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Geng H, Xu Y, Liu R, Xu J, Li X, Yang D, Dai X. Magnetic porous microspheres altering interfacial thermodynamics of sewage sludge to drive metabolic cooperation for efficient methanogenesis. WATER RESEARCH 2024; 261:122022. [PMID: 39002417 DOI: 10.1016/j.watres.2024.122022] [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: 05/08/2024] [Revised: 06/21/2024] [Accepted: 06/28/2024] [Indexed: 07/15/2024]
Abstract
Controllable and recyclable magnetic porous microspheres (MPMs) have been proposed as a means for enhancing the anaerobic digestion (AD) of sludge, as they do not require continuous replenishment and can serve as carriers for anaerobes. However, the effects of MPMs on the interfacial thermodynamics of sludge and the biological responses triggered by abiotic effects in AD systems remain to be clarified. Herein, the underlying mechanisms by which MPMs alter the solid-liquid interface of sludge to drive methanogenesis were investigated. A significant increase in the contents of 13C and 2H (D) in methane molecules was observed in the presence of MPMs, suggesting that MPMs might enhance the CO2-reduction methanogenesis and participation of water in methane generation. Experimental results demonstrated that the addition of MPMs did not promote the anaerobic bioconversion of soluble organics for methanogenesis, suggesting that the enhanced methanogenesis and water participation were not achieved through promotion of the bioconversion of original liquid-state organics in sludge. Analyses of the capillary force, surface adhesion force, and interfacial proton-coupled electron transfer (PCET) of MPMs revealed that MPMs can enhance mass transfer, effective contact, and electron-proton transfer with sludge. These outcomes were confirmed by the statistical analyses of variations in the interfacial thermodynamics and PCET of sludge with and without MPMs during AD. It was thus proposed that the MPMs enhanced the PCET of sludge and PCET-driven release of protons from water by promoting the interfacial Lewis acid-base interactions of sludge, thereby resulting in the enrichment of free and attached methanogenic consortia and the high energy-conserving metabolic cooperation. This proposition was further confirmed by identifying the predominant syntrophic partners, suggesting that PCET-based efficient methanogenesis was attributable to the enrichment of genomes harbouring CO2-reducing pathway and genes encoding water-mediated proton transfer. These findings offer new insights into how substrate properties can be altered by exogenous materials to enable highly efficient methanogenesis.
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Affiliation(s)
- Hui Geng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Ying Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
| | - Rui Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Jun Xu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Xiang Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Dianhai Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Xiaohu Dai
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
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Akram J, Song C, El Mashad HM, Chen C, Zhang R, Liu G. Advances in microbial community, mechanisms and stimulation effects of direct interspecies electron transfer in anaerobic digestion. Biotechnol Adv 2024; 76:108398. [PMID: 38914350 DOI: 10.1016/j.biotechadv.2024.108398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 06/11/2024] [Accepted: 06/21/2024] [Indexed: 06/26/2024]
Abstract
Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes.
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Affiliation(s)
- Jehangir Akram
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chao Song
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hamed M El Mashad
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States; Agricultural Engineering Department, Mansoura University, Egypt
| | - Chang Chen
- College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Ruihong Zhang
- Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, United States.
| | - Guangqing Liu
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Balasundaram G, Gahlot P, Ahmed B, Biswas P, Tyagi VK, Svensson K, Kumar V, Kazmi AA. Advanced steam-explosion pretreatment mediated anaerobic digestion of municipal sludge: Effects on methane yield, emerging contaminants removal, and microbial community. ENVIRONMENTAL RESEARCH 2023; 238:117195. [PMID: 37758117 DOI: 10.1016/j.envres.2023.117195] [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: 08/02/2023] [Revised: 09/05/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Advanced steam explosion pretreatment, i.e., the Thermal hydrolysis process (THP) is applied mainly to improve the sludge solubilization and subsequent methane yield in the downstream anaerobic digestion (AD) process. However, the potential of THP in pretreating the high solids retention time (SRT) sludges, mitigating the risk of emerging organic micropollutants and effects on anaerobic microbiome in digester remains unclear. In this study, sludge from a sequencing batch reactor (SBR) system operating at a SRT of 40 days was subjected to THP using a 5 L pilot plant at the temperature ranges of 120-180 °C for 30-120 min. The effect of THP on organics solubilization, methane yield, organic micropollutant removal, and microbial community dynamics was studied. The highest methane yield of 507 mL CH4/g VSadded and volatile solids (VS) removal of 54% were observed at 160°C- 30min THP condition, i.e., 4.1 and 2.6 times higher than the control (123 mL CH4/gVSadded, 20.7%), respectively. The experimental values of hydrolysis coefficient and methane yield have been predicted using Modified Gompertz, First order, and Logistics models. The observed values fitted well with all three models showing an R2 value between 0.96 and 1.0. THP pretreated sludges showed >80% removal of Trimethoprim, Enrofloxacin, Ciprofloxacin, and Bezafibrate. However, Carbamazepine, 17α-ethinylestradiol, and Progesterone showed recalcitrant behavior, resulting in less than 50% removal. Microbial diversity analysis showed the dominance of Proteobacteria, Firmicutes, Chloroflexi, and Bacteroidetes, collectively accounting for >70-80% of bacterial reads. They are mainly responsible for the fermentation of complex biomolecules like polysaccharides, proteins, and lipids. The THP-mediated anaerobic digestion of sludge shows better performance than the control digestion, improved methane yield, higher VS and micropollutants removal, and a diverse microbiome in the digester.
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Affiliation(s)
- Gowtham Balasundaram
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Pallavi Gahlot
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Banafsha Ahmed
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Pinakshi Biswas
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Vinay Kumar Tyagi
- Environmental Hydrology Division, National Institute of Hydrology, Roorkee, 247667, India.
| | | | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - A A Kazmi
- Department of Civil Engineering, Indian Institute of Technology Roorkee, Roorkee, 247667, India
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Jiang Y, Liu J, Li Y, Xiao P, Liu S, Shao J, Cai Y, Yan X, Fan L. Biochar amendment reduces biological nitrogen fixation and nitrogen use efficiency in cadmium-contaminated paddy fields. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 344:118338. [PMID: 37379629 DOI: 10.1016/j.jenvman.2023.118338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/21/2023] [Accepted: 06/04/2023] [Indexed: 06/30/2023]
Abstract
Cadmium (Cd) contamination poses a considerable threat to human health through grain enrichment and limits biological nitrogen fixation (BNF) in paddy fields. Biochar has shown great potential for agricultural soil remediation because it inactivates Cd, but uncertainties remain as to how biochar amendments affect BNF and grain N use efficiency in paddies. To elucidate these issues, we investigated the effects of biochar amendment on the structure and function of diazotrophic bacterial communities in different rice growth stages in Cd-contaminated paddy fields, and evaluated the contribution of BNF to grain N use efficiency under biochar amendment. The results showed that biochar amendment significantly increased the abundance of diazotrophic bacteria in the tillering and jointing stages. Furthermore, the community structure of soil diazotrophic bacteria markedly changed with biochar amendment, with a significant reduction in the abundances of Euryarchaeota, Desulfobacterales (Proteobacteria), and Sphingomonadales (Bacteroidetes) in the tillering stage. Changes in the soil carbon/nitrogen (C/N) ratio was the main factor driving diazotrophic microbial community characteristics caused by the release of available C from biochar at the tillering stage, rather than the Cd. Moreover, biochar amendment increased the efficiency of BNF (especially for autotrophic N2 fixation) in the vegetative phase of rice growth. Notably, biochar amendment significantly decreased BNF efficiency during the filling stage and reduced grain N use efficiency. The limited available nutrients in biochar and the toxicity of polycyclic aromatics and phenols in biochar-derived dissolved organic matter were responsible for the varied impacts of biochar on BNF in different rice growth stages. For the first time, we report that biochar amendment in paddy soils reduces Cd toxicity but also inhibits BNF and thereby decreases N use efficiency. Therefore, before applying biochar to inactivate Cd in paddy fields, there should be a trade-off between agricultural production and ecological safety to achieve sustainable agriculture.
