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Sakoula D, Schatteman A, Blom P, Jetten MSM, van Kessel MAHJ, Lehtovirta-Morley L, Lücker S. Activity-based labelling of ammonia- and alkane-oxidizing microorganisms including ammonia-oxidizing archaea. ISME COMMUNICATIONS 2024; 4:ycae092. [PMID: 39071849 PMCID: PMC11283641 DOI: 10.1093/ismeco/ycae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Recently, an activity-based labelling protocol for the in vivo detection of ammonia- and alkane-oxidizing bacteria became available. This functional tagging technique enabled targeted studies of these environmentally widespread functional groups, but it failed to capture ammonia-oxidizing archaea (AOA). Since their first discovery, AOA have emerged as key players within the biogeochemical nitrogen cycle, but our knowledge regarding their distribution and abundance in natural and engineered ecosystems is mainly derived from PCR-based and metagenomic studies. Furthermore, the archaeal ammonia monooxygenase is distinctly different from its bacterial counterparts and remains poorly understood. Here, we report on the development of an activity-based labelling protocol for the fluorescent detection of all ammonia- and alkane-oxidizing prokaryotes, including AOA. In this protocol, 1,5-hexadiyne is used as inhibitor of ammonia and alkane oxidation and as bifunctional enzyme probe for the fluorescent labelling of cells via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. Besides efficient activity-based labelling of ammonia- and alkane-oxidizing microorganisms, this method can also be employed in combination with deconvolution microscopy for determining the subcellular localization of their ammonia- and alkane-oxidizing enzyme systems. Labelling of these enzymes in diverse ammonia- and alkane-oxidizing microorganisms allowed their visualization on the cytoplasmic membranes, the intracytoplasmic membrane stacks of ammonia- and methane-oxidizing bacteria, and, fascinatingly, on vesicle-like structures in one AOA species. The development of this novel activity-based labelling method for ammonia- and alkane-oxidizers will be a valuable addition to the expanding molecular toolbox available for research of nitrifying and alkane-oxidizing microorganisms.
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Affiliation(s)
- Dimitra Sakoula
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Arne Schatteman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom
| | - 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
| | - Maartje A H J van Kessel
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Laura Lehtovirta-Morley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, United Kingdom
| | - Sebastian Lücker
- Department of Microbiology, RIBES, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
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Kikuchi S, Fujitani H, Ishii K, Isshiki R, Sekiguchi Y, Tsuneda S. Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:404-416. [PMID: 37078228 PMCID: PMC10472526 DOI: 10.1111/1758-2229.13158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 μM NH3 + NH4 + and 18.5 ± 1.8 μmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.
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Affiliation(s)
- Shuta Kikuchi
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Hirotsugu Fujitani
- Department of Biological SciencesChuo UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Kento Ishii
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
| | - Rino Isshiki
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
| | - Yuji Sekiguchi
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and Technology (AIST)IbarakiJapan
| | - Satoshi Tsuneda
- Department of Life Science and Medical BioscienceWaseda UniversityTokyoJapan
- Research Organization for Nano & Life InnovationWaseda UniversityTokyoJapan
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Oudova-Rivera B, Wright CL, Crombie AT, Murrell JC, Lehtovirta-Morley LE. The effect of methane and methanol on the terrestrial ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. Environ Microbiol 2023; 25:948-961. [PMID: 36598494 DOI: 10.1111/1462-2920.16316] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023]
Abstract
The ammonia monooxygenase (AMO) is a key enzyme in ammonia-oxidizing archaea, which are abundant and ubiquitous in soil environments. The AMO belongs to the copper-containing membrane monooxygenase (CuMMO) enzyme superfamily, which also contains particulate methane monooxygenase (pMMO). Enzymes in the CuMMO superfamily are promiscuous, which results in co-oxidation of alternative substrates. The phylogenetic and structural similarity between the pMMO and the archaeal AMO is well-established, but there is surprisingly little information on the influence of methane and methanol on the archaeal AMO and terrestrial nitrification. The aim of this study was to examine the effects of methane and methanol on the soil ammonia-oxidizing archaeon 'Candidatus Nitrosocosmicus franklandus C13'. We demonstrate that both methane and methanol are competitive inhibitors of the archaeal AMO. The inhibition constants (Ki ) for methane and methanol were 2.2 and 20 μM, respectively, concentrations which are environmentally relevant and orders of magnitude lower than those previously reported for ammonia-oxidizing bacteria. Furthermore, we demonstrate that a specific suite of proteins is upregulated and downregulated in 'Ca. Nitrosocosmicus franklandus C13' in the presence of methane or methanol, which provides a foundation for future studies into metabolism of one-carbon (C1) compounds in ammonia-oxidizing archaea.
