Environmental Dissolved Organic Matter Governs Biofilm Formation and Subsequent Linuron Degradation Activity of a Linuron-Degrading Bacterial Consortium

It was examined whether biofilm growth on dissolved organic matter (DOM) of a three-species consortium whose members synergistically degrade the phenylurea herbicide linuron affected the consortium''s integrity and subsequent linuron-degrading functionality. Citrate as a model DOM and three environmental DOM (eDOM) formulations of different quality were used. Biofilms developed with all DOM formulations, and the three species were retained in the biofilm. However, biofilm biomass, species composition, architecture, and colocalization of member strains depended on DOM and its biodegradability. To assess the linuron-degrading functionality, biofilms were subsequently irrigated with linuron at 10 mg liter⁻¹ or 100 μg liter⁻¹. Instant linuron degradation, the time needed to attain maximal linuron degradation, and hence the total amount of linuron removed depended on both the DOM used for growth and the linuron concentration. At 10 mg liter⁻¹, the final linuron degradation efficiency was as high as previously observed without DOM except for biofilms fed with humic acids which did not degrade linuron. At 100 μg liter⁻¹ linuron, DOM-grown biofilms degraded linuron less efficiently than biofilms receiving 10 mg liter⁻¹ linuron. The amount of linuron removed was more correlated with biofilm species composition than with biomass or structure. Based on visual observations, colocalization of consortium members in biofilms after the DOM feed appears essential for instant linuron-degrading activity and might explain the differences in overall linuron degradation. The data show that DOM quality determines biofilm structure and composition of the pesticide-degrading consortium in periods with DOM as the main carbon source and can affect subsequent pesticide-degrading activity, especially at micropollutant concentrations.     

Selfing for the design of genomic selection experiments in biparental plant populations

Self-fertilization (selfing) is commonly used for population development in plant breeding, and it is well established that selfing increases genetic variance between lines, thus increasing response to phenotypic selection. Furthermore, numerous studies have explored how selfing can be deployed to maximal benefit in the context of traditional plant breeding programs (Cornish in Heredity 65:201–211,1990a, Heredity 65:213–220,1990b; Liu et al. in Theor Appl Genet 109:370–376, 2004; Pooni and Jinks in Heredity 54:255–260, 1985). However, the impact of selfing on response to genomic selection has not been explored. In the current study we examined how selfing impacts the two key aspects of genomic selection—GEBV prediction (training) and selection response. We reach the following conclusions: (1) On average, selfing increases genomic selection gains by more than 70 %. (2) The gains in genomic selection response attributable to selfing hold over a wide range population sizes (100–500), heritabilities (0.2–0.8), and selection intensities (0.01–0.1). However, the benefits of selfing are dramatically reduced as the number of QTLs drops below 20. (3) The major cause of the improved response to genomic selection with selfing is through an increase in the occurrence of superior genotypes and not through improved GEBV predictions. While performance of the training population improves with selfing (especially with low heritability and small population sizes), the magnitude of these improvements is relatively small compared with improvements observed in the selection population. To illustrate the value of these insights, we propose a practical genomic selection scheme that substantially shortens the number of generations required to fully capture the benefits of selfing. Specifically, we provide simulation evidence that indicates the proposed scheme matches or exceeds the selection gains observed in advanced populations (i.e. F ₈ and doubled haploid) across a broad range of heritability and QTL models. Without sacrificing selection gains, we also predict that fully inbred candidates for potential commercialization can be identified as early as the F ₄ generation.     

Fluorometric Quantification of Polyphosphate in Environmental Plankton Samples: Extraction Protocols,Matrix Effects,and Nucleic Acid Interference

Polyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4′,6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.     

Trophodynamics and functional feeding groups of North Sea fauna: a combined stable isotope and fatty acid approach

The trophodynamics of pelagic and benthic animals of the North Sea, North Atlantic shelf, were assessed using stable isotope analysis (SIA) of natural abundance carbon and nitrogen isotopes, lipid fingerprinting and compound-specific SIA (CSIA) of phospholipid-derived fatty acids (PLFAs). Zooplankton (z), epi- and supra-benthic macrofauna were collected in the Southern Bight, at the Oyster Grounds and at North Dogger, 111 km north of the Dogger Bank. The study included 22 taxonomic groups with particular reference to Mollusca (Bivalvia and Gastropoda) and Crustacea. Primary consumers (Bivalvia) were overall most ¹⁵N enriched in the southern North Sea (6.1‰) and more depleted in the Oyster Grounds (5.5‰) and at North Dogger (2.8‰) demonstrating differences in isotopic baselines for bivalve fauna between the study sites. Higher trophic levels also followed this trend. Over an annual cycle, consumers tended to exhibit ¹⁵N depletion during spring followed by ¹⁵N enriched signatures in autumn and winter. The observed seasonal changes of δ ¹⁵N were more pronounced for suspension feeders and deposit feeders (dfs) than for filter feeders (ffs). The position of animals in plots of δ ¹³C and δ ¹⁵N largely concurred with the expected position according to literature-based functional feeding groups. PLFA fingerprints of groups such as z were distinct from benthic groups, e.g. benthic ffs and dfs, and predatory macrobenthos. δ ¹³C_PLFA signatures indicated similarities in ¹³C moiety sources that constituted δ ¹³C_PLFA. Although functional groups of pelagic zooplankton and (supra-) benthic animals represented phylogenetically distinct consumer groups, δ ¹³C_PLFA demonstrated that both groups were supported by pelagic primary production and relied on the same macronutrients such as PLFAs. Errors related to the static categorization of small invertebrates into fixed trophic positions defined by phylogenetic groupings rather than by functional feeding groups, and information on seasonal trophodynamic variability, may have implications for the reliability of numerical marine ecosystem models.     