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Affiliation(s)
- Yuexi Jiang
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Ji Liu
- College of Urban and Environmental Sciences, Central China Normal University, Wuhan, Hubei, 430079, PR China; Department of Ecohydrology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, 12587, Germany
| | - Yanyan Li
- Key Laboratory of Agro-ecological Processes in Subtropical Regions and the Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan, 410125, PR China
| | - Peng Xiao
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Shuang Liu
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Jihai Shao
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China.
| | - Yixiang Cai
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Xiaoqi Yan
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
| | - Li Fan
- College of Environment and Ecology, Hunan Agricultural University, Changsha, Hunan, 410128, PR China
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Cheng X, Du X, Liang Y, Degen AA, Wu X, Ji K, Gao Q, Xin G, Cong H, Yang G. Effect of grape pomace supplement on growth performance, gastrointestinal microbiota, and methane production in Tan lambs. Front Microbiol 2023; 14:1264840. [PMID: 37840727 PMCID: PMC10569316 DOI: 10.3389/fmicb.2023.1264840] [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: 07/21/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Grape pomace (GP), a by-product in wine production, is nutritious and can be used as a feed ingredient for ruminants; however, its role in shaping sheep gastrointestinal tract (GIT) microbiota is unclear. We conducted a controlled trial using a randomized block design with 10 Tan lambs fed a control diet (CD) and 10 Tan lambs fed a pelleted diet containing 8% GP (dry matter basis) for 46 days. Rumen, jejunum, cecum, and colon bacterial and archaeal composition were identified by 16S rRNA gene sequencing. Dry matter intake (DMI) was greater (p < 0.05) in the GP than CD group; however, there was no difference in average daily gain (ADG, p < 0.05) and feed conversion ratio (FCR, p < 0.05) between the two groups. The GP group had a greater abundance of Prevotella 1 and Prevotella 7 in the rumen; of Sharpe, Ruminococcaceae 2, and [Ruminococcus] gauvreauii group in the jejunum; of Ruminococcaceae UCG-014 and Romboutsia in the cecum, and Prevotella UCG-001 in the colon; but lesser Rikenellaceae RC9 gut group in the rumen and cecum, and Ruminococcaceae UCG-005 and Ruminococcaceae UCG-010 in the colon than the CD group. The pathways of carbohydrate metabolism, such as L-rhamnose degradation in the rumen, starch and glycogen degradation in the jejunum, galactose degradation in the cecum, and mixed acid fermentation and mannan degradation in the colon were up-graded; whereas, the pathways of tricarboxylic acid (TCA) cycle VIII, and pyruvate fermentation to acetone in the rumen and colon were down-graded with GP. The archaeal incomplete reductive TCA cycle was enriched in the rumen, jejunum, and colon; whereas, the methanogenesis from H2 and CO2, the cofactors of methanogenesis, including coenzyme M, coenzyme B, and factor 420 biosynthesis were decreased in the colon. The study concluded that a diet including GP at 8% DM did not affect ADG or FCR in Tan lambs. However, there were some potential benefits, such as enhancing propionate production by microbiota and pathways in the GIT, promoting B-vitamin production in the rumen, facilitating starch degradation and amino acid biosynthesis in the jejunum, and reducing methanogenesis in the colon.
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Affiliation(s)
- Xindong Cheng
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Du
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Liang
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Xiukun Wu
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Kaixi Ji
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoxian Gao
- Ningxia Feed Engineering Technology Research Center, Ningxia University, Yinchuan, China
| | - Guosheng Xin
- Ningxia Feed Engineering Technology Research Center, Ningxia University, Yinchuan, China
| | - Haitao Cong
- Shandong Huakun Rural Revitalization Institute Co., Ltd., Jinan, China
| | - Guo Yang
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Yellow River Estuary Tan Sheep Institute of Industrial Technology, Dongying, China
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Bueno de Mesquita CP, Wu D, Tringe SG. Methyl-Based Methanogenesis: an Ecological and Genomic Review. Microbiol Mol Biol Rev 2023; 87:e0002422. [PMID: 36692297 PMCID: PMC10029344 DOI: 10.1128/mmbr.00024-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.
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Affiliation(s)
| | - Dongying Wu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Camargo LSA, Saraiva NZ, Oliveira CS, Carmickle A, Lemos DR, Siqueira LGB, Denicol AC. Perspectives of gene editing for cattle farming in tropical and subtropical regions. Anim Reprod 2023; 19:e20220108. [PMID: 36819485 PMCID: PMC9924776 DOI: 10.1590/1984-3143-ar2022-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/23/2023] [Indexed: 02/19/2023] Open
Abstract
Cattle productivity in tropical and subtropical regions can be severely affected by the environment. Reproductive performance, milk and meat production are compromised by the heat stress imposed by the elevated temperature and humidity. The resulting low productivity contributes to reduce the farmer's income and to increase the methane emissions per unit of animal protein produced and the pressure on land usage. The introduction of highly productive European cattle breeds as well as crossbreeding with local breeds have been adopted as strategies to increase productivity but the positive effects have been limited by the low adaptation of European animals to hot climates and by the reduction of the heterosis effect in the following generations. Gene editing tools allow precise modifications in the animal genome and can be an ally to the cattle industry in tropical and subtropical regions. Alleles associated with production or heat tolerance can be shifted between breeds without the need of crossbreeding. Alongside assisted reproductive biotechnologies and genome selection, gene editing can accelerate the genetic gain of indigenous breeds such as zebu cattle. This review focuses on some of the potential applications of gene editing for cattle farming in tropical and subtropical regions, bringing aspects related to heat stress, milk yield, bull reproduction and methane emissions.
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Affiliation(s)
| | | | | | - Allie Carmickle
- Department of Animal Science, University of California Davis, Davis, CA, USA
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Samal L, Kumar Dash S. Nutritional Interventions to Reduce Methane Emissions in Ruminants. Vet Med Sci 2022. [DOI: 10.5772/intechopen.101763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Methane is the single largest source of anthropogenic greenhouse gases produced in ruminants. As global warming is a main concern, the interest in mitigation strategies for ruminant derived methane has strongly increased over the last years. Methane is a natural by-product of anaerobic microbial (bacteria, archaea, protozoa, and fungi) fermentation of carbohydrates and, to a lesser extent, amino acids in the rumen. This gaseous compound is the most prominent hydrogen sink product synthesized in the rumen. It is formed by the archaea, the so-called methanogens, which utilize excessive ruminal hydrogen. Different nutritional strategies to reduce methane production in ruminants have been investigated such as dietary manipulations, plant extracts, lipids and lipid by-products, plant secondary metabolites, flavonoids, phenolic acid, statins, prebiotics, probiotics, etc. With the range of technical options suggested above, it is possible to develop best nutritional strategies to reduce the ill effects of livestock on global warming. These nutritional strategies seem to be the most developed means in mitigating methane from enteric fermentation in ruminants and some are ready to be applied in the field at the moment.
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Microbial pathways for advanced biofuel production. Biochem Soc Trans 2022; 50:987-1001. [PMID: 35411379 PMCID: PMC9162456 DOI: 10.1042/bst20210764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/25/2022] [Indexed: 01/16/2023]
Abstract
Decarbonisation of the transport sector is essential to mitigate anthropogenic climate change. Microbial metabolisms are already integral to the production of renewable, sustainable fuels and, building on that foundation, are being re-engineered to generate the advanced biofuels that will maintain mobility of people and goods during the energy transition. This review surveys the range of natural and engineered microbial systems for advanced biofuels production and summarises some of the techno-economic challenges associated with their implementation at industrial scales.
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Djemai K, Drancourt M, Tidjani Alou M. Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions. MICROBIAL ECOLOGY 2022; 83:536-554. [PMID: 34169332 DOI: 10.1007/s00248-021-01796-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.
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Affiliation(s)
- Kenza Djemai
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Maryam Tidjani Alou
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-University, 19-12 Bd Jean Moulin, 13005, Marseille, France.
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11
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OUP accepted manuscript. Metallomics 2022; 14:6549566. [DOI: 10.1093/mtomcs/mfac016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/02/2022] [Indexed: 11/12/2022]
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Akinyemi TS, Shao N, Lyu Z, Drake IJ, Liu Y, Whitman WB. Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis. ACS Synth Biol 2021; 10:3028-3039. [PMID: 34665610 DOI: 10.1021/acssynbio.1c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO2 to CH4. The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4- to 6-fold when the medium phosphate drops to growth-limiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5' untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.
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Affiliation(s)
- Taiwo S. Akinyemi
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Nana Shao
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
| | - Zhe Lyu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ian J. Drake
- Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, New Jersey 08801, United States
| | - Yuchen Liu
- Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, New Jersey 08801, United States
| | - William B. Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, United States
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Bueno de Mesquita CP, Zhou J, Theroux SM, Tringe SG. Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. Genes (Basel) 2021; 12:genes12101609. [PMID: 34681003 PMCID: PMC8535929 DOI: 10.3390/genes12101609] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/05/2021] [Accepted: 10/09/2021] [Indexed: 12/12/2022] Open
Abstract
Anaerobic archaeal methanogens are key players in the global carbon cycle due to their role in the final stages of organic matter decomposition in anaerobic environments such as wetland sediments. Here we present the first draft metagenome-assembled genome (MAG) sequence of an unclassified Methanosarcinaceae methanogen phylogenetically placed adjacent to the Methanolobus and Methanomethylovorans genera that appears to be a distinct genus and species. The genome is derived from sediments of a hypersaline (97–148 ppt chloride) unrestored industrial saltern that has been observed to be a significant methane source. The source sediment is more saline than previous sources of Methanolobus and Methanomethylovorans. We propose a new genus name, Methanosalis, to house this genome, which we designate with the strain name SBSPR1A. The MAG was binned with CONCOCT and then improved via scaffold extension and reassembly. The genome contains pathways for methylotrophic methanogenesis from trimethylamine and dimethylamine, as well as genes for the synthesis and transport of compatible solutes. Some genes involved in acetoclastic and hydrogenotrophic methanogenesis are present, but those pathways appear incomplete in the genome. The MAG was more abundant in two former industrial salterns than in a nearby reference wetland and a restored wetland, both of which have much lower salinity levels, as well as significantly lower methane emissions than the salterns.
