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Feehan B, Ran Q, Dorman V, Rumback K, Pogranichniy S, Ward K, Goodband R, Niederwerder MC, Lee STM. Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea. Anim Microbiome 2023; 5:35. [PMID: 37461084 DOI: 10.1186/s42523-023-00256-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination. RESULTS We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.
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Affiliation(s)
- Brandi Feehan
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Qinghong Ran
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Victoria Dorman
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kourtney Rumback
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Sophia Pogranichniy
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Kaitlyn Ward
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA
| | - Robert Goodband
- Department of Animal Sciences and Industry, College of Agriculture, Kansas State University, Manhattan, KS, 66506, USA
| | | | - Sonny T M Lee
- Division of Biology, College of Arts and Sciences, Kansas State University, Manhattan, KS, 66506, USA.
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2
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Yao J, Zeng Y, Wang M, Tang YQ. Energy Availability Determines Strategy of Microbial Amino Acid Synthesis in Volatile Fatty Acid-Fed Anaerobic Methanogenic Chemostats. Front Microbiol 2021; 12:744834. [PMID: 34671332 PMCID: PMC8521154 DOI: 10.3389/fmicb.2021.744834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/30/2021] [Indexed: 12/03/2022] Open
Abstract
In natural communities, microbes exchange a variety of metabolites (public goods) with each other, which drives the evolution of auxotroph and shapes interdependent patterns at community-level. However, factors that determine the strategy of public goods synthesis for a given community member still remains to be elucidated. In anaerobic methanogenic communities, energy availability of different community members is largely varied. We hypothesized that this uneven energy availability contributed to the heterogeneity of public goods synthesis ability among the members in these communities. We tested this hypothesis by analyzing the synthetic strategy of amino acids of the bacterial and archaeal members involved in four previously enriched anaerobic methanogenic communities residing in thermophilic chemostats. Our analyses indicate that most of the members in the communities did not possess ability to synthesize all the essential amino acids, suggesting they exchanged these essential public goods to establish interdependent patterns for survival. Importantly, we found that the amino acid synthesis ability of a functional group was largely determined by how much energy it could obtain from its metabolism in the given environmental condition. Moreover, members within a functional group also possessed different amino acid synthesis abilities, which are related to their features of energy metabolism. Our study reveals that energy availability is a key driver of microbial evolution in presence of metabolic specialization at community level and suggests the feasibility of managing anaerobic methanogenic communities for better performance through controlling the metabolic interactions involved.
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Affiliation(s)
| | | | - Miaoxiao Wang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China
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3
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Lee J, Kim E, Hwang S. Effects of inhibitions by sodium ion and ammonia and different inocula on acetate-utilizing methanogenesis: Methanogenic activity and succession of methanogens. BIORESOURCE TECHNOLOGY 2021; 334:125202. [PMID: 33957457 DOI: 10.1016/j.biortech.2021.125202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 06/12/2023]
Abstract
Acetate-fed anaerobic sequential batch experiments with four different inhibitory conditions (non-inhibitory (Lo), sodium-ion inhibitory (Na), ammonia inhibitory (Am), combined inhibitory (Hi)) were conducted using thirteen different inocula to investigate the inhibition effects by sodium-ion and ammonia and different inocula on acetate-utilizing methanogenesis and succession of methanogens. Sodium-ion and ammonia significantly extended lag-time λ and reduced specific-methanogenic-activity RCH4, and caused synergistic inhibition. The inhibition differed according to the initial methanogen community structures: the inhibition effects on λ and RCH4 were strongest ininocula with Methanosaeta concilii dominant and weakest in inocula with Methanoculleus bourgensis dominant. These inhibitory conditions determined the succession of methanogens: the most competitive methanogens were Methanosaeta concilii in Lo, Methanosarcina sp. in Na, Methanosarcina sp. and Methanoculleus bourgensis in Am, Methanoculleus bourgensis in Hi. This study provides valuable information for microbial management and optimization for AD processes treating wastewater that is rich in protein and/or salt.
