Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

Abstract

Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.

Isolation and Characterization of Bacteria from Lakes Olbolosat and Oloiden, Kenya

“…Hymenobacter sp. belongs to phylum Bactroidetes was also identified in this study by Royo-Llonch et al (2017) who reported that Hymenobacter spp, inhabit different environmental niches like marine, fresh water, air, soil, and glacier. Pseudomonas sp a Proteobacteria identified currently is common in the aquatic environment according to (Mishra et al, 2017) and most strains are known to be phosphate solubilizing bacteria and also produce antagonism to other pathogens (Paul and Sinha, 2016).…”

Genome characteristics of Kordia antarctica IMCC3317T and comparative genome analysis of the genus Kordia

“…Despite enriched taxonomic diversity and wide distribution, physiological, ecological, and genomic studies on the genus Kordia have yet to be performed in-depth beyond those on the algicidal activity of K . algicida strains 10 , 18 – 20 and a recent report detailing microdiversity among uncultured Kordia species identified by single-amplified genomes from a seawater sample of the Indian Ocean 21 .…”

Ecological and functional capabilities of an uncultured Kordia sp.

“…TARA_039_SRF, were selected for genome co-assembly and description of gene content. These SAGs were tested for microdiversity through MLSA analyses, resulting in 100% identity at the nucleotide level in each marker [69]. The five markers were the 16S rRNA gene, partial 23S rRNA gene and the Internally Transcribed Spacer, that could be amplified in the 10 SAGs; the partial RNA polymerase subunit B, amplified in 5 SAGs;…”

“…We have co-assembled 10 Kordia SAGs previously classified as nearly identical genomes [69] into a high-quality draft genome, which is 94.83% complete and meets the set standards regarding contamination (<5%) [11,37]. Recent studies have shown that co-assembling very closely related SAGs helps overcome the main drawback of their genome amplification step: that it rarely exceeds 60% of estimated genome length [36,48].…”

“…TARA_039_SRF) and that the amplified genes (16S rRNA, partial 23S rRNA, partial RNA polymerase subunit B and partial proteorhodopsin genes, as well as Internally Transcribed Spacer) were identical in the whole Kordia SAG population. More details on the phylogeny and distribution of these Kordia SAGs can be found in [69].…”