Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

Ashwag Shami, Rewaa S. Jalal, Ruba A. Ashy, Haneen W. Abuauf, Lina Baz, Mohammed Y. Refai, Aminah A. Barqawi, Hanadi M. Baeissa, Manal A. Tashkandi, Sahar Alshareef and Aala A. Abulfaraj
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Ashwag Shami: Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
Rewaa S. Jalal: Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
Ruba A. Ashy: Department of Biology, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
Haneen W. Abuauf: Department of Biology, Faculty of Applied Science, Umm Al-Qura University, Makkah 24381, Saudi Arabia
Lina Baz: Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
Mohammed Y. Refai: Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
Aminah A. Barqawi: Department of Chemistry, Al-Leith University College, Umm Al Qura University, Makkah 28434, Saudi Arabia
Hanadi M. Baeissa: Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
Manal A. Tashkandi: Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
Sahar Alshareef: Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia
Aala A. Abulfaraj: Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia

Sustainability, 2022, vol. 14, issue 14, 1-21

Abstract: The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus ) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma , which have antagonistic activities against the eukaryotic genus Fusarium . Another example involves Ochrobactrum phage POA1180 , its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others ( Burkholderia and Trichoderma ) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes.

Keywords: relative abundance; non-redundant genes; Archaea; virome; symbiosis; antagonism; nitrogen fixation; ammonia oxidation (search for similar items in EconPapers)
JEL-codes: O13 Q Q0 Q2 Q3 Q5 Q56 (search for similar items in EconPapers)
Date: 2022
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