Understanding temporal variability across trophic levels and spatial scales in freshwater ecosystems.

A tenet of ecology is that temporal variability in ecological structure and processes tends to decrease with increasing spatial scales (from locales to regions) and levels of biological organization (from populations to communities). However, patterns in temporal variability across trophic levels and the mechanisms that produce them remain poorly understood. Here we analyzed the abundance time series of spatially structured communities (i.e., metacommunities) spanning basal resources to top predators from 355 freshwater sites across three continents. Specifically, we used a hierarchical partitioning method to disentangle the propagation of temporal variability in abundance across spatial scales and trophic levels. We then used structural equation modeling to determine if the strength and direction of relationships between temporal variability, synchrony, biodiversity, and environmental and spatial settings depended on trophic level and spatial scale. We found that temporal variability in abundance decreased from producers to tertiary consumers but did so mainly at the local scale. Species population synchrony within sites increased with trophic level, whereas synchrony among communities decreased. At the local scale, temporal variability in precipitation and species diversity were associated with population variability (linear partial coefficient, ß = 0.23) and population synchrony (ß = -0.39) similarly across trophic levels, respectively. At the regional scale, community synchrony was not related to climatic or spatial predictors, but the strength of relationships between metacommunity variability and community synchrony decreased systematically from top predators (ß = 0.73) to secondary consumers (ß = 0.54), to primary consumers (ß = 0.30) to producers (ß = 0). Our results suggest that mobile predators may often stabilize metacommunities by buffering variability that originates at the base of food webs. This finding illustrates that the trophic structure of metacommunities, which integrates variation in organismal body size and its correlates, should be considered when investigating ecological stability in natural systems. More broadly, our work advances the notion that temporal stability is an emergent property of ecosystems that may be threatened in complex ways by biodiversity loss and habitat fragmentation.

A global agenda for advancing freshwater biodiversity research.

Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

The application of metacommunity theory to the management of riverine ecosystems.

River managers strive to use the best available science to sustain biodiversity and ecosystem function. To achieve this goal requires consideration of processes at different scales. Metacommunity theory describes how multiple species from different communities potentially interact with local-scale environmental drivers to influence population dynamics and community structure. However, this body of knowledge has only rarely been used to inform management practices for river ecosystems. In this paper, we present a conceptual model outlining how the metacommunity processes of local niche sorting and dispersal can influence the outcomes of management interventions and provide a series of specific recommendations for applying these ideas as well as research needs. In all cases, we identify situations where traditional approaches to riverine management could be enhanced by incorporating an understanding of metacommunity dynamics. A common theme is developing guidelines for assessing the metacommunity context of a site or region, evaluating how that context may affect the desired outcome, and incorporating that understanding into the planning process and methods used. To maximize the effectiveness of management activities, scientists and resource managers should update the toolbox of approaches to riverine management to reflect theoretical advances in metacommunity ecology.

Genome-enabled discovery of anthraquinone biosynthesis in Senna tora.

Senna tora is a widely used medicinal plant. Its health benefits have been attributed to the large quantity of anthraquinones, but how they are made in plants remains a mystery. To identify the genes responsible for plant anthraquinone biosynthesis, we reveal the genome sequence of S. tora at the chromosome level with 526 Mb (96%) assembled into 13 chromosomes. Comparison among related plant species shows that a chalcone synthase-like (CHS-L) gene family has lineage-specifically and rapidly expanded in S. tora. Combining genomics, transcriptomics, metabolomics, and biochemistry, we identify a CHS-L gene contributing to the biosynthesis of anthraquinones. The S. tora reference genome will accelerate the discovery of biologically active anthraquinone biosynthesis pathways in medicinal plants.

Genome-Wide Association and Prediction of Traits Related to Salt Tolerance in Autotetraploid Alfalfa (Medicago sativa L.).

