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ARS Home » Pacific West Area » Albany, California » Plant Gene Expression Center » Research » Publications at this Location » Publication #322873

Research Project: Molecular Genetics of Ethylene Biosynthesis

Location: Plant Gene Expression Center

Title: Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species.

Author
item Coleman-Derr, Devin
item DESGARENNES, DAMARIS - Guanajuato Campus Of Cinvestav
item FONSECA-GARCIA, CITLATI - Guanajuato Campus Of Cinvestav
item GROSS, STEPHEN - Joint Genome Institute
item CLINGENPEEL, SCOTT - Joint Genome Institute
item WOYKE, TANJA - Joint Genome Institute
item NORTH, GRETCHEN - Joint Genome Institute
item VISEL, AXEL - Joint Genome Institute
item PARTIDA-MARTTINEZ, LAILA - Guanajuato Campus Of Cinvestav
item TRINGE, SUSANNAH - Joint Genome Institute

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2015
Publication Date: N/A
Citation: N/A

Interpretive Summary: Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms (holobiont), and yet these microbial species, the communities they form, and the forces that influence them are poorly understood. Here we report the first comprehensive investigation of the microbial communities associated with species of Agave, which are native to semiarid and arid regions of Central and North America and are emerging as biofuel feedstocks. We examined prokaryotic and fungal communities in the rhizosphere, phyllosphere, leaf and root endosphere, as well as proximal and distal soil samples from cultivated and native agaves, through Illumina amplicon sequencing. Phylogenetic profiling revealed that the composition of prokaryotic communities was primarily determined by the plant compartment, whereas the composition of fungal communities was mainly influenced by the biogeography of the host species. Cultivated A. tequilana exhibited lower levels of prokaryotic diversity compared to native agaves, though no differences in microbial diversity were found in the endosphere. Agaves shared core prokaryotic and fungal taxa known to promote plant growth and confer tolerance to abiotic stress, which suggests common principles underpinning Agave-microbe interactions.

Technical Abstract: The primary goal of this research was to investigate the prokaryotic and fungal communities associated with the bulk soil, the rhizosphere, the phyllosphere, and the root and leaf endospheres, for three Agave species: the cultivated Agave tequilana and the native species, A. salmiana and A. deserti . These species were selected based on their natural geographic distribution, their differentiated management status (cultivated vs. native), and their relevance to both existing and prospective industries. Comparisons across these three Agave species would allow us to infer the impact of biogeography and cultivation status on microbial composition and diversity in the genus Agave. Additionally, we also evaluate the major biotic (i.e. plant species and plant compartment) and abiotic (i.e. season and site) factors shaping both prokaryotic and fungal communities, and identify prominent microbial players in order to develop rational microbiome-based strategies for improving agaves’ yield and productivity.