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

Abstract

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.

Ecological Diversity: Measuring the Unmeasurable

“…In recent years, the era of "Big Data" has spread to ecology, in particular microbial ecology. This has driven a reassessment of which diversity indices to use to summarize and analyze these data [7]. This has led to increased focus on the mathematical behaviour of different measures, since there has been an increasing recognition that ecologists (often non-experts in mathematics) are using measures of diversity without proper consideration of their behaviour and limitations.…”

“…As with the indices themselves, their estimators should be selected carefully to ensure that their formulation is appropriate for the particular application. Interrogation of this point is key, particularly since non-experts often resort to dedicated statistical software or packages whose underlying and disparate estimation techniques can result in different calculations of the same quantity [7].…”

A guide to the application of Hill numbers to DNA‐based diversity analyses

“…Making the right choice requires acknowledgement of the essential concepts and differences between the available approaches, because the final results might depend on the decisions researchers make to measure biodiversity. Given the plethora of metrics available, and since the incorporation of complex attributes like phylogenies increases the level of abstraction, there is an increasing awareness of the need to implement intuitively meaningful diversity measures rather than abstract indices, as the latter can be easily misused and misinterpreted (Jost, ; Leinster & Cobbold, ; Lucas et al, ; Tuomisto, ). In this regard, considerable effort has recently been dedicated to creating frameworks that unify and generalize popular indices (Chao, Chiu, et al, ; Jost, ; Tucker et al, ).…”

Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

“…Specific details on the DNA extraction, sequencing, and data treatment have been described previously [32] and are presented in the Supplementary Information (Text S1). The bacterial and archaeal communities were analysed for community diversity and evenness ( 1 D and 1 E) by calculating the first-order Hill diversity numbers, which have been suggested to be the most important diversity and evenness indices [33]. Non-metric multidimensional scaling (NMDS) based on the "Bray-Curtis" dissimilarities was used to evaluate at which point the microbial communities of TE-depleted reactors began diverging from the control.…”