Soil salinity is a growing problem in world production agriculture. Continued improvement in crop salt tolerance will require the implementation of innovative breeding strategies such as marker-assisted selection (MAS) and genomic selection (GS). Genetic analyses for yield and vigor traits under salt stress in alfalfa breeding populations with three different phenotypic datasets was assessed. Genotype-by-sequencing (GBS) developed markers with allele dosage and phenotypic data were analyzed by genome-wide association studies (GWAS) and GS using different models. GWAS identified 27 single nucleotide polymorphism (SNP) markers associated with salt tolerance. Mapping SNPs markers against the Medicago truncatula reference genome revealed several putative candidate genes based on their roles in response to salt stress. Additionally, eight GS models were used to estimate breeding values of the training population under salt stress. Highest prediction accuracies and root mean square errors were used to determine the best prediction model. The machine learning methods (support vector machine and random forest) performance best with the prediction accuracy of 0.793 for yield. The marker loci and candidate genes identified, along with optimized GS prediction models, were shown to be useful in improvement of alfalfa with enhanced salt tolerance. DNA markers and the outcome of the GS will be made available to the alfalfa breeding community in efforts to accelerate genetic gains, in the development of biotic stress tolerant and more productive modern-day alfalfa cultivars.

Reduction of taxonomic bias in diatom species data.

Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts five elements of sample preparation, taxon identification and enumeration, and quality control (QC) samples. We used six independent datasets to assess the effect of the adjustments on analytical outcomes. The first dataset was produced by five analysts from three laboratories following a standard protocol (Charles et al. 2002). The remaining datasets were produced by 2-3 analysts in 1-3 laboratories following a revised protocol. The revised protocol included the following modifications: 1) use of Battarbee settling chambers to prepare coverslips, 2) development of coordinated pre-count voucher floras based on morphological operational taxonomic units (mOTUs), 3) random assignment of samples to analysts, 4) post-count identification and documentation of taxa, and 5) increased QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.

Genetic Loci Associated with Salt Tolerance in Advanced Breeding Populations of Tetraploid Alfalfa Using Genome-Wide Association Studies.

Many agricultural lands in the western United States consist of soil with high concentrations of salt, which is detrimental to alfalfa ( L.) growth and production, especially in the region where water resource is limited. Developing alfalfa varieties with salt tolerance is imperative for sustainable production under increasing soil salinity. In the present study, we used advanced alfalfa breeding populations and evaluated five traits related to salt tolerance including biomass dry weight (DW) and fresh weight (FW), plant height (PH), leaf relative water content (RWC), and stomatal conductance (SC) under control and salt stress. Stress susceptibility index (SSI) of each trait and single-nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) were used for genome-wide association studies (GWAS) to identify loci associated with salt tolerance. A total of 53 significant SNPs associated with salt tolerance were identified and they were located at 49 loci through eight chromosomes. A Basic Local Alignment Search Tool (BLAST) search of the regions surrounding the SNPs revealed 21 putative candidate genes associated with salt tolerance. The genetic architecture for traits related to salt tolerance characterized in this report could help in understanding the genetic mechanism by which salt stress affects plant growth and production in alfalfa. The markers and candidate genes identified in the present study would be useful for marker-assisted selection (MAS) in breeding salt-tolerant alfalfa after validation of the markers.

Reintroduction of freshwater macroinvertebrates: challenges and opportunities.

Species reintroductions - the translocation of individuals to areas in which a species has been extirpated with the aim of re-establishing a self-sustaining population - have become a widespread practice in conservation biology. Reintroduction projects have tended to focus on terrestrial vertebrates and, to a lesser extent, fishes. Much less effort has been devoted to the reintroduction of invertebrates into restored freshwater habitats. Yet, reintroductions may improve restoration outcomes in regions where impoverished regional species pools limit the self-recolonisation of restored freshwaters. We review the available literature on macroinvertebrate reintroductions, focusing on identifying the intrinsic and extrinsic factors that determine their success or failure. Our study reveals that freshwater macroinvertebrate reintroductions remain rare, are often published in the grey literature and, of the attempts made, approximately one-third fail. We identify life-cycle complexity and remaining stressors as the two factors most likely to affect reintroduction success, illustrating the unique challenges of freshwater macroinvertebrate reintroductions. Consideration of these factors by managers during the planning process and proper documentation - even if a project fails - may increase the likelihood of successful outcomes in future reintroduction attempts of freshwater macroinvertebrates.

Predicting current and future background ion concentrations in German surface water under climate change.

