New cyanobacterial genus Argonema is hiding in soil crusts around the world

Abstract

Cyanobacteria are crucial primary producers in soil and soil crusts. However, their biodiversity in these habitats remains poorly understood, especially in the tropical and polar regions. We employed whole genome sequencing, morphology, and ecology to describe a novel cyanobacterial genus Argonema isolated from Antarctica. Extreme environments are renowned for their relatively high number of endemic species, but whether cyanobacteria are endemic or not is open to much current debate. To determine if a cyanobacterial lineage is endemic is a time consuming, elaborate, and expensive global sampling effort. Thus, we propose an approach that will help to overcome the limits of the sampling effort and better understand the global distribution of cyanobacterial clades. We employed a Sequencing Read Archive, which provides a rich source of data from thousands of environmental samples. We developed a framework for a characterization of the global distribution of any microbial species using Sequencing Read Archive. Using this approach, we found that Argonema is actually cosmopolitan in arid regions. It provides further evidence that endemic microbial taxa are likely to be much rarer than expected.

Population genomics resolves cryptic species of the ecologically flexible genusLaspinema(cyanobacteria)1

“…Strains with the genome sequence were adopted from Stanojković et al (2022) and new samples were collected at several localities in Czechia and Poland (complete list of strains and localities; Table S1). The strain isolation was performed as in our previous taxonomic proposals (Dvořák et al 2017, Skoupý et al 2022). The isolated strains were maintained under the following conditions: Zehnder medium, temperature 22±1°C day temperature, 18±1°C night temperature, illumination 20 µmol photons m −2 .s −1 , light regime 16h light/8h dark.…”

“…The PCR reaction was performed in a total volume of 40 μL containing 17 μL of sterile RNase-free water, 20 μL of EmeraldAMP Master Mix (Takara Bio Europe SAS, Saint Germain en Laye, France), 1 μL of each primer, and 1 μL of template DNA (50 ng/μL). The amplification conditions were as described by Skoupý et al (2022). The PCR products were purified using the E.Z.N.A Cycle Pure Kit (Omega Bio-Tek, Georgia, USA) according to the manufacturer’s instructions.…”

“…Finally, we searched NCBI using BLAST for all 16S rRNA sequences of Laspinema . All sequences were added to the 16S rRNA phylogenetic dataset from Skoupý et al (2022). This way, we could identify the monophyletic clade of Laspinema among all cyanobacteria using two datasets – 16S rRNA only and as well as concatenated 16S rRNA and 16S-23S ITS.…”

“…However, taxonomic studies investigating the genome sequences among the cyanobacterial species are only scarce, although whole genome sequencing became more affordable within the last decade with 5255 genome assemblies of cyanobacteria submitted to the GenBank (https://www.ncbi.nlm.nih.gov/, accessed 23 rd February 2024). For example, the genome sequences were employed to an erection of the new genera Moorena (Engene et al 2012), Elainella (Jahodářová et al 2018), and Argonema (Skoupý et al 2022). If the whole genome sequence is present in the taxonomic study, each taxon is usually represented by one genome sequence.…”

“…Thus, the delimitation is not hurdled by the resolution of conservative markers or low morphological diversity (as we showed above). Population genomics represents the most powerful tool for understanding and delimitating of cryptic species (Skoupý et al 2024, Stanojković et al 2024).…”