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Affiliation(s)
- Joonyeob Lee
- Department of Environmental Engineering, Pukyong National University, Busan 48513, Republic of Korea
| | - Eunji Kim
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seokhwan Hwang
- Division of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
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4
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Chen YT, Zeng Y, Li J, Zhao XY, Yi Y, Gou M, Kamagata Y, Narihiro T, Nobu MK, Tang YQ. Novel Syntrophic Isovalerate-Degrading Bacteria and Their Energetic Cooperation with Methanogens in Methanogenic Chemostats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:9618-9628. [PMID: 32667198 DOI: 10.1021/acs.est.0c01840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Isovalerate is an important intermediate in anaerobic degradation of proteins/amino acids. Little is known about how this compound is degraded due to challenges in cultivation and characterization of isovalerate-degrading bacteria, which are thought to symbiotically depend on methanogenic archaea. In this study, we successfully enriched novel syntrophic isovalerate degraders (uncultivated Clostridiales and Syntrophaceae members) through operation of mesophilic and thermophilic isovalerate-fed anaerobic reactors. Metagenomics- and metatranscriptomics-based metabolic reconstruction of novel putative syntrophic isovalerate metabolizers uncovered the catabolic pathway and byproducts (i.e., acetate, H2, and formate) of isovalerate degradation, mechanisms for electron transduction from isovalerate degradation to H2 and formate generation (via electron transfer flavoprotein; ETF), and biosynthetic metabolism. The identified organisms tended to prefer formate-based interspecies electron transfer with methanogenic partners. The byproduct acetate was further converted to CH4 and CO2 by either Methanothrix (mesophilic) and Methanosarcina (thermophilic), which employed different approaches for acetate degradation. This study presents insights into novel mesophilic and thermophilic isovalerate degraders and their interactions with methanogens.
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Affiliation(s)
- Ya-Ting Chen
- Institute for Disaster Management and Reconstruction, Sichuan University-Hong Kong Polytechnic University, Chengdu, Sichuan 610207, China
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yan Zeng
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Jie Li
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Xin-Yu Zhao
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yue Yi
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Min Gou
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Masaru Konishi Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24, South Section 1, First Ring Road, Chengdu, Sichuan 610065, China
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McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM, Jay ZJ, Klingelsmith KB, Rusch DB, Inskeep WP. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat Microbiol 2019; 4:614-622. [PMID: 30833730 DOI: 10.1038/s41564-019-0362-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 01/07/2019] [Indexed: 11/09/2022]
Abstract
Phylogenetic and geological evidence supports the hypothesis that life on Earth originated in thermal environments and conserved energy through methanogenesis or sulfur reduction. Here we describe two populations of the deeply rooted archaeal phylum Korarchaeota, which were retrieved from the metagenome of a circumneutral, suboxic hot spring that contains high levels of sulfate, sulfide, methane, hydrogen and carbon dioxide. One population is closely related to 'Candidatus Korarchaeum cryptofilum OPF8', while the more abundant korarchaeote, 'Candidatus Methanodesulfokores washburnensis', contains genes that are necessary for anaerobic methane and dissimilatory sulfur metabolisms. Phylogenetic and ancestral reconstruction analyses suggest that methane metabolism originated in the Korarchaeota, whereas genes for dissimilatory sulfite reduction were horizontally transferred to the Korarchaeota from the Firmicutes. Interactions among enzymes involved in both metabolisms could facilitate exergonic, sulfite-dependent, anaerobic oxidation of methane to methanol; alternatively, 'Ca. M. washburnensis' could conduct methanogenesis and sulfur reduction independently. Metabolic reconstruction suggests that 'Ca. M. washburnensis' is a mixotroph, capable of amino acid uptake, assimilation of methane-derived carbon and/or CO2 fixation by archaeal type III-b RuBisCO for scavenging ribose carbon. Our findings link anaerobic methane metabolism and dissimilatory sulfur reduction within a single deeply rooted archaeal population and have implications for the evolution of these traits throughout the Archaea.
