Abstract
Deductions about the ecology of high taxonomic bacterial ranks (i.e., phylum, class, order) are often based on their abundance patterns, yet few studies have quantified how accurately variations in abundance of these bacterial groups represent the dynamics of the taxa within them. Using 454-pyrosequencing of the 16S rRNA gene, we investigated whether the changes in abundance of six dominant bacterial classes (Actinobacteria, Beta-/Alpha-/Gamma-proteobacteria, Flavobacteria, and Sphingobacteria) along a large dam-regulated river are reflected by those of their constituent Operational Taxonomic Units (OTUs; 97% similarity level). The environmental impact generated by the reservoirs promoted clear compositional shifts in all bacterial classes that resulted from changes in the abundance of individual OTUs rather than from the appearance of new taxa along the river. Abundance patterns at the class level represented the dynamics of only a small but variable proportion of their constituting OTUs, which were not necessarily the most abundant ones. Within most classes, we detected sub-groups of OTUs showing contrasting responses to reservoir-induced environmental changes. Overall, we show that the patterns observed at the class level fail to capture the dynamics of a significant fraction of their constituent members, calling for caution when the ecological attributes of high-ranks are to be interpreted.
Highlights
Despite recent advances in our knowledge of bacterial communities associated to the development of high throughput sequencing technologies, it is still under debate whether bacterial high taxonomic ranks form ecologically coherent units and to which extent their constituent taxa share functional traits and environmental preferences (e.g., Fierer et al, 2007; Philippot et al, 2010; Placella et al, 2012)
We evaluated the degree of ecological coherence of the six most abundant bacterial classes in this system by 1) exploring changes in alpha- and beta-diversity in each class; 2) determining which fraction of the Operational Taxonomic Units (OTUs) within them showed the same patterns in abundance as its harboring class; and 3) identifying the existence of sub-groups of taxa with different ecological dynamics within each class
15 bacterial phyla were detected, yet bacterial assemblages were mainly dominated by the phyla Actinobacteria (68% of the total number of classified sequences), followed by Proteobacteria (22%), and Bacteroidetes (7%)
Summary
Despite recent advances in our knowledge of bacterial communities associated to the development of high throughput sequencing technologies, it is still under debate whether bacterial high taxonomic ranks (i.e., phylum, class, order) form ecologically coherent units and to which extent their constituent taxa share functional traits and environmental preferences (e.g., Fierer et al, 2007; Philippot et al, 2010; Placella et al, 2012). Cases where changes in highrank abundance are due to a complete substitution of the existing taxa by other better adapted to the new conditions, or due to a large increase in the relative abundances of previously rare taxa, would imply the presence of ecologically different sub-clusters within that high-rank group. The latter scenarios contradict the idea of functionally coherent units, and could lead to misleading interpretations of the ecological attributes of a particular lineage depending on the fraction of the constituent taxa that holds such attributes
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