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Affiliation(s)
- Clifton P. Bueno de Mesquita
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Jinglie Zhou
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
| | - Susanna M. Theroux
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA;
| | - Susannah G. Tringe
- Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; (C.P.B.d.M.); (J.Z.)
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Correspondence:
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Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses 2021; 13:v13101934. [PMID: 34696364 PMCID: PMC8540584 DOI: 10.3390/v13101934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/14/2021] [Accepted: 09/20/2021] [Indexed: 01/05/2023] Open
Abstract
Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus.
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15
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Lavergne C, Aguilar-Muñoz P, Calle N, Thalasso F, Astorga-España MS, Sepulveda-Jauregui A, Martinez-Cruz K, Gandois L, Mansilla A, Chamy R, Barret M, Cabrol L. Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems. ENVIRONMENT INTERNATIONAL 2021; 154:106575. [PMID: 33901975 DOI: 10.1016/j.envint.2021.106575] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Freshwater ecosystems are responsible for an important part of the methane (CH4) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH4 flux measurements, CH4 production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H2/CO2, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H2/CO2-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H2/CO2 (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H2/CO2-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H2-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.
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Affiliation(s)
- Céline Lavergne
- HUB AMBIENTAL UPLA, Laboratory of Aquatic Environmental Research, Centro de Estudios Avanzados, Universidad de Playa Ancha, Valparaíso, Chile; Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile.
| | - Polette Aguilar-Muñoz
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Natalia Calle
- Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Frédéric Thalasso
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-IPN), Departamento de Biotecnología y Bioingeniería, México, DF, Mexico
| | - Maria Soledad Astorga-España
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Armando Sepulveda-Jauregui
- ENBEELAB, University of Magallanes, Punta Arenas, Chile; Center for Climate and Resilience Research (CR)(2), Santiago, Chile
| | - Karla Martinez-Cruz
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile; ENBEELAB, University of Magallanes, Punta Arenas, Chile
| | - Laure Gandois
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Andrés Mansilla
- Departamento de Ciencias y Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile
| | - Rolando Chamy
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile
| | - Maialen Barret
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse, France
| | - Léa Cabrol
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, 2340950 Valparaíso, Chile; Aix-Marseille University, Univ Toulon, CNRS, IRD, M.I.O. UM 110, Mediterranean Institute of Oceanography, Marseille, France; Institute of Ecology and Biodiversity IEB, Faculty of Sciences, Universidad de Chile, Santiago, Chile.
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16
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Kakuk B, Wirth R, Maróti G, Szuhaj M, Rakhely G, Laczi K, Kovács KL, Bagi Z. Early response of methanogenic archaea to H 2 as evaluated by metagenomics and metatranscriptomics. Microb Cell Fact 2021; 20:127. [PMID: 34217274 PMCID: PMC8254922 DOI: 10.1186/s12934-021-01618-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies. RESULTS The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria. CONCLUSIONS External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.
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Affiliation(s)
- Balázs Kakuk
- Institute of Medical Biology, University of Szeged, Szeged, Hungary
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Wirth
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
| | - Márk Szuhaj
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Gábor Rakhely
- Department of Biotechnology, University of Szeged, Szeged, Hungary
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
| | - Krisztián Laczi
- Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Kornél L Kovács
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
- Department of Oral Biology and Experimental Dental Research, University of Szeged, Szeged, Hungary.
| | - Zoltán Bagi
- Department of Biotechnology, University of Szeged, Szeged, Hungary.
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17
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Archaea: An Agro-Ecological Perspective. Curr Microbiol 2021; 78:2510-2521. [PMID: 34019119 DOI: 10.1007/s00284-021-02537-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Microorganisms inhabiting bulk soil and rhizosphere play an important role in soil biogeochemical cycles leading to enhanced plant growth and productivity. In this context, the role of bacteria is well established, however, not much reports are available about the role archaea plays in this regard. Literature suggests that archaea also play a greater role in nutrient cycling of carbon, nitrogen, sulfur, and other minerals, possess various plant growth promoting attributes, and can impart tolerance to various abiotic stresses (especially osmotic and oxidative) in areas of high salinity, low and high temperatures and hydrogen ion concentrations. Thermoacidophilic archaea have been found to potentially involve in bioleaching of mineral ores and bioremediation of chemical pollutants and aromatic compounds. Looking at immense potential of archaea in promoting plant growth, alleviating abiotic stresses, and remediating contaminated sites, detailed studies are required to establish their role in different ecological processes, and their interactions in rhizosphere with plant and other microflora (bacteria and fungi) in different ecosystems. In this review, a brief discussion on archaea from the agro-ecological point of view is presented.
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18
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Katsyv A, Müller V. Overcoming Energetic Barriers in Acetogenic C1 Conversion. Front Bioeng Biotechnol 2020; 8:621166. [PMID: 33425882 PMCID: PMC7793690 DOI: 10.3389/fbioe.2020.621166] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/19/2020] [Indexed: 11/13/2022] Open
Abstract
Currently one of the biggest challenges for society is to combat global warming. A solution to this global threat is the implementation of a CO2-based bioeconomy and a H2-based bioenergy economy. Anaerobic lithotrophic bacteria such as the acetogenic bacteria are key players in the global carbon and H2 cycle and thus prime candidates as driving forces in a H2- and CO2-bioeconomy. Naturally, they convert two molecules of CO2via the Wood-Ljungdahl pathway (WLP) to one molecule of acetyl-CoA which can be converted to different C2-products (acetate or ethanol) or elongated to C4 (butyrate) or C5-products (caproate). Since there is no net ATP generation from acetate formation, an electron-transport phosphorylation (ETP) module is hooked up to the WLP. ETP provides the cell with additional ATP, but the ATP gain is very low, only a fraction of an ATP per mol of acetate. Since acetogens live at the thermodynamic edge of life, metabolic engineering to obtain high-value products is currently limited by the low energy status of the cells that allows for the production of only a few compounds with rather low specificity. To set the stage for acetogens as production platforms for a wide range of bioproducts from CO2, the energetic barriers have to be overcome. This review summarizes the pathway, the energetics of the pathway and describes ways to overcome energetic barriers in acetogenic C1 conversion.
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Affiliation(s)
- Alexander Katsyv
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
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19
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Kozlova MI, Bushmakin IM, Belyaeva JD, Shalaeva DN, Dibrova DV, Cherepanov DA, Mulkidjanian AY. Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space. BIOCHEMISTRY. BIOKHIMIIA 2020; 85:1518-1542. [PMID: 33705291 DOI: 10.1134/s0006297920120056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.
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Affiliation(s)
- M I Kozlova
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - I M Bushmakin
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - J D Belyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D N Shalaeva
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany.
| | - D V Dibrova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - D A Cherepanov
- Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - A Y Mulkidjanian
- School of Physics, Osnabrueck University, Osnabrueck, 49069, Germany. .,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
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20
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Lowe TB, Hatch BT, Antle C, Nartker S, Ammerman ML. One- and two-stage anaerobic co-digestion of cucumber waste and sewage sludge. ENVIRONMENTAL TECHNOLOGY 2020; 41:3157-3165. [PMID: 30922190 DOI: 10.1080/09593330.2019.1601262] [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: 08/17/2018] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
The demand for uniformly sized and shaped produce that are aesthetically pleasing results in significant food waste throughout the world. Cucumber waste is a major agricultural waste product in a number of countries, especially areas with high pickle production. Opportunity exists for wastewater treatment plants containing anaerobic digesters to utilize cucumber agricultural and industrial waste for biogas production. The biomethane potential of cucumber waste as a substrate for co-digestion with sewage sludge was assessed. The impact of long-term co-digestion of cucumber was then evaluated using mesophilic continuously stirred tank reactors (CSTRs), in both single- and two-stage anaerobic co-digestion with sewage sludge. Ground cucumber waste was added to sewage sludge at 8% of the volume (4.5-4.6% of the organic load) and CSTRs were maintained for five hydraulic retention times (HRTs). One-stage co-digestion of cucumber waste produced comparable gas levels as CSTRs without cucumbers (averaging 219 and 221 m3/kgVS/h, respectively) after two HRTs. The two-stage cucumber co-digestion CSTR averaged 64% higher specific gas than the control and single-stage digester, although the volumetric gas produced was lower (averaging 152 m3/kgVS/h) likely due to gas loss in the first stage resulting in a lower organic load rate. After four HRTs, relative methanogen content showed dramatic differences in levels of hydrogenotrophic methanogens for the two-stage digester, while the one-stage digester containing cucumber waste showed minor differences relative to the control. Cucumber waste co-digestion with sewage sludge is effective although numerous conditions could be utilized to optimize gas production.
