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Predicted Functional Shifts Due to Type of Soil Microbiome and Watering of Two Wild Plants in Western Region of Saudi Arabia

Lina Baz1, Aala A. Abulfaraj2, Manal A. Tashkandi3, Hanadi M. Baeissa3, Mohammed Y. Refai3, Aminah A. Barqawi4, Ashwag Shami5, Haneen W. Abuauf6, Ruba A. Ashy7, Rewaa S. Jalal7,*
1 Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah, 21589, Saudi Arabia
2 Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh, 21911, Saudi Arabia
3 Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
4 Department of Chemistry Al-Leith University College, Umm Al Qura University, Makkah, Saudi Arabia
5 Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
6 Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah, Saudi Arabia
7 Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
* Corresponding Author: Rewaa S. Jalal. Email: rsjalal@uj.edu.sa
(This article belongs to this Special Issue: Plant–Environment Interactions)

Phyton-International Journal of Experimental Botany https://doi.org/10.32604/phyton.2022.021922

Received 13 February 2022; Accepted 23 March 2022; Published online 26 April 2022


The present study aimed to predict differential enrichment of pathways and compounds in the rhizosphere microbiomes of the two wild plants (Abutilon fruticosum and Nitrosalsola vermiculata) and to predict functional shifts in microbiomes due to water. Amplicon sequencing of 16S rRNA region V3–V4 was done and gene-based microbial compositions were enrolled in PICRUSt to predict enriched pathways and compounds. The results indicated that “ABC transporters” and “Quorum sensing” pathways are among the highest enriched pathways in rhizosphere microbiomes of the two wild plants compared with those of the bulk soil microbiomes. The highest enriched compounds in soil microbiomes of the two wild plants included five proteins and three enzymes participating in one or more KEGG pathways. Six of these eight compounds showed higher predicted enrichment in rhizosphere soil microbiomes, while only one, namely phosphate transport system substrate-binding protein, showed higher enrichment in the surrounding bulk soil microbiomes. In terms of differentially enriched compounds due to watering, only the dual-specific aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A showed higher enrichment in rhizosphere soil of the two wild plants after 24 h of watering. Two of the highly enriched compounds namely branched-chain amino acid transport system ATP-binding protein and branched-chain amino acid transport system substrate-binding protein, are encoded by genes stimulated by the plant’s GABA that participates in conferring biotic and abiotic stresses in plants and improves the plant’s growth performance. The 3-Oxoacyl-[ACP] reductase, a member of the short-chain alcohol dehydrogenase/ reductase (SDR) superfamily, participates in fatty acids elongation cycles and contributes to plant-microbe symbiotic relationships, while enoyl-CoA hydratase has a reverse action as it participates in “Fatty acid degradation” pathway. The methyl-accepting chemotaxis protein is an environmental signal that sense “Bacterial chemotaxis” pathway to help establishing symbiosis with plant roots by recruiting/colonizing of microbial partners (symbionts) to plant rhizosphere. This information justifies the high enrichment of compounds in plant rhizosphere. The dual-specific aspartyl-tRNA (Asn)/glutamyl-tRNA (Gln) amidotransferase subunit A contributes to the plant ability to respond to watering as it participates in attaching the correct amino acid during translation to its cognate tRNA species, while hydrolyzing incorrectly attached amino acid. These two actions reduce the influence of oxidative stress in generating misfolded proteins and in reducing fidelity of translation.


Amplicon sequencing; PICRUSt; KEGG; GABA; symbionts; wild plants
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