Identifying critical microbes in guayule-microbe and microbe-microbe associations

Background: Plant-microbe associations play central roles in ecosystem functioning, with some critical microbes significantly influencing the growth and health of plants. Additionally, some microbes are highly associated with other microbes in either competitive or cooperative microbe-microbe associations. Here, we aimed to determine whether there is overlap between critical microbes in plant-microbe and microbe-microbe associations by using guayule (a rubber-producing crop) as a model plant. Methods: Using marker gene amplicon sequencing, we characterized the bacterial/archaeal and fungal communities in soil samples collected from a guayule agroecosystem at six time points that represent changes in guayule productivity and growth stage. The critical microbes in guayule-microbe associations were phylotypes whose relative abundances were positively (positive taxa) or negatively (negative taxa) associated with guayule productivity. Network analysis was used to identify the critical microbes in microbe-microbe associations. Results: Some positive taxa in guayule-microbe associations were ammonia-oxidizing archaea (AOA) and bacteria (AOB) and arbuscular mycorrhizal fungi (AMF), and negative taxa included some microbes resistant to aridity. Some of the critical microbes in microbe-microbe associations were fungal plant pathogens. There were 9 phylotypes representing the overlap between critical microbes in guayule-microbe and microbe-microbe associations. This overlap group included AOB, phototrophic bacteria, AMF, and saprotrophic fungi, along with unique taxa of unknown function. Conclusions: Our study highlighted the association of the soil microbiome with the growth and health of guayule. Our systematic approach narrowed down the immense number of microbial taxa to a ‘most wanted’ list that we define as critical to the entire guayule agroecosystem.