Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae

Abstract

Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.

Keywords: algal-bacterial interactions; genome sequencing; holobiont; metabolic network; phytohormones; symbiosis; transporters; vitamins.

Figure 1

Taxonomic position of “Ca. Phaeomarinobacter ectocarpi” Ec32 within the Alphaproteobacteria. The figure shows a neighbor-joining tree of 236 16S rDNA sequences with bootstrap support values obtained for this and a corresponding maximum likelihood tree, respectively (only values ≥50% are shown). Hyper-variable regions were masked from the alignment. The Gammaproteobacterium Escherichia coli was used as outgroup. A more exhaustive tree of Alphaproteobacteria based on 790 taxa is available in Data sheet 1.

Figure 2

Overview of the “Ca. Phaeomarinobacter ectocarpi” Ec32 genome. (A) illustration of the genome structure generated using CGView (Stothard and Wishart, 2005); (B) summary of subsystems identified using RAST (Aziz et al., 2008).

Figure 3

Carbohydrate modifying enzymes. (A) Number of CAZY families in the genome of “Ca. Phaeomarinobacter ectocarpi” Ec32 and selected Rhizobiales. (B) Organization of genes possibly involved in the degradation of sulfated fucans. GT, glycosyltransferase; ST, sulfotransferase.

Figure 4

Genes involved in tryptophan-dependent auxin synthesis in “Ca. Phaeomarinobacter ectocarpi” Ec32 (blue loci) and E. siliculosus (brown loci).