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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

Inter-samples variability and average relative abundance of the dominant bacterial phyla across soil microbiome collected from different elevational gradients in southwestern highlands of Saudi Arabia. Others; indicate the collective percentage of minor phyla. Sample numbers showed on the x axis and percentage sequences reads classified on the y-axis.
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Fig1: Inter-samples variability and average relative abundance of the dominant bacterial phyla across soil microbiome collected from different elevational gradients in southwestern highlands of Saudi Arabia. Others; indicate the collective percentage of minor phyla. Sample numbers showed on the x axis and percentage sequences reads classified on the y-axis.

Mentions: Bacterial community compositions of the collected soil samples were studied at descending levels of taxonomic classification to find out community membership at different altitudes in the southwestern highlands of Saudi Arabia. Overall, 33 phyla were found across the samples, including a group of unclassified sequences. Twelve phyla were commonly detected within the studied samples. The relative abundances of dominant phyla are presented in Figure 1. Only eight phyla were comprised mean abundance more than 1% in each sample, but they jointly hold 90.4% of the total sequence reads. Most dominant phylum was Proteobacteria with mean relative abundance value of 25.7% ± 8.2 and dominantly detected in ≥20% concentration within all samples except from Swh3 (7.6%). Other dominant phyla were Actinobacteria and Acidobacteria representing bacterial sequences in the range of 4.9–47.1% and 1.5–18.3%, respectively. An average 20.9% of the sequences were unclassified. Concentration of the unclassified sequences were fluctuated in the studied samples, and the sample Swh3 contained highest 65.4% unclassified sequences. There were also identified certain members of Chloroflexi (1.7%–10.3%), Bacteroidetes (0.8%–16.7%), Firmicutes (0.3%–32.9%), Planctomycetes (1.5%–5.1%) and Gemmatimonadetes (0.8%–3.2%), and were designated as minor phyla detected in lower concentration. Of these groups, Firmicutes and Bacteroidetes were detected in higher concentration 32.9% and 16.7%, respectively in the sample Swh6 compared to the other samples. The remaining identified phyla/candidate divisions represent much smaller fraction (2.2%) of the bacterial community.Figure 1


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)

Inter-samples variability and average relative abundance of the dominant bacterial phyla across soil microbiome collected from different elevational gradients in southwestern highlands of Saudi Arabia. Others; indicate the collective percentage of minor phyla. Sample numbers showed on the x axis and percentage sequences reads classified on the y-axis.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: Inter-samples variability and average relative abundance of the dominant bacterial phyla across soil microbiome collected from different elevational gradients in southwestern highlands of Saudi Arabia. Others; indicate the collective percentage of minor phyla. Sample numbers showed on the x axis and percentage sequences reads classified on the y-axis.
Mentions: Bacterial community compositions of the collected soil samples were studied at descending levels of taxonomic classification to find out community membership at different altitudes in the southwestern highlands of Saudi Arabia. Overall, 33 phyla were found across the samples, including a group of unclassified sequences. Twelve phyla were commonly detected within the studied samples. The relative abundances of dominant phyla are presented in Figure 1. Only eight phyla were comprised mean abundance more than 1% in each sample, but they jointly hold 90.4% of the total sequence reads. Most dominant phylum was Proteobacteria with mean relative abundance value of 25.7% ± 8.2 and dominantly detected in ≥20% concentration within all samples except from Swh3 (7.6%). Other dominant phyla were Actinobacteria and Acidobacteria representing bacterial sequences in the range of 4.9–47.1% and 1.5–18.3%, respectively. An average 20.9% of the sequences were unclassified. Concentration of the unclassified sequences were fluctuated in the studied samples, and the sample Swh3 contained highest 65.4% unclassified sequences. There were also identified certain members of Chloroflexi (1.7%–10.3%), Bacteroidetes (0.8%–16.7%), Firmicutes (0.3%–32.9%), Planctomycetes (1.5%–5.1%) and Gemmatimonadetes (0.8%–3.2%), and were designated as minor phyla detected in lower concentration. Of these groups, Firmicutes and Bacteroidetes were detected in higher concentration 32.9% and 16.7%, respectively in the sample Swh6 compared to the other samples. The remaining identified phyla/candidate divisions represent much smaller fraction (2.2%) of the bacterial community.Figure 1

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