Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species
Abstract
Panicum represents a large genus of many North American prairie grass species. These include switchgrass (Panicum virgatum), a biofuel crop candidate with wide geographic range, as well as Panicum hallii, a close relative to switchgrass, which serves as a model system for the study of Panicum genetics due to its diploid genome and short growth cycles. For the advancement of switchgrass as a biofuel crop, it is essential to understand host microbiome interactions, which can be impacted by plant genetics and environmental factors inducing ecotype-specific phenotypic traits. We here compared rhizosphere and root endosphere bacterial communities of upland and lowland P. virgatum and P. hallii genotypes planted at two sites in Texas. Our analysis shows that sampling site predominantly contributed to bacterial community variance in the rhizosphere, however, impacted root endosphere bacterial communities much less. Instead we observed a relatively large core endophytic microbiome dominated by ubiquitously root-colonizing bacterial genera Streptomyces, Pseudomonas, and Bradyrhizobium. Endosphere communities displayed comparable diversity and conserved community structures across genotypes of both Panicum species. Functional insights into interactions between P. hallii and its root endophyte microbiome could hence inform testable hypotheses that are relevant for the improvement of switchgrass as a biofuel crop.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Texas, Austin, TX (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Texas, Austin, TX (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1580863
- Alternate Identifier(s):
- OSTI ID: 1594755
- Grant/Contract Number:
- AC02-05CH11231; SC0014156
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: SEP; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; plant microbiome; Panicum; rhizosphere; root endosphere; core microbiome; biofuel
Citation Formats
Singer, Esther, Bonnette, Jason, Woyke, Tanja, and Juenger, Thomas E. Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species. United States: N. p., 2019.
Web. doi:10.3389/fmicb.2019.02181.
Singer, Esther, Bonnette, Jason, Woyke, Tanja, & Juenger, Thomas E. Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species. United States. doi:10.3389/fmicb.2019.02181.
Singer, Esther, Bonnette, Jason, Woyke, Tanja, and Juenger, Thomas E. Fri .
"Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species". United States. doi:10.3389/fmicb.2019.02181. https://www.osti.gov/servlets/purl/1580863.
@article{osti_1580863,
title = {Conservation of Endophyte Bacterial Community Structure Across Two Panicum Grass Species},
author = {Singer, Esther and Bonnette, Jason and Woyke, Tanja and Juenger, Thomas E.},
abstractNote = {Panicum represents a large genus of many North American prairie grass species. These include switchgrass (Panicum virgatum), a biofuel crop candidate with wide geographic range, as well as Panicum hallii, a close relative to switchgrass, which serves as a model system for the study of Panicum genetics due to its diploid genome and short growth cycles. For the advancement of switchgrass as a biofuel crop, it is essential to understand host microbiome interactions, which can be impacted by plant genetics and environmental factors inducing ecotype-specific phenotypic traits. We here compared rhizosphere and root endosphere bacterial communities of upland and lowland P. virgatum and P. hallii genotypes planted at two sites in Texas. Our analysis shows that sampling site predominantly contributed to bacterial community variance in the rhizosphere, however, impacted root endosphere bacterial communities much less. Instead we observed a relatively large core endophytic microbiome dominated by ubiquitously root-colonizing bacterial genera Streptomyces, Pseudomonas, and Bradyrhizobium. Endosphere communities displayed comparable diversity and conserved community structures across genotypes of both Panicum species. Functional insights into interactions between P. hallii and its root endophyte microbiome could hence inform testable hypotheses that are relevant for the improvement of switchgrass as a biofuel crop.},
doi = {10.3389/fmicb.2019.02181},
journal = {Frontiers in Microbiology},
number = SEP,
volume = 10,
place = {United States},
year = {2019},
month = {9}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 1 work
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
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
Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters: Network analysis of microbial community structure
journal, August 2014
- de Menezes, Alexandre B.; Prendergast-Miller, Miranda T.; Richardson, Alan E.
- Environmental Microbiology, Vol. 17, Issue 8
Mechanism of phosphate solubilization and antifungal activity of Streptomyces spp. isolated from wheat roots and rhizosphere and their application in improving plant growth
journal, April 2014
- Jog, Rahul; Pandya, Maharshi; Nareshkumar, G.
- Microbiology, Vol. 160, Issue 4
Endophytic communities of rhizobacteria and the strategies required to create yield enhancing associations with crops
journal, October 2000
- Sturz, A. V.; Nowak, J.
