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Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

Pascual-García A, Tamames J, Bastolla U - BMC Microbiol. (2014)

Bottom Line: 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 model fails to reproduce.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.We 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.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biología Molecular Severo Ochoa (CSIC-UAM), c. Nicolás Cabrera 1, campus UAM, Madrid, E-28049, Spain. alberto.pascual@csic.es.

ABSTRACT

Background: Since 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.

Results: Here 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 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 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.

Conclusions: We 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.

Show MeSH
Propensity to association versus environmental relatedness (top) and versus phylogenetic relatedness (bottom). In the top figure the x axis labels environmental relatedness at the three levels of subtype, type and supertype. For each level, three values of relatedness are possible: ’Same’ if the preferred habitat is the same, ’Und’ if it is undetermined for one or both taxa, and ’Diff’ if it is different.
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Fig2: Propensity to association versus environmental relatedness (top) and versus phylogenetic relatedness (bottom). In the top figure the x axis labels environmental relatedness at the three levels of subtype, type and supertype. For each level, three values of relatedness are possible: ’Same’ if the preferred habitat is the same, ’Und’ if it is undetermined for one or both taxa, and ’Diff’ if it is different.

Mentions: Figure 2 (top panel) shows the propensity for aggregation versus the environmental relatedness at the level of subtype, type and supertype. We consider a taxon associated with an environment if more than 50% and at least 3 of the samples in which it is observed belong to this environment. We distinguish three types of environmental relatedness for each level, in decreasing order of similarity: Same, if the two taxa are associated with the same environment, Und, if one or both of them are not associated with any specific environment, and Diff if they are associated with different environments. For instance, (Same, Diff, Und) means that the preference is the same at the supertype level, different at the type level and undefined at the subtype level. We represent in the plot only points for which there are at least 10 pairs, for instance no point is shown for same family and same order and (Same, Same, Diff) habitat preferences.Figure 2


Bacteria dialog with Santa Rosalia: Are aggregations of cosmopolitan bacteria mainly explained by habitat filtering or by ecological interactions?

Pascual-García A, Tamames J, Bastolla U - BMC Microbiol. (2014)

Propensity to association versus environmental relatedness (top) and versus phylogenetic relatedness (bottom). In the top figure the x axis labels environmental relatedness at the three levels of subtype, type and supertype. For each level, three values of relatedness are possible: ’Same’ if the preferred habitat is the same, ’Und’ if it is undetermined for one or both taxa, and ’Diff’ if it is different.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4263022&req=5

Fig2: Propensity to association versus environmental relatedness (top) and versus phylogenetic relatedness (bottom). In the top figure the x axis labels environmental relatedness at the three levels of subtype, type and supertype. For each level, three values of relatedness are possible: ’Same’ if the preferred habitat is the same, ’Und’ if it is undetermined for one or both taxa, and ’Diff’ if it is different.
Mentions: Figure 2 (top panel) shows the propensity for aggregation versus the environmental relatedness at the level of subtype, type and supertype. We consider a taxon associated with an environment if more than 50% and at least 3 of the samples in which it is observed belong to this environment. We distinguish three types of environmental relatedness for each level, in decreasing order of similarity: Same, if the two taxa are associated with the same environment, Und, if one or both of them are not associated with any specific environment, and Diff if they are associated with different environments. For instance, (Same, Diff, Und) means that the preference is the same at the supertype level, different at the type level and undefined at the subtype level. We represent in the plot only points for which there are at least 10 pairs, for instance no point is shown for same family and same order and (Same, Same, Diff) habitat preferences.Figure 2

Bottom Line: 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 model fails to reproduce.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.We 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.

View Article: PubMed Central - PubMed

Affiliation: Centro de Biología Molecular Severo Ochoa (CSIC-UAM), c. Nicolás Cabrera 1, campus UAM, Madrid, E-28049, Spain. alberto.pascual@csic.es.

ABSTRACT

Background: Since 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.

Results: Here 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 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 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.

Conclusions: We 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.

Show MeSH