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Affiliation(s)
| | - Chloe L Wright
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich, UK
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Muto H, Miyazaki J, Sawayama S, Takai K, Nakagawa S. A Simple and Effective Method for Solid Medium Cultivation of Strictly Hydrogen- and Sulfur-oxidizing Chemolithoautotrophs Predominant in Deep-sea Hydrothermal Fields. Microbes Environ 2023; 38:ME23072. [PMID: 38104970 PMCID: PMC10728628 DOI: 10.1264/jsme2.me23072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023] Open
Abstract
Strictly hydrogen- and sulfur-oxidizing chemolithoautotrophic bacteria, particularly members of the phyla Campylobacterota and Aquificota, have a cosmopolitan distribution in deep-sea hydrothermal fields. The successful cultivation of these microorganisms in liquid media has provided insights into their physiological, evolutionary, and ecological characteristics. Notably, recent population genetic studies on Sulfurimonas (Campylobacterota) and Persephonella (Aquificota) revealed geographic separation in their populations. Advances in this field of research are largely dependent on the availability of pure cultures, which demand labor-intensive liquid cultivation procedures, such as dilution-to-extinction, given the longstanding assumption that many strictly or facultatively anaerobic chemolithoautotrophs cannot easily form colonies on solid media. We herein describe a simple and cost-effective approach for cultivating these chemolithoautotrophs on solid media. The results obtained suggest that not only the choice of gelling agent, but also the gas phase composition significantly affect the colony-forming ratio of diverse laboratory strains. The use of gellan gum as a gelling agent combined with high concentrations of H2 and CO2 in a pouch bag promoted the formation of colonies. This contrasted with the absence of colony formation on an agar-solidified medium, in which thiosulfate served as an electron donor, nitrate as an electron acceptor, and bicarbonate as a carbon source, placed in anaerobic jars under an N2 atmosphere. Our method efficiently isolated chemolithoautotrophs from a deep-sea vent sample, underscoring its potential value in research requiring pure cultures of hydrogen- and sulfur-oxidizing chemolithoautotrophs.
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Affiliation(s)
- Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Junichi Miyazaki
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Ken Takai
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan
- Deep-Sea and Deep Subsurface Life Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences (NINS), 5–1 Higashiyama Myodaiji, Okazaki 444–8787, Japan
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Sapsirisuk S, Polburee P, Lorliam W, Limtong S. Discovery of Oleaginous Yeast from Mountain Forest Soil in Thailand. J Fungi (Basel) 2022; 8:1100. [PMID: 36294665 PMCID: PMC9605381 DOI: 10.3390/jof8101100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/04/2023] Open
Abstract
As an interesting alternative microbial platform for the sustainable synthesis of oleochemical building blocks and biofuels, oleaginous yeasts are increasing in both quantity and diversity. In this study, oleaginous yeast species from northern Thailand were discovered to add to the topology. A total of 127 yeast strains were isolated from 22 forest soil samples collected from mountainous areas. They were identified by an analysis of the D1/D2 domain of the large subunit rRNA (LSU rRNA) gene sequences to be 13 species. The most frequently isolated species were Lipomyces tetrasporus and Lipomyces starkeyi. Based on the cellular lipid content determination, 78 strains of ten yeast species, and two potential new yeast that which accumulated over 20% of dry biomass, were found to be oleaginous yeast strains. Among the oleaginous species detected, Papiliotrema terrestris and Papiliotrema flavescens have never been reported as oleaginous yeast before. In addition, none of the species in the genera Piskurozyma and Hannaella were found to be oleaginous yeast. L. tetrasporus SWU-NGP 2-5 accumulated the highest lipid content of 74.26% dry biomass, whereas Lipomyces mesembrius SWU-NGP 14-6 revealed the highest lipid quantity at 5.20 ± 0.03 g L-1. The fatty acid profiles of the selected oleaginous yeasts varied depending on the strain and suitability for biodiesel production.
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Affiliation(s)
- Sirawich Sapsirisuk
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Pirapan Polburee
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Wanlapa Lorliam
- Department of Microbiology, Faculty of Science, Srinakharinwirot University, Bangkok 10110, Thailand
| | - Savitree Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center, Kasetsart University, Bangkok 10900, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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