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Bhat EH, Henard JM, Lee SA, McHalffey D, Ravulapati MS, Rogers EV, Yu L, Skiles D, Henard CA. Construction of a broad-host-range Anderson promoter series and particulate methane monooxygenase promoter variants expand the methanotroph genetic toolbox. Synth Syst Biotechnol 2024; 9:250-258. [PMID: 38435708 PMCID: PMC10909576 DOI: 10.1016/j.synbio.2024.02.003] [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: 01/06/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024] Open
Abstract
Methanotrophic bacteria are currently used industrially for the bioconversion of methane-rich natural gas and anaerobic digestion-derived biogas to valuable products. These bacteria may also serve to mitigate the negative effects of climate change by capturing atmospheric greenhouse gases. Several genetic tools have previously been developed for genetic and metabolic engineering of methanotrophs. However, the available tools for use in methanotrophs are significantly underdeveloped compared to many other industrially relevant bacteria, which hinders genetic and metabolic engineering of these biocatalysts. As such, expansion of the methanotroph genetic toolbox is needed to further our understanding of methanotrophy and develop biotechnologies that leverage these unique microbes for mitigation and conversion of methane to valuable products. Here, we determined the copy number of three broad-host-range plasmids in Methylococcus capsulatus Bath and Methylosinus trichosporium OB3b, representing phylogenetically diverse Gammaproteobacterial and Alphaproteobacterial methanotrophs, respectively. Further, we show that the commonly used synthetic Anderson series promoters are functional and exhibit similar relative activity in M. capsulatus and M. trichosporium OB3b, but the synthetic series had limited range. Thus, we mutagenized the native M. capsulatus particulate methane monooxygenase promoter and identified variants with activity that expand the activity range of synthetic, constitutive promoters functional not only in M. capsulatus, but also in Escherichia coli. Collectively, the tools developed here advance the methanotroph genetic engineering toolbox and represent additional synthetic genetic parts that may have broad applicability in Pseudomonadota bacteria.
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Affiliation(s)
| | | | | | - Dustin McHalffey
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Mahith S. Ravulapati
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Elle V. Rogers
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Logan Yu
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - David Skiles
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Calvin A. Henard
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX, USA
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Hirayama H, Takaki Y, Abe M, Miyazaki M, Uematsu K, Matsui Y, Takai K. Methylomarinovum tepidoasis sp. nov., a moderately thermophilic methanotroph of the family Methylothermaceae isolated from a deep-sea hydrothermal field. Int J Syst Evol Microbiol 2024; 74:006288. [PMID: 38478579 PMCID: PMC10950024 DOI: 10.1099/ijsem.0.006288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024] Open
Abstract
A novel aerobic methanotrophic bacterium, designated as strain IN45T, was isolated from in situ colonisation systems deployed at the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. IN45T was a moderately thermophilic obligate methanotroph that grew only on methane or methanol at temperatures between 25 and 56 °C (optimum 45-50 °C). It was an oval-shaped, Gram-reaction-negative, motile bacterium with a single polar flagellum and an intracytoplasmic membrane system. It required 1.5-4.0 % (w/v) NaCl (optimum 2-3 %) for growth. The major phospholipid fatty acids were C16 : 1ω7c, C16 : 0 and C18 : 1ω7c. The major isoprenoid quinone was Q-8. The 16S rRNA gene sequence comparison revealed 99.1 % sequence identity with Methylomarinovum caldicuralii IT-9T, the only species of the genus Methylomarinovum with a validly published name within the family Methylothermaceae. The complete genome sequence of IN45T consisted of a 2.42-Mbp chromosome (DNA G+C content, 64.1 mol%) and a 20.5-kbp plasmid. The genome encodes genes for particulate methane monooxygenase and two types of methanol dehydrogenase (mxaFI and xoxF). Genes involved in the ribulose monophosphate pathway for carbon assimilation are encoded, but the transaldolase gene was not found. The genome indicated that IN45T performs partial denitrification of nitrate to N2O, and its occurrence was indirectly confirmed by N2O production in cultures grown with nitrate. Genomic relatedness indices between the complete genome sequences of IN45T and M. caldicuralii IT-9T, such as digital DNA-DNA hybridisation (51.2 %), average nucleotide identity (92.94 %) and average amino acid identity (93.21 %), indicated that these two methanotrophs should be separated at the species level. On the basis of these results, strain IN45T represents a novel species, for which we propose the name Methylomarinovum tepidoasis sp. nov. with IN45T (=JCM 35101T =DSM 113422T) as the type strain.
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Affiliation(s)
- Hisako Hirayama
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yoshihiro Takaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Mariko Abe
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Masayuki Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | | | - Yohei Matsui
- Research Institute for Global Change (RIGC), JAMSTEC, Yokosuka, Kanagawa, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
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Reis PCJ, Tsuji JM, Weiblen C, Schiff SL, Scott M, Stein LY, Neufeld JD. Enigmatic persistence of aerobic methanotrophs in oxygen-limiting freshwater habitats. THE ISME JOURNAL 2024; 18:wrae041. [PMID: 38470309 PMCID: PMC11008690 DOI: 10.1093/ismejo/wrae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 03/13/2024] [Indexed: 03/13/2024]
Abstract
Methanotrophic bacteria mitigate emissions of the potent greenhouse gas methane (CH4) from a variety of anthropogenic and natural sources, including freshwater lakes, which are large sources of CH4 on a global scale. Despite a dependence on dioxygen (O2) for CH4 oxidation, abundant populations of putatively aerobic methanotrophs have been detected within microoxic and anoxic waters and sediments of lakes. Experimental work has demonstrated active aerobic methanotrophs under those conditions, but how they are able to persist and oxidize CH4 under O2 deficiency remains enigmatic. In this review, we discuss possible mechanisms that underpin the persistence and activity of aerobic methanotrophs under O2-limiting conditions in freshwater habitats, particularly lakes, summarize experimental evidence for microbial oxidation of CH4 by aerobic bacteria under low or no O2, and suggest future research directions to further explore the ecology and metabolism of aerobic methanotrophs in O2-limiting environments.
