skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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); 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:https://doi.org/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:https://doi.org/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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 119 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait: Root bacteria protect plants from drought
journal, March 2014

  • Rolli, Eleonora; Marasco, Ramona; Vigani, Gianpiero
  • Environmental Microbiology, Vol. 17, Issue 2
  • DOI: 10.1111/1462-2920.12439

Feedstocks for Lignocellulosic Biofuels
journal, August 2010

  • Somerville, Cris; Youngs, Heather; Taylor, Caroline
  • Science, Vol. 329, Issue 5993, p. 790-792
  • DOI: 10.1126/science.1189268

Plant-Growth-Promoting Rhizobacteria
journal, October 2009


Diversity and distribution of soil fungal communities in a semiarid grassland
journal, January 2011

  • Porras-Alfaro, Andrea; Herrera, Jose; Natvig, Donald O.
  • Mycologia, Vol. 103, Issue 1
  • DOI: 10.3852/09-297

Highlights for Agave Productivity: AGAVE PRODUCTIVITY
journal, November 2010


Analysis of gene sequences indicates that quantity not quality of chloroplast small HSPs improves thermotolerance in C4 and CAM plants
journal, July 2012


Exploiting the potential of plants with crassulacean acid metabolism for bioenergy production on marginal lands
journal, April 2009

  • Borland, A. M.; Griffiths, H.; Hartwell, J.
  • Journal of Experimental Botany, Vol. 60, Issue 10
  • DOI: 10.1093/jxb/erp118

Saving the agave
journal, December 2005


Structure, variation, and assembly of the root-associated microbiomes of rice
journal, January 2015

  • Edwards, Joseph; Johnson, Cameron; Santos-Medellín, Christian
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 8
  • DOI: 10.1073/pnas.1414592112

Selective progressive response of soil microbial community to wild oat roots
journal, November 2008

  • DeAngelis, Kristen M.; Brodie, Eoin L.; DeSantis, Todd Z.
  • The ISME Journal, Vol. 3, Issue 2
  • DOI: 10.1038/ismej.2008.103

Potential of Plants from the Genus Agave as Bioenergy Crops
journal, October 2011


Practical innovations for high-throughput amplicon sequencing
journal, September 2013

  • Lundberg, Derek S.; Yourstone, Scott; Mieczkowski, Piotr
  • Nature Methods, Vol. 10, Issue 10
  • DOI: 10.1038/nmeth.2634

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Selection on soil microbiomes reveals reproducible impacts on plant function
journal, October 2014

  • Panke-Buisse, Kevin; Poole, Angela C.; Goodrich, Julia K.
  • The ISME Journal, Vol. 9, Issue 4
  • DOI: 10.1038/ismej.2014.196

Photosynthetic acclimation to drought stress in Agave salmiana Otto ex Salm-Dyck seedlings is largely dependent on thermal dissipation and enhanced electron flux to photosystem I
journal, May 2014

  • Campos, Huitziméngari; Trejo, Carlos; Peña-Valdivia, Cecilia B.
  • Photosynthesis Research, Vol. 122, Issue 1
  • DOI: 10.1007/s11120-014-0008-6

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives
journal, December 2013

  • Schlaeppi, K.; Dombrowski, N.; Oter, R. G.
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 2
  • DOI: 10.1073/pnas.1321597111

The Soil Microbiome Influences Grapevine-Associated Microbiota
journal, March 2015

  • Zarraonaindia, Iratxe; Owens, Sarah M.; Weisenhorn, Pamela
  • mBio, Vol. 6, Issue 2
  • DOI: 10.1128/mBio.02527-14

Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States
journal, October 2013


Impact of Shortened Crop Rotation of Oilseed Rape on Soil and Rhizosphere Microbial Diversity in Relation to Yield Decline
journal, April 2013


Defining the core Arabidopsis thaliana root microbiome
journal, August 2012

  • Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera
  • Nature, Vol. 488, Issue 7409
  • DOI: 10.1038/nature11237

