Characterization of Phycoerythrin Physiology in Low-Light Adapted Prochlorococcus Ecotypes

The marine cyanobacteria Prochlorococcus and Synechococcus are the most abundant phototrophs in the oceans. They cohabit the oligotrophic ocean and thus have coevolved together, yet they have distinctly different methods for harvesting light. Synechococcus, like other cyanobacteria, possess phycobilisomes with various combinations of phycobiliproteins to capture wavelengths of light not otherwise available to chlorophyll. Prochlorococcus lack phycobilisomes and use divinyl chlorophyll b (Chl b2) as their primary accessory pigment to divinyl chlorophyll a (Chl a2) to capture light energy. In addition to the divinyl chlorophylls, Prochlorococcus has genes associated with the phycobiliprotein phycoerythrin (PE), the role of which is still not fully understood, though it is unlikely to contribute significantly to photosynthesis. Past studies have focused on characterizing PE expression on a few isolates of Prochlorococcus, the Low Light adapted (LL) II/III ecotype SS120, High Light (HLI) ecotype MED4 and HLII ecotype AS9601. These studies found that the LLII/III SS120 ecotype expressed both PE chromophores, phycoerythrobilin (PEB) and phycourobilin (PUB), whereas the HL ecotypes only expressed PEB. However, the LL ecotypes have more extensive phylogenetic diversity, so I sought to characterize the diversity in PE physiology for Prochlorococcus isolates from three LL ecotypes using a combination of flow cytometry, spectrofluorometry, and pigment measurements. I confirmed that the flow cytometric orange fluorescence (FL2) signal was due to PE in all LL Prochlorococcus strains examined and found differences in phycobilin composition among the LL Prochlorococcus strains. For instance, some LLIV ecotype strains did not have measurable PEB and most strains increased their PE expression per cell when grown at low light irradiances, suggesting PE is photoacclimating in LL Prochlorococcus. The physiological differences observed for LL Prochlorococcus strains and ecotypes highlight the necessity of examining more than one strain from an ecotype to make inferences about ecotypic physiology

Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.Gordon and Betty Moore Foundation (Grant GBMR #495.01)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant OCE-0425602)National Science Foundation (U.S.) (Grant DBI-0424599)Center for Microbial Oceanography: Research and Educatio

Physiology and evolution of nitrate acquisition in Prochlorococcus

Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ~17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.Gordon and Betty Moore Foundation (Grant GBMF495)National Science Foundation (U.S.) (Grant OCE-1153588)National Science Foundation (U.S.) (Grant DBI-0424599

All predicted Prochlorococcus ORFs, amino acid sequence

Set of protein FASTA files containing the predicted amino acid translation for all ORFs in each genome. This file includes ORFs from both the new genomes presented here as well as the re-annotation of previously released Prochlorococcus genomes

Data from: Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus

The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography

Detailed annotation information for Prochlorococcus genomes

Set of tables providing detailed annotation information for each newly sequenced Prochlorococcus genome, as well as re-annotations of previously published genomes

All predicted Prochlorococcus ORFs, nucleotide sequence

Set of nucleotide FASTA files containing the predicted nucleotide sequence for all open reading frames (ORFs) in each genome. This file includes ORFs from both the new genomes presented here as well as the re-annotation of previously released Prochlorococcus genomes

Prochlorococcus genomes and cluster of orthologous groups of proteins (COGs)

Cluster assignments and annotation metadata for genes in the newly sequenced Prochlorococcus genomes described in this work, as well as in previously published genomes

Complete set of initial contig assemblies from non-axenic Prochlorococcus cultures

Set of nucleotide FASTA files containing all assembled contigs (>500 bp) from each culture (i.e. both Prochlorococcus and heterotrophs) sequenced in this work. Each file contains the set of contigs assembled from the raw sequencing data, before any filtering to separate Prochlorococcus from heterotroph contigs

Prochlorococcus genome sequences

Set of nucleotide FASTA-formatted files containing the new Prochlorococcus genome assemblies described in this work