Draft genomes of two Ruegeria spp. isolated from the coral species Pachyseris speciosa in Singapore

TL;DR

This paper presents the draft genomes of two bacteria isolated from a resilient coral in Singapore, highlighting their potential as probiotics for corals.

Contribution

The study provides new insights into the genetic makeup of Ruegeria strains with potential probiotic functions for corals.

Findings

The genomes contain genes involved in dimethylsulfoniopropionate metabolism.

Genes related to denitrification were identified in the Ruegeria isolates.

These isolates show promise as candidate probiotics for coral health.

Abstract

Two Ruegeria strains, SCP10 (JBDZYF000000000) and SCP11 (JBDZYG000000000), were isolated from coral tissue and skeletal macerates of the resilient coral Pachyseris speciosa in Singapore. We present the genomes of these isolates, which contain genes involved in dimethylsulfoniopropionate metabolism and denitrification, good attributes for candidate coral probiotics.

Tables

TABLE 1. Genome features and GenBank accession numbers of the two Ruegeria spp. isolates

Isolate	Source	Genome size (bp)	No. of CDSa	No. of rRNAs	No. of tRNAs	G + C content (%)	No. of contigs	N50 (bp)	L50	Assembly accession no.	SRA accession no.	No. of reads	Average read length (bp)	Genome completeness (%)	Genome contamination (%)
SCP10	Tissue	4,483,924	4,396	3	49	56.9	111	476,927	3	JBDZYF000000000	SRR28745649	10,743,620	151	99.15	0.54
SCP11	Skeleton	5,119,499	4,882	3	52	56.8	82	285,744	7	JBDZYG000000000	SRR28745648	17,564,858	151	99.47	0.25

Full text

ANNOUNCEMENT

The genus Ruegeria is a member of the Roseobacteraceae family (1), an important marine group previously known as the marine Roseobacter clade (2). Species of Ruegeria play a role in marine carbon and sulfur cycling, through the catabolism of dimethylsulfoniopropionate (DMSP), the precursor for the climactically active gas dimethylsulfide (DMS) (3). They can be coral-associated, capable of protecting corals from bleaching through growth inhibition of coral pathogens (4), and forming mutualistic relationships within the coral holobiont to enhance health and survivorship (5), making Ruegeria strong probiotic candidates to enhance coral resilience.

Samples of Pachyseris speciosa were collected from the seawall at the northern side of Kusu Island, Singapore, and maintained in an outdoor aquaria tank with a constant seawater flow. Bacterial isolation methods were performed as described by Loh et al. (6). Briefly, coral samples were ground with a mortar and pestle, treated with proteinase K, vortexed with glass beads, and spread onto marine agar (Difco 2216) incubated at 33°C. SCP10 (for Singapore coral probiotic) was isolated from hydro-blasted coral tissue, and SCP11 was isolated from coral macerates (Table 1). Individual bacterial colonies were subcultured to ensure purity, and a single colony was used for each sample to inoculate marine broth (Difco 2216) and grown aerobically overnight for subsequent processing and sequencing.

Genomic DNA was extracted with the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany). DNA library preparation and sequencing were performed by the SCELSE Sequencing Facility, NTU. DNA library preparation used the Accel-NGS 2S Plus Low Input DNA Library Prep Kit (Swift Biosciences, Ann Arbor, USA). Sequencing was performed using an Illumina HiSeq X Ten platform, version 2.5 (Illumina, San Diego, CA, USA), generating 150 bp paired-end reads.

Quality filtering and adaptor trimming were performed using Trimmomatic version 0.39 (7). Default parameters were used for all software unless specified. Genomes were assembled using the Shovill pipeline version 1.1.0 (https://github.com/tseemann/shovill) and the St. Petersburg Genome Assembler (SPAdes) version 3.15.5 (8). Annotations of the assembled genomes were carried out with Prokaryotic Genome Annotation Pipeline (PGAP) version 6.7 (9). The assemblies (Table 1) were checked for plasmid sequences with PlasmidFinder version 2.0.1 (10), with no plasmids found.

Isolates were identified using the Microbial Genomes Atlas (MiGA) (11) webserver, using the NCBI-Prok function, with the closest similarity of both genomes to Ruegeria sp. THAF33 (NZ_CP045384) based on average amino acid identity (AAI). Phylogenetic relatedness between each isolate and all publicly available Ruegeria reference genomes, as well as each other, was performed using the Orthologous Average Nucleotide Identity Tool, version 0.93.1 (12), and the Genome-To-Genome Distance Calculator, version 3.0 (13), to calculate the average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) scores, respectively. Both genomes are <95% ANI and <70% DDH to each other and against all reference genomes, below the species threshold (14) (78.50% ANI and 80.78% AAI to each other).

Both genomes contained three different isoforms of DMSP lyases (dddD, dddP, and dddQ), which cleave DMSP to the cloud nucleating compound, DMS (15), as well as the anti-herbivory compound, acrylate (16). Analysis using GhostKOALA software version 2.0 (17) revealed the complete pathway for denitrification in SCP11, with the genomic potential to reduce nitrates and nitrites into dinitrogen (18).