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Angius F, Cremers G, Frank J, Witkowski C, Pol A, van Alen TA, Jetten MSM, Op den Camp HJM, Berben T. Gene-centered metagenome analysis of Vulcano Island soil (Aeolian archipelago, Italy) reveals diverse microbial key players in methane, hydrogen and sulfur cycles. Antonie Van Leeuwenhoek 2024; 117:94. [PMID: 38954064 PMCID: PMC11219375 DOI: 10.1007/s10482-024-01995-5] [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: 03/26/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
The Aeolian archipelago is known worldwide for its volcanic activity and hydrothermal emissions, of mainly carbon dioxide and hydrogen sulfide. Hydrogen, methane, and carbon monoxide are minor components of these emissions which together can feed large quantities of bacteria and archaea that do contribute to the removal of these notorious greenhouse gases. Here we analyzed the metagenome of samples taken from the Levante bay on Vulcano Island, Italy. Using a gene-centric approach, the hydrothermal vent community appeared to be dominated by Proteobacteria, and Sulfurimonas was the most abundant genus. Metabolic reconstructions highlight a prominent role of formaldehyde oxidation and the reverse TCA cycle in carbon fixation. [NiFe]-hydrogenases seemed to constitute the preferred strategy to oxidize H2, indicating that besides H2S, H2 could be an essential electron donor in this system. Moreover, the sulfur cycle analysis showed a high abundance and diversity of sulfate reduction genes underpinning the H2S production. This study covers the diversity and metabolic potential of the microbial soil community in Levante bay and adds to our understanding of the biogeochemistry of volcanic ecosystems.
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Affiliation(s)
- Federica Angius
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Jeroen Frank
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Caitlyn Witkowski
- Department of Marine Microbiology and Biogeochemistry, NIOZ, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- School of Earth Sciences, Wills Memorial Building, University of Bristol, Queens Road, Clifton, BS8 1RJ, UK
| | - Arjan Pol
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Theo A van Alen
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | - Tom Berben
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Faculty of Science, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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2
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Leung PM, Grinter R, Tudor-Matthew E, Lingford JP, Jimenez L, Lee HC, Milton M, Hanchapola I, Tanuwidjaya E, Kropp A, Peach HA, Carere CR, Stott MB, Schittenhelm RB, Greening C. Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures. Nat Commun 2024; 15:3219. [PMID: 38622143 PMCID: PMC11018855 DOI: 10.1038/s41467-024-47324-2] [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: 02/03/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024] Open
Abstract
Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.
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Affiliation(s)
- Pok Man Leung
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Eve Tudor-Matthew
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - James P Lingford
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Luis Jimenez
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Han-Chung Lee
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Michael Milton
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Iresha Hanchapola
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Erwin Tanuwidjaya
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Hanna A Peach
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
| | - Carlo R Carere
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Matthew B Stott
- Geomicrobiology Research Group, Department of Geothermal Sciences, Te Pū Ao | GNS Science, Wairakei, Taupō, 3377, Aotearoa New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Platform and Department of Biochemistry, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia.
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3
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Liu C, Schmitz RA, Pol A, Hogendoorn C, Verhagen D, Peeters SH, van Alen TA, Cremers G, Mesman RA, Op den Camp HJM. Active coexistence of the novel gammaproteobacterial methanotroph 'Ca. Methylocalor cossyra' CH1 and verrucomicrobial methanotrophs in acidic, hot geothermal soil. Environ Microbiol 2024; 26:e16602. [PMID: 38454738 DOI: 10.1111/1462-2920.16602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024]
Abstract
Terrestrial geothermal ecosystems are hostile habitats, characterized by large emissions of environmentally relevant gases such as CO2 , CH4 , H2 S and H2 . These conditions provide a niche for chemolithoautotrophic microorganisms. Methanotrophs of the phylum Verrucomicrobia, which inhabit these ecosystems, can utilize these gases and grow at pH levels below 1 and temperatures up to 65°C. In contrast, methanotrophs of the phylum Proteobacteria are primarily found in various moderate environments. Previously, novel verrucomicrobial methanotrophs were detected and isolated from the geothermal soil of the Favara Grande on the island of Pantelleria, Italy. The detection of pmoA genes, specific for verrucomicrobial and proteobacterial methanotrophs in this environment, and the partially overlapping pH and temperature growth ranges of these isolates suggest that these distinct phylogenetic groups could coexist in the environment. In this report, we present the isolation and characterization of a thermophilic and acid-tolerant gammaproteobacterial methanotroph (family Methylococcaceae) from the Favara Grande. This isolate grows at pH values ranging from 3.5 to 7.0 and temperatures from 35°C to 55°C, and diazotrophic growth was demonstrated. Its genome contains genes encoding particulate and soluble methane monooxygenases, XoxF- and MxaFI-type methanol dehydrogenases, and all enzymes of the Calvin cycle. For this novel genus and species, we propose the name 'Candidatus Methylocalor cossyra' CH1.
