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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

Canonical Correspondence Analysis (CCA) of the gene content matrix, using environmental preferences as explanatory variables. Orange crosses show the genera, blue squares the individual COGs in the matrix, and yellow circles represent the projections of the habitat preferences.
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Figure 3: Canonical Correspondence Analysis (CCA) of the gene content matrix, using environmental preferences as explanatory variables. Orange crosses show the genera, blue squares the individual COGs in the matrix, and yellow circles represent the projections of the habitat preferences.

Mentions: We also carried out a Canonical Correspondence Analysis of the gene content matrix using the environmental distribution of taxa as the external variable. The results are shown in Figure 3. Host-associated environments diverged very much from the other environments. The former environments impose a strong selection on the taxa that can live and thrive in them. As in the MDS analysis, archaeal taxa clustered separately (upper right corner of the figure). Since archaea are often associated with thermal and hypersaline habitats, these environments (thermal springs and vents, saline soils and hypersaline habitats) were well segregated in the analysis. A distinction between saline and non-saline environments was also apparent, and a gradient of increased salinity can be seen, from non-saline environments (like freshwaters) to hyposaline, saline and hypersaline habitats. This is in accordance with previous results taking into account just the environmental distribution of taxa (Lozupone and Knight, 2007; Tamames et al., 2010), in which temperature, salinity and association with host tissues were the most determinant environmental characteristics.


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)

Canonical Correspondence Analysis (CCA) of the gene content matrix, using environmental preferences as explanatory variables. Orange crosses show the genera, blue squares the individual COGs in the matrix, and yellow circles represent the projections of the habitat preferences.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Canonical Correspondence Analysis (CCA) of the gene content matrix, using environmental preferences as explanatory variables. Orange crosses show the genera, blue squares the individual COGs in the matrix, and yellow circles represent the projections of the habitat preferences.
Mentions: We also carried out a Canonical Correspondence Analysis of the gene content matrix using the environmental distribution of taxa as the external variable. The results are shown in Figure 3. Host-associated environments diverged very much from the other environments. The former environments impose a strong selection on the taxa that can live and thrive in them. As in the MDS analysis, archaeal taxa clustered separately (upper right corner of the figure). Since archaea are often associated with thermal and hypersaline habitats, these environments (thermal springs and vents, saline soils and hypersaline habitats) were well segregated in the analysis. A distinction between saline and non-saline environments was also apparent, and a gradient of increased salinity can be seen, from non-saline environments (like freshwaters) to hyposaline, saline and hypersaline habitats. This is in accordance with previous results taking into account just the environmental distribution of taxa (Lozupone and Knight, 2007; Tamames et al., 2010), in which temperature, salinity and association with host tissues were the most determinant environmental characteristics.

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