Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

Abstract

The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage and that have different minimum, maximum and optimal light intensities for growth. The high-light-adapted ecotype has the smallest genome (1,657,990 base pairs, 1,716 genes) of any known oxygenic phototroph, whereas the genome of its low-light-adapted counterpart is significantly larger, at 2,410,873 base pairs (2,275 genes). The comparative architectures of these two strains reveal dynamic genomes that are constantly changing in response to myriad selection pressures. Although the two strains have 1,350 genes in common, a significant number are not shared, and these have been differentially retained from the common ancestor, or acquired through duplication or lateral transfer. Some of these genes have obvious roles in determining the relative fitness of the ecotypes in response to key environmental variables, and hence in regulating their distribution and abundance in the oceans.

Towards a better understanding of microbial carbon flux in the sea*

“…The first analyses of marine cyanobacterial genomes provided explanations for divergent patterns of depth distribution of ubiquitous primary producers , Palenik et al 2003, Rocap et al 2003. The first complete genome sequence of a marine 'heterotrophic' bacterioplankton species, Silicibacter pomeroyii, a member of the abundant Roseobacter clade, showed that it uses inorganic compounds like carbon monoxide and sulphide at concentrations found in the oceans to supplement heterotrophy (i.e.…”

Proteomics of marine bacteria

“…[9]. Recently, the genomes of three different members of the cyanobacterium species Prochlorococcus marinus have been sequenced [10,11]. These members of the genus Prochlorococcus dominate phytoplankton communities in most tropical and temperate open ocean ecosystems [12].…”

“…P. marinus is found in two main ecological forms: high-light-adapted genotypes in the upper part of the water column and low-light-adapted genotypes at the bottom of the illuminated layer [10]. The analysis of the genome sequences of the different P. marinus strains led to the identification of genes, which play a role in determining the relative fitness of the ecotypes in response to key environmental variables [11]. Glöckner et al [13] reported the complete genome sequence of Pirellula sp.…”

Cross‐species Transcriptional Network Analysis Reveals Conservation and Variation in Response to Metal Stress in Cyanobacteria

“…Analysis of the transcriptional networks showed that a total of 17, 21, 32 and 28 distinct transcriptional modules can be detected within the transcriptional networks of PMT, PMM, SYG and SYW, respectively (Additional file 2: Figure S2). More transcriptional modules detected in SYG and SYW than PMT and PMM were probably due to the relatively large genome sizes of Synechococcus [32][33][34]. The association analysis between the phenotypes (i.e.…”

“…Therefore, we excluded all samples at 0 hour from our analysis. The updated genome annotation for all four species was downloaded from NCBI and the Comprehensive Microbial Resource (CMR) of TIGR (http://www.tigr.org/ CMR) [32][33][34]. KEGG Pathway and COGs (Cluster of Orthologous Groups of proteins) information was obtained from the KEGG Pathway Databases (http://www.…”