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Affiliation(s)
- Taylor B Lowe
- Department of Chemistry, Biochemistry, Chemical Engineering and Applied Biology, Kettering University, Flint, MI, USA
| | - Benjamin T Hatch
- Department of Chemistry and Physics, Warren Wilson College, Swannanoa, NC, USA
| | | | - Steven Nartker
- Department of Chemistry, Biochemistry, Chemical Engineering and Applied Biology, Kettering University, Flint, MI, USA
| | - Michelle L Ammerman
- Department of Chemistry, Biochemistry, Chemical Engineering and Applied Biology, Kettering University, Flint, MI, USA
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21
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Paulo LM, Hidayat MR, Moretti G, Stams AJM, Sousa DZ. Effect of nickel, cobalt, and iron on methanogenesis from methanol and cometabolic conversion of 1,2-dichloroethene by Methanosarcina barkeri. Biotechnol Appl Biochem 2020; 67:744-750. [PMID: 32282086 PMCID: PMC7687089 DOI: 10.1002/bab.1925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 03/17/2020] [Indexed: 01/28/2023]
Abstract
Methanogens are responsible for the last step in anaerobic digestion (AD), in which methane (a biofuel) is produced. Some methanogens can cometabolize chlorinated pollutants, contributing for their removal during AD. Methanogenic cofactors involved in cometabolic reductive dechlorination, such as F430 and cobalamin, contain metal ions (nickel, cobalt, iron) in their structure. We hypothesized that the supplementation of trace metals could improve methane production and the cometabolic dechlorination of 1,2‐dichloroethene (DCE) by pure cultures of Methanosarcina barkeri. Nickel, cobalt, and iron were added to cultures of M. barkeri growing on methanol and methanol plus DCE. Metal amendment improved DCE dechlorination to vinyl chloride (VC): assays with 20 µM of Fe3+ showed the highest final concentration of VC (5× higher than in controls without Fe3+), but also in assays with 5.5 µM of Co2+ and 5 µM of Ni2+ VC formation was improved (3.5–4× higher than in controls without the respective metals). Dosing of metals could be useful to improve anaerobic removal of chlorinated compounds, and more importantly decrease the detrimental effect of DCE on methane production in anaerobic digesters.
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Affiliation(s)
- Lara M Paulo
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Mohamad R Hidayat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Giulio Moretti
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Laboratory of Microbiology, MESVA Department, University of L'Aquila, Via Vetoio Coppito (AQ), Italy
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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22
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Ozato N, Saito S, Yamaguchi T, Katashima M, Tokuda I, Sawada K, Katsuragi Y, Kakuta M, Imoto S, Ihara K, Nakaji S. Association between breath methane concentration and visceral fat area: a population-based cross-sectional study. J Breath Res 2020; 14:026008. [PMID: 31835267 DOI: 10.1088/1752-7163/ab61c6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
High visceral fat area (VFA) is a stronger predictor of cardiovascular disease and overall mortality, compared with body mass index (BMI) and waist circumference (WC). Recent reports demonstrate that obesity is related to breath gas, which is produced by the intestinal microflora. However, these studies define obesity using BMI, not VFA. In this population-based cross-sectional study, we investigated the relationship between breath gases (methane and hydrogen) and both VFA and BMI. A total of 1033 participants (62% women; age [mean ± standard deviation] 54.4 ± 14.9 years) in the 2015 Iwaki Health Promotion Project in Japan were enrolled in the study. Breath samples were collected using a breath bag and analyzed by gas chromatography. VFA was measured using a visceral fat meter. The proportion of methanogenic bacteria to total intestinal microbiota was measured by polymerase chain reaction and 16S rRNA gene sequencing analysis. Our analysis revealed a significant association between high VFA and low breath methane, even after adjusting for confounding factors (B = -0.024 and P = 0.004). To identify the association between breath methane and VFA in participants with methane-producing bacteria in their intestinal microflora, participants were divided into two groups based on the presence or absence of methanogenic bacteria in their stool. The Methanogen + group was further divided into two subgroups with breath methane higher (Methane-UP) or lower (Methane-LO) than the median breath methane concentration. VFA was significantly lower in the Methane-UP group than in the Methane-LO group. In participants with methanogenic bacteria, breath methane concentration might be an independent biomarker of visceral fat accumulation.
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Affiliation(s)
- Naoki Ozato
- Department of Active Life Promotion Sciences, Graduate School of Medicine, Hirosaki University, Japan. Health Care Food Research Laboratories, Kao Corporation, Japan
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23
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Nguyen CH, Field JA, Sierra-Alvarez R. Microbial toxicity of gallium- and indium-based oxide and arsenide nanoparticles. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2019; 55:168-178. [PMID: 31607225 DOI: 10.1080/10934529.2019.1676065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
III-V semiconductor materials such as gallium arsenide (GaAs) and indium arsenide (InAs) are increasingly used in the fabrication of electronic devices. There is a growing concern about the potential release of these materials into the environment leading to effects on public and environmental health. The waste effluents from the chemical mechanical planarization process could impact microorganisms in biological wastewater treatment systems. Currently, there is only limited information about the inhibition of gallium- and indium-based nanoparticles (NPs) on microorganisms. This study evaluated the acute toxicity of GaAs, InAs, gallium oxide (Ga2O3), and indium oxide (In2O3) particulates using two microbial inhibition assays targeting methanogenic archaea and the marine bacterium, Aliivibrio fischeri. GaAs and InAs NPs were acutely toxic towards these microorganisms; Ga2O3 and In2O3 NPs were not. The toxic effect was mainly due to the release of soluble arsenic species and it increased with decreasing particle size and with increasing time due to the progressive corrosion of the NPs in the aqueous bioassay medium. Collectively, the results indicate that the toxicity exerted by the arsenide NPs under environmental conditions will vary depending on intrinsic properties of the material such as particle size as well as on the dissolution time and aqueous chemistry.
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Affiliation(s)
- Chi H Nguyen
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona, USA
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Odelade KA, Babalola OO. Bacteria, Fungi and Archaea Domains in Rhizospheric Soil and Their Effects in Enhancing Agricultural Productivity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E3873. [PMID: 31614851 PMCID: PMC6843647 DOI: 10.3390/ijerph16203873] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/19/2019] [Accepted: 10/04/2019] [Indexed: 12/24/2022]
Abstract
The persistent and undiscriminating application of chemicals as means to improve crop growth, development and yields for several years has become problematic to agricultural sustainability because of the adverse effects these chemicals have on the produce, consumers and beneficial microbes in the ecosystem. Therefore, for agricultural productivity to be sustained there are needs for better and suitable preferences which would be friendly to the ecosystem. The use of microbial metabolites has become an attractive and more feasible preference because they are versatile, degradable and ecofriendly, unlike chemicals. In order to achieve this aim, it is then imperative to explore microbes that are very close to the root of a plant, especially where they are more concentrated and have efficient activities called the rhizosphere. Extensive varieties of bacteria, archaea, fungi and other microbes are found inhabiting the rhizosphere with various interactions with the plant host. Therefore, this review explores various beneficial microbes such as bacteria, fungi and archaea and their roles in the environment in terms of acquisition of nutrients for plants for the purposes of plant growth and health. It also discusses the effect of root exudate on the rhizosphere microbiome and compares the three domains at molecular levels.
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Affiliation(s)
- Kehinde Abraham Odelade
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Science, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Science, North-West University, Private Bag X2046, Mmabatho 2735, South Africa.
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Energy Conservation and Hydrogenase Function in Methanogenic Archaea, in Particular the Genus Methanosarcina. Microbiol Mol Biol Rev 2019; 83:83/4/e00020-19. [PMID: 31533962 DOI: 10.1128/mmbr.00020-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The biological production of methane is vital to the global carbon cycle and accounts for ca. 74% of total methane emissions. The organisms that facilitate this process, methanogenic archaea, belong to a large and phylogenetically diverse group that thrives in a wide range of anaerobic environments. Two main subgroups exist within methanogenic archaea: those with and those without cytochromes. Although a variety of metabolisms exist within this group, the reduction of growth substrates to methane using electrons from molecular hydrogen is, in a phylogenetic sense, the most widespread methanogenic pathway. Methanogens without cytochromes typically generate methane by the reduction of CO2 with electrons derived from H2, formate, or secondary alcohols, generating a transmembrane ion gradient for ATP production via an Na+-translocating methyltransferase (Mtr). These organisms also conserve energy with a novel flavin-based electron bifurcation mechanism, wherein the endergonic reduction of ferredoxin is facilitated by the exergonic reduction of a disulfide terminal electron acceptor coupled to either H2 or formate oxidation. Methanogens that utilize cytochromes have a broader substrate range, and can convert acetate and methylated compounds to methane, in addition to the ability to reduce CO2 Cytochrome-containing methanogens are able to supplement the ion motive force generated by Mtr with an H+-translocating electron transport system. In both groups, enzymes known as hydrogenases, which reversibly interconvert protons and electrons to molecular hydrogen, play a central role in the methanogenic process. This review discusses recent insight into methanogen metabolism and energy conservation mechanisms with a particular focus on the genus Methanosarcina.
