Draft genome sequence of the marine Rhodobacteraceae strain O3.65, cultivated from oil-polluted seawater of the Deepwater Horizon oil spill

Abstract

The marine alphaproteobacterium strain O3.65 was isolated from an enrichment culture of surface seawater contaminated with weathered oil (slicks) from the Deepwater Horizon (DWH) oil spill and belongs to the ubiquitous, diverse and ecological relevant Roseobacter group within the Rhodobacteraceae. Here, we present a preliminary set of physiological features of strain O3.65 and a description and annotation of its draft genome sequence. Based on our data we suggest potential ecological roles of the isolate in the degradation of crude oil within the network of the oil-enriched microbial community. The draft genome comprises 4,852,484 bp with 4,591 protein-coding genes and 63 RNA genes. Strain O3.65 utilizes pentoses, hexoses, disaccharides and amino acids as carbon and energy source and is able to grow on several hydroxylated and substituted aromatic compounds. Based on 16S rRNA gene comparison the closest described and validated strain is Phaeobacter inhibens DSM 17395, however, strain O3.65 is lacking several phenotypic and genomic characteristics specific for the genus Phaeobacter. Phylogenomic analyses based on the whole genome support extensive genetic exchange of strain O3.65 with members of the genus Ruegeria, potentially by using the secretion system type IV. Our physiological observations are consistent with the genomic and phylogenomic analyses and support that strain O3.65 is a novel species of a new genus within the Rhodobacteraceae.

Keywords: Deepwater Horizon; Hydrocarbon; Marine bacteria; Oil degradation; Oil spill; Rhodobacteraceae; Rhodobacterales; Roseobacter.

Fig. 1

Phylogenetic tree highlighting the position of Rhodobacteraceae strain O3.65 relative to other genome sequenced and type strains within the genera Phaeobacter, Pseudophaeobacter, Ruegeria, Leisingera and additional strains of the Rhodobacteraceae. The tree was inferred from nearly full-length 16S rRNA gene sequences (≥1300 bp) using the neighbour joining tool of the ARB software [28]. Only bootstrap values ≥50 % (derived from 1000 replicates) are shown. Filled circles indicate nodes also recovered reproducibly with maximum-likelihood (RAxML) calculation. Strains and their corresponding GenBank accession numbers are listed in Additional file 1: Table S1. All strains in the tree are genome sequenced, except clone Oil-BE-016 (KJ475503). Type strains are designated by ^T. Three Synechococcus strains (AY946243, CP000951, AF448073) served as outgroup (not shown)

Fig. 2

Tanglegram of genome based trees. a Maximum likelihood tree based on genomic data of organisms affiliated with the genera Phaeobacter, Pseudophaeobacter, Ruegeria, Leisingera and additional strains of the Roseobacter clade inferred with 500 bootstraps (BS) with RAxML after Stamatakis (2014) [100]. The alignment was created from 684 orthologous single-copy genes present in all genomes (Multilocus Sequence Analysis; MLSA) after total protein sequences of the genomes were extracted from the corresponding GenBank files and used for the downstream analysis with an in house pipeline at the Goettingen Genomics Laboratory (J. Vollmers, unpubl.). In brief, clusters of orthologs were generated using proteinortho version 5 [101], inparalogs were removed, the remaining sequences were aligned with MUSCLE [102] and poorly aligned positions automatically filtered from the alignments using Gblocks [103]. b Gene content tree including singletons of the same organisms as in A based on an orthologs-content matrix representing presence or absence of a gene in a certain genome, inferred with Neighbour Joining (1000 BS). Both scripts for this pipeline, PO_2_MLSA.py and PO_2_GENECONTENT.py, are available at github. Numbers at the nodes specify BS values ≥50 %. Scale bars represent 10 % sequence divergence. For Genbank accession numbers see Additional file 1: Table S1. For a clear view only lines were given linking the same species at different positions

Fig. 3

Transmission electron micrographs of Rhodobacteraceae strain O3.65. a The typical rod-shaped morphology of a single cell with intact bundle of flagella, and (b) two cells by binary fission and their flagella. Cells were negatively stained. Scale bars 0.5 μm