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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.

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Related in: MedlinePlus

Alpha diversity of the sequence reads from soil samples collected along elevational gradients from southwestern highland of Saudi Arabia. (A) Chao1 index, (B) rarefaction analysis of the observed species and (C) The Shannon index were computed.
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Fig3: Alpha diversity of the sequence reads from soil samples collected along elevational gradients from southwestern highland of Saudi Arabia. (A) Chao1 index, (B) rarefaction analysis of the observed species and (C) The Shannon index were computed.

Mentions: Chao1 index, rarefaction and the Shannon index were calculated to estimate the alpha diversity. Total 4603 OTUs (defined using a 97% cut off value) were found in the complete data set of processed sequence reads. Chao1 analysis revealed a decreased trend of richness in the samples Swh3, Swh8, Swh9 and Swh7 compared to the samples Swh5, Swh2, Swh1 and Swh10 (Figure 3A). The highest richness value of Chao1 was found in sample Swh5 (2262) and lowest in Swh3 (1060). In rarefaction curves, all the studied samples were tended to approach saturation plateau, and the samples Swh5, Shw10, Swh2 and Swh1 were plotted in the upper part of the graph (Figure 3B). The rarefaction curve indicated variation in OTUs density within the soil samples collected from different altitudes and locations, but the sequence coverage was still sufficient to capture the diversity of bacterial community. The Shannon Wiener index calculated at 3% dissimilarity showed the lowest value of evenness (4.5) for the sample Swh3 compared to the all other samples that revealed the highest value of evenness (>8.0, Figure 3C). Statistically, no significant difference was observed in the Choa1 and the Shannon Wiener index between the groups of samples collected at different altitudes.Figure 3


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)

Alpha diversity of the sequence reads from soil samples collected along elevational gradients from southwestern highland of Saudi Arabia. (A) Chao1 index, (B) rarefaction analysis of the observed species and (C) The Shannon index were computed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig3: Alpha diversity of the sequence reads from soil samples collected along elevational gradients from southwestern highland of Saudi Arabia. (A) Chao1 index, (B) rarefaction analysis of the observed species and (C) The Shannon index were computed.
Mentions: Chao1 index, rarefaction and the Shannon index were calculated to estimate the alpha diversity. Total 4603 OTUs (defined using a 97% cut off value) were found in the complete data set of processed sequence reads. Chao1 analysis revealed a decreased trend of richness in the samples Swh3, Swh8, Swh9 and Swh7 compared to the samples Swh5, Swh2, Swh1 and Swh10 (Figure 3A). The highest richness value of Chao1 was found in sample Swh5 (2262) and lowest in Swh3 (1060). In rarefaction curves, all the studied samples were tended to approach saturation plateau, and the samples Swh5, Shw10, Swh2 and Swh1 were plotted in the upper part of the graph (Figure 3B). The rarefaction curve indicated variation in OTUs density within the soil samples collected from different altitudes and locations, but the sequence coverage was still sufficient to capture the diversity of bacterial community. The Shannon Wiener index calculated at 3% dissimilarity showed the lowest value of evenness (4.5) for the sample Swh3 compared to the all other samples that revealed the highest value of evenness (>8.0, Figure 3C). Statistically, no significant difference was observed in the Choa1 and the Shannon Wiener index between the groups of samples collected at different altitudes.Figure 3

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