Abstract
BackgroundSince the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. Disentangling the role of habitat filtering and interactions with other species is critical for understanding microbial ecology. Macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. These methods have started to be incorporated into microbial ecology relatively recently, due to the inherent experimental difficulties and the coarse grained nature of the data.ResultsHere we investigate the influence of environmental preferences and ecological interactions in the tendency of bacterial taxa to either aggregate or segregate, using a comprehensive dataset of bacterial taxa observed in a wide variety of environments. We assess significance of taxa associations through a null model that takes into account habitat preferences and the global distribution of taxa across samples. The analysis of these associations reveals a surprisingly large number of significant aggregations between taxa, with a marked community structure and a strong propensity to aggregate for cosmopolitan taxa. Due to the coarse grained nature of our data we cannot conclusively reject the hypothesis that many of these aggregations are due to environmental preferences that the null model fails to reproduce. Nevertheless, some observations are better explained by ecological interactions than by habitat filtering. In particular, most pairs of aggregating taxa co-occur in very different environments, which makes it unlikely that these associations are due to habitat preferences, and many are formed by cosmopolitan taxa without well defined habitat preferences. Moreover, known cooperative interactions are retrieved as aggregating pairs of taxa. As observed in similar studies, we also found that phylogenetically related taxa are much more prone to aggregate than to segregate, an observation that may play a role in bacterial speciation.ConclusionsWe hope that these results stimulate experimental verification of the putative cooperative interactions between cosmopolitan bacteria, and we suggest several groups of aggregated cosmopolitan bacteria that are interesting candidates for such an investigation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-014-0284-5) contains supplementary material, which is available to authorized users.
Highlights
Since the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects
We adopt the probabilistic null model proposed by Navarro-Alberto and Manly [27], in which the probability πia that taxon i is observed at sample a in the absence of taxa interactions is parametrized as πia = 1 − exp(−piqa) where the parameter pi is related with the abundance of taxon i and qa is related with the biodiversity supported by sample a, respectively
If taxon i is never found in environment A, pi(A) = 0, implying that πia = 0 if a ∈ A, i.e. the taxon is never found in samples of environment A simulated through the null model either
Summary
Since the landmark Santa Rosalia paper by Hutchinson, niche theory addresses the determinants of biodiversity in terms of both environmental and biological aspects. Macroscopic biogeography explores hypothetical ecological interactions through the analysis of species associations. These methods have started to be incorporated into microbial ecology relatively recently, due to the inherent experimental difficulties and the coarse grained nature of the data. In his seminal paper Homage to Santa Rosalia or Why are there so many kinds of animals? Analysis suggested that ecological patterns are qualitatively similar for macro- and microorganisms [7] and allowed identifying taxa-area and distance decay relationships [8,9] and the influence of environmental variables such as depth [10] or salinity [11], stimulating the emergence of prokaryotic biogeography [12,13]
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