- Applied Soil Ecology, Vol. 15, Issue 2
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Phylogenetic analyses of symbiotic nodulation genes support vertical and lateral gene co-transfer within the Bradyrhizobium genus
journal, March 2004
- Moulin, Lionel; Béna, Gilles; Boivin-Masson, Catherine
- Molecular Phylogenetics and Evolution, Vol. 30, Issue 3
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
PyNAST: a flexible tool for aligning sequences to a template alignment
journal, November 2009
- Caporaso, J. G.; Bittinger, K.; Bushman, F. D.
- Bioinformatics, Vol. 26, Issue 2
Impact of Glyphosate on the Symbiosis with Glyphosate-Resistant Transgenic Soybean
journal, January 2004
- Zablotowicz, Robert M.; Reddy, Krishna N.
- Journal of Environment Quality, Vol. 33, Issue 3
Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence
journal, August 2017
- Yeoh, Yun Kit; Dennis, Paul G.; Paungfoo-Lonhienne, Chanyarat
- Nature Communications, Vol. 8, Issue 1
Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation
journal, June 2017
- He, Shubin; Guo, Lixiang; Niu, Mengying
- Scientific Reports, Vol. 7, Issue 1
Practical innovations for high-throughput amplicon sequencing
journal, September 2013
- Lundberg, Derek S.; Yourstone, Scott; Mieczkowski, Piotr
- Nature Methods, Vol. 10, Issue 10
Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria
journal, May 2011
- Mendes, R.; Kruijt, M.; de Bruijn, I.
- Science, Vol. 332, Issue 6033
The gut microbiome in health and in disease
journal, January 2015
- Shreiner, Andrew B.; Kao, John Y.; Young, Vincent B.
- Current Opinion in Gastroenterology, Vol. 31, Issue 1
New extractant for soil test evaluation of phosphorus, potassium, magnesium, calcium, sodium, manganese and zinc
journal, January 1978
- Mehlich, A.
- Communications in Soil Science and Plant Analysis, Vol. 9, Issue 6
Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation
journal, July 2014
- Laine, Anna-Liisa; Burdon, Jeremy J.; Nemri, Adnane
- Proceedings of the Royal Society B: Biological Sciences, Vol. 281, Issue 1787
Glycoside Hydrolase Activities of Thermophilic Bacterial Consortia Adapted to Switchgrass
journal, July 2011
- Gladden, John M.; Allgaier, Martin; Miller, Christopher S.
- Applied and Environmental Microbiology, Vol. 77, Issue 16, p. 5804-5812
Root-induced changes in the rhizosphere: Importance for the mineral nutrition of plants
journal, January 1986
- Marschner, H.; Römheld, V.; Horst, W. J.
- Zeitschrift für Pflanzenernährung und Bodenkunde, Vol. 149, Issue 4
Historical and current climate drive spatial and temporal patterns in fungal endophyte diversity
journal, April 2016
- Giauque, Hannah; Hawkes, Christine V.
- Fungal Ecology, Vol. 20
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Defining the core Arabidopsis thaliana root microbiome
journal, August 2012
- Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera
- Nature, Vol. 488, Issue 7409
Primer and platform effects on 16S rRNA tag sequencing
journal, August 2015
- Tremblay, Julien; Singh, Kanwar; Fern, Alison
- Frontiers in Microbiology, Vol. 6
Dedicated Energy Crops and Crop Residues for Bioenergy Feedstocks in the Central and Eastern USA
journal, June 2016
- Mitchell, R. B.; Schmer, M. R.; Anderson, W. F.
- BioEnergy Research, Vol. 9, Issue 2
Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling
journal, July 2014
- Piao, Hailan; Lachman, Medora; Malfatti, Stephanie
- Frontiers in Microbiology, Vol. 5
Endophytic bacteria improve nodule function and plant nitrogen in soybean on co-inoculation with Bradyrhizobium japonicum MN110
journal, October 2014
- Subramanian, Parthiban; Kim, Kiyoon; Krishnamoorthy, Ramasamy
- Plant Growth Regulation, Vol. 76, Issue 3
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
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
journal, July 2002
- Katoh, K.
- Nucleic Acids Research, Vol. 30, Issue 14
Plant–Soil–Microorganism Interactions: Heritable Relationship Between Plant Genotype and Associated soil Microorganisms
journal, March 2008
- Schweitzer, Jennifer A.; Bailey, Joseph K.; Fischer, Dylan G.
- Ecology, Vol. 89, Issue 3
Development of switchgrass (Panicum virgatum) as a bioenergy feedstock in the United States
journal, June 2005
- McLaughlin, Samuel B.; Adams Kszos, Lynn
- Biomass and Bioenergy, Vol. 28, Issue 6
One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation
journal, June 2019
- Chen, Huaihai; Yang, Zamin K.; Yip, Dan
- PLOS ONE, Vol. 14, Issue 6
Switchgrass as a biofuels feedstock in the USA
journal, December 2006
- Sanderson, M. A.; Adler, P. R.; Boateng, A. A.