Salinization of surface waters is a global environmental issue that can pose a regional risk to freshwater organisms, potentially leading to high environmental and economic costs. Global environmental change including climate and land use change can increase the transport of ions into surface waters. We fit both multiple linear regression (LR) and random forest (RF) models on a large spatial dataset to predict Ca2+ (266 sites), Mg2+ (266 sites), and [Formula: see text] (357 sites) ion concentrations as well as electrical conductivity (EC-a proxy for total dissolved solids with 410 sites) in German running water bodies. Predictions in both types of models were driven by the major factors controlling salinity including geologic and soil properties, climate, vegetation and topography. The predictive power of the two types of models was very similar, with RF explaining 71-76% of the spatial variation in ion concentrations and LR explaining 70-75% of the variance. Mean squared errors for predictions were all smaller than 0.06. The factors most strongly associated with stream ion concentrations varied among models but rock chemistry and climate were the most dominant. The RF model was subsequently used to forecast the changes in EC that were likely to occur for the period of 2070 to 2100 in response to just climate change-i.e. no additional effects of other anthropogenic activities. The future forecasting shows approximately 10% and 15% increases in mean EC for representative concentration pathways 2.6 and 8.5 (RCP2.6 and RCP8.5) scenarios, respectively.This article is part of the theme issue 'Salt in freshwaters: causes, ecological consequences and future prospects'.

Landscape heterogeneity strengthens the relationship between ß-diversity and ecosystem function.

Consensus has emerged in the literature that increased biodiversity enhances the capacity of ecosystems to perform multiple functions. However, most biodiversity/ecosystem function studies focus on a single ecosystem, or on landscapes of homogenous ecosystems. Here, we investigate how increased landscape-level environmental dissimilarity may affect the relationship between different metrics of diversity (α, ß, or γ) and ecosystem function. We produced a suite of simulated landscapes, each of which contained four experimental outdoor aquatic mesocosms. Differences in temperature and nutrient conditions of the mesocosms allowed us to simulate landscapes containing a range of within-landscape environmental heterogeneities. We found that the variation in ecosystem functions was primarily controlled by environmental conditions, with diversity metrics accounting for a smaller (but significant) amount of variation in function. When landscapes were more homogeneous, α, ß, and γ diversity was not associated with differences in primary production, and only γ was associated with changes in decomposition. In these homogeneous landscapes, differences in these two ecosystem functions were most strongly related to nutrient and temperature conditions in the ecosystems. However, as landscape-level environmental dissimilarity increased, the relationship between α, ß, or γ and ecosystem functions strengthened, with ß being a greater predictor of variation in decomposition at the highest levels of environmental dissimilarity than α or γ. We propose that when all ecosystems in a landscape have similar environmental conditions, species sorting is likely to generate a single community composition that is well suited to those environmental conditions, ß is low, and the efficiency of diversity-ecosystem function couplings is similar across communities. Under this low ß, the effect of abiotic conditions on ecosystem function will be most apparent. However, when environmental conditions vary among ecosystems, species sorting pressures are different among ecosystems, producing different communities among locations in a landscape. These conditions lead to stronger relationships between ß and the magnitude of ecosystem functions. Our results illustrate that abiotic conditions and the homogeneity of communities influence ecosystem function expressed at the landscape scale.

Thermal and hydrologic responses to climate change predict marked alterations in boreal stream invertebrate assemblages.

Air temperature at the northernmost latitudes is predicted to increase steeply and precipitation to become more variable by the end of the 21st century, resulting in altered thermal and hydrological regimes. We applied five climate scenarios to predict the future (2070-2100) benthic macroinvertebrate assemblages at 239 near-pristine sites across Finland (ca. 1200 km latitudinal span). We used a multitaxon distribution model with air temperature and modeled daily flow as predictors. As expected, projected air temperature increased the most in northernmost Finland. Predicted taxonomic richness also increased the most in northern Finland, congruent with the predicted northwards shift of many species' distributions. Compositional changes were predicted to be high even without changes in richness, suggesting that species replacement may be the main mechanism causing climate-induced changes in macroinvertebrate assemblages. Northern streams were predicted to lose much of the seasonality of their flow regimes, causing potentially marked changes in stream benthic assemblages. Sites with the highest loss of seasonality were predicted to support future assemblages that deviate most in compositional similarity from the present-day assemblages. Macroinvertebrate assemblages were also predicted to change more in headwaters than in larger streams, as headwaters were particularly sensitive to changes in flow patterns. Our results emphasize the importance of focusing protection and mitigation on headwater streams with high-flow seasonality because of their vulnerability to climate change.

An eFP browser for visualizing strawberry fruit and flower transcriptomes.

