Algal biogeography: metagenomics shows distribution of a picoplanktonic pelagophyte

Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans

A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.

Insights Into the Evolution of Picocyanobacteria and Phycoerythrin Genes (mpeBA and cpeBA)

Marine picocyanobacteria, Prochlorococcus and Synechococcus, substantially contribute to marine primary production and have been the subject of extensive ecological and genomic studies. Little is known about their close relatives from freshwater and non-marine environments. Phylogenomic analyses (using 136 proteins) provide strong support for the monophyly of a clade of non-marine picocyanobacteria consisting of Cyanobium, Synechococcus and marine Sub-cluster 5.2; this clade itself is sister to marine Synechococcus and Prochlorococcus. The most basal lineage within the Syn/Pro clade, Sub-Cluster 5.3, includes marine and freshwater strains. Relaxed molecular clock (SSU, LSU) analyses show that while ancestors of the Syn/Pro clade date as far back as the end of the Pre-Cambrian, modern crown groups evolved during the Carboniferous and Triassic. Comparative genomic analyses reveal novel gene cluster arrangements involved in phycobilisome (PBS) metabolism in freshwater strains. Whilst PBS genes in marine Synechococcus are mostly found in one type of phycoerythrin (PE) rich gene cluster (Type III), strains from non-marine habitats, so far, appear to be more diverse both in terms of pigment content and gene arrangement, likely reflecting a wider range of habitats. Our phylogenetic analyses show that the PE genes (mpeBA) evolved via a duplication of the cpeBA genes in an ancestor of the marine and non-marine picocyanobacteria and of the symbiotic strains Synechococcus spongiarum. A 'primitive' Type III-like ancestor containing cpeBA and mpeBA had thus evolved prior to the divergence of the Syn/Pro clade and S. spongiarum. During the diversification of Synechococcus lineages, losses of mpeBA genes may explain the emergence of pigment cluster Types I, II, IIB, and III in both marine and non-marine habitats, with few lateral gene transfer events in specific taxa.

Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics

Metagenomic analyses are challenging in metazoans, but high-copy number and repeat regions can be assembled from low-coverage sequencing by "genome skimming," which is applied here as a new way of characterizing metagenomes obtained in an ecological or taxonomic context. Illumina shotgun sequencing on two pools of Coleoptera (beetles) of approximately 200 species each were assembled into tens of thousands of scaffolds. Repeated low-coverage sequencing recovered similar scaffold sets consistently, although approximately 70% of scaffolds could not be identified against existing genome databases. Identifiable scaffolds included mitochondrial DNA, conserved sequences with hits to expressed sequence tag and protein databases, and known repeat elements of high and low complexity, including numerous copies of rRNA and histone genes. Assemblies of histones captured a diversity of gene order and primary sequence in Coleoptera. Scaffolds with similarity to multiple sites in available coleopteran genome sequences for Dendroctonus and Tribolium revealed high specificity of scaffolds to either of these genomes, in particular for high-copy number repeats. Numerous "clusters" of scaffolds mapped to the same genomic site revealed intra- and/or intergenomic variation within a metagenome pool. In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear. Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts. The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.

Localization of enzymes relating to C4 organic acid metabolisms in the marine diatom, Thalassiosira pseudonana

In the genome of the marine diatom-Thalassiosira pseudonana, there are several putative genes encoding enzymes potentially constitute a classical C4 type biochemical CO2-concentrating mechanism. Two genes encode a carboxylation enzyme phosphoenolpyruvate carboxylase (PEPC)1 and PEPC2; and another two encode decarboxylation enzymes, NAD(+)-dependent malic enzyme (NAD-ME) and phosphoenolpyruvate carboxykinase (PEPCK). These genes were tagged by the enhanced-green fluorescence protein, egfp, ligated in the transformation vector, and transformed into the cells of T. pseudonana for localization of GFP fusion products. The PEPC1:GFP fusion was localized at the matrix of the periplastidal compartment, while the PEPC2:GFP fusion was localized at the mitochondria. The NAD-ME:GFP fusion was localized in the cytosol and the PEPCK:GFP fusion at the mitochondria. The transcripts level of NAD-ME was extremely low, and PEPCK transcript was significantly induced under the dark, suggesting that PEPCK is involved in the dark metabolism such as respiration and amino acid metabolism in the mitochondria. Treatments of low-CO2grown T. pseudonana cells with inhibitors for PEPCK and PEPC efficiently dissipated the maximum rate of photosynthesis while these treatments did not affect high-affinity photosynthesis. These data strongly suggest that classical C4 enzymes play little role in the CCM in T. pseudonana.

Iron acquisition and allocation in stramenopile algae

The essential element iron has a low biological availability in the surface ocean where photosynthetic organisms live. Recent advances in our understanding of iron acquisition mechanisms in brown algae and diatoms (stramenopile algae) show the importance of the reduction of ferric to ferrous iron prior to, or during, transport in the uptake process. The uses of iron in photosynthetic stramenopiles resembles that in other oxygenic organisms, although (with the exception of the diatom Thalassiosira oceanica from an iron-deficient part of the ocean) they lack plastocyanin, instead using cytochrome c 6, This same diatom further economizes genotypically on the use of iron in photosynthesis by decreasing the expression of photosystem I, cytochrome c 6, and the cytochrome b 6 f complex per cell and per photosystem II relative to the coastal Thalassiosira pseudonana; similar changes occur phenotypically in response to iron deficiency in other diatoms such as Phaeodactylum tricornutum. In some diatoms grown under iron-limiting conditions, essentially all of the iron in the cells can be accounted for by the iron occurring in catalytic proteins. However, stramenopiles can store iron. Genomic studies show that pennate, but not centric, diatoms have the iron storage protein ferritin. While Mössbauer and X-ray analysis of (57)Fe-labelled Ectocarpus siliculosus shows iron in an amorphous mineral phase resembling the core of ferritin, the genome shows no protein with significant sequence similarity to ferritin.