The Leinster and Cobbold indices improve inferences about microbial diversity

Decomposing diversity into measures of evenness, similarity, and richness

It has long been recognized that diversity has many measurable aspects, such as richness, evenness, and similarity among species. However, given a diversity index, it is unclear whether it necessarily can be decomposed into components that reflect these different aspects. Here, we present a scheme to decompose the Leinster and Cobbold diversity index, which subsumes and generalizes many other indices, into the components of richness, evenness and taxonomic similarity. Our approach addresses the problem that in general a vector of equal relative abundances does not maximize diversity. Furthermore, our approach uses all available information to give unbiased estimates of both evenness and similarity.

Arbuscular Mycorrhizal Fungi Alter the Community Structure of Ammonia Oxidizers at High Fertility via Competition for Soil NH4. MICROBIAL ECOLOGY 2019;78:147-158. [PMID: 30402724 DOI: 10.1007/s00248-018-1281-2]

Nitrification represents a central process in the cycling of nitrogen (N) which in high-fertility habitats can occasionally be undesirable. Here, we explore how arbuscular mycorrhiza (AM) impacts nitrification when N availability is not limiting to plant growth. We wanted to test which of the mechanisms that have been proposed in the literature best describes how AM influences nitrification. We manipulated the growth settings of Plantago lanceolata so that we could control the mycorrhizal state of our plants. AM induced no changes in the potential nitrification rates or the estimates of ammonium oxidizing (AO) bacteria. However, we could observe a moderate shift in the community of ammonia-oxidizers, which matched the shift we saw when comparing hyphosphere to rhizosphere soil samples and mirrored well changes in the availability of ammonium in soil. We interpret our results as support that it is competition for N that drives the interaction between AM and AO. Our experiment sheds light on an understudied interaction which is pertinent to typical management practices in agricultural systems.

Disentangling the influence of climate, soil and belowground microbes on local species richness in a dryland ecosystem of Northwest China

Xinjiang Uygur Autonomous Region (XUAR) covers one of the largest drylands in the world, while the relative effects of different environmental factors on plant diversity are poorly understood. We sampled 66 sites in a typical dryland of XUAR, which covers more than 450,000 km², to evaluate the relative influences of different factors on the patterns of local plant species richness (LPSR). We found that overall and herbaceous LPSR were positively correlated with water availability, soil nutrients but negatively correlated with energy availability, while the shrub LPSR showed the opposite response. Climate, soil attributes together explained 53.2% and 59.2% of the variance in overall and herbaceous LPSR, respectively; revealing that LPSR patterns were shaped by abiotic and underground biotic factors together. Only 31.5% of the variance in the shrub LPSR was explained by soil attributes, indicating that shrub LPSR was mainly limited by non-climatic factors. There findings provide robust evidence that relative contribution of climate and soil attributes differ markedly depending on the plant functional group. Furthermore, we found the different relationship between microbes and plant diversity, indicating that the linkages between soil microbial diversity and plant diversity may vary across functional groups of microbes and plant. These findings provide robust evidence that the relative roles of climate, soil and microbes differ markedly depending on the plant functional group. Microbial richness showed a significantly pure influence on the LPSR of all groups, suggesting that microbes play a non-negligible role in regulating plant diversity in dryland ecosystems.

Plant community, geographic distance and abiotic factors play different roles in predicting AMF biogeography at the regional scale in northern China

Arbuscular mycorrhizal fungi (AMF) are ubiquitous mutualists of terrestrial plants and play key roles in regulating various ecosystem processes, but little is known about AMF biogeography at regional scale. This study aims at exploring the key predictors of AMF communities across a 5000-km transect in northern China. We determined the soil AMF species richness and community composition at 47 sites representative of four vegetation types (meadow steppe, typical steppe, desert steppe and desert) and related them to plant community characteristics, abiotic factors and geographic distance. The results showed that soil pH was the strongest predictor of AMF richness and phylogenetic diversity. However, abiotic factors only have a low predictive effect on AMF community composition or phylogenetic patterns. By contrast, we found a significant relationship between community composition of AMF and plants, which was a surprising result given the extent of heterogeneity in the plant community across this transect. Moreover, the geographic distance predominantly explained the AMF phylogenetic structure, implying that history evolutionary may play a role in shaping AMF biogeographic patterns. This study highlighted the different roles of main factors in predicting AMF biogeography, and bridge landscape-scale studies to more recent global-scale efforts.

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.

Relative Importance of Individual Climatic Drivers Shaping Arbuscular Mycorrhizal Fungal Communities

The physiological tolerance hypothesis (PTH) postulates that it is the tolerance of species to climatic factors that determines overall community richness. Here, we tested whether a group of mutualistic microbes, Glomeromycota, is distributed in semi-arid environments in ways congruent with the PTH. For this purpose, we modeled with climatic predictors the niche of each of the four orders of Glomeromycota and identified predictors of arbuscular mycorrhizal (AM) fungal operational taxonomic unit (OTU) richness. Our dataset consisted of 50 paired grassland and farmland sites in the farming-pastoral ecotone of northern China. We observed shifts in the relative abundance of AM fungal orders in response to climatic variables but also declines in OTU richness in grassland sites that had experienced high precipitation during the preceding year which was incongruous with the PTH. We found pronounced differences across groups of Glomeromycotan fungi in their responses to climatic variables and identified strong dependencies of AM fungal communities on precipitation. Given that precipitation is expected to further decline in the farming-pastoral ecotone over the coming years and that mycorrhiza represents an integral constituent of ecosystem functioning, it is likely that the ecosystem services in the region will change accordingly.