A Rhizobium bacterium and its population dynamics under different culture conditions of its associated toxic dinoflagellate Gambierdiscus balechii

Abstract

Rhizobium bacteria are known as symbionts of legumes for developing nodules on plant roots and fixing N₂ for the host plants but unknown for associations with dinoflagellates. Here, we detected, isolated, and characterized a Rhizobium species from the marine toxic dinoflagellate Gambierdiscus culture. Its 16S rRNA gene (rDNA) is 99% identical to that of Rhizobium rosettiformans, and the affiliation is supported by the phylogenetic placement of its cell wall hydrolase -encoding gene (cwh). Using quantitative PCR of 16S rDNA and cwh, we found that the abundance of this bacterium increased during the late exponential growth phase of Gambierdiscus and under nitrogen limitation, suggesting potential physiological interactions between the dinoflagellate and the bacterium. This is the first report of dinoflagellate-associated Rhizobium bacterium, and its prevalence and ecological roles in dinoflagellate-Rhizobium relationships remain to be investigated in the future.

Supplementary information: The online version contains supplementary material available at 10.1007/s42995-021-00102-1.

Keywords: 16S rRNA gene; Cell wall hydrola; Gambierdiscus; Rhizobium.

Fig. 1

Maximum likelihood tree based on 16S rDNA sequences showing the phylogenetic position of the bacterium isolated from G. balechii. Values at nodes are bootstrap support values (only those > 50% are shown). Scale bar indicates mutation per site

Fig. 2

Maximum likelihood tree based on CWH amino acid sequences from bacterial strains showing the phylogenetic position of cwh from G. balechii. Values at nodes are bootstrap support values (only those > 50% are shown). Scale bar indicates mutation per site

Fig. 3

Alignment of residues surrounding the 4Fe-4S coordinating cysteine residues (vertical arrows) for NifH and BchX homologs. The sequence from our strain is boxed. a Block of alignment that contains Cys119 of the 4Fe-4S cluster ligand; b block of alignment that contains Cys156 of the 4Fe-4S cluster ligand. Numbering is based on alignment. Np: Nostoc punctiforme PCC 73102; Ct: Chlorobium tepidum; Aa: Anabaena azotica FACHB-118; Am: Azomonas macrocytogenes; Mj: Methanocaldococcus jannaschii; Rs: Roseobacter sp. COLSP; Rr: R. rosettiformans stain GAMBA01

Fig. 4

Relative cell concentration (a), chlorophyll a content (b), and cell size (c) of G. balechii under N-replete and N-limited conditions. Each spot shown is means of triplicates with error bars representing stardard deviations. Significant differences between the treatment groups are indicated by an asterisk (P < 0.05)

Fig. 5

Abundances of R. rosettiformans GAMBA-01 16S rDNA (a) and cwh (b) normalized to per algal cell in different N treatment groups of G. balechii during the early and late exponential phases. Significant difference between the treatment groups is indicated by an asterisk (P < 0.05)