The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome
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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-12-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1285791/full |
| _version_ | 1797394668194889728 |
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| author | Ate H. Jaarsma Athanasios Zervas Katie Sipes Francisco Campuzano Jiménez Andrea Claire Smith Liessel Victoria Svendsen Mariane S. Thøgersen Peter Stougaard Liane G. Benning Liane G. Benning Martyn Tranter Alexandre M. Anesio |
| author_facet | Ate H. Jaarsma Athanasios Zervas Katie Sipes Francisco Campuzano Jiménez Andrea Claire Smith Liessel Victoria Svendsen Mariane S. Thøgersen Peter Stougaard Liane G. Benning Liane G. Benning Martyn Tranter Alexandre M. Anesio |
| author_sort | Ate H. Jaarsma |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T00:23:06Z |
| format | Article |
| id | doaj.art-3ab6abe2b9474af08cfd5fae68baa675 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-09T00:23:06Z |
| publishDate | 2023-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-3ab6abe2b9474af08cfd5fae68baa6752023-12-12T05:20:52ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-12-011410.3389/fmicb.2023.12857911285791The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiomeAte H. Jaarsma0Athanasios Zervas1Katie Sipes2Francisco Campuzano Jiménez3Andrea Claire Smith4Liessel Victoria Svendsen5Mariane S. Thøgersen6Peter Stougaard7Liane G. Benning8Liane G. Benning9Martyn Tranter10Alexandre M. Anesio11Department of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkGerman Research Centre for Geosciences, Helmholtz Centre Potsdam, Potsdam, GermanyDepartment of Earth Sciences, Freie Universität Berlin, Berlin, GermanyDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkDepartment of Environmental Science, Aarhus University, Roskilde, DenmarkThe 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.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1285791/fullsupraglacial habitatsextremophilesmetagenomic sequencingbiosynthetic gene clustersgenome miningbioprospecting |
| spellingShingle | Ate H. Jaarsma Athanasios Zervas Katie Sipes Francisco Campuzano Jiménez Andrea Claire Smith Liessel Victoria Svendsen Mariane S. Thøgersen Peter Stougaard Liane G. Benning Liane G. Benning Martyn Tranter Alexandre M. Anesio The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome Frontiers in Microbiology supraglacial habitats extremophiles metagenomic sequencing biosynthetic gene clusters genome mining bioprospecting |
| title | The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome |
| title_full | The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome |
| title_fullStr | The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome |
| title_full_unstemmed | The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome |
| title_short | The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome |
| title_sort | undiscovered biosynthetic potential of the greenland ice sheet microbiome |
| topic | supraglacial habitats extremophiles metagenomic sequencing biosynthetic gene clusters genome mining bioprospecting |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1285791/full |
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