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Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms.

Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C - Front Microbiol (2016)

Bottom Line: The combination of these three datasets made it possible to describe and quantify the relationships among them.We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations.Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain.

ABSTRACT
Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.

No MeSH data available.


Related in: MedlinePlus

Three-dimensional representation of genomic, environmental, and phylogenetic distances among all pairs of bacterial and archaeal genera. Each point in the plot corresponds to a pair of genera, indicating their particular gene content, environmental and phylogenetic distances. Examples discussed in the text are highlighted.
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Figure 4: Three-dimensional representation of genomic, environmental, and phylogenetic distances among all pairs of bacterial and archaeal genera. Each point in the plot corresponds to a pair of genera, indicating their particular gene content, environmental and phylogenetic distances. Examples discussed in the text are highlighted.

Mentions: We compared the pairs of genera by plotting their values of phylogenetic distance and environmental and gene content correlation, as shown in Figure 4. The two large clusters, corresponding to long or short phylogenetic distances, correspond to interdomain (between bacteria ad archaea) and intradomain (bacteria-bacteria or archaea-archaea) pairs, respectively. Phylogenetic closeness was usually associated with gene content similarity, but with a wide range of different environmental preferences. There were many instances of closely related organisms sharing similar environmental preferences, such as the many Enterobacteria taxa living preferentially in the digestive tract of animals, but closely related organisms could also diversify to live in different habitats. This was the case of Pantoea, a genus of the same Enterobacteria clade, and therefore closely related to the gut bacteria, but comprising pathogenic bacteria that can also be found on the surface of plants (Brady et al., 2008). Another example was methanogenic archaea, that despite being close phylogenetic relatives and metabolically similar, thrive in environments so different as anoxygenic sediments in the deep sea (genus Methanobacterium) and in the human gut (genus Methanobrevibacter; Liu and Whitman, 2008).


Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms.

Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C - Front Microbiol (2016)

Three-dimensional representation of genomic, environmental, and phylogenetic distances among all pairs of bacterial and archaeal genera. Each point in the plot corresponds to a pair of genera, indicating their particular gene content, environmental and phylogenetic distances. Examples discussed in the text are highlighted.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4814473&req=5

Figure 4: Three-dimensional representation of genomic, environmental, and phylogenetic distances among all pairs of bacterial and archaeal genera. Each point in the plot corresponds to a pair of genera, indicating their particular gene content, environmental and phylogenetic distances. Examples discussed in the text are highlighted.
Mentions: We compared the pairs of genera by plotting their values of phylogenetic distance and environmental and gene content correlation, as shown in Figure 4. The two large clusters, corresponding to long or short phylogenetic distances, correspond to interdomain (between bacteria ad archaea) and intradomain (bacteria-bacteria or archaea-archaea) pairs, respectively. Phylogenetic closeness was usually associated with gene content similarity, but with a wide range of different environmental preferences. There were many instances of closely related organisms sharing similar environmental preferences, such as the many Enterobacteria taxa living preferentially in the digestive tract of animals, but closely related organisms could also diversify to live in different habitats. This was the case of Pantoea, a genus of the same Enterobacteria clade, and therefore closely related to the gut bacteria, but comprising pathogenic bacteria that can also be found on the surface of plants (Brady et al., 2008). Another example was methanogenic archaea, that despite being close phylogenetic relatives and metabolically similar, thrive in environments so different as anoxygenic sediments in the deep sea (genus Methanobacterium) and in the human gut (genus Methanobrevibacter; Liu and Whitman, 2008).

Bottom Line: The combination of these three datasets made it possible to describe and quantify the relationships among them.We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations.Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain.

ABSTRACT
Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments.

No MeSH data available.


Related in: MedlinePlus