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Hsu D, Flynn JR, Schuler CJ, Santelli CM, Toner BM, Bond DR, Gralnick JA. Isolation and genomic analysis of " Metallumcola ferriviriculae" MK1, a Gram-positive, Fe(III)-reducing bacterium from the Soudan Underground Mine, an iron-rich Martian analog site. Appl Environ Microbiol 2024:e0004424. [PMID: 39007603 DOI: 10.1128/aem.00044-24] [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: 01/10/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
The Soudan Underground Mine State Park, found in the Vermilion Iron Range in northern Minnesota, provides access to a ~ 2.7 billion-year-old banded iron formation. Exploratory boreholes drilled between 1958 and 1962 on the 27th level (713 m underground) of the mine intersect calcium and iron-rich brines that have recently been subject to metagenomic analysis and microbial enrichments. Using concentrated brine samples pumped from a borehole depth of up to 55 m, a novel Gram-positive bacterium was enriched under anaerobic, acetate-oxidizing, and Fe(III) citrate-reducing conditions. The isolated bacterium, designated strain MK1, is non-motile, rod-shaped, spore-forming, anaerobic, and mesophilic, with a growth range between 24°C and 30°C. The complete circular MK1 genome was found to be 3,720,236 bp and encodes 25 putative multiheme cytochromes, including homologs to inner membrane cytochromes in the Gram-negative bacterium Geobacter sulfurreducens and cytoplasmic membrane and periplasmic cytochromes in the Gram-positive bacterium Thermincola potens. However, MK1 does not encode homologs of the peptidoglycan (CwcA) and cell surface-associated (OcwA) multiheme cytochromes proposed to be required by T. potens to perform extracellular electron transfer. The 16S rRNA gene sequence of MK1 indicates that its closest related isolate is Desulfitibacter alkalitolerans strain sk.kt5 (91% sequence identity), which places MK1 in a novel genus within the Desulfitibacteraceae family and Moorellales order. Within the Moorellales order, only Calderihabitans maritimus strain KKC1 has been reported to reduce Fe(III), and only D. alkalitolerans can also grow in temperatures below 40°C. Thus, MK1 represents a novel species within a novel genus, for which we propose the name "Metallumcola ferriviriculae" strain MK1, and provides a unique opportunity to study a cytochrome-rich, mesophilic, Gram-positive, spore-forming Fe(III)-reducing bacterium.IMPORTANCEThe Soudan Underground Mine State Park gives access to understudied regions of the deep terrestrial subsurface that potentially predate the Great Oxidation Event. Studying organisms that have been relatively unperturbed by surface conditions for as long as 2.7 billion years may give us a window into ancient life before oxygen dominated the planet. Additionally, studying microbes from anoxic and iron-rich environments can help us better understand the requirements of life in analogous environments, such as on Mars. The isolation and characterization of "Metallumcola ferriviriculae" strain MK1 give us insights into a novel genus and species that is distinct both from its closest related isolates and from iron reducers characterized to date. "M. ferriviriculae" strain MK1 may also act as a model organism to study how the processes of sporulation and germination are affected by insoluble extracellular acceptors, as well as the impact of spores in the deep terrestrial biosphere.
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Affiliation(s)
- David Hsu
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jack R Flynn
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Christopher J Schuler
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Cara M Santelli
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | - Brandy M Toner
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Department of Soil, Water, and Climate, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Daniel R Bond
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
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Kato J, Fujii T, Kato S, Wada K, Watanabe M, Nakamichi Y, Aoi Y, Morita T, Murakami K, Nakashimada Y. Genetic engineering of a thermophilic acetogen, Moorella thermoacetica Y72, to enable acetoin production. Front Bioeng Biotechnol 2024; 12:1398467. [PMID: 38812916 PMCID: PMC11133584 DOI: 10.3389/fbioe.2024.1398467] [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: 03/10/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
Acetogens are among the key microorganisms involved in the bioproduction of commodity chemicals from diverse carbon resources, such as biomass and waste gas. Thermophilic acetogens are particularly attractive because fermentation at higher temperatures offers multiple advantages. However, the main target product is acetic acid. Therefore, it is necessary to reshape metabolism using genetic engineering to produce the desired chemicals with varied carbon lengths. Although such metabolic engineering has been hampered by the difficulty involved in genetic modification, a model thermophilic acetogen, M. thermoacetica ATCC 39073, is the case with a few successful cases of C2 and C3 compound production, other than acetate. This brief report attempts to expand the product spectrum to include C4 compounds by using strain Y72 of Moorella thermoacetica. Strain Y72 is a strain related to the type strain ATCC 39073 and has been reported to have a less stringent restriction-modification system, which could alleviate the cumbersome transformation process. A simplified procedure successfully introduced a key enzyme for acetoin (a C4 chemical) production, and the resulting strains produced acetoin from sugars and gaseous substrates. The culture profile revealed varied acetoin yields depending on the type of substrate and culture conditions, implying the need for further engineering in the future. Thus, the use of a user-friendly chassis could benefit the genetic engineering of M. thermoacetica.
