ddrage: A data set generator to evaluate ddRADseq analysis software

High‐throughput sequencing makes it possible to evaluate thousands of genetic markers across genomes and populations. Reduced‐representation sequencing approaches, like double‐digest restriction site‐associated DNA sequencing (ddRADseq), are frequently applied to screen for genetic variation. In particular in nonmodel organisms where whole‐genome sequencing is not yet feasible, ddRADseq has become popular as it allows genomewide assessment of variation patterns even in the absence of other genomic resources. However, while many tools are available for the analysis of ddRADseq data, few options exist to simulate ddRADseq data in order to evaluate the accuracy of downstream tools. The available tools either focus on the optimization of ddRAD experiment design or do not provide the information necessary for a detailed evaluation of different ddRAD analysis tools. For this task, a ground truth, that is, the underlying information of all effects in the data set, is required. Therefore, we here present ddrage , the ddRA D Data Set Ge nerator, that allows both developers and users to evaluate their ddRAD analysis software. ddrage allows the user to adjust many parameters such as coverage and rates of mutations, sequencing errors or allelic dropouts, in order to generate a realistic simulated ddRADseq data set for given experimental scenarios and organisms. The simulated reads can be easily processed with available analysis software such as stacks or pyrad and evaluated against the underlying parameters used to generate the data to gauge the impact of different parameter values used during downstream data processing.     

Increasing the okra salt threshold value with biochar amendments

Soil salinity is a severe worldwide environmental problem that adversely affects soil properties and the crop growth such as okra. We hypothesized that biochar soil amendments could increase the okra salt threshold, alleviate salt stress and improve soil productivity. In this study, a pot experiment was conducted to investigate whether biochar could ameliorate the effects of salinity on okra plants. Three biochar amendment (BA) soil applications (0%, 5% and 10% by mass of soil) were considered for seven irrigation water salinity levels (0.75, 1.0, 2.0, 4.0, 5.0, 6.0 and 7.0?dS?m^?1) in a randomized block design with three replications. The Maas and Hoffman salt tolerance model was used to evaluate the effects of BA on okra plant growth parameters (e.g. yield, biomass) and water use efficiency for each salinity treatment. The results showed that increasing the soil salinity levels caused significant decreases in plant yields and yield components. However, biochar application rates of 5% and 10% increased the okra threshold by 19.7% and 81.2%, respectively, compared to the control (0%). The 10% biochar application rate also resulted in the greatest okra plant growth and increased yield, indicating that the effects of salt stress were ameliorated; moreover, the soil bulk density was decreased, and the water content was increased. Hence, biochar soil amendments could be considered as an important agronomic practice that could potentially overcome the adverse effects of salt stress.     

Production of some oligochaete species in large Estonian lakes

The production of Potamothrix hammoniensis, Lamprodrilus isoporus, and Uncinais uncinata was estimated in the eutrophic lakes Peipsi-Pihkva and Vôrtsjärv. Growth characteristics of these species are briefly described. Calculated production values were 6–32 (P. hammoniensis), 19–79 (L. isoporus), and 1–4 kJ m² (U. uncinata), respectively. The annual P/B ratios for the same species were, 0.8–1.7, 2.5–4.8, and 4.4–5.4, respectively.     

Propappidae and aquatic Enchytraeidae (Oligochaeta) from the farthest southeast of Russia

Two mountain streams north and northeast of Vladivostok were studied in 1983–1984. In the Komarovka Stream, a great variety of Mesenchytraeus occurred in the spring zone, among them M. crenobius sp. n. with giant setae in the ventral bundles of VI–VIII and M. vshivkovae sp. n. with numerous spermathecal diverticula. In the stream zone of the Frolovka Stream Cernosvitoviella pensau sp. n., characterized by a complicated penial bulb and a very long spermathecal ampulla, was the dominant oligochaete. Propappus arhynchotus Sokolskaya was the second most abundant oligochaete in this stream. It proved to be a true member of this genus and not synonymous with any other species. These are the first records of aquatic enchytraeids for the Primorski Region of Russia.     

Diversity of Pseudomonas Genomes,Including Populus-Associated Isolates,as Revealed by Comparative Genome Analysis

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.     

Changes in size of Baltic field voles over the last 50 years: are they really shrinking?

Using museum materials and recently trapped specimens of field voles (Microtus agrestis (Linnaeus, 1761)) from Lithuania and Estonia, we assessed temporal and latitudinal trends in body and skull size, comparing the periods 1980–1996 and 2014–2016. We measured four body and 23 skull characters, size-adjusting them using the geometric mean procedure. A pronounced decrease in the size of M. agrestis was noted in Estonia, where 23 out of 27 adjusted body and skull characters had decreased by up to 21.9%, with only the tail length, hind foot length, maximum height of mandibula excluding coronoid process and coronoid height of mandibula increasing significantly. Decreases were less marked in voles from Lithuania – most pronounced were a 6.1% decrease in adjusted body length, an 11.6% decrease in adjusted length of the braincase, a 3.85% decrease in the breadth of the braincase, measured at the widest part, a 2.9% decrease in condylobasal skull length and a 2.2% decrease in the height of the braincase. The coronoid height of the mandibula of Lithuanian individuals showed an 8.4% size increase. In both countries, the confounding effect of sex on the size changes of M. agrestis from 1980 to 2016 was much smaller than the effect of time period. Concluding, voles in Estonia became significantly smaller, while changes in the measured characters in Lithuania were heterogeneous.     

Non-canonical localization of RubisCO under high-light conditions in the toxic cyanobacterium Microcystis aeruginosa PCC7806

The frequent production of the hepatotoxin microcystin (MC) and its impact on the lifestyle of bloom-forming cyanobacteria are poorly understood. Here, we report that MC interferes with the assembly and the subcellular localization of RubisCO, in Microcystis aeruginosa PCC7806. Immunofluorescence, electron microscopic and cellular fractionation studies revealed a pronounced heterogeneity in the subcellular localization of RubisCO. At high cell density, RubisCO particles are largely separate from carboxysomes in M. aeruginosa and relocate to the cytoplasmic membrane under high-light conditions. We hypothesize that the binding of MC to RubisCO promotes its membrane association and enables an extreme versatility of the enzyme. Steady-state levels of the RubisCO CO₂ fixation product 3-phosphoglycerate are significantly higher in the MC-producing wild type. We also detected noticeable amounts of the RubisCO oxygenase reaction product secreted into the medium that may support the mutual interaction of M. aeruginosa with its heterotrophic microbial community.