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Affiliation(s)
- Changqing Liu
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Schmitz
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Arjan Pol
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Carmen Hogendoorn
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Daniël Verhagen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Theo A van Alen
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Rob A Mesman
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Faculty of Science, Radboud Institute for Biological and Environmental Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
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4
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Zhang RY, Wang YR, Liu RL, Rhee SK, Zhao GP, Quan ZX. Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment. MICROBIOME 2024; 12:7. [PMID: 38191433 PMCID: PMC10773090 DOI: 10.1186/s40168-023-01728-2] [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: 07/01/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking. RESULTS In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways. CONCLUSIONS One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.
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Affiliation(s)
- Ru-Yi Zhang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan-Ren Wang
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Ru-Long Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju, Republic of Korea
| | - Guo-Ping Zhao
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhe-Xue Quan
- Fudan Microbiome Center, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China.
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5
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Kadnikov VV, Mardanov AV, Beletsky AV, Karnachuk OV, Ravin NV. Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics. BIOLOGY 2023; 12:biology12050723. [PMID: 37237535 DOI: 10.3390/biology12050723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023]
Abstract
The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.
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Affiliation(s)
- Vitaly V Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Olga V Karnachuk
- Laboratory of Biochemistry and Molecular Biology, Tomsk State University, 634050 Tomsk, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
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6
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Hogendoorn C, Pol A, de Graaf R, White PB, Mesman R, van Galen PM, van Alen TA, Cremers G, Jansen RS, Jetten MSM, Op den Camp HJM. " Candidatus Hydrogenisulfobacillus filiaventi" strain R50 gen. nov. sp. nov., a highly efficient producer of extracellular organic compounds from H 2 and CO 2. Front Microbiol 2023; 14:1151097. [PMID: 37032882 PMCID: PMC10080006 DOI: 10.3389/fmicb.2023.1151097] [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: 01/25/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Production of organic molecules is largely depending on fossil fuels. A sustainable alternative would be the synthesis of these compounds from CO2 and a cheap energy source, such as H2, CH4, NH3, CO, sulfur compounds or iron(II). Volcanic and geothermal areas are rich in CO2 and reduced inorganic gasses and therefore habitats where novel chemolithoautotrophic microorganisms for the synthesis of organic compounds could be discovered. Here we describe "Candidatus Hydrogenisulfobacillus filiaventi" R50 gen. nov., sp. nov., a thermoacidophilic, autotrophic H2-oxidizing microorganism, that fixed CO2 and excreted no less than 0.54 mol organic carbon per mole fixed CO2. Extensive metabolomics and NMR analyses revealed that Val, Ala and Ile are the most dominant form of excreted organic carbon while the aromatic amino acids Tyr and Phe, and Glu and Lys were present at much lower concentrations. In addition to these proteinogenic amino acids, the excreted carbon consisted of homoserine lactone, homoserine and an unidentified amino acid. The biological role of the excretion remains uncertain. In the laboratory, we noticed the production under high growth rates (0.034 h-1, doubling time of 20 h) in combination with O2-limitation, which will most likely not occur in the natural habitat of this strain. Nevertheless, this large production of extracellular organic molecules from CO2 may open possibilities to use chemolithoautotrophic microorganisms for the sustainable production of important biomolecules.
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Affiliation(s)
- Carmen Hogendoorn
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Arjan Pol
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Rob de Graaf
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Paul B. White
- Department of Synthetic Organic Chemistry, IMM, Radboud University, Nijmegen, Netherlands
| | - Rob Mesman
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Peter M. van Galen
- Department of Systems Chemistry, IMM, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Geert Cremers
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Robert S. Jansen
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
| | - Huub J. M. Op den Camp
- Department of Microbiology, RIBES, Radboud University, Nijmegen, Netherlands
- *Correspondence: Huub J. M. Op den Camp,
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7
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Harirchi S, Sar T, Ramezani M, Aliyu H, Etemadifar Z, Nojoumi SA, Yazdian F, Awasthi MK, Taherzadeh MJ. Bacillales: From Taxonomy to Biotechnological and Industrial Perspectives. Microorganisms 2022; 10:2355. [PMID: 36557608 PMCID: PMC9781867 DOI: 10.3390/microorganisms10122355] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
For a long time, the genus Bacillus has been known and considered among the most applicable genera in several fields. Recent taxonomical developments resulted in the identification of more species in Bacillus-related genera, particularly in the order Bacillales (earlier heterotypic synonym: Caryophanales), with potential application for biotechnological and industrial purposes such as biofuels, bioactive agents, biopolymers, and enzymes. Therefore, a thorough understanding of the taxonomy, growth requirements and physiology, genomics, and metabolic pathways in the highly diverse bacterial order, Bacillales, will facilitate a more robust designing and sustainable production of strain lines relevant to a circular economy. This paper is focused principally on less-known genera and their potential in the order Bacillales for promising applications in the industry and addresses the taxonomical complexities of this order. Moreover, it emphasizes the biotechnological usage of some engineered strains of the order Bacillales. The elucidation of novel taxa, their metabolic pathways, and growth conditions would make it possible to drive industrial processes toward an upgraded functionality based on the microbial nature.
