title: 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.
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.
authors: Rico
authors: R
authors: Lucas
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.|Institute of Forest Growth and Computer Science, Technische Universität Dresden, PO 1117, 01735 Tharandt, Germany.
authors: Jürgen
authors: J
authors: Groeneveld
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany.
authors: Hauke
authors: H
authors: Harms
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.
authors: Karin
authors: K
authors: Johst
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e, 04103 Leipzig, Germany.
authors: Karin
authors: K
authors: Frank
authors: UFZ-Helmholtz Centre for Environmental Research, Department of Environmental Microbiology, Permoserstr. 15, 04318 Leipzig, Germany sabine.kleinsteuber@ufz.de.
authors: Sabine
authors: S
authors: Kleinsteuber
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D004463:Ecology; D017753:Ecosystem
keywords: T-RFLP; anaerobic digestion; diversity concept; effective numbers, evenness; next-generation sequencing