Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater
Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore...
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crfrontiers:10.3389/fmicb.2024.1328083 2024-05-19T07:30:44+00:00 Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater Lumian, Jessica Sumner, Dawn Y. Grettenberger, Christen L. Jungblut, Anne D. Irber, Luiz Pierce-Ward, N. Tessa Brown, C. Titus 2024 http://dx.doi.org/10.3389/fmicb.2024.1328083 https://www.frontiersin.org/articles/10.3389/fmicb.2024.1328083/full unknown Frontiers Media SA https://creativecommons.org/licenses/by/4.0/ Frontiers in Microbiology volume 15 ISSN 1664-302X journal-article 2024 crfrontiers https://doi.org/10.3389/fmicb.2024.1328083 2024-05-01T06:48:37Z Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones. Article in Journal/Newspaper Antarc* Antarctic Antarctica Frontiers (Publisher) Frontiers in Microbiology 15 |
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Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones. |
format |
Article in Journal/Newspaper |
author |
Lumian, Jessica Sumner, Dawn Y. Grettenberger, Christen L. Jungblut, Anne D. Irber, Luiz Pierce-Ward, N. Tessa Brown, C. Titus |
spellingShingle |
Lumian, Jessica Sumner, Dawn Y. Grettenberger, Christen L. Jungblut, Anne D. Irber, Luiz Pierce-Ward, N. Tessa Brown, C. Titus Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
author_facet |
Lumian, Jessica Sumner, Dawn Y. Grettenberger, Christen L. Jungblut, Anne D. Irber, Luiz Pierce-Ward, N. Tessa Brown, C. Titus |
author_sort |
Lumian, Jessica |
title |
Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
title_short |
Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
title_full |
Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
title_fullStr |
Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
title_full_unstemmed |
Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
title_sort |
biogeographic distribution of five antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater |
publisher |
Frontiers Media SA |
publishDate |
2024 |
url |
http://dx.doi.org/10.3389/fmicb.2024.1328083 https://www.frontiersin.org/articles/10.3389/fmicb.2024.1328083/full |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
Frontiers in Microbiology volume 15 ISSN 1664-302X |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3389/fmicb.2024.1328083 |
container_title |
Frontiers in Microbiology |
container_volume |
15 |
_version_ |
1799466619420803072 |