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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

Networks based analysis of samples/OTUs interaction. (A) Network showed the connection of OTUs at family and (B) genera level among the studied samples. Square nodes represent samples and circle nodes represent the bacterial OTUs. The white circle nodes represent bacterial OTUs commonly found in different samples and connected with more than one edge. Unique bacterial OTUs to a specific samples were connected with a respective sample node by single line.
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Fig2: Networks based analysis of samples/OTUs interaction. (A) Network showed the connection of OTUs at family and (B) genera level among the studied samples. Square nodes represent samples and circle nodes represent the bacterial OTUs. The white circle nodes represent bacterial OTUs commonly found in different samples and connected with more than one edge. Unique bacterial OTUs to a specific samples were connected with a respective sample node by single line.

Mentions: All the sequence reads were assigned into 329 OTUs at the family level of the taxonomy. Out of 329, the 193 (58.7%) OTUs were unclassified to any define family. Average, 162.1 ± 25.3 OTUs at family level were observed per sample. Fifty seven OTUs were commonly detected within samples and were representing 74% of the total sequence reads. Only few OTUs were present exclusively in each sample with mean relative abundance of 7.0 ± 5.7 ranged (1–20). Maximum number of unique family level OTUs were identified in the sample Swh10 and minimum number in Swh1 (Figure 2A). The highest diversity was observed in the sample Swh10 containing 219 taxa at family level followed by Swh4 (183), Swh5 (173) and Swh2 (170). Apart from unclassified taxa OTUs, other dominant taxa at family level were Actinomycetales fam. (4.3 ± 3.2), Micromonosporaceae (3.1 ± 2.7%), Geodermatophilaceae (3.0 ± 3.1%), Chloracidobacteria fam. (2.9 ± 2.3%) and Acidobacteria–6 fam. 1 (2.7 ± 2.0). All the dominant families >1% mean concentration were commonly present within the studied samples except from Clostridiaceae (1.2 ± 3.3%) that was detected at 10.5% in sample Swh6 and present at a rare concentration in the other 4 samples Swh4, Swh5, Swh9 and Swh10.Figure 2


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)

Networks based analysis of samples/OTUs interaction. (A) Network showed the connection of OTUs at family and (B) genera level among the studied samples. Square nodes represent samples and circle nodes represent the bacterial OTUs. The white circle nodes represent bacterial OTUs commonly found in different samples and connected with more than one edge. Unique bacterial OTUs to a specific samples were connected with a respective sample node by single line.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig2: Networks based analysis of samples/OTUs interaction. (A) Network showed the connection of OTUs at family and (B) genera level among the studied samples. Square nodes represent samples and circle nodes represent the bacterial OTUs. The white circle nodes represent bacterial OTUs commonly found in different samples and connected with more than one edge. Unique bacterial OTUs to a specific samples were connected with a respective sample node by single line.
Mentions: All the sequence reads were assigned into 329 OTUs at the family level of the taxonomy. Out of 329, the 193 (58.7%) OTUs were unclassified to any define family. Average, 162.1 ± 25.3 OTUs at family level were observed per sample. Fifty seven OTUs were commonly detected within samples and were representing 74% of the total sequence reads. Only few OTUs were present exclusively in each sample with mean relative abundance of 7.0 ± 5.7 ranged (1–20). Maximum number of unique family level OTUs were identified in the sample Swh10 and minimum number in Swh1 (Figure 2A). The highest diversity was observed in the sample Swh10 containing 219 taxa at family level followed by Swh4 (183), Swh5 (173) and Swh2 (170). Apart from unclassified taxa OTUs, other dominant taxa at family level were Actinomycetales fam. (4.3 ± 3.2), Micromonosporaceae (3.1 ± 2.7%), Geodermatophilaceae (3.0 ± 3.1%), Chloracidobacteria fam. (2.9 ± 2.3%) and Acidobacteria–6 fam. 1 (2.7 ± 2.0). All the dominant families >1% mean concentration were commonly present within the studied samples except from Clostridiaceae (1.2 ± 3.3%) that was detected at 10.5% in sample Swh6 and present at a rare concentration in the other 4 samples Swh4, Swh5, Swh9 and Swh10.Figure 2

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