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Teoh R, Caro E, Holman DB, Joseph S, Meale SJ, Chaves AV. Effects of Hardwood Biochar on Methane Production, Fermentation Characteristics, and the Rumen Microbiota Using Rumen Simulation. Front Microbiol 2019; 10:1534. [PMID: 31354652 PMCID: PMC6635593 DOI: 10.3389/fmicb.2019.01534] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022] Open
Abstract
Biochar is a novel carbonized feed additive sourced from pyrolyzed biomass. This compound is known to adsorb gasses and carbon, participate in biological redox reactions and provide habitat biofilms for desirable microbiota proliferation. Therefore, biochar holds potential to modify rumen fermentation characteristics and reduce enteric CH4 emissions. The objective of this study was to investigate the effect of hardwood biochar supplementation on fermentation parameters, methane (CH4) production and the ruminal archaeal, bacterial, and fungal microbiota using the in vitro RUSITEC (rumen simulation technique) system. Treatments consisted of a control diet (oaten pasture: maize silage: concentrate, 35:35:30 w/w) and hardwood biochar included at 400 or 800 mg per day (3.6 and 7.2% of substrate DM, respectively), over a 15-day period. Biochar supplementation had no effect (P ≥ 0.37) on pH, effluent (mL/d), total gas (mL/d), dry matter (DM) digestibility or CH4 production (mg/d). The addition of 800 mg biochar per day had the tendency (P = 0.10) to lower the % of CH4 released in fermentation compared to 400 mg/d biochar treatment. However, no effect (P ≥ 0.44) was seen on total VFA, acetate, propionate, butyric, branched-chain VFA, valerate and caproate production and the ratio of acetate to propionate. No effect (P > 0.05) was observed on bacterial, archaeal or fungal community structure. However, biochar supplementation at 800 mg/d decreased the abundance of one Methanomethylophilaceae OTU (19.8-fold, P = 0.046) and one Lactobacillus spp. OTU (31.7-fold, P < 0.01), in comparison to control treatments. Two fungal OTUs classified as Vishniacozyma victoriae (5.4 × 107 increase) and Sporobolomyces ruberrimus (5.4 × 107-fold increase) were more abundant in the 800 mg/d biochar samples. In conclusion, hardwood biochar had no effects on ruminal fermentation characteristics and may potentially lower the concentration of enteric CH4 when included at higher dosages by manipulating ruminal microbiota abundances.
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Affiliation(s)
- Rebecca Teoh
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
| | - Eleonora Caro
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
- Department of Agricultural, Forestry and Food Science, University of Turin, Turin, Italy
| | - Devin B. Holman
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Stephen Joseph
- School of Materials Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Sarah J. Meale
- School of Agriculture and Food Sciences, Faculty of Science, The University of Queensland, Gatton, QLD, Australia
| | - Alex V. Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW, Australia
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Yang C, McKain N, McCartney CA, Wallace RJ. Consequences of inhibiting methanogenesis on the biohydrogenation of fatty acids in bovine ruminal digesta. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2019.05.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kröninger L, Steiniger F, Berger S, Kraus S, Welte CU, Deppenmeier U. Energy conservation in the gut microbeMethanomassiliicoccus luminyensisis based on membrane‐bound ferredoxin oxidation coupled to heterodisulfide reduction. FEBS J 2019; 286:3831-3843. [DOI: 10.1111/febs.14948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/17/2019] [Accepted: 06/01/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Lena Kröninger
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Fabian Steiniger
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Stefanie Berger
- Department of Microbiology IWWR Radboud University Nijmegen The Netherlands
| | - Sebastian Kraus
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
| | - Cornelia U. Welte
- Department of Microbiology IWWR Radboud University Nijmegen The Netherlands
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology University of Bonn Bonn Germany
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Cunha CS, Marcondes MI, Veloso CM, Mantovani HC, Pereira LGR, Tomich TR, Dill-McFarland KA, Suen G. Compositional and structural dynamics of the ruminal microbiota in dairy heifers and its relationship to methane production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:210-218. [PMID: 29851082 DOI: 10.1002/jsfa.9162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Heifers emit more enteric methane (CH4 ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for these pre-production animals. Given its direct role in CH4 production, altering the rumen microbiota is another potential avenue for reducing CH4 production by ruminants. However, to identify effective microbial targets, a better understanding of the rumen microbiota and its relationship to CH4 production across heifer development is needed. RESULTS Here, we investigate the relationship between rumen bacterial, archaeal, and fungal communities as well as CH4 emissions and a number of production traits in prepubertal (PP), pubertal (PB), and pregnant heifers (PG). Overall, PG heifers emitted the most CH4 , followed by PB and PP heifers. The bacterial genus Acetobacter and the archaeal genus Methanobrevibacter were positively associated, while Eubacterium and Methanosphaera were negatively associated with raw CH4 production by heifers. When corrected for dietary intake, both Eubacterium and Methanosphaera remained negatively associated with CH4 production. CONCLUSION We suggest that Eubacterium and Methanosphaera represent likely targets for CH4 mitigation efforts in heifers as they were negatively associated with CH4 production and not significantly associated with production traits. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Camila S Cunha
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Marcos I Marcondes
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Cristina M Veloso
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Thierry R Tomich
- Brazilian Agricultural Research Corporation, EMBRAPA Dairy Cattle, Juiz de Fora, Brazil
| | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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Characterization of the lytic archaeal virus Drs3 infecting Methanobacterium formicicum. Arch Virol 2018; 164:667-674. [DOI: 10.1007/s00705-018-04120-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/19/2018] [Indexed: 01/21/2023]
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Müller V, Chowdhury NP, Basen M. Electron Bifurcation: A Long-Hidden Energy-Coupling Mechanism. Annu Rev Microbiol 2018; 72:331-353. [PMID: 29924687 DOI: 10.1146/annurev-micro-090816-093440] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A decade ago, a novel mechanism to drive thermodynamically unfavorable redox reactions was discovered that is used in prokaryotes to drive endergonic electron transfer reactions by a direct coupling to an exergonic redox reaction in one soluble enzyme complex. This process is referred to as flavin-based electron bifurcation, or FBEB. An important function of FBEB is that it allows the generation of reduced low-potential ferredoxin (Fdred) from comparably high-potential electron donors such as NADH or molecular hydrogen (H2). Fdred is then the electron donor for anaerobic respiratory chains leading to the synthesis of ATP. In many metabolic scenarios, Fd is reduced by metabolic oxidoreductases and Fdred then drives endergonic metabolic reactions such as H2 production by the reverse, electron confurcation. FBEB is energetically more economical than ATP hydrolysis or reverse electron transport as a driving force for endergonic redox reactions; thus, it does "save" cellular ATP. It is essential for autotrophic growth at the origin of life and also allows for heterotrophic growth on certain low-energy substrates.
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Affiliation(s)
- Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
| | - Mirko Basen
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, 60438 Frankfurt, Germany;
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Kröninger L, Gottschling J, Deppenmeier U. Growth Characteristics of Methanomassiliicoccus luminyensis and Expression of Methyltransferase Encoding Genes. ARCHAEA (VANCOUVER, B.C.) 2017; 2017:2756573. [PMID: 29230105 PMCID: PMC5688252 DOI: 10.1155/2017/2756573] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 09/24/2017] [Indexed: 11/17/2022]
Abstract
DNA sequence analysis of the human gut revealed the presence a seventh order of methanogens referred to as Methanomassiliicoccales. Methanomassiliicoccus luminyensis is the only member of this order that grows in pure culture. Here, we show that the organism has a doubling time of 1.8 d with methanol + H2 and a growth yield of 2.4 g dry weight/mol CH4. M. luminyensis also uses methylamines + H2 (monomethylamine, dimethylamine, and trimethylamine) with doubling times of 2.1-2.3 d. Similar cell yields were obtained with equimolar concentrations of methanol and methylamines with respect to their methyl group contents. The transcript levels of genes encoding proteins involved in substrate utilization indicated increased amounts of mRNA from the mtaBC2 gene cluster in methanol-grown cells. When methylamines were used as substrates, mRNA of the mtb/mtt operon and of the mtmBC1 cluster were found in high abundance. The transcript level of mtaC2 was almost identical in methanol- and methylamine-grown cells, indicating that genes for methanol utilization were constitutively expressed in high amounts. The same observation was made with resting cells where methanol always yielded the highest CH4 production rate independently from the growth substrate. Hence, M. luminyensis is adapted to habitats that provide methanol + H2 as substrates.