Leaf litter inputs decrease phosphate sorption in a strongly weathered tropical soil over two time scales

In strongly weathered soils, leaf litter not only returns phosphorus (P) to the soil environment, it may also modify soil properties and soil solution chemistry, with the potential to decrease phosphate sorption and increase plant available P. Using a radioactive phosphate tracer (³²P) and 1 h laboratory incubations we investigated the effect of litter inputs on phosphate sorption over two time scales: (1) long-term field litter manipulations (litter addition, control and litter removal) and (2) pulses of litter leachate (i.e. water extracts of leaf litter) from five species. Leachate pulse effects were compared to a simulated throughfall, which served as a control solution. Soil receiving long-term doubling of leaf litter maintained five-fold more phosphate in solution than the litter removal soil. In addition to the quantity of phosphate sorbed, the field litter addition treatment decreased the strength of phosphate sorption, as evaluated through extraction of sorbed ³²P using a weakly acidic ammonium fluoride solution (Bray 1). In litter removal soil, leachate pulses significantly reduced phosphate sorption in comparison to the throughfall control for all five species evaluated. However, the ability of leachate pulses to reduce phosphate sorption decreased when soil had received field litter inputs. Across soils the effect of leachate pulses on phosphate sorption increased with net sorption of dissolved organic C, with the exception of leachate from one species that had a higher index of aromatic C concentration. These results demonstrate that litter inputs, as both long-term inputs and short-term leachate pulses, can decrease the quantity and strength of phosphate sorption, which may increase the biological availability of this key nutrient.     

Drosophila pupal macrophages – A versatile tool for combined ex vivo and in vivo imaging of actin dynamics at high resolution

Molecular understanding of actin dynamics requires a genetically traceable model system that allows live cell imaging together with high-resolution microscopy techniques. Here, we used Drosophila pupal macrophages that combine many advantages of cultured cells with a genetic in vivo model system. Using structured illumination microscopy together with advanced spinning disk confocal microscopy we show that these cells provide a powerful system for single gene analysis. It allows forward genetic screens to characterize the regulatory network controlling cell shape and directed cell migration in a physiological context. We knocked down components regulating lamellipodia formation, including WAVE, single subunits of Arp2/3 complex and CPA, one of the two capping protein subunits and demonstrate the advantages of this model system by imaging mutant macrophages ex vivo as well as in vivo upon laser-induced wounding.     

Dimensions of Animal Personalities in Guinea Pigs

Behavioural phenotypes can be studied from a variety of perspectives. Recent developments have focused on the individual, seeking patterns of behaviour that are stable over time and/or across different contexts (animal personalities). This study applied this method of understanding individual behavioural variability to domestic guinea pigs. Two behavioural domains were investigated: emotionality and social behaviour. Additionally, individual cortisol–stress reactivity and dominance status were examined. Adult male domestic guinea pigs living in large mixed‐sex colonies were subjected to a series of behavioural and physiological tests twice with an intertest interval of 8 wk. Individual consistency over time was found regarding social behaviour, cortisol reactivity and dominance status, whereas no stability regarding emotional behaviour was detected. Furthermore, no stability over contexts was found. Our results suggest that the concept of animal personality is applicable to domestic guinea pigs. The ecological relevance of these data is underscored by the fact that they were obtained in animals from a very rich, socially complex scenario. Moreover, our study highlights that behaviour alone is not sufficient to describe individual phenotypic consistency. Physiological parameters such as stress reactivity should be included in animal personality research. Furthermore dominance – a relative measure which is not an absolute attribute of individuals – proved to be stable over time and thus also shed light on individuality.     

A PARAMETRIC METHOD FOR ASSESSING DIVERSIFICATION‐RATE VARIATION IN PHYLOGENETIC TREES

Phylogenetic hypotheses are frequently used to examine variation in rates of diversification across the history of a group. Patterns of diversification‐rate variation can be used to infer underlying ecological and evolutionary processes responsible for patterns of cladogenesis. Most existing methods examine rate variation through time. Methods for examining differences in diversification among groups are more limited. Here, we present a new method, parametric rate comparison (PRC), that explicitly compares diversification rates among lineages in a tree using a variety of standard statistical distributions. PRC can identify subclades of the tree where diversification rates are at variance with the remainder of the tree. A randomization test can be used to evaluate how often such variance would appear by chance alone. The method also allows for comparison of diversification rate among a priori defined groups. Further, the application of the PRC method is not restricted to monophyletic groups. We examined the performance of PRC using simulated data, which showed that PRC has acceptable false‐positive rates and statistical power to detect rate variation. We apply the PRC method to the well‐studied radiation of North American Plethodon salamanders, and support the inference that the large‐bodied Plethodon glutinosus clade has a higher historical rate of diversification compared to other Plethodon salamanders.