Draft Genome Sequence of Nereida sp. Strain MMG025, Isolated from Giant Kelp

ABSTRACT

Here, we report the draft genome sequence of Nereida sp. strain MMG025, isolated from the surface of giant kelp and assembled and analyzed by undergraduate students participating in a marine microbial genomics course. A genomic comparison suggests that MMG025 is a novel species, providing a resource for future microbiology and biotechnology investigations.

ANNOUNCEMENT

To engage undergraduates in discovery-based research, novel marine bacteria were isolated and cultured and their genomes sequenced, assembled, annotated, and analyzed by students in a marine microbial genomics (MMG) course at San Diego State University. Strain MMG025 was isolated from the surface of a giant kelp, Macrocystis pyrifera, from the La Jolla Tide Pools, CA, USA (32.8411°N, 117.2817°W), using a sterile cotton swab. A single colony was obtained on marine agar 2216 (BD Difco, Franklin Lakes, NJ, USA) and incubated at 28°C for 72 h. The colonies were transferred to marine broth 2216 and incubated for 72 h at 25°C before storage, DNA isolation, and imaging by scanning electron microscopy (SEM) (Fig. 1).

FIG 1.

(A) Scanning electron micrograph of Nereida sp. MMG025. Bacteria were fixed onto coverslips with 2.5% glutaraldehyde, 4% paraformaldehyde, 0.15% Alcian blue, 0.0075% lysine, and 0.1 M cacodylate buffer. The coverslips were dehydrated and critical point dried prior to coating with 6 nm platinum. Images were obtained on an FEI Quanta 450 variable pressure SEM. (B) Maximum likelihood phylogeny constructed using the codon tree method through PATRIC with 100 single-copy genes and proteins identified using cross-genus families (PGfams) (10, 21–27). The phylogeny root is indicated by an arrow for clarity. The GenBank accession numbers of the sequences used in this analysis are as follows: CVPC00000000 (Nereida ignava CECT 5292), CP003744 (Octadecabacter arcticus 238), CP006967 (Phaeobacter gallaeciensis DSM 26640), and QBKU00000000 (Sulfitobacter mediterraneus DSM 12244).

Genomic DNA was extracted using a Quick-DNA fungal/bacterial miniprep kit (Zymo Research, Irvine, CA, USA). Using 16S rRNA gene amplification with the primers 27F-1492R (1) and Sanger sequencing (Eton Biosciences, San Diego, CA, USA), the closest strain was identified as Nereida ignava CECT 5292 (identity, 97.99%; E value, 0.0). DNA was submitted to the Microbial Genome Sequencing Center (Pittsburgh, PA, USA) for library preparation (Illumina DNA prep kit; San Diego, CA, USA) and whole-genome sequencing (NextSeq 550 platform; Illumina), producing 2 × 150-bp paired-end reads. The reads were trimmed using Trim Galore v0.6.5 (2), assembled using Unicycler v0.4.8 (3) integrated in PATRIC v3.6.12 (4), and annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) v5.1 (5) with default parameters. MMG025 has a 3.1-Mb genome, a total GC content of 56% with 40 contigs at 242.493× coverage, and an N₅₀ value of 628,545 bp, with 3,260 predicted coding sequences. Default parameters were used except where otherwise noted.

A phylogenetic analysis revealed that strain MMG025 falls into the genus Nereida (Fig. 1), which is part of the Roseobacter group, in the family Rhodobacteraceae and class Alphaproteobacteria (6–9). Comparing strain MMG025 with Nereida ignava CECT 5292 yields an average nucleotide identity (ANI) value of 72.47% (4, 10, 11), a distance that is below the 95% threshold that delineates species (12), suggesting that MMG025 is a new species. We designate the current isolate Nereida sp. strain MMG025.

Species within and related to the Nereida genus have been found in association with diverse marine eukaryotes. Nereida ignava CECT 5292 is related to an uncultured gall symbiont from red algae (7). Related species from the genus Octadecabacter were isolated from an ascidian or compose 70 to 80% of the microbiome of a brittle star (13, 14). Roseobacter species are associated with algae and reef-building corals, where they are thought to play important roles in global sulfur cycling, in part through the degradation of dimethylsulfoniopropionate (DMSP) (15). We found that strain MMG025 harbors a homolog of the DMSP demethylase gene dmdA (identity, 80%; query coverage, 100%; E value, 0) (16). Because of their natural occurrence with plants and animals and antagonistic properties against pathogenic bacteria, Roseobacter species are promising candidates for use as probiotics in aquaculture or for environmental restoration (17–20). The isolation and genome sequence of Nereida sp. MMG025 provides a valuable resource for studying the ecology of Roseobacter bacteria and serves as an asset for biotechnology applications.

Data availability.

The genome sequencing and assembly project for strain MMG025 has been deposited at DDBJ/EMBL/GenBank under BioProject accession number PRJNA716944, the raw sequencing data under SRA accession number SRR17607627, and the whole-genome sequence under GenBank accession number JAKFZN000000000.