The community ecology perspective of omics data.

The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (ß-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and ß-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.

Soil chemistry turned upside down: a meta-analysis of invasive earthworm effects on soil chemical properties.

Recent studies have shown that invasive earthworms can dramatically reduce native biodiversity, both above and below the ground. However, we still lack a synthetic understanding of the underlying mechanisms behind these changes, such as whether earthworm effects on soil chemical properties drive such relationships. Here, we investigated the effects of invasive earthworms on soil chemical properties (pH, water content, and the stocks and fluxes of carbon, nitrogen, and phosphorus) by conducting a meta-analysis. Invasive earthworms generally increased soil pH, indicating that the removal of organic layers and the upward transport of more base-rich mineral soil caused a shift in soil pH. Moreover, earthworms significantly decreased soil water content, suggesting that the burrowing activities of earthworms may have increased water infiltration of and/or increased evapotranspiration from soil. Notably, invasive earthworms had opposing effects on organic and mineral soil for carbon and nitrogen stocks, with decreases in organic, and increases in mineral soil. Nitrogen fluxes were higher in mineral soil, whereas fluxes in organic soil were not significantly affected by the presence of invasive earthworms, indicating that earthworms mobilize and redistribute nutrients among soil layers and increase overall nitrogen loss from the soil. Invasive earthworm effects on element stocks increased with ecological group richness only in organic soil. Earthworms further decreased ammonium stocks with negligible effects on nitrate stocks in organic soil, whereas they increased nitrate stocks but not ammonium stocks in mineral soil. Notably, all of these results were consistent across forest and grassland ecosystems underlining the generality of our findings. However, we found some significant differences between studies that were conducted in the field (observational and experimental settings) and in the lab, such as that the effects on soil pH decreased from field to lab settings, calling for a careful interpretation of lab findings. Our meta-analysis provides strong empirical evidence that earthworm invasion may lead to substantial changes in soil chemical properties and element cycling in soil. Furthermore, our results can help explain the dramatic effects of invasive earthworms on native biodiversity, for example, shifts towards the dominance of grass species over herbaceous ones, as shown by recent meta-analyses.