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The open-source programming language R has gained a central place in the hydrological sciences over the last decade, driven by the availability of diverse hydro-meteorological data archives and the development of open-source computational tools. The growth of R's usage in hydrology is reflected in the number of newly published hydrological packages, the strengthening of online user communities, and the popularity of training courses and events. In this paper, we explore the benefits and advantages of R's usage in hydrology, such as the democratization of data science and numerical literacy, the enhancement of reproducible research and open science, the access to statistical tools, the ease of connecting R to and from other languages, and the support provided by a growing community. This paper provides an overview of a typical hydrological workflow based on reproducible principles and packages for retrieval of hydro-meteorological data, spatial analysis, hydrological modelling, statistics, and the design of static and dynamic visualizations and documents. We discuss some of the challenges that arise when using R in hydrology and useful tools to overcome them, including the use of hydrological libraries, documentation, and vignettes (long-form guides that illustrate how to use packages); the role of integrated development environments (IDEs); and the challenges of big data and parallel computing in hydrology. Lastly, this paper provides a roadmap for R's future within hydrology, with R packages as a driver of progress in the hydrological sciences, application programming interfaces (APIs) providing new avenues for data acquisition and provision, enhanced teaching of hydrology in R, and the continued growth of the community via short courses and events.

Nitrate pollution of freshwaters and methane emissions into the atmosphere are crucial factors in deteriorating the quality of drinking water and in contributing to global climate change. The n-damo (nitrite-dependent anaerobic methane oxidation), nitrate-dependent anaerobic methane oxidation and the anaerobic oxidation of ammonium (anammox) represent two microbially mediated processes that can reduce nitrogen loading of aquatic ecosystems and associated methane emissions to the atmosphere. Here, we report vertical concentration and stable-isotope profiles of CH4, NO−3, NO−2, and NH+4 in the water column of Fohnsee (lake in southern Bavaria, Germany) that may indicate linkages between denitrification, anaerobic oxidation of methane (AOM), and anammox. At a water depth from 12 to 20 m, a methane–nitrate transition zone (NMTZ) was observed, where δ13C values of methane and δ15N and δ18O of dissolved nitrate markedly increased in concert with decreasing concentrations of methane and nitrate. These data patterns, together with the results of a simple 1-D diffusion model linked with a degradation term, show that the nonlinear methane concentration profile cannot be explained by diffusion and that microbial oxidation of methane coupled with denitrification under anaerobic conditions is the most parsimonious explanation for these data trends. In the methane zone at the bottom of the NMTZ (20 to 22 m) δ15N of ammonium increased by 4 ‰, while ammonium concentrations decreased. In addition, a strong 15N enrichment of dissolved nitrate was observed at a water depth of 20 m, suggesting that anammox is occurring together with denitrification. The conversion of nitrite to N2 and nitrate during anammox is associated with an inverse N isotope fractionation and may explain the observed increasing offset (Δδ15N) of 26 ‰ between δ15N values of dissolved nitrate and nitrite at a water depth of 20 m compared to the Δδ15Nnitrate-nitrite of 11 ‰ obtained in the NMTZ at a water depth between 16 and 18 m. The associated methane concentration and stable-isotope profiles indicate that some of the denitrification may be coupled to AOM, an observation supported by an increased concentration of bacteria known to be involved in n-damo/denitrification with AOM (NC10 and Crenothrix) and anammox (“Candidatus Anammoximicrobium”) whose concentrations were highest in the methane and ammonium oxidation zones, respectively. This study shows the potential for a coupling of microbially mediated nitrate-dependent methane oxidation with anammox in stratified freshwater ecosystems, which may be important for affecting both methane emissions and nitrogen concentrations in lakes.