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Affiliation(s)
- Lena Kröninger
- Institut für Mikrobiologie und Biotechnologie, Universität Bonn, Bonn, Germany
| | | | - Uwe Deppenmeier
- Institut für Mikrobiologie und Biotechnologie, Universität Bonn, Bonn, Germany
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Gilmore SP, Henske JK, Sexton JA, Solomon KV, Seppälä S, Yoo JI, Huyett LM, Pressman A, Cogan JZ, Kivenson V, Peng X, Tan Y, Valentine DL, O'Malley MA. Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. BMC Genomics 2017; 18:639. [PMID: 28826405 PMCID: PMC5563889 DOI: 10.1186/s12864-017-4036-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/08/2017] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. RESULTS Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. CONCLUSIONS Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO2 metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO2 and formate are common electron carriers in microbial communities.
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Affiliation(s)
- Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Jessica A Sexton
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA.,Present Address: Agricultural & Biological Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Justin I Yoo
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Lauren M Huyett
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Abe Pressman
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - James Z Cogan
- Biology Program, College of Creative Studies, University of California, Santa Barbara, California, USA
| | - Veronika Kivenson
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, California, USA
| | - Xuefeng Peng
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA.,Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, California, USA
| | - YerPeng Tan
- California NanoScience Institute, University of California, Santa Barbara, California, USA
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, California, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA.
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Martínez-Núñez MA, Rodríguez-Escamilla Z, Rodríguez-Vázquez K, Pérez-Rueda E. Tracing the Repertoire of Promiscuous Enzymes along the Metabolic Pathways in Archaeal Organisms. Life (Basel) 2017; 7:life7030030. [PMID: 28703743 PMCID: PMC5617955 DOI: 10.3390/life7030030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/10/2023] Open
Abstract
The metabolic pathways that carry out the biochemical transformations sustaining life depend on the efficiency of their associated enzymes. In recent years, it has become clear that promiscuous enzymes have played an important role in the function and evolution of metabolism. In this work we analyze the repertoire of promiscuous enzymes in 89 non-redundant genomes of the Archaea cellular domain. Promiscuous enzymes are defined as those proteins with two or more different Enzyme Commission (E.C.) numbers, according the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. From this analysis, it was found that the fraction of promiscuous enzymes is lower in Archaea than in Bacteria. A greater diversity of superfamily domains is associated with promiscuous enzymes compared to specialized enzymes, both in Archaea and Bacteria, and there is an enrichment of substrate promiscuity rather than catalytic promiscuity in the archaeal enzymes. Finally, the presence of promiscuous enzymes in the metabolic pathways was found to be heterogeneously distributed at the domain level and in the phyla that make up the Archaea. These analyses increase our understanding of promiscuous enzymes and provide additional clues to the evolution of metabolism in Archaea.
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Affiliation(s)
- Mario Alberto Martínez-Núñez
- Laboratorio de Estudios Ecogenómicos, Facultad de Ciencias, Unidad Académica de Ciencias y Tecnología de la UNAM en Yucatán, Universidad Nacional Autónoma de México, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
| | - Zuemy Rodríguez-Escamilla
- Departamento de Microbiología, Instituto de Biotecnología, Universidad Nacional, Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
| | - Katya Rodríguez-Vázquez
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Ciudad de México, Mexico.
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, C.P. 62210, Cuernavaca, Morelos, Mexico.
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Carretera Sierra Papacal-Chuburna Km. 5, C.P. 97302, Mérida, Yucatán, Mexico.
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Duarte AC, Holman DB, Alexander TW, Kiri K, Breves G, Chaves AV. Incubation Temperature, But Not Pequi Oil Supplementation, Affects Methane Production, and the Ruminal Microbiota in a Rumen Simulation Technique (Rusitec) System. Front Microbiol 2017; 8:1076. [PMID: 28701999 PMCID: PMC5487375 DOI: 10.3389/fmicb.2017.01076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 05/29/2017] [Indexed: 01/05/2023] Open
Abstract
Lipid supplementation is a promising strategy for methane mitigation in cattle and has been evaluated using several different lipid sources. However, limited studies have assessed the effect of temperature on methane emissions from cattle and changes in incubation temperature have also not been extensively evaluated. The aim of this study was to evaluate the combined effect of pequi oil (high in unsaturated fatty acids) and incubation temperature on fermentation characteristics and microbial communities using the rumen simulation technique. A completely randomized experiment was conducted over a 28-day period using a Rusitec system. The experiment was divided into four periods of 7 days each, the first of which was a 7-day adaptation period followed by three experimental periods. The two treatments consisted of a control diet (no pequi oil inclusion) and a diet supplemented with pequi oil (1.5 mL/day) which increased the dietary fat content to 6% (dry matter, DM-basis). Three fermenter vessels (i.e., replicates) were allocated to each treatment. In the first experimental period, the incubation temperature was maintained at 39°C, decreased to 35°C in the second experimental period and then increased again to 39°C in the third. Pequi oil was continuously supplemented during the experiment. Microbial communities were assessed using high-throughput sequencing of the archaeal and bacterial 16S rRNA gene. Methane production was reduced by 57% following a 4°C decrease in incubation temperature. Supplementation with pequi oil increased the dietary fat content to 6% (DM-basis) but did not affect methane production. Analysis of the microbiota revealed that decreasing incubation temperature to 35°C affected the archaeal and bacterial diversity and richness of liquid-associated microbes, but lipid supplementation did not change microbial diversity.
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Affiliation(s)
- Andrea C Duarte
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, SydneyNSW, Australia
| | - Devin B Holman
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Trevor W Alexander
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada
| | - Kerstin Kiri
- Department of Physiology, University of Veterinary MedicineHannover, Germany
| | - Gerhard Breves
- Department of Physiology, University of Veterinary MedicineHannover, Germany
| | - Alexandre V Chaves
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, SydneyNSW, Australia
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Wu WL, Lai SJ, Yang JT, Chern J, Liang SY, Chou CC, Kuo CH, Lai MC, Wu SH. Phosphoproteomic analysis of Methanohalophilus portucalensis FDF1(T) identified the role of protein phosphorylation in methanogenesis and osmoregulation. Sci Rep 2016; 6:29013. [PMID: 27357474 PMCID: PMC4928046 DOI: 10.1038/srep29013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/10/2016] [Indexed: 02/02/2023] Open
Abstract
Methanogens have gained much attention for their metabolic product, methane, which could be an energy substitute but also contributes to the greenhouse effect. One factor that controls methane emission, reversible protein phosphorylation, is a crucial signaling switch, and phosphoproteomics has become a powerful tool for large-scale surveying. Here, we conducted the first phosphorylation-mediated regulation study in halophilic Methanohalophilus portucalensis FDF1(T), a model strain for studying stress response mechanisms in osmoadaptation. A shotgun approach and MS-based analysis identified 149 unique phosphoproteins. Among them, 26% participated in methanogenesis and osmolytes biosynthesis pathways. Of note, we uncovered that protein phosphorylation might be a crucial factor to modulate the pyrrolysine (Pyl) incorporation and Pyl-mediated methylotrophic methanogenesis. Furthermore, heterologous expression of glycine sarcosine N-methyltransferase (GSMT) mutant derivatives in the osmosensitive Escherichia coli MKH13 revealed that the nonphosphorylated T68A mutant resulted in increased salt tolerance. In contrast, mimic phosphorylated mutant T68D proved defective in both enzymatic activity and salinity tolerance for growth. Our study provides new insights into phosphorylation modification as a crucial role of both methanogenesis and osmoadaptation in methanoarchaea, promoting biogas production or reducing future methane emission in response to global warming and climate change.
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Affiliation(s)
- Wan-Ling Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Jung Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
| | - Jhih-Tian Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Ph.D program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung 40227, Taiwan
| | - Jeffy Chern
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Suh-Yuen Liang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Core Facilities for Protein Structural Analysis, Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Mei-Chin Lai
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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Cardinali-Rezende J, Rojas-Ojeda P, Nascimento AMA, Sanz JL. Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology. CHEMOSPHERE 2016; 146:519-525. [PMID: 26741558 DOI: 10.1016/j.chemosphere.2015.12.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/09/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Biomethanization entails a good means to reduce the organic fraction (OF) derived from municipal solid wastes (MSW). The bacterial diversity of a full scale MSW anaerobic reactor located in Madrid (Spain) was investigated using high-throughput 454 pyrosequencing. Even though the proteolytic bacteria prevailed throughout all of the process, community shifts were observed from the start-up to the steady-state conditions, with an increasing biodiversity displayed over time. The Bacteroidetes and the Firmicutes were the majority phyla: 55.1 and 40.2% (start-up) and 18.7 and 78.7 (steady-state) of the total reads. The system's lack of evenness remains noteworthy as the sequences affiliated to the proteolytic non-saccharolytic Proteiniphylum, Gallicola and Fastidiosipila genera, together with the saccharolytic Saccharofermentans, were predominant on the system and this predominance appears to correlate with the presence of a high ammonium concentration. The 454 pyrosequencing revealed a great diversity of rare organisms which seemingly do not sustain any metabolic roles in the course of the OF-MSW degradation. However, this scarce and unique microbiota can confer great resilience to the system as a buffer against nutritional and environmental changing conditions, thus opening the door to increase the current knowledge about the bacterial community dynamics taking place during MSW treatment processes.
