Limits...
Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

Yasir M, Azhar EI, Khan I, Bibi F, Baabdullah R, Al-Zahrani IA, Al-Ghamdi AK - BMC Microbiol. (2015)

Bottom Line: The identified OTUs unique to each sample were very low irrespective of the altitude.Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients.The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

View Article: PubMed Central - PubMed

Affiliation: Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia. yasirkhattak.mrl@gmail.com.

ABSTRACT

Background: Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands.

Results: In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples.

Conclusions: Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Show MeSH

Related in: MedlinePlus

Principal coordinates analysis (PCoA) of bacterial communities in different soil samples collected along elevational gradients from southwestern highlands of Saudi Arabia. (A) Unweighted PCoA explained 43%variation and (B) weighted PCoA explained 64% of variation along the first three axes. Ellipses around center points represent the interquartile range.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4374494&req=5

Fig4: Principal coordinates analysis (PCoA) of bacterial communities in different soil samples collected along elevational gradients from southwestern highlands of Saudi Arabia. (A) Unweighted PCoA explained 43%variation and (B) weighted PCoA explained 64% of variation along the first three axes. Ellipses around center points represent the interquartile range.

Mentions: Jackknifed PCoA was performed using Unifrac metrics to compare overall composition of bacterial community within the samples and to cluster the bacterial community along axes of maximal variance according to their diversity (qualitative/unweighted) and concentration (quantitative/weighted). Jackknifed unweighted PCoA explained relatively small variation (43%) along the first three axes (Figure 4A). Jackknifed weighted PCoA explained 64% of variation along the first three axes demonstrating that overall differences between bacterial communities within the samples were more related to the richness of specific taxa OTUs compared to their presence or absence (Figure 4B). In the three-dimensional plot visualized from Unifrac unweighted distance matrix PCoA, samples Swh7, Swh8, Swh9 grouped in one cluster and samples Swh1, Swh2 and Swh5 made another cluster. The other four samples were scattered in the plot. The samples were broadly distributed along PC1, PC2 and PC3 in the weighted distance matrix principle coordinate plot except for the sample Shw1 and Swh5.Figure 4


Composition of soil microbiome along elevation gradients in southwestern highlands of Saudi Arabia.

Yasir M, Azhar EI, Khan I, Bibi F, Baabdullah R, Al-Zahrani IA, Al-Ghamdi AK - BMC Microbiol. (2015)

Principal coordinates analysis (PCoA) of bacterial communities in different soil samples collected along elevational gradients from southwestern highlands of Saudi Arabia. (A) Unweighted PCoA explained 43%variation and (B) weighted PCoA explained 64% of variation along the first three axes. Ellipses around center points represent the interquartile range.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374494&req=5

Fig4: Principal coordinates analysis (PCoA) of bacterial communities in different soil samples collected along elevational gradients from southwestern highlands of Saudi Arabia. (A) Unweighted PCoA explained 43%variation and (B) weighted PCoA explained 64% of variation along the first three axes. Ellipses around center points represent the interquartile range.
Mentions: Jackknifed PCoA was performed using Unifrac metrics to compare overall composition of bacterial community within the samples and to cluster the bacterial community along axes of maximal variance according to their diversity (qualitative/unweighted) and concentration (quantitative/weighted). Jackknifed unweighted PCoA explained relatively small variation (43%) along the first three axes (Figure 4A). Jackknifed weighted PCoA explained 64% of variation along the first three axes demonstrating that overall differences between bacterial communities within the samples were more related to the richness of specific taxa OTUs compared to their presence or absence (Figure 4B). In the three-dimensional plot visualized from Unifrac unweighted distance matrix PCoA, samples Swh7, Swh8, Swh9 grouped in one cluster and samples Swh1, Swh2 and Swh5 made another cluster. The other four samples were scattered in the plot. The samples were broadly distributed along PC1, PC2 and PC3 in the weighted distance matrix principle coordinate plot except for the sample Shw1 and Swh5.Figure 4

Bottom Line: The identified OTUs unique to each sample were very low irrespective of the altitude.Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients.The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

View Article: PubMed Central - PubMed

Affiliation: Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia. yasirkhattak.mrl@gmail.com.

ABSTRACT

Background: Saudi Arabia is mostly barren except the southwestern highlands that are susceptible to environmental changes, a hotspot for biodiversity, but poorly studied for microbial diversity and composition. In this study, 454-pyrosequencing of 16S rRNA gene hypervariable region V6 was used to analyze soil bacterial community along elevation gradients of the southwestern highlands.

Results: In general, lower percentage of total soil organic matter (SOM) and nitrogen were detected in the analyzed soil samples. Total 33 different phyla were identified across the samples, including dominant phyla Proteobacteria, Actinobacteria and Acidobacteria. Representative OTUs were grouped into 329 and 508 different taxa at family and genus level taxonomic classification, respectively. The identified OTUs unique to each sample were very low irrespective of the altitude. Jackknifed principal coordinates analysis (PCoA) revealed, overall differences in the bacterial community were more related to the quantity of specific OTUs than to their diversity among the studied samples.

Conclusions: Bacterial diversity and soil physicochemical properties did not show consistent changes along the elevation gradients. The large number of OTUs shared between the studied samples suggest the presence of a core soil bacterial community in the southwestern highlands of Saudi Arabia.

Show MeSH
Related in: MedlinePlus