Background Initial characterization of the flax genome showed that Ty1 -copia retrotransposons are abundant, with several members being recently inserted, and in close association with genes. Recent insertions indicate a potential for ongoing transpositional activity that can create genomic diversity among accessions, cultivars or varieties. The polymorphisms generated constitute a good source of molecular markers that may be associated with phenotype if the insertions alter gene activity. Flax, where accessions are bred mainly for seed nutritional properties or for fibers, constitutes a good model for studying the relationship of transpositional activity with diversification and breeding. In this study, we estimated copy number and used a type of transposon display known as Sequence-Specific Amplification Polymorphisms (SSAPs), to characterize six families of Ty1- copia elements across 14 flax accessions. Polymorphic insertion sites were sequenced to find insertions that could potentially alter gene expression, and a preliminary test was performed with selected genes bearing transposable element (TE) insertions. Results Quantification of six families of Ty1 -copia elements indicated different abundances among TE families and between flax accessions, which suggested diverse transpositional histories. SSAPs showed a high level of polymorphism in most of the evaluated retrotransposon families, with a trend towards higher levels of polymorphism in low-copy number families. Ty1- copia insertion polymorphisms among cultivars allowed a general distinction between oil and fiber types, and between spring and winter types, demonstrating their utility in diversity studies. Characterization of polymorphic insertions revealed an overwhelming association with genes, with insertions disrupting exons, introns or within 1 kb of coding regions. A preliminary test on the potential transcriptional disruption by TEs of four selected genes evaluated in three different tissues, showed one case of significant impact of the insertion on gene expression. Conclusions We demonstrated that specific Ty1 -copia families have been active since breeding commenced in flax. The retrotransposon-derived polymorphism can be used to separate flax types, and the close association of many insertions with genes defines a good source of potential mutations that could be associated with phenotypic changes, resulting in diversification processes.

Plant communities are shaped by bottom-up processes such as competition for nutrients and top-down processes such as herbivory. Although much theoretical work has studied how herbivores can mediate plant species coexistence, indirect effects caused by the carnivores that consume herbivores have been largely ignored. These carnivores can have significant indirect effects on plants by altering herbivore density (density-mediated effects) and behavior (trait-mediated effects). Carnivores that differ in traits, particularly in their hunting mode, cause different indirect effects on plants and, ultimately, different plant community compositions. We analyze a food-web model to determine how plant coexistence is affected by herbivore-consuming carnivores, contrasting those causing only density-mediated effects with those causing trait-mediated effects as well. In the latter case, herbivores can adjust their consumption of a refuge plant species. We derive a general graphical model to study the interplay of density- and trait-mediated effects. We show that carnivores eliciting both effects can sustain plant species coexistence, given intermediate intensities of behavioral adjustments. Coexistence is more likely, and more stable, if the refuge plant is competitively dominant. These results extend our understanding of carnivore indirect effects in food webs and show that behavioral effects can have major consequences on plant community structure, stressing the need for theoretical approaches that incorporate dynamical traits.

Genotype by genotype indirect genetic effects (G x G IGEs) occur when the phenotype of an individual is influenced by an interaction between its own genotype and those of neighbour individuals. Little is known regarding the relative importance of G x G IGEs compared with other forms of direct and indirect genetic effects. We quantified the relative importance of IGEs in the filamentous fungus Aspergillus nidulans, a species in which IGEs are likely to be important as air-borne social interactions are known to affect growth. We used a collection of distantly related wild isolates, lab strains and a set of closely related mutation accumulation lines to estimate the contribution of direct and indirect genetic effects on mycelium growth rate, a key fitness component. We found that indirect genetic effects were dominated by G x G IGEs that occurred primarily between a focal genotype and its immediate neighbour within a vertical stack, and these accounted for 11% of phenotypic variation. These results indicate that G x G IGEs may be substantial, at least in some systems, and that the evolutionary importance of these interactions may be underappreciated, especially in microbes. We advocate for a wider use of the IGE framework in both applied (for example, choice of varietal mixtures in plant breeding) and evolutionary genetics (kin selection/kin competition studies).

Ongoing intensification and specialisation of livestock production lead to increasing volumes of manure to be managed, which are a source of the greenhouse gases (GHGs) methane (CH4) and nitrous oxide (N2O). Net emissions of CH4 and N2O result from a multitude of microbial activities in the manure environment. Their relative importance depends not only on manure composition and local management practices with respect to treatment, storage and field application, but also on ambient climatic conditions. The diversity of livestock production systems, and their associated manure management, is discussed on the basis of four regional cases (Sub-Saharan Africa, Southeast Asia, China and Europe) with increasing levels of intensification and priorities with respect to nutrient management and environmental regulation. GHG mitigation options for production systems based on solid and liquid manure management are then presented, and potentials for positive and negative interactions between pollutants, and between management practices, are discussed. The diversity of manure properties and environmental conditions necessitate a modelling approach for improving estimates of GHG emissions, and for predicting effects of management changes for GHG mitigation, and requirements for such a model are discussed. Finally, we briefly discuss drivers for, and barriers against, introduction of GHG mitigation measures for livestock production. There is no conflict between efforts to improve food and feed production, and efforts to reduce GHG emissions from manure management. Growth in livestock populations are projected to occur mainly in intensive production systems where, for this and other reasons, the largest potentials for GHG mitigation may be found.