Dataset Information

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

ABSTRACT: Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the scarcity of genome sequences from fresh- and brackish water-adapted strains. To remediate this, we analysed genomes assembled from metagenomic samples collected along a natural salinity gradient, and over the course of a growth season, in the Baltic Sea. We found that while PBS gene clusters in picocyanobacteria sampled in marine habitats were highly similar to known references, brackish-adapted genotypes harboured a novel type not seen in previously sequenced genomes. Phylogenetic analyses showed that the novel gene cluster belonged to a clade of uncultivated picocyanobacteria that dominate the brackish Baltic Sea throughout the summer season, but are uncommon in other examined aquatic ecosystems. Further, our data suggest that the PE genes were lost in the ancestor of PC-containing coastal picocyanobacteria and that multiple horizontal gene transfer events have re-introduced PE genes into brackish-adapted strains, including the novel clade discovered here.

SUBMITTER: Larsson J

PROVIDER: S-EPMC4139726 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Larsson John J Celepli Narin N Ininbergs Karolina K Dupont Christopher L CL Yooseph Shibu S Bergman Bigitta B Ekman Martin M

The ISME journal 20140313 9

Photoautotrophic picocyanobacteria harvest light via phycobilisomes (PBS) consisting of the pigments phycocyanin (PC) and phycoerythrin (PE), encoded by genes in conserved gene clusters. The presence and arrangement of these gene clusters give picocyanobacteria characteristic light absorption properties and allow the colonization of specific ecological niches. To date, a full understanding of the evolution and distribution of the PBS gene cluster in picocyanobacteria has been hampered by the sca ...[more]

PMID: 24621524

Similar Datasets

Project description:BackgroundOur knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches.Methodology/principal findingsA combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species.Conclusions/significanceThese findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.

Project description:The Baltic Sea is one of the largest brackish water bodies in the world. Redoxclines that form between oxic and anoxic layers in the deepest sub-basins are a semi-permanent character of the pelagic Baltic Sea. The microbially mediated nitrogen removal processes in these redoxclines have been recognized as important ecosystem service that removes large proportion of the nitrogen load originating from the drainage basin. However, nitrification, which links mineralization of organic nitrogen and nitrogen removal processes, has remained poorly understood. To gain better understanding of the nitrogen cycling in the Baltic Sea, we analyzed the assemblage of ammonia oxidizing bacteria and archaea in the central Baltic Sea using functional gene microarrays and measured the biogeochemical properties along with potential nitrification rates. Overall, the ammonia oxidizer communities in the Baltic Sea redoxcline were very evenly distributed. However, the communities were clearly different between the eastern and western Gotland Basin and the correlations between different components of the ammonia oxidizer assemblages and environmental variables suggest ecological basis for the community composition. The more even community ammonia oxidizer composition in the eastern Gotland Basin may be related to the constantly oscillating redoxcline that does not allow domination of single archetype. The oscillating redoxcline also creates long depth range of optimal nitrification conditions. The rate measurements suggest that nitrification in the central Baltic Sea is able to produce all nitrate required by denitrification occurring below the nitrification zone. Two color array (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5. Three replicate probes were printed for each archetype. Two replicate arrays were run on duplicate targets.

Project description:BackgroundOil spills can cause severe damage within a marine ecosystem. Following a spill, the soluble fraction of polycyclic aromatic hydrocarbons is rapidly released into the water column. These remain dissolved in seawater over an extended period of time, even should the insoluble fraction be removed. The vertical distribution of the aromatic hydrocarbon component and how these become transferred is poorly understood in brackish waters. This study examines the vertical distribution of polycyclic aromatic hydrocarbons having been released from a controlled film of spilled oil onto the surface of brackish water.MethodsThe study was undertaken under controlled conditions so as to minimize the variability of environmental factors such as temperature and hydrodynamics. The distribution of polycyclic aromatic hydrocarbons was measured in the dissolved and suspended phases throughout the 1 m water column with different intensity of water sampling: 1, 2, 4, 7, 72, 120, 336, 504 and 984 h.ResultsThe total concentration of polycyclic aromatic hydrocarbons ranged from 19.01 to 214.85 ng L-1 in the dissolved phase and from 5.14 to 63.92 ng L-1 in the suspended phase. These hydrocarbons were released immediately following a controlled spill attaining 214.9 ng L-1 in the dissolved phase and 54.4 ng L-1 in the suspended phase near the cylinder bottom after 1-2 h. The 2-3 ring polycyclic aromatic hydrocarbons dominated in the dissolved phase (60-80%), whereas the greater amount of 4-6 ring polycyclic aromatic hydrocarbons (55-90%) occurred in the suspended phase. A relatively low negative correlation (rS = -0.41) was determined between the concentration of phenanthrene and suspended matter, whereas a high negative correlation (r = - 0.79) was found between the concentration of pyrene and suspended matter. Despite the differences in the relationships between the concentration ratio and amount of suspended matter the obtained regressions allow roughly to predict the concentration of polycyclic aromatic hydrocarbons.

Dataset Information

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Publications

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets