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

Coleman-Derr, Devin; Desgarennes, Damaris; Fonseca-Garcia, Citlali; Gross, Stephen; Clingenpeel, Scott; Woyke, Tanja; North, Gretchen; Visel, Axel; Partida-Martinez, Laila P.; Tringe, Susannah G.

doi:10.1111/nph.13697

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

Journal Article · Thu Oct 15 00:00:00 EDT 2015 · New Phytologist

DOI:https://doi.org/10.1111/nph.13697· OSTI ID:1378714

Coleman-Derr, Devin ^[1]; Desgarennes, Damaris ^[2]; Fonseca-Garcia, Citlali ^[2]; Gross, Stephen ^[3]; Clingenpeel, Scott ^[3]; Woyke, Tanja ^[3]; North, Gretchen ^[4]; Visel, Axel ^[5];

^[2]; Tringe, Susannah G. ^[3]

USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division; USDA Agricultural Research Service (ARS), Albany, CA (United States). Plant Gene Expression Center
Center for Research and Advanced Studies (CINVESTAV), Irapuato (Mexico). Dept. of Genetic Engineering
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Occidental College, Los Angeles, CA (United States). Dept. of Biology
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division; Univ. of California, Merced, CA (United States). School of Natural Sciences

Desert plants are hypothesized to survive the environmental stress inherent to these regions in part thanks to symbioses with microorganisms, 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 with native agaves, although 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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); National Council of Science and Technology (CONACYT) (Mexico)

Contributing Organization:: USDA Agricultural Research Service (ARS), Albany, CA (United States); Occidental College, Los Angeles, CA (United States); Univ. of California, Merced, CA (United States)

Grant/Contract Number:: AC02-05CH11231; CB-2010-01-151007; INFR-2012-01-197799

OSTI ID:: 1378714

Journal Information:: New Phytologist, Vol. 209, Issue 2; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 453 works

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Not only priming: Soil microbiota may protect tomato from root pathogens Chialva, Matteo; Zhou, Yang; Spadaro, Davide Plant Signaling & Behavior https://doi.org/10.1080/15592324.2018.1464855	journal	April 2018
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The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ Wei, Na; Ashman, Tia-Lynn Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-23518-9	journal	March 2018
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A Friend in Need (of Nutrients) Is a… Liberman, Louisa M.; Benfey, Philip N. Cell, Vol. 165, Issue 2 https://doi.org/10.1016/j.cell.2016.03.036	journal	April 2016
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Putting the Mess in Order: Aspergillus welwitschiae (and Not A. niger) Is the Etiological Agent of Sisal Bole Rot Disease in Brazil Duarte, Elizabeth A. A.; Damasceno, Caroline L.; de Oliveira, Thiago A. S. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01227	journal	June 2018

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