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Affiliation(s)
- Juliana Cardinali-Rezende
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain; Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31.270-901, Brazil
| | - Patricia Rojas-Ojeda
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain
| | - Andréa M A Nascimento
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Belo Horizonte, MG 31.270-901, Brazil
| | - José L Sanz
- Department of Molecular Biology, Universidad Autónoma de Madrid, c/ Darwin 2, Madrid 28049, Spain.
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Kröninger L, Berger S, Welte C, Deppenmeier U. Evidence for the involvement of two heterodisulfide reductases in the energy-conserving system ofMethanomassiliicoccus luminyensis. FEBS J 2015; 283:472-83. [DOI: 10.1111/febs.13594] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/30/2015] [Accepted: 11/09/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Lena Kröninger
- Institute of Microbiology and Biotechnology; University of Bonn; Germany
| | - Stefanie Berger
- Institute of Microbiology and Biotechnology; University of Bonn; Germany
| | - Cornelia Welte
- Department of Microbiology; Institute for Water and Wetland Research; Radboud University; Nijmegen The Netherlands
| | - Uwe Deppenmeier
- Institute of Microbiology and Biotechnology; University of Bonn; Germany
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Mbakwa CA, Penders J, Savelkoul PH, Thijs C, Dagnelie PC, Mommers M, Arts ICW. Gut colonization with methanobrevibacter smithii is associated with childhood weight development. Obesity (Silver Spring) 2015; 23:2508-16. [PMID: 26524691 DOI: 10.1002/oby.21266] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To prospectively investigate the presence and counts of archaea in feces of 472 children in association with weight development from 6 to 10 years of age. METHODS Within the KOALA Birth Cohort Study, a single fecal sample from each child was analyzed by quantitative polymerase chain reaction to quantify archaea (Methanobrevibacter smithii, Methanosphera stadtmanae). Anthropometric outcomes (overweight [body mass index {BMI} ≥ 85th percentile], age- and sex-standardized BMI, weight, and height z-scores) were repeatedly measured at ages (mean ± SD) of 6.2 ± 0.5, 6.8 ± 0.5, 7.8 ± 0.5, and 8.8 ± 0.5 years. Generalized estimating equation was used for statistical analysis while controlling for confounders. RESULTS Methanobrevibacter smithii colonization was associated with an increased risk of overweight (adjusted odds ratio [OR] = 2.69; 95% confidence interval [CI] 0.96-7.54) from 6 to 10 years of age. Children with high levels (>7 log10 copies/g feces) of this archaeon were at highest risk for overweight (OR = 3.27; 95% CI 1.09-9.83). Moreover, M. smithii colonization was associated with higher weight z-scores (adj. β 0.18; 95% CI 0.00-0.36), but not with height. For BMI z-scores, the interaction (P = 0.008) between M. smithii and age was statistically significant, implying children colonized with M. smithii had increasing BMI z-scores with age. CONCLUSIONS Presence and higher counts of M. smithii in the gut of children are associated with higher weight z-scores, higher BMI z-scores, and overweight.
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Affiliation(s)
- Catherine A Mbakwa
- Top Institute Food and Nutrition, Wageningen, the Netherlands
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
| | - John Penders
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
- Department of Medical Microbiology, Maastricht University Medical Centre, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht, the Netherlands
| | - Paul H Savelkoul
- Department of Medical Microbiology, Maastricht University Medical Centre, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht, the Netherlands
| | - Carel Thijs
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
| | - Pieter C Dagnelie
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
- Department of Epidemiology, Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, the Netherlands
| | - Monique Mommers
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
| | - Ilja C W Arts
- Department of Epidemiology, Maastricht University, CAPHRI School for Public Health and Primary Care, Maastricht, the Netherlands
- Department of Epidemiology, Maastricht University, CARIM School for Cardiovascular Diseases, Maastricht, the Netherlands
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Abstract
Low-molecular-weight (LMW) thiols are extensively involved in the maintenance of cellular redox potentials and the protection of cells from a variety of reactive chemical and electrophilic species. However, we recently found that the metabolic coupling of two LMW thiols - mycothiol (MSH) and ergothioneine (EGT) - programs the biosynthesis of the anti-infective agent lincomycin A. Remarkably, such a constructive role of the thiols in the biosynthesis of natural products has so far received relatively little attention. We speculate that the unusual thiol EGT might function as a chiral thiolation carrier (for modification) and a novel activator (for glycosylation) of sugar. Additionally, we examine recent evidence for LMW thiols (MSH and others) as sulfur donors of sulfur-containing natural products. Clearly, the LMW thiols have more diverse activities beyond cell protection, and more attention should be paid to the correlation of their functions with thiol-dependent enzymes.
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Affiliation(s)
- Min Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Qunfei Zhao
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.,Huzhou Center of Bio-Synthetic Innovation, Huzhou, China
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Guzman CE, Bereza-Malcolm LT, De Groef B, Franks AE. Presence of Selected Methanogens, Fibrolytic Bacteria, and Proteobacteria in the Gastrointestinal Tract of Neonatal Dairy Calves from Birth to 72 Hours. PLoS One 2015; 10:e0133048. [PMID: 26186002 PMCID: PMC4505879 DOI: 10.1371/journal.pone.0133048] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 06/22/2015] [Indexed: 12/12/2022] Open
Abstract
The microbial communities in the gastrointestinal tract of a young calf are essential for the anatomical and physiological development that permits a transition from milk to solid feed. Selected methanogens, fibrolytic bacteria, and proteobacteria were quantified in the rumen fluid and tissue, abomasum fluid, cecum fluid and tissue, and feces of Holstein bull calves on day 0 (0-20 mins after birth), day 1 (24 ± 1 h after birth), day 2 (48 ± 1 h after birth), and day 3 (72 ± 1 h after birth). Methanogens, fibrolytic bacteria, and Geobacter spp. were found to be already present from birth, indicating that microbial colonization of the gastrointestinal tract occurred before or during delivery. The abundance of methanogens and Geobacter spp. differed between the days tested and between compartments of the digestive tract and feces, but such difference was not observed for fibrolytic bacteria. Our findings suggests that methanogens might have an alternative hydrogen provider such as Geobacter spp. during these early stages of postnatal development. In addition, fibrolytic bacteria were present in the rumen well before the availability of fibrous substrates, suggesting that they might use nutrients other than cellulose and hemicellose.
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Affiliation(s)
- Cesar E. Guzman
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Lara T. Bereza-Malcolm
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Ashley E. Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, Victoria, Australia
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Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production. Appl Environ Microbiol 2015; 81:6528-37. [PMID: 26162885 PMCID: PMC4561719 DOI: 10.1128/aem.01162-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/27/2015] [Indexed: 11/20/2022] Open
Abstract
Methanogens are anaerobic archaea that grow by producing methane, a gas that is both an efficient renewable fuel and a potent greenhouse gas. We observed that overexpression of the cytoplasmic heterodisulfide reductase enzyme HdrABC increased the rate of methane production from methanol by 30% without affecting the growth rate relative to the parent strain. Hdr enzymes are essential in all known methane-producing archaea. They function as the terminal oxidases in the methanogen electron transport system by reducing the coenzyme M (2-mercaptoethane sulfonate) and coenzyme B (7-mercaptoheptanoylthreonine sulfonate) heterodisulfide, CoM-S-S-CoB, to regenerate the thiol-coenzymes for reuse. In Methanosarcina acetivorans, HdrABC expression caused an increased rate of methanogenesis and a decrease in metabolic efficiency on methylotrophic substrates. When acetate was the sole carbon and energy source, neither deletion nor overexpression of HdrABC had an effect on growth or methane production rates. These results suggest that in cells grown on methylated substrates, the cell compensates for energy losses due to expression of HdrABC with an increased rate of substrate turnover and that HdrABC lacks the appropriate electron donor in acetate-grown cells.
