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Oliva B, Zervas A, Stougaard P, Westh P, Thøgersen MS. Metagenomic exploration of cold-active enzymes for detergent applications: Characterization of a novel, cold-active and alkali-stable GH8 endoglucanase from ikaite columns in SW Greenland. Microb Biotechnol 2024; 17:e14466. [PMID: 38829370 PMCID: PMC11146146 DOI: 10.1111/1751-7915.14466] [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: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 06/05/2024] Open
Abstract
Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture-independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate-modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired. Seventeen selected ORFs, representing eight enzyme families were synthesized and expressed in two host organisms, Escherichia coli and Aliivibrio wodanis. Aliivibrio wodanis demonstrated expression of a more diverse range of enzyme classes compared to E. coli, emphasizing the importance of alternative expression systems for enzymes from extremophilic microorganisms. To demonstrate the validity of the screening strategy, we chose a recombinantly expressed cellulolytic enzyme from the metagenome for further characterization. The enzyme, Cel240, exhibited close to 40% of its relative activity at low temperatures (4°C) and demonstrated endoglucanase characteristics, with a preference for cellulose substrates. Despite low sequence similarity with known enzymes, computational analysis and structural modelling confirmed its cellulase-family affiliation. Cel240 displayed activity at low temperatures and good stability at 25°C, activity at alkaline pH and increased activity in the presence of CaCl2, making it a promising candidate for detergent and washing industry applications.
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Affiliation(s)
- Bianca Oliva
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
- Present address:
Synthetic and Molecular Biology Laboratory, Department of Biotechnology, Lorena School of EngineeringUniversity of São PauloLorenaSPBrazil
| | - Athanasios Zervas
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Stougaard
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Westh
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Mariane Schmidt Thøgersen
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
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Ruiz A, Gisbert E, Andree KB. Impact of the diet in the gut microbiota after an inter-species microbial transplantation in fish. Sci Rep 2024; 14:4007. [PMID: 38369563 PMCID: PMC10874947 DOI: 10.1038/s41598-024-54519-6] [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: 10/31/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024] Open
Abstract
Inter-species microbial transplantations offer the possibility of transferring species-specific microbes and their associated functionality. As a conceptual approach, an intestinal microbiota transplant (IMT) between two marine carnivorous fish species that thrive in different environmental conditions was conducted: from donor Atlantic salmon (Salmo salar) to recipient gilthead seabream (Sparus aurata), after obliterating its basal microbiota with an antibiotic treatment. To confirm that the gut microbiota was able to recover after antibiotics without the influence of the diet, a group of gilthead seabream not submitted to the IMT was kept fasted as an internal control. To assess the effect of the diet after the IMT, two groups of gilthead seabream were respectively fed with their typical diet and with Atlantic salmon diet. At 36 days post-IMT, the gut of the individuals fed with their typical diet was dominated by the feed-associated bacteria, while those fed with the salmon diet had developed a unique microbiota from the convergence of the diet, donor, and recipient microbiota. These results suggested that an intestinal microbiota transplantation may be effective if the basal microbiota from the gut is first cleared and a targeted dietary modification is provided to maintain and enrich the novel bacteria species over time.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain.
| | - Enric Gisbert
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
| | - Karl B Andree
- Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
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Kastner PD, Noell SE, Essig DA. Complete genome sequence of a winter season Vibrio facilitates discovery of a novel subclade of cold-adapted species in the albus clade. Microb Genom 2024; 10:001178. [PMID: 38230915 PMCID: PMC10868602 DOI: 10.1099/mgen.0.001178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
In temperate marine climate zones, seasonal changes in water temperature contribute to distinct populations of warm- and cold-water vibrios. We report here the complete genome sequence (BUSCO score=94.8) of the novel strain Vibrio sp. VB16 isolated in late winter from the intertidal zone near Virginia Beach, Virginia, USA with the ability to form colonies at 4 °C. The 5.2 Mbp genome is composed of a large (3.6 Mbp) and small (1.6 Mbp) chromosome. Based on paired average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH), V. sp. VB16 is the same species as V. sp. UBA2437 from a North Sea tidal flat and is closely related to V. sp. DW001 from Antarctic sea ice. Our phylogenomic and bioinformatic analyses placed VB16, UBA2437 and DW001 into a cold-tolerant subclade within the albus clade, along with two non-cold-tolerant subclades. Orthovenn analysis indicated that VB16 and its other albus clade members shared 1544 gene orthologue clusters, including clusters for biosynthesis of polar flagella and tight adhesion pili that predict multiple lifestyles, either free-living or as an opportunistic pathogen within a marine eukaryotic host. The cold-tolerant subclade shared 552 orthologue proteins, including genes known to promote survival in cold or freezing temperatures, such as the eicosapentaenoic acid biosynthetic gene cluster, syp exopolysaccharide gene cluster and novel giant proteins with ice-binding domains. This subclade represents a group of psychrotolerant or 'moderate psychrophile' winter season Vibrio species. The discovery of this subclade opens the door for experimental work on the physiological features, virulence potential and ecological importance of this subclade.