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Affiliation(s)
- Luke J McKay
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA. .,Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
| | - Mensur Dlakić
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Tom O Delmont
- Department of Medicine, University of Chicago, Chicago, IL, USA.,Genoscope, Évry, France
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL, USA.,Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Zackary J Jay
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA
| | | | | | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA. .,Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
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6
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Manesis AC, Musselman BW, Keegan BC, Shearer J, Lehnert N, Shafaat HS. A Biochemical Nickel(I) State Supports Nucleophilic Alkyl Addition: A Roadmap for Methyl Reactivity in Acetyl Coenzyme A Synthase. Inorg Chem 2019; 58:8969-8982. [PMID: 30788970 PMCID: PMC6635881 DOI: 10.1021/acs.inorgchem.8b03546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Nickel-containing
enzymes such as methyl coenzyme M reductase (MCR) and carbon monoxide
dehydrogenase/acetyl coenzyme A synthase (CODH/ACS) play a critical
role in global energy conversion reactions, with significant contributions
to carbon-centered processes. These enzymes are implied to cycle through
a series of nickel-based organometallic intermediates during catalysis,
though identification of these intermediates remains challenging.
In this work, we have developed and characterized a nickel-containing
metalloprotein that models the methyl-bound organometallic intermediates
proposed in the native enzymes. Using a nickel(I)-substituted azurin
mutant, we demonstrate that alkyl binding occurs via nucleophilic
addition of methyl iodide as a methyl donor. The paramagnetic NiIII-CH3 species initially generated can be rapidly
reduced to a high-spin NiII-CH3 species in the
presence of exogenous reducing agent, following a reaction sequence
analogous to that proposed for ACS. These two distinct bioorganometallic
species have been characterized by optical, EPR, XAS, and MCD spectroscopy,
and the overall mechanism describing methyl reactivity with nickel
azurin has been quantitatively modeled using global kinetic simulations.
A comparison between the nickel azurin protein system and existing
ACS model compounds is presented. NiIII-CH3 Az
is only the second example of two-electron addition of methyl iodide
to a NiI center to give an isolable species and the first
to be formed in a biologically relevant system. These results highlight
the divergent reactivity of nickel across the two intermediates, with
implications for likely reaction mechanisms and catalytically relevant
states in the native ACS enzyme. A bioorganometallic model
for acetyl coenzyme A synthase has been developed. This model protein
is able to bind a cationic methyl group via direct addition to the
nickel(I) center. The resultant nickel(III)-methyl species has been
characterized via optical and electron paramagnetic resonance spectroscopy,
and the reduced nickel(II)-methyl state has been characterized using
magnetic circular dichroism and X-ray spectroscopy. Implications for
further reactivity with CO are gleaned from electronic structure analysis
of the nickel-methyl species.
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Affiliation(s)
- Anastasia C Manesis
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
| | - Bradley W Musselman
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Brenna C Keegan
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Jason Shearer
- Department of Chemistry , Trinity University , One Trinity Place , San Antonio , Texas 78212 , United States
| | - Nicolai Lehnert
- Department of Chemistry , University of Michigan , 930 N. University Avenue , Ann Arbor , Michigan 48109 , United States
| | - Hannah S Shafaat
- Department of Chemistry and Biochemistry , The Ohio State University , 100 W. 18th Avenue , Columbus , Ohio 43210 , United States
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7
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Bennett RK, Steinberg LM, Chen W, Papoutsakis ET. Engineering the bioconversion of methane and methanol to fuels and chemicals in native and synthetic methylotrophs. Curr Opin Biotechnol 2017; 50:81-93. [PMID: 29216497 DOI: 10.1016/j.copbio.2017.11.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 10/18/2022]
Abstract
Methylotrophy describes the ability of organisms to utilize reduced one-carbon compounds, notably methane and methanol, as growth and energy sources. Abundant natural gas supplies, composed primarily of methane, have prompted interest in using these compounds, which are more reduced than sugars, as substrates to improve product titers and yields of bioprocesses. Engineering native methylotophs or developing synthetic methylotrophs are emerging fields to convert methane and methanol into fuels and chemicals under aerobic and anaerobic conditions. This review discusses recent progress made toward engineering native methanotrophs for aerobic and anaerobic methane utilization and synthetic methylotrophs for methanol utilization. Finally, strategies to overcome the limitations involved with synthetic methanol utilization, notably methanol dehydrogenase kinetics and ribulose 5-phosphate regeneration, are discussed.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Lisa M Steinberg
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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