Wild strawberry Fragaria vesca is emerging as an important model system for the cultivated strawberry due to its diploid genome and availability of extensive transcriptome data and a range of molecular genetic tools. Being able to better utilize these tools, especially the transcriptome data, will greatly facilitate research progress in strawberry and other Rosaceae fruit crops. The electronic fluorescent pictograph (eFP) software is a useful and popular tool to display transcriptome data visually, and is widely used in other model organisms including Arabidopsis and mouse. Here we applied eFP to display wild strawberry RNA sequencing (RNA-seq) data from 42 different tissues and stages, including various flower and fruit developmental stages. In addition, we generated eight additional RNA-seq data sets to represent tissues from ripening-stage receptacle fruit from yellow-colored and red-colored wild strawberry varieties. Differential gene expression analysis between these eight data sets provides additional information for understanding fruit-quality traits. Together, this work greatly facilitates the utility of the extensive transcriptome data for investigating strawberry flower and fruit development as well as fruit-quality traits.

Global synthesis of the temperature sensitivity of leaf litter breakdown in streams and rivers.

Streams and rivers are important conduits of terrestrially derived carbon (C) to atmospheric and marine reservoirs. Leaf litter breakdown rates are expected to increase as water temperatures rise in response to climate change. The magnitude of increase in breakdown rates is uncertain, given differences in litter quality and microbial and detritivore community responses to temperature, factors that can influence the apparent temperature sensitivity of breakdown and the relative proportion of C lost to the atmosphere vs. stored or transported downstream. Here, we synthesized 1025 records of litter breakdown in streams and rivers to quantify its temperature sensitivity, as measured by the activation energy (Ea , in eV). Temperature sensitivity of litter breakdown varied among twelve plant genera for which Ea could be calculated. Higher values of Ea were correlated with lower-quality litter, but these correlations were influenced by a single, N-fixing genus (Alnus). Ea values converged when genera were classified into three breakdown rate categories, potentially due to continual water availability in streams and rivers modulating the influence of leaf chemistry on breakdown. Across all data representing 85 plant genera, the Ea was 0.34 ± 0.04 eV, or approximately half the value (0.65 eV) predicted by metabolic theory. Our results indicate that average breakdown rates may increase by 5-21% with a 1-4 °C rise in water temperature, rather than a 10-45% increase expected, according to metabolic theory. Differential warming of tropical and temperate biomes could result in a similar proportional increase in breakdown rates, despite variation in Ea values for these regions (0.75 ± 0.13 eV and 0.27 ± 0.05 eV, respectively). The relative proportions of gaseous C loss and organic matter transport downstream should not change with rising temperature given that Ea values for breakdown mediated by microbes alone and microbes plus detritivores were similar at the global scale.

Genome-scale DNA variant analysis and functional validation of a SNP underlying yellow fruit color in wild strawberry.

Fragaria vesca is a species of diploid strawberry being developed as a model for the octoploid garden strawberry. This work sequenced and compared the genomes of three F. vesca accessions: 'Hawaii 4', 'Rügen', and 'Yellow Wonder'. Genome-scale analyses of shared and distinct SNPs among these three accessions have revealed that 'Rügen' and 'Yellow Wonder' are more similar to each other than they are to 'Hawaii 4'. Though all three accessions are inbred seven generations, each accession still possesses extensive heterozygosity, highlighting the inherent differences between individual plants even of the same accession. The identification of the impact of each SNP as well as the large number of Indel markers provides a foundation for locating candidate mutations underlying phenotypic variations among these F. vesca accessions and for mapping new mutations generated through forward genetics screens. Through systematic analysis of SNP variants affecting genes in anthocyanin biosynthesis and regulation, a candidate SNP in FveMYB10 was identified and then functionally confirmed to be responsible for the yellow color fruits made by many F. vesca accessions. As a whole, this study provides further resources for F. vesca and establishes a foundation for linking traits of economic importance to specific genes and variants.

A model for an early role of auxin in Arabidopsis gynoecium morphogenesis.

