Abstract
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.
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Data availability
The raw sequence data reported have been deposited in the Sequence Read Archive under BioProject accession no. PRJNA940315.
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Acknowledgements
We acknowledge the help of Lia Q.R. Ossanna, Jessica Ledesma, and Ben Yang with soil sampling. We acknowledge the help of Adalee Martinez with DNA extraction. An allocation of computer resource from the UA Research Computing High Performance Computing (HPC) at the University of Arizona is gratefully acknowledged. The research was supported by USDA-NIFA grant 2017-68005-26867, Sustainable Bioeconomy for Arid Lands. Opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the view of US Department of Agriculture.
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DTR, AB, RMM, and JWN conceived the research. DAD, G(S)W, and DEME guided field work. YC and JWN performed soil sampling. YC analyzed the data and, along with JWN, led the writing of the manuscript. All authors contributed critically to manuscript writing and revisions.
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Chen, Y., Dierig, D.A., Wang, G.(. et al. Identifying critical microbes in guayule-microbe and microbe-microbe associations. Plant Soil 494, 269–284 (2024). https://doi.org/10.1007/s11104-023-06269-z
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DOI: https://doi.org/10.1007/s11104-023-06269-z