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Affiliation(s)
- Paul D. Kastner
- School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Stephen E. Noell
- Te Aka Mātuatua – School of Science, Thermophile Research Unit, Te Whare Wānanga o Waikato – University of Waikato, Hamilton, New Zealand
| | - David A. Essig
- Department of Biology, Geneva College, Beaver Falls, PA, USA
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Jaarsma AH, Zervas A, Sipes K, Campuzano Jiménez F, Smith AC, Svendsen LV, Thøgersen MS, Stougaard P, Benning LG, Tranter M, Anesio AM. The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome. Front Microbiol 2023; 14:1285791. [PMID: 38149278 PMCID: PMC10749974 DOI: 10.3389/fmicb.2023.1285791] [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: 08/30/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
The Greenland Ice Sheet is a biome which is mainly microbially driven. Several different niches can be found within the glacial biome for those microbes able to withstand the harsh conditions, e.g., low temperatures, low nutrient conditions, high UV radiation in summer, and contrasting long and dark winters. Eukaryotic algae can form blooms during the summer on the ice surface, interacting with communities of bacteria, fungi, and viruses. Cryoconite holes and snow are also habitats with their own microbial community. Nevertheless, the microbiome of supraglacial habitats remains poorly studied, leading to a lack of representative genomes from these environments. Under-investigated extremophiles, like those living on the Greenland Ice Sheet, may provide an untapped reservoir of chemical diversity that is yet to be discovered. In this study, an inventory of the biosynthetic potential of these organisms is made, through cataloging the presence of biosynthetic gene clusters in their genomes. There were 133 high-quality metagenome-assembled genomes (MAGs) and 28 whole genomes of bacteria obtained from samples of the ice sheet surface, cryoconite, biofilm, and snow using culturing-dependent and -independent approaches. AntiSMASH and BiG-SCAPE were used to mine these genomes and subsequently analyze the resulting predicted gene clusters. Extensive sets of predicted Biosynthetic Gene Clusters (BGCs) were collected from the genome collection, with limited overlap between isolates and MAGs. Additionally, little overlap was found in the biosynthetic potential among different environments, suggesting specialization of organisms in specific habitats. The median number of BGCs per genome was significantly higher for the isolates compared to the MAGs. The most talented producers were found among Proteobacteria. We found evidence for the capacity of these microbes to produce antimicrobials, carotenoid pigments, siderophores, and osmoprotectants, indicating potential survival mechanisms to cope with extreme conditions. The majority of identified BGCs, including those in the most prevalent gene cluster families, have unknown functions, presenting a substantial potential for bioprospecting. This study underscores the diverse biosynthetic potential in Greenland Ice Sheet genomes, revealing insights into survival strategies and highlighting the need for further exploration and characterization of these untapped resources.
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Affiliation(s)
- Ate H. Jaarsma
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Katie Sipes
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | | | | | | | | | - Peter Stougaard
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Liane G. Benning
- German Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, Germany
- Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - Martyn Tranter
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
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Maharajan AD, Hansen H, Khider M, Willassen NP. Quorum sensing in Aliivibrio wodanis 06/09/139 and its role in controlling various phenotypic traits. PeerJ 2021; 9:e11980. [PMID: 34513327 PMCID: PMC8395575 DOI: 10.7717/peerj.11980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background Quorum Sensing (QS) is a cell-to-cell communication system that bacteria utilize to adapt to the external environment by synthesizing and responding to signalling molecules called autoinducers. The psychrotrophic bacterium Aliivibrio wodanis 06/09/139, originally isolated from a winter ulcer of a reared Atlantic salmon, produces the autoinducer N-3-hydroxy-decanoyl-homoserine-lactone (3OHC10-HSL) and encodes the QS systems AinS/R and LuxS/PQ, and the master regulator LitR. However, the role of QS in this bacterium has not been investigated yet. Results In the present work we show that 3OHC10-HSL production is cell density and temperature-dependent in A. wodanis 06/09/139 with the highest production occurring at a low temperature (6 °C). Gene inactivation demonstrates that AinS is responsible for 3OHC10-HSL production and positively regulated by LitR. Inactivation of ainS and litR further show that QS is involved in the regulation of growth, motility, hemolysis, protease activity and siderophore production. Of these QS regulated activities, only the protease activity was found to be independent of LitR. Lastly, supernatants harvested from the wild type and the ΔainS and ΔlitR mutants at high cell densities show that inactivation of QS leads to a decreased cytopathogenic effect (CPE) in a cell culture assay, and strongest attenuation of the CPE was observed with supernatants harvested from the ΔlitR mutant. Conclusion A. wodanis 06/09/139 use QS to regulate a number of activities that may prove important for host colonization or interactions. The temperature of 6 °C that is in the temperature range at which winter ulcer occurs, plays a role in AHL production and development of CPE on a Chinook Salmon Embryo (CHSE) cell line.
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Affiliation(s)
- Amudha Deepalakshmi Maharajan
- Norwegian Structural Biology Center and The Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Norwegian Structural Biology Center and The Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Miriam Khider
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, NTNU-Norwegian University of Science and Technology, Trondheim, Norway
| | - Nils Peder Willassen
- Norwegian Structural Biology Center and The Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, Tromsø, Norway.,Centre for Bioinformatics, Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, Tromsø, Norway
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