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Affiliation(s)
- Paula C J Reis
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jackson M Tsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Cerrise Weiblen
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sherry L Schiff
- Department of Earth & Environmental Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Matthew Scott
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Molari M, Hassenrueck C, Laso-Pérez R, Wegener G, Offre P, Scilipoti S, Boetius A. A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nat Microbiol 2023; 8:651-665. [PMID: 36894632 PMCID: PMC10066037 DOI: 10.1038/s41564-023-01342-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 02/10/2023] [Indexed: 03/11/2023]
Abstract
Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, USulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, US. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of US. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.
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Affiliation(s)
- Massimiliano Molari
- Max Planck Institute for Marine Microbiology, Bremen, Germany. .,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | | | - Rafael Laso-Pérez
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.,Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
| | - Stefano Scilipoti
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Electromicrobiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Antje Boetius
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Abstract
Microbes with the capacity to use methane (CH4) as a carbon source (methanotrophs) have significant potential for the bioconversion of CH4-containing natural gas and anaerobic digestion-derived biogas to high value products. These organisms also play a vital role in the biogeochemical cycling of atmospheric CH4 by serving as the only known biological sink of this gas in terrestrial and aquatic ecosystems. Much is known regarding the enzymes and central metabolic pathways mediating CH4 utilization in these bacteria. However, large fundamental knowledge gaps exist regarding methanotroph physiology and responses to environmental stimuli, primarily due to a lack of efficient molecular tools to probe gene-function relationships. In this chapter, we describe several recently developed genetic tools and optimized genome editing methods that can be used for methanotroph metabolic engineering and to probe metabolic and physiological governing mechanisms in these unique bacteria.
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Affiliation(s)
- Sreemoye Nath
- Department of Biological Sciences, University of North Texas, Denton, TX, USA
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Jessica M Henard
- BioDiscovery Institute, University of North Texas, Denton, TX, USA
| | - Calvin A Henard
- Department of Biological Sciences, University of North Texas, Denton, TX, USA.
- BioDiscovery Institute, University of North Texas, Denton, TX, USA.
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Multispecies populations of methanotrophic Methyloprofundus and cultivation of a likely dominant species from the Iheya North deep-sea hydrothermal field. Appl Environ Microbiol 2021; 88:e0075821. [PMID: 34788070 PMCID: PMC8788690 DOI: 10.1128/aem.00758-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Methyloprofundus clade is represented by uncultivated methanotrophic bacterial endosymbionts of deep-sea bathymodiolin mussels, but only a single free-living species has been cultivated to date. This study reveals the existence of free-living Methyloprofundus variants in the Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough. A clade-targeted amplicon analysis of the particulate methane monooxygenase gene (pmoA) detected 647 amplicon sequence variants (ASVs) of the Methyloprofundus clade in microbial communities newly formed in in situ colonization systems. Such systems were deployed at colonies of bathymodiolin mussels and a galatheoid crab in diffuse-flow areas. These ASVs were classified into 161 species-like groups. The proportion of the species-like groups representing endosymbionts of mussels was unexpectedly low. A methanotrophic bacterium designated INp10, a likely dominant species in the Methyloprofundus population in this field, was enriched in a biofilm formed in a methane-fed cultivation system operated at 10°C. Genomic characterization with the gene transcription data set of INp10 from the biofilm suggested traits advantageous to niche competition in environments, such as mobility, chemotaxis, biofilm formation, offensive and defensive systems, and hypoxia tolerance. The notable metabolic traits that INp10 shares with some Methyloprofundus members are the use of lanthanide-dependent XoxF as the sole methanol dehydrogenase due to the absence of the canonical MxaFI, the glycolytic pathway using fructose-6-phosphate aldolase instead of fructose-1,6-bisphosphate aldolase, and the potential to perform partial denitrification from nitrate under oxygen-limited conditions. These findings help us better understand the ecological strategies of this possibly widespread marine-specific methanotrophic clade. IMPORTANCE The Iheya North deep-sea hydrothermal field in the mid-Okinawa Trough is characterized by abundant methane derived from organic-rich sediments and diverse chemosynthetic animal species, including those harboring methanotrophic bacterial symbionts, such as bathymodiolin mussels Bathymodiolus japonicus and “Bathymodiolus” platifrons and a galatheoid crab, Shinkaia crosnieri. Symbiotic methanotrophs have attracted significant attention, and yet free-living methanotrophs in this environment have not been studied in detail. We focused on the free-living Methyloprofundus spp. that thrive in this hydrothermal field and identified an unexpectedly large number of species-like groups in this clade. Moreover, we enriched and characterized a methanotroph whose genome sequence indicated that it corresponds to a new species in the genus Methyloprofundus. This species might be a dominant member of the indigenous Methyloprofundus population. New information on free-living Methyloprofundus populations suggests that the hydrothermal field is a promising locale at which to investigate the adaptive capacity and associated genetic diversity of Methyloprofundus spp.
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