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Background: Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results: The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion: High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. [ABSTRACT FROM AUTHOR]

The abundance and diversity of aerobic anoxygenic phototrophs ( AAPs) were studied for a year cycle at the Blanes Bay Microbial Observatory ( NW Mediterranean) and their potential links to an array of environmental variables were explored. Cell numbers were low in winter and peaked in summer, showing a marked seasonality that positively correlated with day length and light at the surface. Bacteriochlorophyll a concentration, their light-harvesting pigment, was only detected between April and October, and pigment cell quota showed large variations during this period. Pyrosequencing analysis of the puf M gene revealed that the most abundant operational taxonomic units ( OTUs) were affiliated to phylogroup K ( Gammaproteobacteria) and uncultured phylogroup C, although they were outnumbered by alphaproteobacterial OTUs in spring. Overall, richness was higher in winter than in summer, showing an opposite trend to abundance and day length. Clustering of samples by multivariate analyses showed a clear seasonality that suggests a succession of different AAP subpopulations over time. Temperature, chlorophyll a and day length were the environmental drivers that best explained the distribution of AAP assemblages. These results indicate that AAP bacteria are highly dynamic and undergo seasonal variations in diversity and abundance mostly dictated by environmental conditions as exemplified by light availability. [ABSTRACT FROM AUTHOR]

Growth is one of the basic attributes of any living organism. Surprisingly, the growth rates of marine bacterioplankton are only poorly known. Current data suggest that marine bacteria grow relatively slowly, having generation times of several days. However, some bacterial groups, such as the aerobic anoxygenic phototrophic (AAP) bacteria, have been shown to grow much faster. Two manipulation experiments, in which grazing, viruses, and resource competition were reduced, were conducted in the coastal Mediterranean Sea (Blanes Bay Microbial Observatory). The growth rates of AAP bacteria and of several important phylogenetic groups (the Bacteroidetes, the aiphaproteobacterial groups Roseobacter and SAR11, and the Gammaproteobacteria group and its subgroups the Alteromonadaceae and the NOR5/0M60 dade) were calculated from changes in cell numbers in the manipulation treatments. In addition, we examined the role that top-down (mortality due to grazers and viruses) and bottom-up (resource availability) factors play in determining the growth rates of these groups. Manipulations resulted in an increase of the growth rates of all groups studied, but its extent differed largely among the individual treatments and among the different groups. Interestingly, higher growth rates were found for the AAP bacteria (up to 3.71 day1) and for the Alteromonadaceae (up to 5.44 day'), in spite of the fact that these bacterial groups represented only a very low percentage of the total prokaryotic community. In contrast, the SARi! dade, which was the most abundant group, was the slower grower in all treatments. Our results show that, in general, the least abundant groups exhibited the highest rates, whereas the most abundant groups were those growing more slowly, indicating that some minor groups, such the AAP bacteria, very likely contribute much more to the recycling of organic matter in the ocean than what their abundances alone would predict. [ABSTRACT FROM AUTHOR]

