Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent

Abstract

Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we present the 7.2-megabase genome of the marine bacterium Hahella chejuensis including genes responsible for the biosynthesis of a pigment which has the lytic activity against a red-tide dinoflagellate. H.chejuensis is the first sequenced species in the Oceanospiralles clade, and sequence analysis revealed its distant relationship to the Pseudomonas group. The genome was well equipped with genes for basic metabolic capabilities and contained a large number of genes involved in regulation or transport as well as with characteristics as a marine heterotroph. Sequence analysis also revealed a multitude of genes of functional equivalence or of possible foreign origin. Functions encoded in the genomic islands include biosynthesis of exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigmentation. Molecular structure of the algicidal pigment, which was determined through LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium.

Figure 1

Phylogenetic position of H.chejuensis based on 16S rDNA sequences. Sequences were retrieved from GenBank and an unrooted neighbor-joining tree was calculated. A maximum parsimony analysis gave similar topology. IUB was used as DNA weight matrix and the scale bar represents number of substitutions per site.

Figure 2

Circular representation of the H.chejuensis chromosome. Blue patches on the outermost circle indicate genomic islands. Circles 2 and 3 show CDSs transcribed clockwise and counter-clockwise, which are color-coded according to the COG functional classes as designated in the inset. Detailed function description for each one-letter classification code is available from . Next three circles indicate the locations of homologous genes in P.aeruginosa PAO1, Vibrio cholerae El Tor N16961 and E.coli K-12 (reciprocal best hits, BLASTP bit score/self-score >0.3). Circles 7 and 8 denote rRNA genes and tRNA genes, respectively. Circles 9 and 10 are plots of G+C content and cumulative (G−C)/(G+C) deviation (>0, yellow; <0, orange).

Figure 3

TTSSs and flagellar biogenesis systems in the H.chejuensis genome. (A) Genetic organizations of two TTSSs and two flagellar biogenesis systems found in H.chejuensis. Genes with similar functions are indicated in the same color. Genes conserved between the two TTSSs are shown by gray boxes. Homologous genes between TTSSs and the flagellar systems are shown by red color. (B) Phylogenetic tree based on SctV/FlhA protein sequences. Gonnet 250 was used as a protein weight matrix and proteins are neighbor-joined. Bootstrap values of >50% (for 1000 iterations) are shown and the scale bar represents number of substitutions per site.

Figure 4

Algicidal activity of the purified red pigment (RP10356) of H.chejuensis against C.polykrikoides strain BWE0109 at various concentrations.

Figure 5

Biosynthesis and structure of the red pigment of H.chejuensis. (A) The genomic region involved in pigment biosynthesis. Genes homologous to those in the S.coelicolor A3(2) red cluster are indicated by filled arrows. Horizontal lines indicate fosmid clones containing some or all of the pigment-synthetic genes. Colony colors: red, filled circles; white, open circles; white with some constitutively red variants, half-filled circle. Open lollipops: locations of the Tn5 insertions that result in loss of the colony color in a red variant of HC81006F09. (B) Structural determination of the red pigment. Upper part, LC-ESI-MS in the positive-ion mode; lower part, MS/MS fragmentation pattern of the base peak (23.73 min).