Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale

Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plantassociated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature

Bottom-up effects of plant diversity on multitrophic interactions in a biodiversity experiment

Biodiversity is rapidly declining1, and this may negatively affect ecosystem processes, including economically important ecosystem services. Previous studies have shown that biodiversity has positive effects on organisms and processes4 across trophic levels. However, only a few studies have so far incorporated an explicit food-web perspective. In an eight-year biodiversity experiment, we studied an unprecedented range of above- and below-ground organisms and multitrophic interactions. A multitrophic data set originating from a single long-term experiment allows mechanistic insights that would not be gained from meta-analysis of different experiments. Here we show that plant diversity effects dampen with increasing trophic level and degree of omnivory. This was true both for abundance and species richness of organisms. Furthermore, we present comprehensive above-ground/below-ground biodiversity food webs. Both above ground and below ground, herbivores responded more strongly to changes in plant diversity than did carnivores or omnivores. Density and richness of carnivorous taxa was independent of vegetation structure. Below-ground responses to plant diversity were consistently weaker than above-ground responses. Responses to increasing plant diversity were generally positive, but were negative for biological invasion, pathogen infestation and hyperparasitism. Our results suggest that plant diversity has strong bottom-up effects on multitrophic interaction networks, with particularly strong effects on lower trophic levels. Effects on higher trophic levels are indirectly mediated through bottom-up trophic cascades

Biodiversity–multifunctionality relationships depend on identity and number of measured functions

Biodiversity ensures ecosystem functioning and provisioning of ecosystem services, but it remains unclear how biodiversity–ecosystem multifunctionality relationships depend on the identity and number of functions considered. Here, we demonstrate that ecosystem multifunctionality, based on 82 indicator variables of ecosystem functions in a grassland biodiversity experiment, increases strongly with increasing biodiversity. Analysing subsets of functions showed that the effects of biodiversity on multifunctionality were stronger when more functions were included and that the strength of the biodiversity effects depended on the identity of the functions included. Limits to multifunctionality arose from negative correlations among functions and functions that were not correlated with biodiversity. Our findings underline that the management of ecosystems for the protection of biodiversity cannot be replaced by managing for particular ecosystem functions or services and emphasize the need for specific management to protect biodiversity. More plant species from the experimental pool of 60 species contributed to functioning when more functions were considered. An individual contribution to multifunctionality could be demonstrated for only a fraction of the species

Biodiversity–multifunctionality relationships depend on identity and number of measured functions

Biodiversity ensures ecosystem functioning and provisioning of ecosystem services, but it remains unclear how biodiversity–ecosystem multifunctionality relationships depend on the identity and number of functions considered. Here, we demonstrate that ecosystem multifunctionality, based on 82 indicator variables of ecosystem functions in a grassland biodiversity experiment, increases strongly with increasing biodiversity. Analysing subsets of functions showed that the effects of biodiversity on multifunctionality were stronger when more functions were included and that the strength of the biodiversity effects depended on the identity of the functions included. Limits to multifunctionality arose from negative correlations among functions and functions that were not correlated with biodiversity. Our findings underline that the management of ecosystems for the protection of biodiversity cannot be replaced by managing for particular ecosystem functions or services and emphasize the need for specific management to protect biodiversity. More plant species from the experimental pool of 60 species contributed to functioning when more functions were considered. An individual contribution to multifunctionality could be demonstrated for only a fraction of the species

Effects of biodiversity strengthen over time as ecosystem functioning declines at low and increases at high biodiversity

Human-caused declines in biodiversity have stimulated intensive research on the consequences of biodiversity loss for ecosystem services and policy initiatives to preserve the functioning of ecosystems. Short-term biodiversity experiments have documented positive effects of plant species richness on many ecosystem functions, and longer-term studies indicate, for some ecosystem functions, that biodiversity effects can become stronger over time. Theoretically, a biodiversity effect can strengthen over time by an increasing performance of high-diversity communities, by a decreasing performance of low-diversity communities, or a combination of both processes. Which of these two mechanisms prevail, and whether the increase in the biodiversity effect over time is a general property of many functions remains currently unclear. These questions are an important knowledge gap as a continuing decline in the performance of low-diversity communities would indicate an ecosystem-service debt resulting from delayed effects of species loss on ecosystem functioning. Conversely, an increased performance of high-diversity communities over time would indicate that the benefits of biodiversity are generally underestimated in short-term studies. Analyzing 50 ecosystem variables over 11 years in the world's largest grassland biodiversity experiment, we show that overall plant diversity effects strengthened over time. Strengthening biodiversity effects were independent of the considered compartment (above- or belowground), organizational level (ecosystem variables associated with the abiotic habitat, primary producers, or higher trophic levels such as herbivores and pollinators), and variable type (measurements of pools or rates). We found evidence that biodiversity effects strengthened because of both a progressive decrease in functioning in species-poor and a progressive increase in functioning in species-rich communities. Our findings provide evidence that negative feedback effects at low biodiversity are as important for biodiversity effects as complementarity among species at high biodiversity. Finally, our results indicate that a current loss of species will result in a future impairment of ecosystem functioning, potentially decades beyond the moment of species extinction