Functional diversity and redundancy across fish gut, sediment and water bacterial communities.

This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (ß) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed.

A unifying quantitative framework for exploring the multiple facets of microbial biodiversity across diverse scales.

Recent developments of molecular tools have revolutionized our knowledge of microbial biodiversity by allowing detailed exploration of its different facets and generating unprecedented amount of data. One key issue with such large datasets is the development of diversity measures that cope with different data outputs and allow comparison of biodiversity across different scales. Diversity has indeed three components: local (α), regional (γ) and the overall difference between local communities (ß). Current measures of microbial diversity, derived from several approaches, provide complementary but different views. They only capture the ß component of diversity, compare communities in a pairwise way, consider all species as equivalent or lack a mathematically explicit relationship among the α, ß and γ components. We propose a unified quantitative framework based on the Rao quadratic entropy, to obtain an additive decomposition of diversity (γ = α + ß), so the three components can be compared, and that integrate the relationship (phylogenetic or functional) among Microbial Diversity Units that compose a microbial community. We show how this framework is adapted to all types of molecular data, and we highlight crucial issues in microbial ecology that would benefit from this framework and propose ready-to-use R-functions to easily set up our approach.

Decomposing phylogenetic entropy into α, ß and γ components.

Measuring the phylogenetic diversity of communities has become a key issue for biogeography and conservation. However, most diversity indices that rely on interspecies phylogenetic distances may increase with species loss and thus violate the principle of weak monotonicity. Moreover, most published phylogenetic diversity indices ignore the abundance distribution along phylogenetic trees, even though lineage abundances are crucial components of biodiversity. The recently introduced concept of phylogenetic entropy overcomes these limitations, but has not been decomposed across scales, i.e. into α, ß and γ components. A full understanding of mechanisms sustaining biological diversity within and between communities needs such decomposition. Here, we propose an additive decomposition framework for estimating α, ß and γ components of phylogenetic entropy. Based on simulated trees, we demonstrate its robustness to phylogenetic tree shape and species richness. Our decomposition fulfils the requirements of both independence between components and weak monotonicity. Finally, our decomposition can also be adapted to the partitioning of functional diversity across different scales with the same desirable properties.

Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints.

Considering the major involvement of gut microflora in the digestive function of various macro-organisms, bacterial communities inhabiting fish guts may be the main actors of organic matter degradation by fish. Nevertheless, the extent and the sources of variability in the degradation potential of gut bacterial communities are largely overlooked. Using Biolog Ecoplate™ and denaturing gradient gel electrophoresis (DGGE), we explored functional (i.e. the ability to degrade organic matter) and genetic (i.e. identification of DGGE banding patterns) diversity of fish gut bacterial communities, respectively. Gut bacterial communities were extracted from fish species characterized by different diets sampled along a salinity gradient in the Patos-Mirim lagoons complex (Brazil). We found that functional diversity was surprisingly unrelated to genetic diversity of gut bacterial communities. Functional diversity was not affected by the sampling site but by fish species and diet, whereas genetic diversity was significantly influenced by all three factors. Overall, the functional diversity was consistently high across fish individuals and species, suggesting a wide functional niche breadth and a high potential of organic matter degradation. We conclude that fish gut bacterial communities may strongly contribute to nutrient cycling regardless of their genetic diversity and environment.