Community Structure and Metabolic Potentials of Keystone Taxa within Rice Root Endophytic Microbiome in Response to Multiple Metal(Loid)S Contamination

Abstract

Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress and promoting plant growth. The metabolic potentials of the endophytes, especially under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Accordingly, this study aims to characterize the composition and metabolic potential of endophytic microbiome in HM contaminated sites. Members of Burkholderiales and Rhizobiales were identified as keystone taxa in root endosphere microbiome under HM stress. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested they held diverse genetic potentials related to metal resistance and plant growth promotion. Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance and nitrogen and phosphate acquisition metabolisms were identified, suggesting these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages under HM stress. This knowledge provided valuable insights on future applications of employing root microbiome for safety management of agriculture productions.

Keywords: Heavy metal, Rice safety, plant growth, Keystone taxa, Metabolic potentials