Seasonal Community Succession of the Phyllosphere Microbiome
journal, March 2015

  • Copeland, Julia K.; Yuan, Lijie; Layeghifard, Mehdi
  • Molecular Plant-Microbe Interactions, Vol. 28, Issue 3
  • DOI: 10.1094/MPMI-10-14-0331-FI

Associations with rhizosphere bacteria can confer an adaptive advantage to plants
journal, May 2015


Agave for tequila and biofuels: an economic assessment and potential opportunities: ECONOMIC ASSESSMENT AND OPPORTUNITIES OF AGAVE
journal, December 2010


The importance of the microbiome of the plant holobiont
journal, February 2015

  • Vandenkoornhuyse, Philippe; Quaiser, Achim; Duhamel, Marie
  • New Phytologist, Vol. 206, Issue 4
  • DOI: 10.1111/nph.13312

Rhizosphere microbiome assemblage is affected by plant development
journal, November 2013

  • Chaparro, Jacqueline M.; Badri, Dayakar V.; Vivanco, Jorge M.
  • The ISME Journal, Vol. 8, Issue 4
  • DOI: 10.1038/ismej.2013.196

Microbial community biogeographic patterns in the rhizosphere of two Brazilian semi-arid leguminous trees
journal, February 2013

  • Lançoni, Milena Duarte; Taketani, Rodrigo Gouvêa; Kavamura, Vanessa Nessner
  • World Journal of Microbiology and Biotechnology, Vol. 29, Issue 7
  • DOI: 10.1007/s11274-013-1286-4

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees
journal, October 2013


The Phylogenetic Diversity of Metagenomes
journal, August 2011


UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013


Going back to the roots: the microbial ecology of the rhizosphere
journal, September 2013

  • Philippot, Laurent; Raaijmakers, Jos M.; Lemanceau, Philippe
  • Nature Reviews Microbiology, Vol. 11, Issue 11
  • DOI: 10.1038/nrmicro3109

Fungal Community Analysis by Large-Scale Sequencing of Environmental Samples
journal, September 2005


Identifying Factors Controlling the Continuous Corn Yield Penalty
journal, January 2013

  • Gentry, Laura F.; Ruffo, Matias L.; Below, Fred E.
  • Agronomy Journal, Vol. 105, Issue 2
  • DOI: 10.2134/agronj2012.0246

Taxonomical and functional microbial community selection in soybean rhizosphere
journal, February 2014

  • Mendes, Lucas W.; Kuramae, Eiko E.; Navarrete, Acácio A.
  • The ISME Journal, Vol. 8, Issue 8
  • DOI: 10.1038/ismej.2014.17

Conversion of the Amazon rainforest to agriculture results in biotic homogenization of soil bacterial communities
journal, December 2012

  • Rodrigues, J. L. M.; Pellizari, V. H.; Mueller, R.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 3
  • DOI: 10.1073/pnas.1220608110

Identification and Characterisation of Bacteria Causing Soft-rot in Agave tequilana
journal, March 2004


The global potential for Agave as a biofuel feedstock: AGAVE AS A BIOFUEL FEEDSTOCK
journal, November 2010


Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species
journal, November 2014

  • Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J.
  • FEMS Microbiology Ecology, Vol. 90, Issue 3
  • DOI: 10.1111/1574-6941.12438

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa
journal, July 2015


Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns
journal, October 2013

  • Meiser, Anjuli; Bálint, Miklós; Schmitt, Imke
  • New Phytologist, Vol. 201, Issue 2
  • DOI: 10.1111/nph.12532

Microbial inoculants and organic amendment improves plant establishment and soil rehabilitation under semiarid conditions
journal, February 2014


Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
journal, March 2015

  • Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C.
  • Cell Host & Microbe, Vol. 17, Issue 3
  • DOI: 10.1016/j.chom.2015.01.011

Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution
journal, August 2008


The plant microbiome
journal, June 2013


Genome-wide association study of Arabidopsis thaliana leaf microbial community
journal, November 2014

  • Horton, Matthew W.; Bodenhausen, Natacha; Beilsmith, Kathleen
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms6320

Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom Fungi
journal, October 2006

  • Taylor, John W.; Turner, Elizabeth; Townsend, Jeffrey P.
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1475
  • DOI: 10.1098/rstb.2006.1923

The Microbe-Free Plant: Fact or Artifact?
journal, January 2011


Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota
journal, August 2012

  • Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus
  • Nature, Vol. 488, Issue 7409
  • DOI: 10.1038/nature11336

Agave as a biofuel feedstock in Australia: AGAVE IN AUSTRALIA
journal, December 2010


A strong species?area relationship for eukaryotic soil microbes: island size matters for ectomycorrhizal fungi
journal, June 2007


Genetic transformation of Agave salmiana by Agrobacterium tumefaciens and particle bombardment
journal, September 2007

  • Flores-Benítez, Silvia; Jiménez-Bremont, Juan F.; Rosales-Mendoza, Sergio
  • Plant Cell, Tissue and Organ Culture, Vol. 91, Issue 3
  • DOI: 10.1007/s11240-007-9287-3

The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms
journal, September 2013

  • Mendes, Rodrigo; Garbeva, Paolina; Raaijmakers, Jos M.
  • FEMS Microbiology Reviews, Vol. 37, Issue 5
  • DOI: 10.1111/1574-6976.12028

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide
journal, March 2013

  • Lindahl, Björn D.; Nilsson, R. Henrik; Tedersoo, Leho
  • New Phytologist, Vol. 199, Issue 1
  • DOI: 10.1111/nph.12243

Diversity and heritability of the maize rhizosphere microbiome under field conditions
journal, April 2013

  • Peiffer, J. A.; Spor, A.; Koren, O.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 16
  • DOI: 10.1073/pnas.1302837110

Inside the root microbiome: Bacterial root endophytes and plant growth promotion
journal, September 2013

  • Gaiero, Jonathan R.; McCall, Crystal A.; Thompson, Karen A.
  • American Journal of Botany, Vol. 100, Issue 9
  • DOI: 10.3732/ajb.1200572

Light to liquid fuel: theoretical and realized energy conversion efficiency of plants using Crassulacean Acid Metabolism (CAM) in arid conditions
journal, April 2014

  • Davis, Sarah C.; LeBauer, David S.; Long, Stephen P.
  • Journal of Experimental Botany, Vol. 65, Issue 13
  • DOI: 10.1093/jxb/eru163

Agave proves to be a low recalcitrant lignocellulosic feedstock for biofuels production on semi-arid lands
journal, January 2014

  • Li, Hongjia; Pattathil, Sivakumar; Foston, Marcus B.
  • Biotechnology for Biofuels, Vol. 7, Issue 1
  • DOI: 10.1186/1754-6834-7-50

A Drought Resistance-Promoting Microbiome Is Selected by Root System under Desert Farming
journal, October 2012


Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys
journal, December 2011

  • Werner, Jeffrey J.; Zhou, Dennis; Caporaso, J. Gregory
  • The ISME Journal, Vol. 6, Issue 7
  • DOI: 10.1038/ismej.2011.186

    Works referencing / citing this record:

    Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities
    journal, September 2018


    Rhizocompartments and environmental factors affect microbial composition and variation in native plants
    journal, June 2019


    Putting the Mess in Order: Aspergillus welwitschiae (and Not A. niger) Is the Etiological Agent of Sisal Bole Rot Disease in Brazil
    journal, June 2018

    • Duarte, Elizabeth A. A.; Damasceno, Caroline L.; de Oliveira, Thiago A. S.
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.01227

    Bacterial endophyte communities in Pinus flexilis are structured by host age, tissue type, and environmental factors
    journal, May 2018


    Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions
    journal, May 2018


    Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling
    journal, July 2019


    Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes
    journal, June 2019


    Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
    journal, July 2016

    • Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms12151

    Drought and host selection influence bacterial community dynamics in the grass root microbiome
    journal, July 2017