Summary The distribution of aerobic anoxygenic phototrophs (AAPs) was surveyed in various regions of the Mediterranean Sea in spring and summer. These phototrophic bacteria were present within the euphotic layer at all sampled stations. The AAP abundances increased with increasing trophic status ranging from 2.5 × 103 cells per ml in oligotrophic Eastern Mediterranean up to 90 × 103 cells per ml in the Bay of Villefranche. Aerobic anoxygenic phototrophs made up on average 1-4% of total prokaryotes in low nutrient areas, whereas in coastal and more productive stations these organisms represented 3-11% of total prokaryotes. Diel bacteriochlorophyll a decay measurements showed that AAP community in the Western Mediterranean grew rapidly, at rates from 1.13 to 1.42 day−1. The lower AAP abundances registered in the most oligotrophic waters suggest that they are relatively poor competitors under nutrient limiting conditions. Instead, AAPs appear to be metabolically active organisms, which thrive better in more eutrophic environments providing the necessary substrates to maintain high growth rates. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic (AAP) bacteria play significant roles in the bacterioplankton productivity and biogeochemical cycles of the surface ocean. In this study, we applied both cultivation and mRNA-based molecular methods to explore the diversity of AAP bacteria along an oligotrophic gradient in the Mediterranean Sea in early summer 2008. Colony-forming units obtained on three different agar media were screened for the production of bacteriochlorophyll-α (BChl-α), the light-harvesting pigment of AAP bacteria. BChl-α-containing colonies represented a low part of the cultivable fraction. In total, 54 AAP strains were isolated and the phylogenetic analyses based on their 16S rRNA and pufM genes showed that they were all affiliated to the Alphaproteobacteria. The most frequently isolated strains belonged to Citromicrobium bathyomarinum, and Erythrobacter and Roseovarius species. Most other isolates were related to species not reported to produce BChl-alpha; and/or may represent novel taxa. Direct extraction of RNA from seawater samples enabled the analysis of the expression of pufM, the gene coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis. Clone libraries of pufM gene transcripts revealed that most phylotypes were highly similar to sequences previously recovered from the Mediterranean Sea and a large majority (~94%) was affiliated to the Gammaproteobacteria. The most abundantly detected phylotypes occurred in the western and eastern Mediterranean basins. However, some were exclusively detected in the eastern basin, reflecting the highest diversity of pufM transcripts observed in this ultra-oligotrophic region. To our knowledge, this is the first study to document extensively the diversity of AAP isolates and to unveil the active AAP community in an oligotrophic marine environment. By pointing out the discrepancies between culture-based and molecular methods, this study highlights the existing gaps in the understanding of the AAP bacteria ecology, especially in the Mediterranean Sea and likely globally. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophic prokaryotes able to use both light and organic substrates for energy production. They are widely distributed in coastal and oceanic environments and may contribute significantly to the carbon cycle in the upper ocean. To better understand questions regarding links between the ecology of these photoheterotrophic bacteria and the trophic status of water masses, we examined their horizontal and vertical distribution and the effects of nutrient additions on their growth along an oligotrophic gradient in the Mediterranean Sea. Concentrations of bacteriochlorophyll-a (BChl-a) and AAP bacterial abundance decreased from the western to the eastern basin of the Mediterranean Sea and were linked with concentrations of chlorophyll-a, nutrient and dissolved organic carbon. Inorganic nutrient and glucose additions to surface seawater samples along the oligotrophic gradient revealed that AAP bacteria were nitrogen- and carbon-limited in the ultraoligotrophic eastern basin. The intensity of the AAP bacterial growth response generally differed from that of the total bacterial growth response. BChl-a quota of AAP bacterial communities was significantly higher in the eastern basin than in the western basin, suggesting that reliance on phototrophy varied along the oligotrophic gradient and that nutrient and/or carbon limitation favors BChl-a synthesis. [ABSTRACT FROM AUTHOR]

Aerobic anoxygenic phototrophic bacteria (AAP) represent an important fraction of bacterioplankton assemblages in various oceanic regimes. Although their abundance and distribution have been explored recently in diverse oceanic regions, the environmental factors controlling the population structure and diversity of these photoheterotrophic bacteria remain poorly understood. Here, we investigate the horizontal and vertical distributions and the genetic diversity of AAP populations collected in late summer throughout the Mediterranean Sea using pufM-temporal temperature gel gradient electrophoresis (TTGE) and clone library analyses. The TTGE profiles and clone libraries analyzed using multivariate statistical methods demonstrated a horizontal and vertical zonation of AAP assemblages. Physicochemical parameters such as pH, inorganic nitrogen compounds, photosynthetically active radiation, total organic carbon and to a lesser extent particulate organic nitrogen and phosphorus, and biogenic activities (e.g. bacterial production, cell densities), acted in synergy to explain the population changes with depth. About half of the pufM sequences were <94% identical to known sequences. The AAP populations were predominantly (∼80%) composed of Gammaproteobacteria, unlike most previously explored marine systems. Our results suggest that genetically distinct ecotypes inhabiting different niches may exist in natural AAP populations of the Mediterranean Sea whose genetic diversity is typical of oligotrophic environments. [ABSTRACT FROM AUTHOR]

Bacteriochlorophyll a-containing aerobic anoxygenic phototrophs (AAnP) have been proposed to account for up to 11% of the total surface water microbial community and to potentially have great ecological importance in the world's oceans. Recently, environmental and genomic data based on analysis of the pufM gene identified the existence of α-proteobacteria as well as possible γ-like proteobacteria among AAnP in the Pacific Ocean. Here we report on analyses of environmental samples from the Red and Mediterranean Seas by using pufM as well as the bchX and bchL genes as molecular markers. The majority of photosynthesis genes retrieved from these seas were related to Roseobacter-like AAnP sequences. Furthermore, the sequence of a novel photosynthetic operon organization from an uncultured Roseobacter-like bacterial artificial chromosome retrieved from the Red Sea is described. The data show the presence of Roseobacter-like bacteria in Red and Mediterranean Sea AAnP populations in the seasons analyzed. [ABSTRACT FROM AUTHOR]