The relationship between biodiversity and ecosystem function (BEF) captivates ecologists, but the factors responsible for the direction of this relationship remain unclear. While higher ecosystem functioning at higher biodiversity levels (‘positive BEF’) is not universal in nature, negative BEF relationships seem puzzlingly rare. Here, we develop a dynamical consumer-resource model inspired by microbial decomposer communities in pitcher plant leaves to investigate BEF. We manipulate microbial diversity via controlled colonization and measure their function as total ammonia production. We test how niche partitioning among bacteria and other ecological processes influence BEF in the leaves. We find that a negative BEF can emerge from reciprocal interspecific inhibition in ammonia production causing a negative complementarity effect, or from competitive hierarchies causing a negative selection effect. Absent these factors, a positive BEF was the typical outcome. Our findings provide a potential explanation for the rarity of negative BEF in empirical data.

As primary determinants of microbial community dynamics, viruses play a central role in key ecological processes, including respiration, organic and inorganic nutrient cycling, and greenhouse gas production and sequestration. However, the majority of studies of viruses in natural environments are from oceans, where the size and complexity of ecological communities pose major challenges for studying detailed mechanisms and gaining a full picture of host-virus networks. We characterize viruses in 16 metagenomes from carnivorous pitcher plant natural microcosms, which are an emerging model system for studying community ecology and ecosystem function. We find that pitcher plant microcosms possess a relatively high proportion of lysogenic viruses compared to other freshwater systems. In addition, viruses from pitcher plant microcosms appear to possess auxiliary metabolic genes for chitin degradation, an important ecological function in pitcher plants where the primary energy source is the plant's insect prey. The reduced size and complexity of pitcher plant natural microcosms, as well as their well-defined ecological function, position them as an excellent model system for characterizing whole host-virus networks and understanding the mechanisms through which viruses alter microbial diversity and function.