A metagenomic alpha-diversity index for microbial functional biodiversity

Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.

Temperature and predators as interactive drivers of community properties

The effects of warming on ecological communities emerge from a range of potentially asymmetric impacts on individual physiology and development. Understanding these responses, however, is limited by our ability to connect mechanisms or emergent patterns across the many processes that drive variation in demography. Further complicating this understanding is the gain or loss of predators to many communities, which may interact with changes in temperature to drive community change. Here we conducted a factorial warming and predation experiment to test generalized predictions about responses to warming. We used microcosms with a range of protists, rotifers, and a gastrotrich, with and without the predator Actinosphaerium, to assess changes in diversity, body size, function, and composition in response to warming. We find that community respiration and predator:prey biovolume ratios peak at intermediate temperatures, while species richness declined with temperature. We also found that overall biomass increased with species richness, driven by the effect of temperature on richness. There was little evidence of an interaction between predation and temperature change, likely because the predator was mostly limited to the intermediate temperatures. Overall, our results suggest that general predictions about community change are still challenging to make but may benefit by considering multiple dimensions of community patterns in an integrated way.

Larger Area Facilitates Richness-Function Effects in Experimental Microcosms

Species-area relationships (SAR) and biodiversity-ecosystem function (BEF) relationships are central patterns in community ecology. Although research on both patterns often invokes mechanisms of community assembly, both SARs and BEFs are generally treated as separate phenomena. Here we link the two by creating an experimental SAR in microcosm communities and show that greater species richness in larger areas is accompanied by greater ecosystem function. We then explore mechanisms of community assembly by determining whether rare, large, or high-biomass species are more likely to persist in the larger microcosms. Our results indicate that larger areas harbor more rare species of a wider range of body sizes and have higher functional diversity, implying that the addition of niche space that supports rare species underlies the effect of area on species richness and function. Our results suggest that the preservation of large areas is a potentially useful way of maximizing the provisioning of ecosystem services through the maintenance of biodiversity.

Effects of grasshoppers on prairies: Herbivore composition matters more than richness in three grassland ecosystems

Understanding how biodiversity affects ecosystem processes is a key question in ecology. Previous research has found that increasing plant diversity often enhances many ecosystem processes, but less is known about the role of consumer diversity to ecosystem processes, especially in terrestrial ecosystems. Furthermore, we do not know how general biodiversity responses are among ecosystem types. We examined the role of insect herbivore (Orthoptera) diversity on plant production using parallel field experiments in three grassland ecosystems (mixed grass prairie, tallgrass prairie and coastal tallgrass prairie) to determine whether the effects of grasshopper diversity were consistent among sites. Using mesocosms, we manipulated orthopteran species richness (0, 1, 2, 3 or 4 species), functional richness (number of functional feeding groups present; 0, 1 or 2 functional groups) and functional composition (composition of functional groups present; mixed-feeders only, grass-feeders only, both mixed-feeders and grass-feeders). Diversity treatments were maintained throughout the experiment by replacing dead individuals. Plant biomass was destructively sampled at the end of the experiment. We found no effect of species richness or functional richness on plant biomass. However, herbivore functional composition was important, and effects were qualitatively similar across sites: The presence of only grass-feeding species reduced plant biomass more than either mixed-feeding species alone or both groups together. Orthopterans had consistent effects across a range of abiotic conditions, as well as different plant community and orthopteran community compositions. Our results suggest that functional composition of insect herbivores affects plant communities in grasslands more than herbivore species richness or functional richness, and this pattern was robust among grassland types.

Size matters: nest colonization patterns for twig-nesting ants

Understanding the drivers of ant diversity and co-occurrence in agroecosystems is fundamental because ants participate in interactions that influence agroecosystem processes. Multiple local and regional factors influence ant community assembly.We examined local factors that influence the structure of a twig-nesting ant community in a coffee system in Mexico using an experimental approach. We investigated whether twig characteristics (nest entrance size and diversity of nest entrance sizes) and nest strata (canopy shade tree or coffee shrub) affected occupation, species richness, and community composition of twig-nesting ants and whether frequency of occupation of ant species varied with particular nest entrance sizes or strata.We conducted our study in a shaded coffee farm in Chiapas, Mexico, between March and June 2012. We studied ant nest colonization by placing artificial nests (bamboo twigs) on coffee shrubs and shade trees either in diverse or uniform treatments. We also examined whether differences in vegetation (no. of trees, canopy cover and coffee density) influenced nest colonization.We found 33 ant species occupying 73% of nests placed. Nest colonization did not differ with nest strata or size. Mean species richness of colonizing ants was significantly higher in the diverse nest size entrance treatment, but did not differ with nest strata. Community composition differed between strata and also between the diverse and uniform size treatments on coffee shrubs, but not on shade trees. Some individual ant species were more frequently found in certain nest strata and in nests with certain entrance sizes.Our results indicate that twig-nesting ants are nest-site limited, quickly occupy artificial nests of many sizes, and that trees or shrubs with twigs of a diversity of entrance sizes likely support higher ant species richness. Further, individual ant species more frequently occupy nests with different sized entrances promoting ant richness on individual coffee plants and trees.