Rhodoalgimonas zhirmunskyi gen. nov., sp. nov., a Marine Alphaproteobacterium Isolated from the Pacific Red Alga Ahnfeltia tobuchiensis: Phenotypic Characterization and Pan-Genome Analysis

Abstract

A novel Gram-staining negative, strictly aerobic, rod-shaped, and non-motile bacterium, designated strain 10Alg 79^T, was isolated from the red alga Ahnfeltia tobuchiensis. A phylogenetic analysis based on 16S rRNA gene sequences placed the novel strain within the family Roseobacteraceae, class Alphaproteobacteria, phylum Pseudomonadota, where the nearest neighbor was Shimia sediminis ZQ172^T (97.33% of identity). However, a phylogenomic study clearly showed that strain 10Alg 79^T forms a distinct evolutionary lineage at the genus level within the family Roseobacteraceae combining with strains Aquicoccus porphyridii L1 8-17^T, Marimonas arenosa KCTC 52189^T, and Lentibacter algarum DSM 24677^T. The ANI, AAI, and dDDH values between them were 75.63-78.15%, 67.41-73.08%, and 18.8-19.8%, respectively. The genome comprises 3,754,741 bp with a DNA GC content of 62.1 mol%. The prevalent fatty acids of strain 10Alg 79^T were C_{18:1 ω7c} and C_16:0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. A pan-genome analysis showed that the unique part of the 10Alg 79^T genome consists of 13 genus-specific clusters and 413 singletons. The annotated singletons were more often related to transport protein systems, transcriptional regulators, and enzymes. A functional annotation of the draft genome sequence revealed that this bacterium could be a source of a new phosphorylase, which may be used for phosphoglycoside synthesis. A combination of the genotypic and phenotypic data showed that the bacterial isolate represents a novel species and a novel genus, for which the name Rhodoalgimonas zhirmunskyi gen. nov., sp. nov. is proposed. The type strain is 10Alg 79^T (=KCTC 72611^T = KMM 6723^T).

Keywords: Roseobacteraceae; marine bacteria Rhodoalgimonas zhirmunskyi; pan-genome analysis; red alga Ahnfeltia tobuchiensis; whole genome sequence.

Figure 1

ML 16S rRNA tree showing phylogenetic relationships between the novel strain 10Alg 79^T (KMM 6723^T) and members of the family Rosebacteraceae (formerly Rhodobacteriaceae). Bootstrap values shown as percentage are based on 500 replicates. Bars are 0.5 substitutions per nucleotide. Strain Caulobacter vibrioides CB51^T/DSM 9893^T was used as an outgroup. GenBank/EMBL/DDB accession numbers are given in parentheses.

Figure 2

ML RpoC tree showing phylogenetic relationships between the novel strain 10Alg 79^T (KMM 6723^T) and 43 members of the family Rosebacteraceae (formerly Rhodobacteriaceae). Bootstrap values are based on 500 replicates and shown as percentages greater than 50. Bars are 0.5 substitutions per amino acid position. Strain Caulobacter vibrioides DSM 9893^T was used as an outgroup. GeBank/EMBL/DDB accession numbers are given in parentheses.

Figure 3

ML genomic tree showing phylogenetic relationships between the strain 10Alg 79^T (KMM 6723^T) and members of the family Rosebacteraceae (formerly Rhodobacteriaceae). Bootstrap values shown as percentages greater than 50 are based on 100 replicates. Bar is 0.2 substitutions per amino acid position. Strain Caulobacter vibrioides DSM 9893^T was used as an outgroup. GenBank/EMBL/DDB accession numbers are given in parentheses.

Figure 4

Venn diagram showing the distribution of shared orthologous clusters among genomes of 10Alg 79^T, A. porphyridii L1 8-17^T, M. arenosa KCTC 52189^T, and L. algarum DSM 24677^T. The orthologous clusters are comprised of proteins predicted using RAST [36]. The number of orthologous clusters for each genome is shown in vertical bar chart.

Figure 5

The distribution of CAZymes across genomes of KMM 6723^T (=10Alg 79^T) and close relatives. The heat maps show the number of genes assigned to individual CAZyme families. Rows are clustered using Euclidean distances. GH, glycoside hydrolases; GT, glycosyltransferases, CE, carbohydrate esterase; AA, auxiliary activity; CBM, carbohydrate-binding module.

Figure 6

Comparative analysis of synteny between NRPS-like fragment and Type I PKS BGCs in the genomes of strain 10Alg 79^T (KMM 6723^T) and close relatives. Genes are colored based on their annotation as indicated at the bottom. The locus regions are NOI20_03420 to NOI20_03580 in the KMM 6723^T genome, NO357_05410 to NO357_05560 in the M. arenosa KCTC 52189^T genome, BLV93_RS04080 to BLV93_RS03920 in the L. algarum DSM 24677^T genome, and FLO80_RS04395 to FLO80_RS04560 in the A. porphyridii JCM 31543^T genome.