Insights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains

Abstract

Planktothrix is a dominant cyanobacterial genus forming toxic blooms in temperate freshwater ecosystems. We sequenced the genome of planktic and non planktic Planktothrix strains to better represent this genus diversity and life style at the genomic level. Benthic and biphasic strains are rooting the Planktothrix phylogenetic tree and widely expand the pangenome of this genus. We further investigated in silico the genetic potential dedicated to gas vesicles production, nitrogen fixation as well as natural product synthesis and conducted complementary experimental tests by cell culture, microscopy and mass spectrometry. Significant differences for the investigated features could be evidenced between strains of different life styles. The benthic Planktothrix strains showed unexpected characteristics such as buoyancy, nitrogen fixation capacity and unique natural product features. In comparison with Microcystis, another dominant toxic bloom-forming genus in freshwater ecosystem, different evolutionary strategies were highlighted notably as Planktothrix exhibits an overall greater genetic diversity but a smaller genomic plasticity than Microcystis. Our results are shedding light on Planktothrix evolution, phylogeny and physiology in the frame of their diverse life styles.

Figure 1

Sizes estimation of the core genome in number of conserved genes (a) and pangenome in number of specific genes (b) of all Planktothrix (in black) and the planktic strains only (in red).

Figure 2. Genetic relationships between the fifteen available Planktothrix genomes.

(a) Phylogenetic tree obtained using a Maximum Likelihood method on 586 concatenated proteins.(b) Phenetic tree (UPGMA) obtained from the ANIm values between all genomes. Grey rectangle contains all the planktic strains.

Figure 3. Scheme of the structure of GvpC proteins of Planktothrix.

(a) Alignment of GvpC protein variants of Planktothrix sp. with GvpC⁴⁰ from PCC 11201, PCC 8927, PCC 9214 and PCC 9631, GvpC²⁸ from P. agardhii PCC 7805 and P. mougeotti NIVA CYA 56-3, GvpC²⁶ from NIVA CYA 34 and NIVA CYA 405, GvpC²⁴ from NIVA CYA 15, GvpC²⁰ from PCC 7821 and GvpC¹⁶ from NIVA CYA 540. The red lines indicate the localisation of the four degenerated repeats R1, R2, R3, and R4. The blue line indicate the N terminal domain presenting homology with GvpN; (b) Consensus sequence found between the R1, R2, R3, and R4 repeats. LRF residues are conserved in Anabaena and Calothrix repeats as well.

Figure 4. Organization of the Nif gene clusters in two benthic Planktothrix strains PCC 8927 and PCC 9214 compared to the ones in other non-heterocystous cyanobacteria.

The conserved genes of the nif cluster locus are indicated in grey, the genes indicated in black are present and rearranged between the clusters, the genes indicated in white are not conserved.

Figure 5. Genomic island dedicated to natural products in Planktothrix.

Similar genomic islands containing biosynthetic gene clusters of apt (green), oci (red) and mdn (blue) were found in P. sp. PCC 11201, P. rubescens PCC 7821 identical to the one found in nine planktonic Planktothrix spp. (NIVA-CYA 15, NIVA-CYA 34, NIVA-CYA 56/3, NIVA-CYA 98, NIVA-CYA 126/8, NIVA-CYA 405, NIVA-CYA 406, NIVA-CYA 407 and NIVA-CYA 540) and in P. agardhii PCC 7805. In the latter, the genomic island is not evidenced by the current assembly of the contigs, but one remaining gene of apt and the flanking regions witness a previous occurrence of the same genomic island organization. Clusters with conserved sequence and domain organization are connected in grey and in black when reorganized. The genetic island in addition of apt, oci and mdn gene clusters contained other genes putatively involved in these pathways (in grey), flanking genes (in white) and genes of mobility such as insertion sequences and transposases (in yellow).