Optical map guided genome assembly

Background The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly. Results We proposeOpticalKermitwhich directly integrates genome wide optical maps into contig assembly. We show how genome wide optical maps can be used to localize reads on the genome and then we adapt the Kermit method, which originally incorporated genetic linkage maps to the miniasm assembler, to use this information in contig assembly. Our experimental results show that incorporating genome wide optical maps to the contig assembly of miniasm increases NGA50 while the number of misassemblies decreases or stays the same. Furthermore, when compared to the Canu assembler,OpticalKermitproduces an assembly with almost three times higher NGA50 with a lower number of misassemblies on realA. thalianareads. Conclusions OpticalKermitsuccessfully incorporates optical mapping data directly to contig assembly of eukaryotic genomes. Our results show that this is a promising approach to improve the contiguity of genome assemblies.Peer reviewe

Increasing nitrogen limitation in the Bothnian Sea, potentially caused by inflow of phosphate-rich water from the Baltic Proper

The study showed that the open water of the Bothnian Sea (BS) is likely to have shifted from altering nitrogen and phosphorous limitations of the spring bloom to more nitrogen-limited conditions during the last 20 years. This is affected by the by inflow of phosphate-rich and oxygen-depleted water from depths near the halocline in the northern Baltic Proper, where severe oxygen conditions currently cause extreme phosphate concentrations in the deep water. The change in relation between inorganic nitrogen and phosphorous in the BS occurs first in the deep water and then progresses to the surface water. The change can potentially cause increased production in the BS and more frequent cyanobacterial blooms. There does not appear to be any immediate concern in the short-term perspective for the state of the BS, but a progression of the processes may lead to a more eutrophic state of the BS. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13280-015-0675-3) contains supplementary material, which is available to authorized users

Small-scale carbon and nitrogen fluxes associated with Aphanizomenon sp. in the Baltic Sea.

Carbon and nitrogen fluxes in Aphanizomenon sp. colonies in the Baltic Sea were measured using a combination of microsensors, stable isotopes, mass spectrometry, and nanoscale secondary ion mass spectrometry (nanoSIMS). Cell numbers varied between 956 and 33 000 in colonies ranging in volume between 1.4 × 10−4 and 230 × 10−4 mm−3. The high cell content and their productivity resulted in steep O2 gradients at the colony–water interface as measured with an O2 microsensor. Colonies were highly autotrophic communities with few heterotrophic bacteria attached to the filaments. Volumetric gross photosynthesis in colonies was 78 nmol O2 mm−3 h−1. Net photosynthesis was 64 nmol O2 mm−3 h−1, and dark respiration was on average 15 nmol O2 mm−3 h−1 or 16% of gross photosynthesis. These volumetric photosynthesis rates belong to the highest measured in aquatic systems. The average cell-specific net carbon-fixation rate was 38 and 40 fmol C cell−1 h−1 measured by microsensors and by using stable isotopes in combination with mass spectrometry and nanoSIMS, respectively. In light, the net C:N fixation ratio of individual cells was 7.3±3.4. Transfer of fixed N2 from heterocysts to vegetative cells was fast, but up to 35% of the gross N2 fixation in light was released as ammonium into the surrounding water. Calculations based on a daily cycle showed a net C:N fixation ratio of 5.3. Only 16% of the bulk N2 fixation in dark was detected in Aphanizomenon sp. Hence, other organisms appeared to dominate N2 fixation and NH4+ release during darkness

Dissolved iron (II) in the Baltic Sea surface water and implications for cyanobacterial bloom development

Iron chemistry measurements were conducted during summer 2007 at two distinct locations in the Baltic Sea (Gotland Deep and Landsort Deep) to evaluate the role of iron for cyanobacterial bloom development in these estuarine waters. Depth profiles of Fe(II) were measured by chemiluminescent flow injection analysis (CL-FIA) and reveal several origins of Fe(II) to the water column. Photoreduction of Fe(III)-complexes and deposition by rain are main sources of Fe(II) (up to 0.9 nmol L−1) in light penetrated surface waters. Indication for organic Fe(II) complexation resulting in prolonged residence times in oxygenated water was observed. Surface dwelling heterocystous cyanobacteria where mainly responsible for Fe(II) consumption in comparison to other phytoplankton. The significant Fe(II) concentrations in surface waters apparently play a major role in cyanobacterial bloom development in the Baltic Sea and are a major contributor to the Fe requirements of diazotrophs. Second, Fe(II) concentrations up to 1.44 nmol L−1 were observed at water depths below the euphotic zone, but above the oxic anoxic interface. Finally, all Fe(III) is reduced to Fe(II) in anoxic deep water. However, only a fraction thereof is present as ferrous ions (up to 28 nmol L−1) and was detected by the CL-FIA method applied. Despite their high concentrations, it is unlikely that ferrous ions originating from sub-oxic waters could be a temporary source of bioavailable iron to the euphotic zone since mixed layer depths after strong wind events are not deep enough in summer time

Dissolved iron (II) in the Baltic Sea surface water and implications for cyanobacterial bloom development

Iron chemistry measurements were conducted during summer 2007 at two distinct locations in the Baltic Sea (Gotland Deep and Landsort Deep) to evaluate the role of iron for cyanobacterial bloom development in these estuarine waters. Depth profiles of Fe(II) were measured by chemiluminescent flow injection analysis (CL-FIA). Up to 0.9 nmol Fe(II) L−1 were detected in light penetrated surface waters, which constitutes up to 20% to the dissolved Fe pool. This bioavailable iron source is a major contributor to the Fe requirements of Baltic Sea phytoplankton and apparently plays a major role for cyanobacterial bloom development during our study. Measured Fe(II) half life times in oxygenated water exceed predicted values and indicate organic Fe(II) complexation. Potential sources for Fe(II) ligands, including rainwater, are discussed. Fe(II) concentrations of up to 1.44 nmol L−1 were detected at water depths below the euphotic zone, but above the oxic anoxic interface. Mixed layer depths after strong wind events are not deep enough in summer time to penetrate the oxic-anoxic boundary layer. However, Fe(II) from anoxic bottom water may enter the sub-oxic zone via diapycnal mixing and diffusion.Validerad; 2009; 20091106 (jgn)</p