducers were dominated by fermentative genera Clostridium, Bacillus, and Desulfotomaculum in the treatment of IG gut, while they were dominated by dissimilatory iron(III)-reducing genera Geobacter in the treatment of IG soil. The iron(III)-reducing microbial community shared several genera with denitrifers in the treatment of IG gut, revealing a close link between iron(III) reduction and denitrification in the gut of earthworms. Collectively, our findings demonstrated that iron(III) reduction occurred along the gut and provided novel insights into the great contribution of earthworm gut microbiota on Fe and the associated C and N cycling in soil environments.
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Affiliation(s)
- Guo-Wei Zhou
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - An-Qi Sun
- Department of Environmental Science and Engineering , Huaqiao University , Xiamen 361021 , People's Republic of China
| | - Hu Li
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
| | - Simon Bo Lassen
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- Department of Plant and Environmental Sciences, Faculty of Science , University of Copenhagen , Thorvaldsensvej 40 , Frederiksberg 1871 , Denmark
| | - Bang-Xiao Zheng
- Falculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme , University of Helsinki , Niemenkatu 73 , Lahti 15140 , Finland
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , People's Republic of China
- State Key Lab of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , People's Republic of China
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Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle. Nat Microbiol 2019; 4:864-875. [PMID: 30858574 DOI: 10.1038/s41564-019-0384-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 01/22/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbial associations enhance the fitness of most living organisms, and wood-feeding insects offer some of the most striking examples of this. Odontotaenius disjunctus is a wood-feeding beetle that possesses a digestive tract with four main compartments, each of which contains well-differentiated microbial populations, suggesting that anatomical properties and separation of these compartments may enhance energy extraction from woody biomass. Here, using integrated chemical analyses, we demonstrate that lignocellulose deconstruction and fermentation occur sequentially across compartments, and that selection for microbial groups and their metabolic pathways is facilitated by gut anatomical features. Metaproteogenomics showed that higher oxygen concentration in the midgut drives lignocellulose depolymerization, while a thicker gut wall in the anterior hindgut reduces oxygen diffusion and favours hydrogen accumulation, facilitating fermentation, homoacetogenesis and nitrogen fixation. We demonstrate that depolymerization continues in the posterior hindgut, and that the beetle excretes an energy- and nutrient-rich product on which its offspring subsist and develop. Our results show that the establishment of beneficial microbial partners within a host requires both the acquisition of the microorganisms and the formation of specific habitats within the host to promote key microbial metabolic functions. Together, gut anatomical properties and microbial functional assembly enable lignocellulose deconstruction and colony subsistence on an extremely nutrient-poor diet.
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46
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Chen X, Ottosen LDM, Kofoed MVW. How Low Can You Go: Methane Production of Methanobacterium congolense at Low CO 2 Concentrations. Front Bioeng Biotechnol 2019; 7:34. [PMID: 30899758 PMCID: PMC6416169 DOI: 10.3389/fbioe.2019.00034] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/05/2019] [Indexed: 01/21/2023] Open
Abstract
Autotrophic hydrogenotrophic methanogens use H2/CO2 as sole carbon and energy source. In contrast to H2, CO2 is present in high concentrations in environments dominated by methanogens e.g., anaerobic digesters (AD), and is therefore rarely considered to be a limiting factor. Nonetheless, potential CO2 limitation can be relevant in the process of biomethanation, a power-to-gas technology, where biogas is upgraded by the addition of H2 and ideally reduce the CO2 concentration in the produced biogas to 0-6%. H2 is effectively utilized by methanogens even at very low concentrations, but little is known about the impact of low CO2 concentrations on methanogenic activity. In this study, CO2 consumption and CH4 production kinetics under low CO2 concentrations were studied, using a hydrogenotrophic methanogen, Methanobacterium congolense, as model organism. We found that both cellular growth and methane production were limited at low CO2 concentrations (here expressed as Dissolved Inorganic Carbon, DIC). Maximum rates (V max) were reached at [DIC] of 100 mM (extrapolated), with a CO2 consumption rate of 69.2 fmol cell-1 d-1 and a CH4 production rate of 48.8 fmol cell-1 d-1. In our experimental setup, 80% of V max was achieved at [DIC] >9 mM. DIC half-saturation concentrations (K m) was about 2.5 mM for CO2 consumption and 2.2 mM for CH4 production. No CH4 production could be detected below 44.4 μM [DIC]. These data revealed that the limiting concentration of DIC may be much higher than that of H2 for a hydrogenotrophic methanogen. However, DIC is not a limiting factor in ADs running under standard operating conditions. For biomethanation, the results are applicable for both in situ and ex situ biomethanation reactors and show that biogas can be upgraded to concentrations of 2% CO2 (98% CH4) while still retaining 80% V max at pH 7.5 evaluated from M. congolense. Since DIC concentration can vary significantly with pH and pCO2 during biomethanation, monitoring DIC concentration through pH and pCO2 is therefore important for keeping optimal operational conditions for the biomethanation process.
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Lan W, Yang C. Ruminal methane production: Associated microorganisms and the potential of applying hydrogen-utilizing bacteria for mitigation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:1270-1283. [PMID: 30841400 DOI: 10.1016/j.scitotenv.2018.11.180] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 05/16/2023]
Abstract
Methane emission from ruminants not only causes serious environmental problems, but also represents a significant source of energy loss to animals. The increasing demand for sustainable animal production is driving researchers to explore proper strategies to mitigate ruminal methanogenesis. Since hydrogen is the primary substrate of ruminal methanogenesis, hydrogen metabolism and its associated microbiome in the rumen may closely relate to low- and high-methane phenotypes. Using candidate microbes that can compete with methanogens and redirect hydrogen away from methanogenesis as ruminal methane mitigants are promising avenues for methane mitigation, which can both prevent the adverse effects deriving from chemical additives such as toxicity and resistance, and increase the retention of feed energy. This review describes the ruminal microbial ecosystem and its association with methane production, as well as the effects of interspecies hydrogen transfer on methanogenesis. It provides a scientific perspective on using bacteria that are involved in hydrogen utilization as ruminal modifiers to decrease methanogenesis. This information will be helpful in better understanding the key role of ruminal microbiomes and their relationship with methane production and, therefore, will form the basis of valuable and eco-friendly methane mitigation methods while improving animal productivity.
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Affiliation(s)
- Wei Lan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China
| | - Chunlei Yang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China; MoE Key Laboratory of Molecular Animal Nutrition, China.
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Role of hydrogen (H 2) mass transfer in microbiological H 2-threshold studies. Biodegradation 2019; 30:113-125. [PMID: 30788623 DOI: 10.1007/s10532-019-09870-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Gas-to-liquid mass transfer of hydrogen (H2) was investigated in a gas-liquid reactor with a continuous gas phase, a batch liquid phase, and liquid mixing regimes relevant to assessing kinetics of microbial H2 consumption. H2 transfer was quantified in real-time with a H2 microsensor for no mixing, moderate mixing [100 rotations per minute (rpm)], and rapid mixing (200 rpm). The experimental results were simulated by mathematical models to find best-fit values of volumetric mass transfer coefficients-kLa-for H2, which were 1.6/day for no mixing, 7/day for 100 rpm, and 30/day for 200 rpm. Microbiological H2-consumption experiments were conducted with Methanobacterium bryantii M.o.H. to assess effects of H2 mass transfer on microbiological H2-threshold studies. The results illustrate that slow mixing reduced the gas-to-liquid H2 transfer rate, which fell behind the rate of microbiological H2 consumption in the liquid phase. As a result, the liquid-phase H2 concentration remained much lower than the liquid-phase H2 concentration that would be in equilibrium with the gas-phase H2 concentration. Direct measurements of the liquid-phase H2 concentration by an in situ probe demonstrated the problems associated with slow H2 transfer in past H2 threshold studies. The findings indicate that some of the previously reported H2-thresholds most likely were over-estimates due to slow gas-to-liquid H2 transfer. Essential requirements to conduct microbiological H2 threshold experiments are to have vigorous mixing, large gas-to-liquid volume, large interfacial area, and low initial biomass concentration.
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Gregory SP, Barnett MJ, Field LP, Milodowski AE. Subsurface Microbial Hydrogen Cycling: Natural Occurrence and Implications for Industry. Microorganisms 2019; 7:E53. [PMID: 30769950 PMCID: PMC6407114 DOI: 10.3390/microorganisms7020053] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/01/2019] [Accepted: 02/03/2019] [Indexed: 12/21/2022] Open
Abstract
Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry.
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Affiliation(s)
- Simon P Gregory
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Megan J Barnett
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Lorraine P Field
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
| | - Antoni E Milodowski
- British Geological Survey, Environmental Science Centre, Keyworth, Nottingham NG12 5GG, UK.
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50
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Beaton D, Pelletier P, Goulet RR. Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste. Front Microbiol 2019; 10:204. [PMID: 30814985 PMCID: PMC6381020 DOI: 10.3389/fmicb.2019.00204] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
Deep geologic repositories (DGR) in Canada are designed to contain and isolate low- and intermediate-level radioactive waste. Microbial degradation of the waste potentially produces methane, carbon dioxide and hydrogen gas. The generation of these gases increase rock cavity pressure and limit water ingress which delays the mobility of water soluble radionuclides. The objective of this study was to measure gas pressure and composition over 7 years in experiments containing cellulosic material with various starting conditions relevant to a DGR and to identify micro-organisms generating gas. For this purpose, we conducted experiments in glass bottles containing (1) wet cellulosic material, (2) wet cellulosic material with compost Maker, and (3) wet cellulosic material with compost Accelerator. Results demonstrated that compost accelerated the pressure build-up in the containers and that methane gas was produced in one experiment with compost and one experiment without compost because the pH remained neutral for the duration of the 464 days experiment. Methane was not formed in the other experiment because the pH became acidic. Once the pressure became similar in all containers after 464 days, we then monitored gas pressure and composition in glass bottle containing wet cellulosic material in (1) acidic conditions, (2) neutral conditions, and (3) with an enzyme that accelerated degradation of cellulose over 1965 days. In these experiments, acetogenic bacteria degraded cellulose and produced acetic acid, which acidity suppressed methane production. Microbial community analyses suggested a diverse community of archaea, bacteria and fungi actively degrading cellulose. DNA analyses also confirmed the presence of methanogens and acetogens in our experiments. This study suggests that methane gas will be generated in DGRs if pH remains neutral. However, our results showed that microbial degradation of cellulose not only generated gas, but also generated acidity. This finding is important as acids can limit bentonite swelling and potentially degrade cement and rock barriers, thus this requires consideration in the safety case as appropriate.
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Affiliation(s)
- Danielle Beaton
- Chalk River Laboratories, Canadian Nuclear Laboratories, Chalk River, ON, Canada
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
| | | | - Richard R. Goulet
- Orillia Soldiers’ Memorial Hospital, Ottawa, ON, Canada
- Canadian Nuclear Safety Commission, Ottawa, ON, Canada
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