The female reproductive organ of angiosperms, the gynoecium, often consists of the fusion of multiple ovule-bearing carpels. It serves the important function of producing and protecting ovules as well as mediating pollination. The gynoecium has likely contributed to the tremendous success of angiosperms over their 160 million year history. In addition, being a highly complex plant organ, the gynoecium is well suited to serving as a model system for use in the investigation of plant morphogenesis and development. The longstanding model of gynoecium morphogenesis in Arabidopsis holds that apically localized auxin biosynthesis in the gynoecium results in an apical to basal gradient of auxin that serves to specify along its length the development of style, ovary, and gynophore in a concentration-dependent manner. This model is based primarily on the observed effects of the auxin transport blocker N-1-naphthylphthalamic acid (NPA) as well as analyses of mutants of Auxin Response Factor (ARF) 3/ETTIN (ETT). Both NPA treatment and ett mutation disrupt gynoecium morphological patterns along the apical-basal axis. More than a decade after the model's initial proposal, however, the auxin gradient on which the model critically depends remains elusive. Furthermore, multiple observations are inconsistent with such an auxin-gradient model. Chiefly, the timing of gynoecium emergence and patterning occurs at a very early stage when the organ has little-to-no apical-basal dimension. Based on these observations and current models of early leaf patterning, we propose an alternate model for gynoecial patterning. Under this model, the action of auxin is necessary for the early establishment of adaxial-abaxial patterning of the carpel primordium. In this case, the observed gynoecial phenotypes caused by NPA and ett are due to the disruption of this early adaxial-abaxial patterning of the carpel primordia. Here we present the case for this model based on recent literature and current models of leaf development.

Increased male reproductive success in Ts65Dn "Down syndrome" mice.

The Ts65Dn mouse is trisomic for orthologs of about half the genes on Hsa21. A number of phenotypes in these trisomic mice parallel those in humans with trisomy 21 (Down syndrome), including cognitive deficits due to hippocampal malfunction that are sufficiently similar to human that "therapies" developed in Ts65Dn mice are making their way to human clinical trials. However, the impact of the model is limited by availability. Ts65Dn cannot be completely inbred and males are generally considered to be sterile. Females have few, small litters and they exhibit poor care of offspring, frequently abandoning entire litters. Here we report identification and selective breeding of rare fertile males from two working colonies of Ts65Dn mice. Trisomic offspring can be propagated by natural matings or by in vitro fertilization (IVF) to produce large cohorts of closely related siblings. The use of a robust euploid strain as recipients of fertilized embryos in IVF or as the female in natural matings greatly improves husbandry. Extra zygotes cultured to the blastocyst stage were used to create trisomic and euploid embryonic stem (ES) cells from littermates. We developed parameters for cryopreserving sperm from Ts65Dn males and used it to produce trisomic offspring by IVF. Use of cryopreserved sperm provides additional flexibility in the choice of oocyte donors from different genetic backgrounds, facilitating rapid production of complex crosses. This approach greatly increases the power of this important trisomic model to interrogate modifying effects of trisomic or disomic genes that contribute to trisomic phenotypes.

Assessing macroinvertebrate biodiversity in freshwater ecosystems: advances and challenges in DNA-based approaches.

Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics.

Lubiprostone activates non-CFTR-dependent respiratory epithelial chloride secretion in cystic fibrosis mice.

Periciliary fluid balance is maintained by the coordination of sodium and chloride channels in the apical membranes of the airways. In the absence of the cystic fibrosis transmembrane regulator (CFTR), chloride secretion is diminished and sodium reabsorption exaggerated. ClC-2, a pH- and voltage-dependent chloride channel, is present on the apical membranes of airway epithelial cells. We hypothesized that ClC-2 agonists would provide a parallel pathway for chloride secretion. Using nasal potential difference (NPD) measurements, we quantified lubiprostone-mediated Cl(-) transport in sedated cystic fibrosis null (gut-corrected), C57Bl/6, and A/J mice during nasal perfusion of lubiprostone (a putative ClC-2 agonist). Baseline, amiloride-inhibited, chloride-free gluconate-substituted Ringer with amiloride and low-chloride Ringer plus lubiprostone (at increasing concentrations of lubiprostone) were perfused, and the NPD was continuously recorded. A clear dose-response relationship was detected in all murine strains. The magnitude of the NPD response to 20 muM lubiprostone was -5.8 +/- 2.1 mV (CF, n = 12), -8.1 +/- 2.6 mV (C57Bl/6 wild-type, n = 12), and -5.3 +/- 1.2 mV (AJ wild-type, n = 8). A cohort of ClC-2 knockout mice did not respond to 20 muM lubiprostone (n = 6, P = 0.27). In C57Bl/6 mice, inhibition of CFTR with topical application of CFTR inhibitor-172 did not abolish the lubiprostone response, thus confirming the response seen is independent of CFTR regulation. RT-PCR confirmed expression of ClC-2 mRNA in murine lung homogenate. The direct application of lubiprostone in the CF murine nasal airway restores nearly normal levels of chloride secretion in nasal epithelia.