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

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.

Severe and mild drought cause distinct phylogenetically linked shifts in the blue grama (Bouteloua gracilis) rhizobiome

“…We hypothesize that the small diameter of our pots (6.4 cm) did not allow for sufficient coring distance from plant roots to make this distinction as the roots largely filled the available space. This finding challenges a common working definition of rhizosphere soil as that which is specifically attached to roots (Chaparro et al, 2014;Zhu et al, 2020;Shami et al, 2022). Kuzyakov and Razavi (2019) reviewed the temporal dynamics and spatial stationarity of plant rhizospheres and found that the rhizosphere generally extends 0.5-4 mm from plant roots.…”

Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

“… Citrus rhizosphere [ 102 ] Rhizophagus , Burkholderia , Trichoderma , Fusarium , Ochrobactrum phage POA1180 , Blastococcus , Microvirga , Nocardioides , Geodermatophilus , Belnapia , Solirubrobacter , Arthrobacter , Mycobacterium phage Edugator , and Mycobacterium phage Kratio Not identified. Cleome pallida (Desert plant) rhizosphere [ 103 ] Kaistobacter and Rubrobacter Bacillus Nocardioides , Cellulomonas , Skermanella , Methylobacterium , Modestobacter and Aeromicrobium , Rhizobiales , Kaistobacter , Rubrobacter or Bacillus Metabolism of carbohydrate (especially C degradation) and membrane transporters. Carbohydrate degradation metabolism, carbohydrate synthesis, and its related energy metabolism.…”