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

Abstract

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.

Authors:
 [1];  [2];  [2];  [3];  [3];  [3];  [4];  [5]; ORCiD logo [2];  [3]
  1. 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
  2. Center for Research and Advanced Studies (CINVESTAV), Irapuato (Mexico). Dept. of Genetic Engineering
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
  4. Occidental College, Los Angeles, CA (United States). Dept. of Biology
  5. 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
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Council of Science and Technology (CONACYT) (Mexico)
Contributing Org.:
USDA Agricultural Research Service (ARS), Albany, CA (United States); Occidental College, Los Angeles, CA (United States); Univ. of California, Merced, CA (United States)
OSTI Identifier:
1378714
Grant/Contract Number:  
AC02-05CH11231; CB-2010-01-151007; INFR-2012-01-197799
Resource Type:
Accepted Manuscript
Journal Name:
New Phytologist
Additional Journal Information:
Journal Volume: 209; Journal Issue: 2; Journal ID: ISSN 0028-646X
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Agave; biogeography; cultivation; desert; iTags; microbial diversity; plant microbiome; plant-microbe interactions

Citation Formats

Coleman-Derr, Devin, Desgarennes, Damaris, Fonseca-Garcia, Citlali, Gross, Stephen, Clingenpeel, Scott, Woyke, Tanja, North, Gretchen, Visel, Axel, Partida-Martinez, Laila P., and Tringe, Susannah G. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. United States: N. p., 2015. Web. doi:10.1111/nph.13697.
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. Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species. United States. doi:10.1111/nph.13697.
Coleman-Derr, Devin, Desgarennes, Damaris, Fonseca-Garcia, Citlali, Gross, Stephen, Clingenpeel, Scott, Woyke, Tanja, North, Gretchen, Visel, Axel, Partida-Martinez, Laila P., and Tringe, Susannah G. Thu . "Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species". United States. doi:10.1111/nph.13697. https://www.osti.gov/servlets/purl/1378714.
@article{osti_1378714,
title = {Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species},
author = {Coleman-Derr, Devin and Desgarennes, Damaris and Fonseca-Garcia, Citlali and Gross, Stephen and Clingenpeel, Scott and Woyke, Tanja and North, Gretchen and Visel, Axel and Partida-Martinez, Laila P. and Tringe, Susannah G.},
abstractNote = {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.},
doi = {10.1111/nph.13697},
journal = {New Phytologist},
number = 2,
volume = 209,
place = {United States},
year = {2015},
month = {10}
}

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