    • Naylor, Dan; DeGraaf, Stephanie; Purdom, Elizabeth
    • The ISME Journal, Vol. 11, Issue 12
    • DOI: 10.1038/ismej.2017.118

    Genomic features of bacterial adaptation to plants
    journal, December 2017

    • Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian
    • Nature Genetics, Vol. 50, Issue 1
    • DOI: 10.1038/s41588-017-0012-9

    A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens
    journal, November 2018

    • Daru, Barnabas H.; Bowman, Elizabeth A.; Pfister, Donald H.
    • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, Issue 1763
    • DOI: 10.1098/rstb.2017.0395

    Environmental filtering structures fungal endophyte communities in tree bark
    journal, October 2019

    • Pellitier, Peter T.; Zak, Donald R.; Salley, Sydney O.
    • Molecular Ecology, Vol. 28, Issue 23
    • DOI: 10.1111/mec.15237

    Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies
    journal, May 2016


    Bacterial endophyte communities in Pinus flexilis are structured by host age, tissue type, and environmental factors
    journal, May 2018


    Rhizocompartments and environmental factors affect microbial composition and variation in native plants
    journal, June 2019


    Influence of phylogenetic conservatism and trait convergence on the interactions between fungal root endophytes and plants
    journal, November 2016

    • Kia, Sevda Haghi; Glynou, Kyriaki; Nau, Thomas
    • The ISME Journal, Vol. 11, Issue 3
    • DOI: 10.1038/ismej.2016.140

    Drought and host selection influence bacterial community dynamics in the grass root microbiome
    journal, July 2017

    • Naylor, Dan; DeGraaf, Stephanie; Purdom, Elizabeth
    • The ISME Journal, Vol. 11, Issue 12
    • DOI: 10.1038/ismej.2017.118

    Host genotype and age shape the leaf and root microbiomes of a wild perennial plant
    journal, July 2016

    • Wagner, Maggie R.; Lundberg, Derek S.; del Rio, Tijana G.
    • Nature Communications, Vol. 7, Issue 1
    • DOI: 10.1038/ncomms12151

    Genomic features of bacterial adaptation to plants
    journal, December 2017

    • Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian
    • Nature Genetics, Vol. 50, Issue 1
    • DOI: 10.1038/s41588-017-0012-9

    Host species identity in annual Brassicaceae has a limited effect on the assembly of root-endophytic fungal communities
    journal, September 2018


    A novel proof of concept for capturing the diversity of endophytic fungi preserved in herbarium specimens
    journal, November 2018

    • Daru, Barnabas H.; Bowman, Elizabeth A.; Pfister, Donald H.
    • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 374, Issue 1763
    • DOI: 10.1098/rstb.2017.0395

    Environmental filtering structures fungal endophyte communities in tree bark
    journal, October 2019

    • Pellitier, Peter T.; Zak, Donald R.; Salley, Sydney O.
    • Molecular Ecology, Vol. 28, Issue 23
    • DOI: 10.1111/mec.15237

    Revegetation on abandoned salt ponds relieves the seasonal fluctuation of soil microbiomes
    journal, June 2019


    Performance of 16s rDNA Primer Pairs in the Study of Rhizosphere and Endosphere Bacterial Microbiomes in Metabarcoding Studies
    journal, May 2016


    Putting the Mess in Order: Aspergillus welwitschiae (and Not A. niger) Is the Etiological Agent of Sisal Bole Rot Disease in Brazil
    journal, June 2018

    • Duarte, Elizabeth A. A.; Damasceno, Caroline L.; de Oliveira, Thiago A. S.
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.01227

    Plant Phenotypic Traits Eventually Shape Its Microbiota: A Common Garden Test
    journal, November 2018


    Microbiome of the Black-Lipped Pearl Oyster Pinctada margaritifera, a Multi-Tissue Description With Functional Profiling
    journal, July 2019


    Microbiome Dynamics Associated With the Atacama Flowering Desert
    journal, January 2020

    • Araya, Juan Pablo; González, Máximo; Cardinale, Massimiliano
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.03160

    Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions
    journal, May 2018


    Mycobiota of maize seeds revealed by rDNAITS sequence analysis of samples with varying storage times
    journal, March 2018

    • Xing, Hui‐Qin; Ma, Jian‐Cang; Xu, Bing‐Liang
    • MicrobiologyOpen, Vol. 7, Issue 6
    • DOI: 10.1002/mbo3.609

    Fungal Communities of the Canola Rhizosphere: Keystone Species and Substantial Between-Year Variation of the Rhizosphere Microbiome
    journal, January 2020


    The effect of environment on the microbiome associated with the roots of a native woody plant under different climate types in China
    journal, March 2019

    • Chen, Peilin; Zhao, Meilin; Tang, Feng
    • Applied Microbiology and Biotechnology, Vol. 103, Issue 9
    • DOI: 10.1007/s00253-019-09747-6

    Assembly of root-associated microbial community of typical rice cultivars in different soil types
    journal, December 2019


    Distinct factors drive the assembly of quinoa-associated microbiomes along elevation
    journal, January 2020


    Strengthening desert plant biotechnology research in the United Arab Emirates: a viewpoint
    journal, May 2018

    • Gairola, Sanjay; Al Shaer, Khawla I.; Al Harthi, Eman K.
    • Physiology and Molecular Biology of Plants, Vol. 24, Issue 4
    • DOI: 10.1007/s12298-018-0551-2

    Building plant microbiome vault: a future biotechnological resource
    journal, September 2018


    Prospecting the characteristics and significance of the phyllosphere microbiome
    journal, March 2018


    Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota
    journal, April 2017


    The stage of soil development modulates rhizosphere effect along a High Arctic desert chronosequence
    journal, January 2018


    In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana
    journal, May 2018


    Root microbiota assembly and adaptive differentiation among European Arabidopsis populations
    journal, December 2019

    • Thiergart, Thorsten; Durán, Paloma; Ellis, Thomas
    • Nature Ecology & Evolution, Vol. 4, Issue 1
    • DOI: 10.1038/s41559-019-1063-3

    Insights into the functionality of endophytic actinobacteria with a focus on their biosynthetic potential and secondary metabolites production
    journal, September 2017


    Bacterial communities associated to Chilean altiplanic native plants from the Andean grasslands soils
    journal, January 2019

    • Fernández-Gómez, Beatriz; Maldonado, Jonathan; Mandakovic, Dinka
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-018-37776-0

    Metabarcoding reveals that rhizospheric microbiota of Quercus pyrenaica is composed by a relatively small number of bacterial taxa highly abundant
    journal, February 2019

    • Lasa, Ana V.; Fernández-González, Antonio J.; Villadas, Pablo J.
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-018-38123-z

    Deciphering the microbiome shift during fermentation of medicinal plants
    journal, September 2019


    Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil
    journal, October 2019

    • Brisson, Vanessa L.; Schmidt, Jennifer E.; Northen, Trent R.
    • Scientific Reports, Vol. 9, Issue 1
    • DOI: 10.1038/s41598-019-52148-y

    Root-associated fungal microbiota of nonmycorrhizal Arabis alpina and its contribution to plant phosphorus nutrition
    journal, October 2017

    • Almario, Juliana; Jeena, Ganga; Wunder, Jörg
    • Proceedings of the National Academy of Sciences, Vol. 114, Issue 44
    • DOI: 10.1073/pnas.1710455114

    Characterization of Microbial Communities Populating the Inflorescences of Humulus lupulus L.
    journal, October 2019

    • Allen, Mary E.; Piefer, Andrew J.; Cole, Sean N.
    • Journal of the American Society of Brewing Chemists, Vol. 77, Issue 4
    • DOI: 10.1080/03610470.2019.1667739

    Plants exhibit significant effects on the rhizospheric microbiome across contrasting soils in tropical and subtropical China
    journal, July 2019

    • Xu, Shangqi; Tian, Lei; Chang, Chunling
    • FEMS Microbiology Ecology, Vol. 95, Issue 8
    • DOI: 10.1093/femsec/fiz100

