The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos

Roseibium album (1) (homotypic synonyms, Stappia alba [2] and Labrenzia alba [3]) is a Gram-negative, marine alphaproteobacterium (order Hyphomicrobiales, family Stappiaceae) that has frequently been isolated from sessile, filter-feeding invertebrates such as sponges, corals, and oysters (2, 4–6). To date, however, only a few genomes of this species are available. To illuminate the putative roles of R. album in association with marine animals, here we report the genomes of eight R. album strains that were isolated from the octocoral Eunicella labiata (Table 1), and we present symbiosis factors and environmental resistance traits common to all genomes (Fig. 1).

The eight R. album strains were isolated from E. labiata specimens that had been collected off the coast of Faro, Portugal, after plating of host-derived homogenates on half-strength marine agar medium followed by incubation at 18°C for 4 weeks (4). Genomic DNA was extracted from pure cultures using the Wizard genomic DNA purification kit (Promega, Madison, WI, USA) as described previously (4). The isolates were sequenced at the Joint Genome Institute (JGI) as part of the Genomic Encyclopedia of Type Strains Phase IV (KMG-V) project. Default parameters were used for all software unless otherwise specified. Genome libraries (300 bp) were prepared with the KAPA HyperPrep kit (KAPA Biosystems) and sequenced using the Illumina NovaSeq 6000 platform (S4 flow cell). Raw reads were quality filtered per JGI standard operating practice (SOP) protocol 1061 using BBTools v38.86 (http://bbtools.jgi.doe.gov). Filtered reads were assembled into contigs using SPAdes v3.14.1 (7) with 25, 55, and 95 k-mers, and contigs were annotated using the Integrated Microbial Genomes and Microbiomes (IMG/M) pipeline v5.0.17 (8). We report the Clusters of Orthologous Groups of proteins (COG) profiles obtained for all eight strains using the IMG/M platform (9). Average nucleotide identity (ANI) values obtained on the IMG/M platform (9) for all pairwise combinations among the strains were above 98.3%, supporting the same-species status of the strains. Genome completeness and contamination scores were assessed with the Microbial Genomes Atlas (MiGA) (10) (Table 1). AntiSMASH v6.0 (11) was used to identify secondary metabolite biosynthetic gene clusters (SM-BGCs).

Analysis of the R. album genomes revealed the presence of various COGs important for the establishment of symbiotic relationships, including eukaryotic-like WD40, ankyrin, and tetratricopeptide repeats (Fig. 1). COG functions related to drug (e.g., COG1566) and heavy metal resistance were common to all eight genomes, including traits specific for tellurite resistance that are usually encoded on plasmids (12) (Fig. 1). The eight strains harbor genes for the utilization of chitin, a trait that was previously reported for sponge and coral symbionts (13), as revealed by the presence of polysaccharide deacetylases and exochitinases. Other features included a coding potential for a possible role in sulfur cycling, e.g., through the catabolism of the sulfolipid cerebroside 3-sulfate and of the amino-sulfonic acid taurine, two compounds that are widely synthesized in animal tissue and utilized by bacterial symbionts (14). Moreover, all R. album genomes possess the potential to produce a diverse range of secondary metabolites. Indeed, we found a variety of SM-BGCs encoding terpenes, trans-AT-polyketide synthases and type III polyketide synthases, nonribosomal peptide synthetases, and several ribosomally synthesized peptides in this genome pool (Fig. 1).

This study was financed by the Fundo Azul program of Direção-Geral de Política do Mar (DGPM) (Ministry of the Sea, Portugal) through grant FA_05_2017_032. Sequencing, assembly, and annotation of the eight Roseibium album/Labrenzia alba genomes were performed at the JGI within the framework of the KMG-V. The work conducted by the JGI, a U.S. Department of Energy (DOE) Office of Science User Facility, is supported by the Office of Science of the DOE under contract DE-AC02-05CH11231. Further support was provided to the Institute for Bioengineering and Biosciences by Programa Operacional Regional de Lisboa (project 007317), the Fundação para a Ciência e a Tecnologia (FCT), and the European Regional Development Fund (ERDF) through grant UIDB/04565/2020. T.K.-C. is the recipient of a research scientist contract conceded by FCT (grant CEECIND/00788/2017).