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Affiliation(s)
- Junya Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Tatsuya Fujii
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Keisuke Wada
- National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan
| | - Masahiro Watanabe
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Yusuke Nakamichi
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Yoshiteru Aoi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Tomotake Morita
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Katsuji Murakami
- National Institute of Advanced Industrial Science and Technology (AIST), Higashihiroshima, Hiroshima, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
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Jia D, Deng W, Hu P, Jiang W, Gu Y. Thermophilic Moorella thermoacetica as a platform microorganism for C1 gas utilization: physiology, engineering, and applications. BIORESOUR BIOPROCESS 2023; 10:61. [PMID: 38647965 PMCID: PMC10992200 DOI: 10.1186/s40643-023-00682-z] [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: 06/27/2023] [Accepted: 08/29/2023] [Indexed: 04/25/2024] Open
Abstract
In the context of the rapid development of low-carbon economy, there has been increasing interest in utilizing naturally abundant and cost-effective one-carbon (C1) substrates for sustainable production of chemicals and fuels. Moorella thermoacetica, a model acetogenic bacterium, has attracted significant attention due to its ability to utilize carbon dioxide (CO2) and carbon monoxide (CO) via the Wood-Ljungdahl (WL) pathway, thereby showing great potential for the utilization of C1 gases. However, natural strains of M. thermoacetica are not yet fully suitable for industrial applications due to their limitations in carbon assimilation and conversion efficiency as well as limited product range. Over the past decade, progresses have been made in the development of genetic tools for M. thermoacetica, accelerating the understanding and modification of this acetogen. Here, we summarize the physiological and metabolic characteristics of M. thermoacetica and review the recent advances in engineering this bacterium. Finally, we propose the future directions for exploring the real potential of M. thermoacetica in industrial applications.
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Affiliation(s)
- Dechen Jia
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wangshuying Deng
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Hu
- Shanghai GTLB Biotech Co., Ltd, 1688 North Guoquan Road, Shanghai, 200438, China
| | - Weihong Jiang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yang Gu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
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Harahap BM, Ahring BK. Acetate Production from Syngas Produced from Lignocellulosic Biomass Materials along with Gaseous Fermentation of the Syngas: A Review. Microorganisms 2023; 11:microorganisms11040995. [PMID: 37110418 PMCID: PMC10143712 DOI: 10.3390/microorganisms11040995] [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: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Biotransformation of lignocellulose-derived synthetic gas (syngas) into acetic acid is a promising way of creating biochemicals from lignocellulosic waste materials. Acetic acid has a growing market with applications within food, plastics and for upgrading into a wide range of biofuels and bio-products. In this paper, we will review the microbial conversion of syngas to acetic acid. This will include the presentation of acetate-producing bacterial strains and their optimal fermentation conditions, such as pH, temperature, media composition, and syngas composition, to enhance acetate production. The influence of syngas impurities generated from lignocellulose gasification will further be covered along with the means to alleviate impurity problems through gas purification. The problem with mass transfer limitation of gaseous fermentation will further be discussed as well as ways to improve gas uptake during the fermentation.