    Potentials and pitfalls in the analysis of bipartite networks to understand plant–microbe interactions in changing environments
    journal, October 2018

    • Bennett, Alison E.; Evans, Darren M.; Powell, Jeff R.
    • Functional Ecology, Vol. 33, Issue 1
    • DOI: 10.1111/1365-2435.13223

    Can dynamic network modelling be used to identify adaptive microbiomes?
    journal, December 2019


    Soil compartment is a major determinant of the impact of simulated rainfall on desert microbiota: Microbial responses to watering desert soils
    journal, August 2016

    • Aslam, Shazia N.; Dumbrell, Alex J.; Sabir, Jamal S.
    • Environmental Microbiology, Vol. 18, Issue 12
    • DOI: 10.1111/1462-2920.13474

    Temperature drives the assembly of endophytic communities' seasonal succession
    journal, July 2017

    • Campisano, Andrea; Albanese, Davide; Yousaf, Sohail
    • Environmental Microbiology, Vol. 19, Issue 8
    • DOI: 10.1111/1462-2920.13843

    Plant compartment and genetic variation drive microbiome composition in switchgrass roots
    journal, January 2019

    • Singer, Esther; Bonnette, Jason; Kenaley, Shawn C.
    • Environmental Microbiology Reports, Vol. 11, Issue 2
    • DOI: 10.1111/1758-2229.12727

    Disentangling the factors shaping microbiota composition across the plant holobiont
    journal, December 2015


    Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana
    journal, November 2018

    • Fabiańska, Izabela; Gerlach, Nina; Almario, Juliana
    • New Phytologist, Vol. 221, Issue 4
    • DOI: 10.1111/nph.15538

    Native and Invading Yellow Starthistle ( Centaurea solstitialis ) Microbiomes Differ in Composition and Diversity of Bacteria
    journal, February 2019


    Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees
    journal, February 2017


    The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome
    journal, February 2018


    Microbial interactions within the plant holobiont
    journal, March 2018


    Soil productivity and structure of bacterial and fungal communities in unfertilized arable soil
    journal, September 2018


    Desert plant bacteria reveal host influence and beneficial plant growth properties
    journal, December 2018


    Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genus Dioon
    journal, February 2019


    Back to the Origin: In Situ Studies Are Needed to Understand Selection during Crop Diversification
    journal, October 2017

    • Chen, Yolanda H.; Shapiro, Lori R.; Benrey, Betty
    • Frontiers in Ecology and Evolution, Vol. 5
    • DOI: 10.3389/fevo.2017.00125

    The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity
    journal, February 2016

    • Fonseca-García, Citlali; Coleman-Derr, Devin; Garrido, Etzel
    • Frontiers in Microbiology, Vol. 7
    • DOI: 10.3389/fmicb.2016.00150

    Genome Sequences of a Plant Beneficial Synthetic Bacterial Community Reveal Genetic Features for Successful Plant Colonization
    journal, August 2019

    • de Souza, Rafael Soares Correa; Armanhi, Jaderson Silveira Leite; Damasceno, Natália de Brito
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.01779

    Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species
    journal, September 2019


    Dominant Groups of Potentially Active Bacteria Shared by Barley Seeds become Less Abundant in Root Associated Microbiome
    journal, June 2017


    A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome
    journal, January 2018

    • Armanhi, Jaderson Silveira Leite; de Souza, Rafael Soares Correa; Damasceno, Natália de Brito
    • Frontiers in Plant Science, Vol. 8
    • DOI: 10.3389/fpls.2017.02191

    Biostimulant Action of Protein Hydrolysates: Unraveling Their Effects on Plant Physiology and Microbiome
    journal, December 2017


    Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes
    journal, January 2019


    Exploration of Plant-Microbe Interactions for Sustainable Agriculture in CRISPR Era
    journal, August 2019


    Niche differentiation in the rhizosphere and endosphere fungal microbiome of wild Paris polyphylla Sm.
    journal, January 2020