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45
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Identification of the Final Two Genes Functioning in Methanofuran Biosynthesis in Methanocaldococcus jannaschii. J Bacteriol 2015; 197:2850-8. [PMID: 26100040 DOI: 10.1128/jb.00401-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED All methanofuran structural variants contain a basic core structure of 4-[N-(γ-l-glutamyl)-p-(β-aminoethyl)phenoxymethyl]-(aminomethyl)furan (APMF-Glu) but have different side chains depending on the source organism. Recently, we identified four genes (MfnA, MfnB, MfnC, and MfnD) that are responsible for the biosynthesis of the methanofuran precursor γ-glutamyltyramine and 5-(aminomethyl)-3-furanmethanol-phosphate (F1-P) from tyrosine, glutamate, glyceraldehyde-3-P, and alanine in Methanocaldococcus jannaschii. How γ-glutamyltyramine and F1-P couple together to form the core structure of methanofuran was previously unknown. Here, we report the identification of two enzymes encoded by the genes mj0458 and mj0840 that catalyze the formation of F1-PP from ATP and F1-P and the condensation of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. We have annotated these enzymes as MfnE and MfnF, respectively, representing the fifth and sixth enzymes in the methanofuran biosynthetic pathway to be identified. Although MfnE was previously reported as an archaeal adenylate kinase, our present results show that MfnE is a promiscuous enzyme and that its possible physiological role is to produce F1-PP. Unlike other enzymes catalyzing coupling reactions involving pyrophosphate as the leaving group, MfnF exhibits a distinctive α/β two-layer sandwich structure. By comparing MfnF with thiamine synthase and dihydropteroate synthase, a substitution nucleophilic unimolecular (SN-1) reaction mechanism is proposed for MfnF. With the identification of MfnE and MfnF, the biosynthetic pathway for the methanofuran core structure APMF-Glu is complete. IMPORTANCE This work describes the identification of the final two enzymes responsible for catalyzing the biosynthesis of the core structure of methanofuran. The gene products of mj0458 and mj0840 catalyze the formation of F1-PP and the coupling of F1-PP with γ-glutamyltyramine, respectively, to form APMF-Glu. Although the chemistry of such a coupling reaction is widespread in biochemistry, we provide here the first evidence that such a mechanism is used in methanofuran biosynthesis. MfnF belongs to the hydantoinase A family (PF01968) and exhibits a unique α/β two-layer sandwich structure that is different from the enzymes catalyzing similar reactions. Our results show that MfnF catalyzes the formation of an ether bond during methanofuran biosynthesis. Therefore, this work further expands the functionality of this enzyme family.
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46
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Wang Y, Jones MK, Xu H, Ray WK, White RH. Mechanism of the Enzymatic Synthesis of 4-(Hydroxymethyl)-2-furancarboxaldehyde-phosphate (4-HFC-P) from Glyceraldehyde-3-phosphate Catalyzed by 4-HFC-P Synthase. Biochemistry 2015; 54:2997-3008. [DOI: 10.1021/acs.biochem.5b00176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Wang
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Michael K. Jones
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Huimin Xu
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - W. Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Robert H. White
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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Li J, Wong CF, Wong MT, Huang H, Leung FC. Modularized evolution in archaeal methanogens phylogenetic forest. Genome Biol Evol 2014; 6:3344-59. [PMID: 25502908 PMCID: PMC4986457 DOI: 10.1093/gbe/evu259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2014] [Indexed: 11/13/2022] Open
Abstract
Methanogens are methane-producing archaea that plays a key role in the global carbon cycle. To date, the evolutionary history of methanogens and closely related nonmethanogen species remains unresolved among studies conducted upon different genetic markers, attributing to horizontal gene transfers (HGTs). With an effort to decipher both congruent and conflicting evolutionary events, reconstruction of coevolved gene clusters and hierarchical structure in the archaeal methanogen phylogenetic forest, comprehensive evolution, and network analyses were performed upon 3,694 gene families from 41 methanogens and 33 closely related archaea. Our results show that 1) greater than 50% of genes are in topological dissonance with others; 2) the prevalent interorder HGTs, even for core genes, in methanogen genomes led to their scrambled phylogenetic relationships; 3) most methanogenesis-related genes have experienced at least one HGT; 4) greater than 20% of the genes in methanogen genomes were transferred horizontally from other archaea, with genes involved in cell-wall synthesis and defense system having been transferred most frequently; 5) the coevolution network contains seven statistically robust modules, wherein the central module has the highest average node strength and comprises a majority of the core genes; 6) different coevolutionary module genes boomed in different time and evolutionary lineage, constructing diversified pan-genome structures; 7) the modularized evolution is also closely related to the vertical evolution signals and the HGT rate of the genes. Overall, this study presented a modularized phylogenetic forest that describes a combination of complicated vertical and nonvertical evolutionary processes for methanogenic archaeal species.
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Affiliation(s)
- Jun Li
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China
| | - Chi-Fat Wong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China School of Biological Sciences, Faculty of Science, The University of Hong Kong, China
| | - Mabel Ting Wong
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Present address: Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada
| | - He Huang
- Center for Marine Environmental Studies, Ehime University, Japan
| | - Frederick C Leung
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, China Bioinformatics Center, Nanjing Agricultural University, People's Republic of China
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Purwantini E, Torto-Alalibo T, Lomax J, Setubal JC, Tyler BM, Mukhopadhyay B. Genetic resources for methane production from biomass described with the Gene Ontology. Front Microbiol 2014; 5:634. [PMID: 25520705 PMCID: PMC4253957 DOI: 10.3389/fmicb.2014.00634] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 11/05/2014] [Indexed: 11/21/2022] Open
Abstract
Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).
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Affiliation(s)
- Endang Purwantini
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Trudy Torto-Alalibo
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Jane Lomax
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Hinxton, UK
| | - João C Setubal
- Department of Biochemistry, Universidade de São Paulo São Paulo, Brazil ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Center for Genome Research and Biocomputing, Oregon State University Corvallis, OR, USA
| | - Biswarup Mukhopadhyay
- Department of Biochemistry, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University Blacksburg, VA, USA ; Department of Biological Sciences, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
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Gonzalez-Estrella J, Puyol D, Sierra-Alvarez R, Field JA. Role of biogenic sulfide in attenuating zinc oxide and copper nanoparticle toxicity to acetoclastic methanogenesis. JOURNAL OF HAZARDOUS MATERIALS 2014; 283:755-763. [PMID: 25464319 DOI: 10.1016/j.jhazmat.2014.10.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 06/04/2023]
Abstract
Soluble ions released by zinc oxide (ZnO) and copper (Cu(0)) nanoparticles (NPs) have been associated with toxicity to methanogens. This study evaluated the role of biogenic sulfide in attenuating ZnO and Cu(0) NP toxicity to methanogens. Short- and long-term batch experiments were conducted to explore ZnO and Cu(0) NPs toxicity to acetoclastic methanogens in sulfate-containing (0.4mM) and sulfate-free conditions. ZnO and Cu(0) were respectively 14 and 7-fold less toxic in sulfate-containing than in sulfate-free assays as indicated by inhibitory constants (Ki). The Ki with respect to residual soluble metal indicated that soluble metal was well correlated with toxicity irrespective of the metal ion source or presence of biogenic sulfide. Long-term assays indicated that ZnO and Cu(0) NPs caused different effects on methanogens. ZnO NPs without protection of sulfide caused a chronic effect, whereas Cu(0) NPs caused an acute effect and recovered. This study confirms that biogenic sulfide effectively attenuates ZnO and Cu(0) NPs toxicity to methanogens by the formation of metal sulfides.
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Affiliation(s)
- Jorge Gonzalez-Estrella
- Department of Chemical and Environmental Engineering, University of Arizona, P.O. Box 210011, Tucson, AZ 85721, USA.
| | - Daniel Puyol
- Department of Chemical and Environmental Engineering, University of Arizona, P.O. Box 210011, Tucson, AZ 85721, USA
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, P.O. Box 210011, Tucson, AZ 85721, USA
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, P.O. Box 210011, Tucson, AZ 85721, USA
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50
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Zhang S, Winestrand S, Chen L, Li D, Jönsson LJ, Hong F. Tolerance of the nanocellulose-producing bacterium Gluconacetobacter xylinus to lignocellulose-derived acids and aldehydes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:9792-9. [PMID: 25186182 DOI: 10.1021/jf502623s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Lignocellulosic biomass serves as a potential alternative feedstock for production of bacterial nanocellulose (BNC), a high-value-added product of bacteria such as Gluconacetobacter xylinus. The tolerance of G. xylinus to lignocellulose-derived inhibitors (formic acid, acetic acid, levulinic acid, furfural, and 5-hydroxymethylfurfural) was investigated. Whereas 100 mM formic acid completely suppressed the metabolism of G. xylinus, 250 mM of either acetic acid or levulinic acid still allowed glucose metabolism and BNC production to occur. Complete suppression of glucose utilization and BNC production was observed after inclusion of 20 and 30 mM furfural and 5-hydroxymethylfurfural, respectively. The bacterium oxidized furfural and 5-hydroxymethylfurfural to furoic acid and 5-hydroxymethyl-2-furoic acid, respectively. The highest yields observed were 88% for furoic acid/furfural and 76% for 5-hydroxymethyl-2-furoic acid/5-hydroxymethylfurfural. These results are the first demonstration of the capability of G. xylinus to tolerate lignocellulose-derived inhibitors and to convert furan aldehydes.
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Affiliation(s)
- Shuo Zhang
- China-Sweden Associated Research Laboratory in Industrial Biotechnology and ‡Group of Microbiological Engineering and Industrial Biotechnology, College of Chemistry, Chemical Engineering and Biotechnology, and #School of Environmental Science and Engineering, Donghua University , Shanghai 201620, China
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