1. Wochenbericht AL509

Wochenbericht FS Alkor Reise 509, Fahrtabschnitt 15.05 – 20.05.201

Cruise Report AL509 R.V. Alkor

Dates of Cruise: 15.05. – 30.05.2018 Areas of Research: Physical, chemical, biological and fishery oceanography Port Calls: Riga. Latvia, 22.05.201

1. Wochenbericht AL522

Wochenbericht FS Alkor Reise 522 "Ostsee Mai", 1. Fahrtabschnitt 15.05 – 25.05.201

Eco-Evolutionary Interaction in Competing Phytoplankton: Nutrient Driven Genotype Sorting Likely Explains Dominance Shift and Species Responses to CO2

How ecological and evolutionary processes interact and together determine species and community responses to climate change is poorly understood. We studied long-term dynamics (over approximately 200 asexual generations) in two phytoplankton species, a coccolithophore (Emiliania huxleyi), and a diatom (Chaetoceros affinis), to increased CO2 growing alone, or competing with one another in co-occurrence. To allow for rapid evolutionary responses, the experiment started with a standing genetic variation of nine genotypes in each of the species. Under co-occurrence of both species, we observed a dominance shift from C. affinis to E. huxleyi after about 120 generations in both CO2 treatments, but more pronounced under high CO2. Associated with this shift, we only found weak adaptation to high CO2 in the diatom and none in the coccolithophore in terms of species’ growth rates. In addition, no adaptation to interspecific competition could be observed by comparing the single to the two-species treatments in reciprocal assays, regardless of the CO2 treatment. Nevertheless, highly reproducible genotype sorting left only one genotype remaining for each of the species among all treatments. This strong evolutionary selection coincided with the dominance shift from C. affinis to E. huxleyi. Since all other conditions were kept constant over time, the most parsimonious explanation for the dominance shift is that the strong evolutionary selection was driven by the experimental nutrient conditions, and in turn potentially altered competitive ability of the two species. Thus, observed changes in the simplest possible two-species phytoplankton “community” demonstrated that eco-evolutionary interactions can be critical for predicting community responses to climate change in rapidly dividing organisms such as phytoplankton

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

An improved filtering algorithm for big read datasets and its application to single-cell assembly

Background: For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots of redundant data. A filtering of this data prior to assembly is advisable. Brown et al. (2012) presented the algorithm Diginorm for this purpose, which filters reads based on the abundance of their k-mers. Methods: We present Bignorm, a faster and quality-conscious read filtering algorithm. An important new algorithmic feature is the use of phred quality scores together with a detailed analysis of the k-mer counts to decide which reads to keep. Results: We qualify and recommend parameters for our new read filtering algorithm. Guided by these parameters, we remove in terms of median 97.15% of the reads while keeping the mean phred score of the filtered dataset high. Using the SDAdes assembler, we produce assemblies of high quality from these filtered datasets in a fraction of the time needed for an assembly from the datasets filtered with Diginorm. Conclusions: We conclude that read filtering is a practical and efficient method for reducing read data and for speeding up the assembly process. This applies not only for single cell assembly, as shown in this paper, but also to other projects with high mean coverage datasets like metagenomic sequencing projects. Our Bignorm algorithm allows assemblies of competitive quality in comparison to Diginorm, while being much faster. Bignorm is available for download at https://git.informatik.uni-kiel.de/axw/Bignorm

Light-chain-induced renal tubular acidosis: effect of sodium bicarbonate on sodium-proton exchange

We measured sodium-proton (Na+/H+) exchange in lymphocytes and platelets of a 46-year-old woman with the adult Fanconi syndrome before, during, and after treatment with NaHCO3. Kappa light chains in her urine and unique but rarely observed crystalline structures confirmed the presence of light-chain nephropathy. Her glomerular filtration rate was only moderately impaired at 72 ml/min. NaHCO3 at 1, 3, and 5 mmol/kg/day for 5 days increased her serum HCO3 and pH from 17 to 21 mmol/l and 7.28 to 7.39 respectively. Plasma renin and aldosterone values were decreased by NaHCO3. Na+/H+ exchange (δHi/min) was measured with the fluorescent marker BCECF after acidification of lymphocytes and platelets with sodium propionate at five (10-50mM) doses. Na+/H+ exchange was accelerated in this patient compared to normal controls. NaHCO3 treatment significantly decreased Na+/H+ exchange in lymphocytes, but not in platelets. These findings suggest that Na+/H+ exchange can be influenced by NaHCO3 ingestion at doses that only modestly affect systemic pH. Since Na+/H+ exchange is involved in stimulus response coupling, cell growth regulation, cell differentiation, and perhaps the progression of nephrosclerosis, these observations may have clinical relevanc