Evidence for Divergence of the Genus ' Solwaraspora' Within the Bacterial Family Micromonosporaceae

Abstract

The purpose of this study was to investigate the taxonomic and phylogenomic placement of the proposed genus 'Solwaraspora' within the context of other marine genera using a dual-omics approach. Initially, we isolated bacteria from marine tunicates, squirts, and sponges, which were morphologically similar to an emerging genus (identified as 'Micromonospora_E' by the GTDB-tk2 database using whole genome sequence data) by colony shape, size, and clustering pattern, but only found five strains in our dataset belonging to this distinction. Due to the minimally explored nature of this genus, we sought to identify more bacterial strains with similar morphology to Micromonospora'Micromonospora_E' by whole genome sequencing (WGS). Within our collection, we noted 35 strains that met this criterion and extracted genomic information to perform WGS on these strains. With this information, we studied taxonomic and phylogenomic relationships among these organisms. Using the data gathered from WGS, we were able to identify an additional five strains labeled by the GTDB-tk2 database as Micromonospora'Micromonospora_E', as well as construct phylogenomic trees to examine the evolutionary relationships between these strains. ANI values were calculated between strains from our dataset and type strains of Micromonospora and Plantactinospora as well as against an outgroup Streptomyces strain. No type strains are available for 'Solwaraspora'. Using MALDI-TOF MS, we positively identified 'Solwaraspora', which was supported by the phylogenomic tree showing Micromonospora'Micromonospora_E' ('Solwaraspora') in a distinct clade from Plantactinospora and Micromonospora. Additionally, we discovered gene cluster families (GCFs) in alignment with genera, as well as a large representation of biosynthetic gene clusters (BGCs) coming from the 'Solwaraspora' strains. These findings suggest significant potential to discover novel chemistry from 'Solwaraspora', adding to the importance of investigating this new genus of bacteria.

Keywords: biosynthetic gene cluster; drug discovery; genomics; marine-derived; natural products.

Figure 1

WGS maximum-likelihood phylogenomic tree for the strains of interest labeled by genus with a focus on ‘Solwaraspora’ and Plantactinospora. The tree was constructed using iTOL v6 with the output from GTo Tree. ‘Solwaraspora’ strains are in a separate clade from Micromonospora and Plantactinospora strains, with Plantactinospora more closely aligning with Micromonospora (n = 35). Type strain references were included for Micromonospora and Plantactinospora, as well as an outgroup type strain of Streptomyces. Strain name is accompanied by NCBI accession number. GenBank and RefSeq assemblies can be found via the supplemental materials. The tree scale represents bootstrap values calculated by MUSCLEv5 in GToTree.

Figure 2

(A) Percentage of BGCs from the 35 strains by BiG-SCAPE predicted natural product BGC classification, including the singletons, and excluding MIBiG BGCs from the MIBiG repository. (B) CytoScape matrix visualization of BiG-SCAPE output for 35 total genomes’ BGC product type. Included in this visual are 657 total BGCs, with GCFs that contain 2 or fewer BGCs removed for better visualization, 168 of which were singletons and 41 were GCFs with 2 BGCs. The colors represent the different BGC product class as per BiG-SCAPE distinctions, and the node shape represents the taxonomy with emphasis on ‘Solwaraspora’ and Plantactinospora, and Micromonospora. There were 18 GCFs containing MIBiG BGCs. MIBiG repository BGCs are also represented by a differing node shape. A box is drawn around GCFs containing ‘Solwaraspora’ BGCs, as well as three GCFs that contained ‘Solwaraspora’ and MIBiG BGCs.

Figure 3

MALDI-TOF MS protein dendrogram constructed using IDBac. Strains WMMD406 and WMMA335 from the original dataset are absent from the dendrogram as there were difficulties with growth. The y axis relates individual samples, and the x axis shows the cosine score of the spectra vectors.