Abstract
Genetic diversity of phylogenetic or functional markers is widely used as a proxy of microbial diversity. However, it remains unclear to what extent functional diversity (FD), gene sequence diversity and community functioning are linked. For a range of denitrifying bacteria, we analyzed the relationships between (i) the similarity of functional traits evaluated from metabolic profiles (BIOLOG plates) or from N2O accumulation patterns on different carbon sources and (ii) the similarity of phylogenetic (16S rRNA gene) or functional (nir gene) markers. We also calculated different proxies for the diversity of denitrifier community based on taxa richness, phylogenetic (16S rRNA gene) or functional similarities (based either on metabolic profiles or N2O accumulation patterns), and evaluated their performance in inferring the functioning of assembled denitrifying communities. For individual strains, the variation in the 16S rRNA gene sequence was weakly correlated with the variation in metabolic patterns (ρ = 0.35) and was not related to N2O accumulation. The latter was correlated with the similarity of nitrite reductase residues. When nir genes were analyzed separately, the similarity in amino acids coded by the nirS genes was highly correlated with the observed patterns of N2O accumulation (ρ = 0.62), whereas nirK amino acid residues were unrelated to N2O accumulation. For bacterial assemblages, phylogenetic diversity (average similarity among species in a community) and mean community dissimilarity (average distance between species) calculated using 16S rRNA gene sequences, and FD measures associated with metabolic profiles, poorly predicted the variation in the functioning of assembled communities (≤15%). In contrast, the proxies of FD based on N2O accumulation patterns performed better and explained from 23 to 42% of the variation in denitrification. Amongst those, community niche was the best metric, indicating the importance of complementarity for resources in the context of bacterial community functioning.
Highlights
As biodiversity is threatened by global changes, understanding the relationship between diversity and the functioning of ecosystems or biological communities has received increasing attention (Hooper et al, 2005)
Many studies evaluating the effects of biodiversity on ecosystem functioning have focused on species richness, despite the fact that ecosystem functioning is not governed by the phylogenetic content of its organisms but rather by the functional traits of the individuals present, the distribution and abundance of these individuals, and their biological activity (Hooper et al, 2002; Naeem and Wright, 2003; Giller et al, 2004; Salles et al, 2009)
One could argue that this search for appropriate functional traits represents a more feasible task, as the functional genes coding for the well-studied functions such as denitrification are mostly known (Philippot and Hallin, 2005; Philippot et al, 2007)
Summary
As biodiversity is threatened by global changes, understanding the relationship between diversity and the functioning of ecosystems or biological communities has received increasing attention (Hooper et al, 2005). As 10 g of soil might contain 104– 106 distinct taxa (Torsvik and Ovreas, 2002; Gans et al, 2005), a complete understanding of microbial diversity is still a challenge Despite this overwhelming prokaryotic diversity, the potential loss of diversity at the microbial scale is of concern. In this context, it remains unclear to what extent microbial community structure, especially when based on the 16S rRNA gene as phylogenetic marker, can be used to explain differences in ecosystem processes related to carbon and nitrogen cycles (Wertz et al, 2006; Fierer et al, 2007; Le Roux et al, 2008; Philippot et al, 2010). From a biodiversity-ecosystem functioning point of view, it remains unclear the extent to which microbial community composition can be used to predict its impact on ecosystem processes and how community composition should be characterized in this context
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