- Canadian Journal of Plant Science, Vol. 86, Issue Special Issue
Plant growth stimulation by inoculation with symbiotic and associative rhizosphere microorganisms
journal, October 1994
- Höflich, G.; Wiehe, W.; Kühn, G.
- Experientia, Vol. 50, Issue 10
The rhizosphere microbiome and plant health
journal, August 2012
- Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M.
- Trends in Plant Science, Vol. 17, Issue 8
Impacts of biodiversity on the emergence and transmission of infectious diseases
journal, December 2010
- Keesing, Felicia; Belden, Lisa K.; Daszak, Peter
- Nature, Vol. 468, Issue 7324
Associative nitrogen fixation (ANF) in switchgrass (Panicum virgatum) across a nitrogen input gradient
journal, June 2018
- Roley, Sarah S.; Duncan, David S.; Liang, Di
- PLOS ONE, Vol. 13, Issue 6
Microbial phylotype composition and diversity predicts plant productivity and plant-soil feedbacks
journal, December 2012
- Bever, James D.; Broadhurst, Linda M.; Thrall, Peter H.
- Ecology Letters, Vol. 16, Issue 2
Plant growth promotion induced by phosphate solubilizing endophytic Pseudomonas isolates
journal, July 2015
- Oteino, Nicholas; Lally, Richard D.; Kiwanuka, Samuel
- Frontiers in Microbiology, Vol. 6
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
Isolation and characterization of indigenous endophytic bacteria associated with leaves of switchgrass ( Panicum virgatum L.) cultivars
journal, January 2013
- Gagne-Bourgue, F.; Aliferis, K. A.; Seguin, P.
- Journal of Applied Microbiology, Vol. 114, Issue 3
Bioactive secondary metabolites produced by microorganisms associated with plants
journal, January 2007
- Firáková, Silvia; Šturdíková, Mária; Múčková, Marta
- Biologia, Vol. 62, Issue 3
The genomic landscape of molecular responses to natural drought stress in Panicum hallii
journal, December 2018
- Lovell, John T.; Jenkins, Jerry; Lowry, David B.
- Nature Communications, Vol. 9, Issue 1
A framework for community and ecosystem genetics: from genes to ecosystems
journal, July 2006
- Whitham, Thomas G.; Bailey, Joseph K.; Schweitzer, Jennifer A.
- Nature Reviews Genetics, Vol. 7, Issue 7
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
The Measurement of Soil pH
journal, April 1955
- Schofield, R. K.; Taylor, A. Wormald
- Soil Science Society of America Journal, Vol. 19, Issue 2
The plant growth-promoting effect of the nitrogen-fixing endophyte Pseudomonas stutzeri A15
journal, January 2017
- Pham, Van T. K.; Rediers, Hans; Ghequire, Maarten G. K.
- Archives of Microbiology, Vol. 199, Issue 3
Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?: Root exudates and rhizosphere bacteria
journal, March 2010
- Dennis, Paul G.; Miller, Anthony J.; Hirsch, Penny R.
- FEMS Microbiology Ecology, Vol. 72, Issue 3
Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species
journal, October 2015
- Coleman-Derr, Devin; Desgarennes, Damaris; Fonseca-Garcia, Citlali
- New Phytologist, Vol. 209, Issue 2
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
journal, July 2013
- D'haeseleer, Patrik; Gladden, John M.; Allgaier, Martin
- PLoS ONE, Vol. 8, Issue 7, Article No. e68465
Targeted Discovery of Glycoside Hydrolases from a Switchgrass-Adapted Compost Community
journal, January 2010
- Allgaier, Martin; Reddy, Amitha; Park, Joshua I.
- PLoS ONE, Vol. 5, Issue 1
Plant growth promotion by streptomycetes: ecophysiology, mechanisms and applications
journal, August 2016
- Sousa, Jucimara Anunciação de Jesus; Olivares, Fabio Lopes
- Chemical and Biological Technologies in Agriculture, Vol. 3, Issue 1
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification
journal, November 2016
- Wagner, Josef; Coupland, Paul; Browne, Hilary P.
- BMC Microbiology, Vol. 16, Issue 1
Characterization of culturable bacterial endophytes of switchgrass ( Panicum virgatum L.) and their capacity to influence plant growth
journal, September 2012
- Xia, Ye; Greissworth, Eliana; Mucci, Curtis
- GCB Bioenergy, Vol. 5, Issue 6