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Affiliation(s)
- Sharareh Harirchi
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Taner Sar
- Swedish Centre for Resource Recovery, University of Borås, 50190 Borås, Sweden
| | - Mohaddaseh Ramezani
- Microorganisms Bank, Iranian Biological Resource Centre (IBRC), Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Habibu Aliyu
- Institute of Process Engineering in Life Science II: Technical Biology, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Zahra Etemadifar
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 8174673441, Iran
| | - Seyed Ali Nojoumi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran 1316943551, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran 1316943551, Iran
| | - Fatemeh Yazdian
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran 1439957131, Iran
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road 3#, Yangling, Xianyang 712100, China
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Sakoula D, Smith GJ, Frank J, Mesman RJ, Kop LFM, Blom P, Jetten MSM, van Kessel MAHJ, Lücker S. Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria. THE ISME JOURNAL 2022; 16:958-971. [PMID: 34743174 PMCID: PMC8941013 DOI: 10.1038/s41396-021-01144-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
- Division of Microbial Ecology, Center for Microbiology and Environmental Systems Science, University of Vienna, Althanstraße 14, 1090, Vienna, Austria.
| | - Garrett J Smith
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Jeroen Frank
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Rob J Mesman
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Linnea F M Kop
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Pieter Blom
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Maartje A H J van Kessel
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
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Greening C, Islam ZF, Bay SK. Hydrogen is a major lifeline for aerobic bacteria. Trends Microbiol 2021; 30:330-337. [PMID: 34462186 DOI: 10.1016/j.tim.2021.08.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/31/2022]
Abstract
Molecular hydrogen (H2) is available in trace amounts in most ecosystems through atmospheric, biological, geochemical, and anthropogenic sources. Aerobic bacteria use this energy-dense gas, including at atmospheric concentrations, to support respiration and carbon fixation. While it was thought that aerobic H2 consumers are rare community members, here we summarize evidence suggesting that they are dominant throughout soils and other aerated ecosystems. Bacterial cultures from at least eight major phyla can consume atmospheric H2. At the ecosystem scale, H2 consumers are abundant, diverse, and active across diverse soils and are key primary producers in extreme environments such as hyper-arid deserts. On this basis, we propose that H2 is a universally available energy source for the survival of aerobic bacteria.
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Affiliation(s)
- Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; Centre to Impact AMR, Monash University, Clayton, VIC 3800, Australia.
| | - Zahra F Islam
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; STEM College, RMIT University, Bundoora, VIC 3083, Australia
| | - Sean K Bay
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Securing Antarctica's Environmental Future, Monash University, Clayton, VIC 3800, Australia; School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
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A widely distributed hydrogenase oxidises atmospheric H 2 during bacterial growth. ISME JOURNAL 2020; 14:2649-2658. [PMID: 32647310 PMCID: PMC7784904 DOI: 10.1038/s41396-020-0713-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/25/2020] [Accepted: 06/30/2020] [Indexed: 11/09/2022]
Abstract
Diverse aerobic bacteria persist by consuming atmospheric hydrogen (H2) using group 1h [NiFe]-hydrogenases. However, other hydrogenase classes are also distributed in aerobes, including the group 2a [NiFe]-hydrogenase. Based on studies focused on Cyanobacteria, the reported physiological role of the group 2a [NiFe]-hydrogenase is to recycle H2 produced by nitrogenase. However, given this hydrogenase is also present in various heterotrophs and lithoautotrophs lacking nitrogenases, it may play a wider role in bacterial metabolism. Here we investigated the role of this enzyme in three species from different phylogenetic lineages and ecological niches: Acidithiobacillus ferrooxidans (phylum Proteobacteria), Chloroflexus aggregans (phylum Chloroflexota), and Gemmatimonas aurantiaca (phylum Gemmatimonadota). qRT-PCR analysis revealed that the group 2a [NiFe]-hydrogenase of all three species is significantly upregulated during exponential growth compared to stationary phase, in contrast to the profile of the persistence-linked group 1h [NiFe]-hydrogenase. Whole-cell biochemical assays confirmed that all three strains aerobically respire H2 to sub-atmospheric levels, and oxidation rates were much higher during growth. Moreover, the oxidation of H2 supported mixotrophic growth of the carbon-fixing strains C. aggregans and A. ferrooxidans. Finally, we used phylogenomic analyses to show that this hydrogenase is widely distributed and is encoded by 13 bacterial phyla. These findings challenge the current persistence-centric model of the physiological role of atmospheric H2 oxidation and extend this process to two more phyla, Proteobacteria and Gemmatimonadota. In turn, these findings have broader relevance for understanding how bacteria conserve energy in different environments and control the biogeochemical cycling of atmospheric trace gases.
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