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Affiliation(s)
- Budi Mandra Harahap
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
| | - Birgitte K Ahring
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Wegner Hall, Pullman, WA 99164, USA
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Perchlorate-Coupled Carbon Monoxide (CO) Oxidation by Moorella glycerini, an Obligately Anaerobic, Thermophilic, Nickel-Dependent Carboxydotroph. Microorganisms 2023; 11:microorganisms11020462. [PMID: 36838427 PMCID: PMC9964509 DOI: 10.3390/microorganisms11020462] [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: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Many facultative and obligate anaerobes reduce perchlorate. Likewise, carbon monoxide (CO) oxidation has been documented in many aerobes, facultative anaerobes, and obligate anaerobes. A molybdenum-dependent CO dehydrogenase (Mo-CODH) and a nickel-dependent CO dehydrogenase (Ni-CODH) distinguish the former from the latter. Some Mo-dependent CO oxidizers (Mo-COX) couple CO oxidation to perchlorate reduction, but only at low concentrations of both under conditions that do not support growth in cultures. In contrast, CO-coupled perchlorate reduction has not been documented in Ni-dependent CO oxidizers (Ni-COX). To assess the potential for Ni-COX to reduce perchlorate, a model, obligately anaerobic homoacetogen, Moorella glycerini DSM 11254T, was cultivated with or without perchlorate, usiing CO or glycerol as its sole carbon and energy source. It grew with glycerol with or without perchlorate, and its maximum cell densities were only weakly affected by the perchlorate. However, when CO (at a 30% headspace concentration) was used as a carbon and energy source, perchlorate reduction supported greater cell densities and more rapid growth rates. The stoichiometry of CO uptake, perchlorate reduction, and chloride production were consistent with the cryptic pathway for perchlorate reduction with chlorite as an end product. Chloride production occurred abiologically in the medium due to a reaction between chlorite and the sulfide used as a reducing agent. These results provide the first demonstration of CO-coupled perchlorate reduction supporting growth in Ni-COX, and they provide constraints on the potential for perchlorate-coupled, anaerobic CO oxidation in engineered systems as well as terrestrial systems and hypothetical, sub-surface, serpentinite-hosted systems on Mars.
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Zeldes B, Poehlein A, Jain S, Baum C, Daniel R, Müller V, Basen M. DNA uptake from a laboratory environment drives unexpected adaptation of a thermophile to a minor medium component. ISME COMMUNICATIONS 2023; 3:2. [PMID: 37938748 PMCID: PMC9834392 DOI: 10.1038/s43705-022-00211-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 06/01/2023]
Abstract
DNA uptake is widespread among microorganisms and considered a strategy for rapid adaptation to new conditions. While both DNA uptake and adaptation are referred to in the context of natural environments, they are often studied in laboratories under defined conditions. For example, a strain of the thermophile Thermoanaerobacter kivui had been adapted to growth on high concentrations of carbon monoxide (CO). Unusual phenotypes of the CO-adapted strain prompted us to examine it more closely, revealing a horizontal gene transfer (HGT) event from another thermophile, Thermoanaerobacter sp. strain X514, being cultured in the same laboratory. The transferred genes conferred on T. kivui the ability to utilize trehalose, a trace component of the yeast-extract added to the media during CO-adaptation. This same HGT event simultaneously deleted a native operon for thiamine biosynthesis, which likely explains why the CO-adapted strain grows poorly without added vitamins. Attempts to replicate this HGT by providing T. kivui with genomic DNA from Thermoanaerobacter sp. strain X514 revealed that it is easily reproducible in the lab. This subtle form of "genome contamination" is difficult to detect, since the genome remains predominantly T. kivui, and no living cells from the original contamination remain. Unexpected HGT between two microorganisms as well as simultaneous adaptation to several conditions may occur often and unrecognized in laboratory environments, requiring caution and careful monitoring of phenotype and genotype of microorganisms that are naturally-competent for DNA uptake.
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Affiliation(s)
- Benjamin Zeldes
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Surbhi Jain
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Christoph Baum
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Göttingen, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, Rostock, Germany.
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Slobodkina GB, Merkel AY, Kuchierskaya AA, Slobodkin AI. Moorella sulfitireducens sp. nov., a thermophilic anaerobic bacterium isolated from a terrestrial thermal spring. Extremophiles 2022; 26:33. [DOI: 10.1007/s00792-022-01285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
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Judicial Opinions 112–122. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Opinion 112 denies the request to place
Seliberia
Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject
Shewanella irciniae
Lee et al. 2006 and Opinion 114 denies the request to reject the name
Enterobacter siamensis
Khunthongpan et al. 2014. Opinion 115 rejects the epithet of
Moorella thermoautotrophica
(Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate
Methylothermus subterraneus
Hirayama et al. 2011 as the type species of the genus
Methylothermus
is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name
Flaviaesturariibacter
is treated, as are the analogous cases of
Fredinandcohnia
and
Hydrogeniiclostidium
. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and
Hydrogeniiclostridium
, respectively. Opinion 119 concludes that assigning
Actinomycetales
Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class
Actinobacteria
Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but
Actinomycetales
is also assigned as type of
Actinomycetes
Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name
Amycolatopsis albidoflavus
is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of
Mollicutes
proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.
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Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. Int J Syst Evol Microbiol 2020; 70:4061-4090. [DOI: 10.1099/ijsem.0.004245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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