Biogeographic Distribution of Five Antarctic Cyanobacteria Using Large-Scale k-mer Searching with sourmash branchwater

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 Lakes Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi, a Microcoleus, a Leptolyngbya, a Pseudanabaena, and a Neosynechococcus (Lumian et al., 2021, Lumian et al., 2022, in prep.) in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus MAG was found in a wide variety of environments, P. pseudopriestleyi was found in environments with challenging conditions, the Neosynechococcus was only found in Antarctica, and the Leptolyngbya and Pseudanabaena 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.

Sourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search

“…estimated abundances) on top of the minimal information provided by branchwater. FracMinHash generally and Branchwater specifically have been validated bioinformatically with read mapping (see [14,16]). This is discussed further below.…”

“…K-mer search via branchwater has been used in two projects so far - Lumian et al (2022) [16] and Viehweger et al (2021) [15]. Viehweger et al used branchwater to find a metagenome containing an additional Klebsiella pneumoniae for a large scale analysis of outbreak data, while Lumian et al conducted a global biogeography analysis of five new antarctic cyanobacteria.…”

“…We have built two custom tools in concert with sourmash and branchwater, genome-grist and spacegraphcats. Genome-grist performs an entirely automated reference-based characterization of individual metagenomes that follows the minimum metagenome cover produced by sourmash gather with mapping of short reads; it is described in Irber et al [14] and was used in Lumian et al [16]. While genome-grist does download the entire data set in order to map the reads, it is still reference based and thus relatively lightweight.…”

“…The availability of relatively lightweight content-based search of SRA metagenomes helps address many of the biological use cases in Table 1 (see 3rd column). Some of these use cases have already been explored with Branchwater: Viehweger et al (2021) [15] used Branchwater to discover a metagenomic sample containing Klebsiella pneumonia that was subsequently included in an outbreak analysis, and Lumian et al (2022) [16] conducted a biogeographical study on five newly generated cyanobacterial genomes from Antarctic samples.…”

Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics

“…For this, we considered only matches with ≥95% identity and ≥75% coverage. We also used sourmash branchwater [69,70] and IMNGS [71] to search the two Gloeobacterales MAGs against metagenomic and amplicon sequencing datasets in the Sequence Read Archive (SRA), respectively. For the first, we used the mastiff implementation of sourmash branchwater (github.com/sourmash-bio/2022search-sra-with-mastiff).…”