Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater

Jessica Lumian; Dawn Y Sumner; Christen L Grettenberger; Anne D Jungblut; Luiz Irber; N Tessa Pierce-Ward; C Titus Brown

doi:10.3389/fmicb.2024.1328083

Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater

Front Microbiol. 2024 Feb 19:15:1328083. doi: 10.3389/fmicb.2024.1328083. eCollection 2024.

Authors

Jessica Lumian¹, Dawn Y Sumner², Christen L Grettenberger^{2

3}, Anne D Jungblut⁴, Luiz Irber⁵, N Tessa Pierce-Ward⁵, C Titus Brown⁵

Affiliations

¹ Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States.
² Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States.
³ Department of Environmental Toxicology, University of California Davis, Davis, CA, United States.
⁴ Department of Science, The Natural History Museum, London, United Kingdom.
⁵ Population Health and Reproduction, University of California Davis, Davis, CA, United States.

Abstract

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.

Keywords: biogeography; bioinformatics; cyrosphere; metagenomics; polar cyanobacteria.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4551, as well as US National Science Foundation grant BIO-2018911, both to C. Titus Brown. Support was also provided by US National Science Foundation grant OPP-1937748 to Sumner.