Genomic and Functional Variation of the Chlorophyll d-Producing Cyanobacterium Acaryochloris marina

Abstract

The Chlorophyll d-producing cyanobacterium Acaryochloris marina is widely distributed in marine environments enriched in far-red light, but our understanding of its genomic and functional diversity is limited. Here, we take an integrative approach to investigate A. marina diversity for 37 strains, which includes twelve newly isolated strains from previously unsampled locations in Europe and the Pacific Northwest of North America. A genome-wide phylogeny revealed both that closely related A. marina have migrated within geographic regions and that distantly related A. marina lineages can co-occur. The distribution of traits mapped onto the phylogeny provided evidence of a dynamic evolutionary history of gene gain and loss during A. marina diversification. Ancestral genes that were differentially retained or lost by strains include plasmid-encoded sodium-transporting ATPase and bidirectional NiFe-hydrogenase genes that may be involved in salt tolerance and redox balance under fermentative conditions, respectively. The acquisition of genes by horizontal transfer has also played an important role in the evolution of new functions, such as nitrogen fixation. Together, our results resolve examples in which genome content and ecotypic variation for nutrient metabolism and environmental tolerance have diversified during the evolutionary history of this unusual photosynthetic bacterium.

Keywords: Acaryochloris; chlorophyll; cyanobacteria; far-red photosynthesis; genomics; horizontal gene transfer; plasmid.

Figure 1

Sampling locations for A. marina strains and their evolutionary relationships. The genome-wide maximum likelihood phylogeny was reconstructed for a concatenation of 1369 protein sequences from single-copy orthologs according to the JTT+F+R5 model of sequence evolution and outgroup-rooted with Cyanothece sp. PCC 7425. Branch lengths are in units of the expected number of amino acid substitutions per site. Bootstrap support values of 100% (closed circles) and >90% (open circle) are shown for 1000 ultrafast bootstrap replicates. Selected traits discussed in the text are color coded as indicated. For the map of collection sites, note that the markers for the S. China Sea and Arabian Sea strains are approximate, as the exact sampling locations are unknown.

Figure 2

Venn diagram of shared and idiosyncratic protein-coding gene content among the A. marina core genome, the Acaryochloris thomasi RCC1774 genome, and Cyanothece PCC 7425 genomes. The diagram was generated with the R package VennDiagram.

Figure 3

(A). Multiple alignment of plasmids from A. marina strains MBIC11017, CCMEE 5410, and S15 encoding sodium-transporting ATPase and bidirectional hydrogenase genes. Homologous blocks of aligned sequence share the same color, with missing DNA transparent. Traces within blocks indicate sequence similarity. (B). Gene map of the sodium-transporting ATPase region for A. marina CCMEE 5410. (C). Gene map of the bidirectional hydrogenase region for A. marina CCMEE 5410.

Figure 4

(A). Population growth rate in the presence (+) or absence (−) of combined nitrogen for nif-containing strains MU08 and MU09 and for nif-lacking strain CCMEE 5410. Error bars are standard errors. (B). Maximum likelihood phylogenies for nifHDK and 16S rRNA genes reconstructed with a GTR+I+G model. Bootstrap support values greater than 50% are shown for 1000 bootstrap replicates. Branch lengths are in units of expected number of nucleotide substitutions per site. The two topologies were significantly different by an SH test (p < 0.0001).

Figure 5

Population growth rates at different NaCl concentrations for upper intertidal A. marina strains S1 and HP9, subtidal strains S15 and MBIC11017, estuarine strain FH11, and saline lake strain CCMEE 5410. Error bars are standard errors. Note that 0.43 M is the NaCl concentration of standard marine ASN-III medium. Rates were estimated if growth was sustained for at least three generations. Pigments of strains for which growth was not observed at 0.2 M or 0.8 M NaCl did not bleach, whereas all strains bleached at 0 M and 1.6 M.

Figure 6

Distribution of genes involved in the regulation, acquisition, and storage of iron among A. marina strains based on both gene count and percent of genes in the genome. A dendrogram clustered strains into two groups based on high (purple) and low (green) total iron gene content. The approximately unbiased p-value of each cluster was 99%. See Figure S2 for the hierarchical clustering dendrogram.

Figure 7

Representative gene maps for CRISPR-Cas systems detected in A. marina genomes (strain is indicated in parentheses).