Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes
Abstract
Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soil conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended tomore »
- Authors:
-
- Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Natural Resources and Environmental Sciences
- Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Crop Sciences
- Publication Date:
- Research Org.:
- South Dakota State Univ., Brookings, SD (United States)
- Sponsoring Org.:
- USDOE Office of Energy Efficiency and Renewable Energy (EERE), Sustainable Transportation Office. Bioenergy Technologies Office (BETO); Univ. of Illinois at Urbana-Champaign, IL (United States). Energy Farm; U.S. Department of Agriculture (USDA). Cooperative State Research, Education, and Extension Service (CSREES)
- OSTI Identifier:
- 1438470
- Alternate Identifier(s):
- OSTI ID: 1361197; OSTI ID: 1400692
- Grant/Contract Number:
- FC36-05GO85041; ILLU 875‐374
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Global Change Biology. Bioenergy
- Additional Journal Information:
- Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 1757-1693
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; bacterial community composition; bioenergy feedstock; diazotroph; endophytic compartment; Miscanthus 9 giganteus; rhizosphere; Miscanthus x giganteus
Citation Formats
Li, Dongfang, Voigt, Thomas B., and Kent, Angela D. Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes. United States: N. p., 2015.
Web. doi:10.1111/gcbb.12252.
Li, Dongfang, Voigt, Thomas B., & Kent, Angela D. Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes. United States. https://doi.org/10.1111/gcbb.12252
Li, Dongfang, Voigt, Thomas B., and Kent, Angela D. Thu .
"Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes". United States. https://doi.org/10.1111/gcbb.12252. https://www.osti.gov/servlets/purl/1438470.
@article{osti_1438470,
title = {Plant and soil effects on bacterial communities associated with Miscanthus × giganteus rhizosphere and rhizomes},
author = {Li, Dongfang and Voigt, Thomas B. and Kent, Angela D.},
abstractNote = {Here, bacterial assemblages, especially diazotroph assemblages residing in the rhizomes and the rhizosphere soil of Miscanthus × giganteus, contribute to plant growth and nitrogen use efficiency. However, the composition of these microbial communities has not been adequately explored nor have the potential ecological drivers for these communities been sufficiently studied. This knowledge is needed for understanding and potentially improving M. × giganteus – microbe interactions, and further enhancing sustainability of M. × giganteus production. In this study, cultivated M. × giganteus from four sites in Illinois, Kentucky, Nebraska, and New Jersey were collected to examine the relative influences of soil conditions and plant compartments on assembly of the M. × giganteus-associated microbiome. Automated ribosomal intergenic spacer (ARISA) and terminal restriction fragment length polymorphism (T-RFLP) targeting the nifH gene were applied to examine the total bacterial communities and diazotroph assemblages that reside in the rhizomes and the rhizosphere. Distinct microbial assemblages were detected in the endophytic and rhizosphere compartments. Site soil conditions had strong correlation with both total bacterial and diazotroph assemblages, but in different ways. Nitrogen treatments showed no significant effect on the composition of diazotroph assemblages in most sites. Endophytic compartments of different M. × giganteus plants tended to harbor similar microbial communities across all sites, whereas the rhizosphere soil of different plant tended to harbor diverse microbial assemblages that were distinct among sites. These observations offer insight into better understanding of the associative interactions between M. × giganteus and diazotrophs, and how this relationship is influenced by agronomic and edaphic factors.},
doi = {10.1111/gcbb.12252},
journal = {Global Change Biology. Bioenergy},
number = 1,
volume = 8,
place = {United States},
year = {Thu Apr 30 00:00:00 EDT 2015},
month = {Thu Apr 30 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
Annual Patterns in Bacterioplankton Community Variability in a Humic Lake
journal, October 2004
- Kent, A. D.; Jones, S. E.; Yannarell, A. C.
- Microbial Ecology, Vol. 48, Issue 4
The communities of endophytic diazotrophic bacteria in cultivated rice (Oryza sativa L.)
journal, June 2009
- Prakamhang, Janpen; Minamisawa, Kiwamu; Teamtaisong, Kamonluck
- Applied Soil Ecology, Vol. 42, Issue 2
Variations in the 15N natural abundance of plant-available N with soil depth: Their influence on estimates of contributions of biological N2 fixation to sugar cane
journal, January 2014
- Baptista, Rafael Butke; de Morais, Rafael Fiusa; Leite, José Marcos
- Applied Soil Ecology, Vol. 73
Microbiotas are Transmitted Between Holobiont Generations
book, January 2013
- Rosenberg, Eugene; Zilber-Rosenberg, Ilana
- The Hologenome Concept: Human, Animal and Plant Microbiota
Assembly and response rules: two goals for predictive community ecology
journal, April 1992
- Keddy, Paul A.
- Journal of Vegetation Science, Vol. 3, Issue 2
Soil and plant specific effects on bacterial community composition in the rhizosphere
journal, September 2001
- Marschner, P.; Yang, C. -H; Lieberei, R.
- Soil Biology and Biochemistry, Vol. 33, Issue 11
Properties of bacterial endophytes and their proposed role in plant growth
journal, October 2008
- Hardoim, Pablo R.; van Overbeek, Leo S.; Elsas, Jan Dirk van
- Trends in Microbiology, Vol. 16, Issue 10
Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics
journal, January 2004
- Rees, Gavin N.; Baldwin, Darren S.; Watson, Garth O.
- Antonie van Leeuwenhoek, Vol. 86, Issue 4
Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum ( Sorghum bicolor ) treated with contrasting levels of nitrogen fertilizer
journal, February 2008
- Rodrigues Coelho, Marcia Reed; de Vos, Marjon; Carneiro, Newton Portilho
- FEMS Microbiology Letters, Vol. 279, Issue 1
Comparison of nifH Gene Pools in Soils and Soil Microenvironments with Contrasting Properties
journal, May 2001
- Poly, F.; Ranjard, L.; Nazaret, S.
- Applied and Environmental Microbiology, Vol. 67, Issue 5
Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology
journal, January 2014
- Jami, Elie; Shterzer, Naama; Mizrahi, Itzhak
- Pathogens, Vol. 3, Issue 1
Biological nitrogen fixation associated with tropical pasture grasses
journal, January 2001
- Reis, Veronica M.; Jr, Fábio B. dos Reis; Quesada, Diego M.
- Functional Plant Biology, Vol. 28, Issue 9
Geographic and Environmental Sources of Variation in Lake Bacterial Community Composition
journal, January 2005
- Yannarell, A. C.; Triplett, E. W.
- Applied and Environmental Microbiology, Vol. 71, Issue 1
Miscanthus × giganteus productivity: the effects of management in different environments
journal, December 2011
- Maughan, Matt; Bollero, Germán; Lee, D. K.
- GCB Bioenergy, Vol. 4, Issue 3
Comparative Biogeochemical Cycles of Bioenergy Crops Reveal Nitrogen-Fixation and Low Greenhouse Gas Emissions in a Miscanthus × giganteus Agro-Ecosystem
journal, December 2009
- Davis, Sarah C.; Parton, William J.; Dohleman, Frank G.
- Ecosystems, Vol. 13, Issue 1
Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants.
journal, January 2001
- Kirchhof, G.; Reis, V. M.; Baldani, J. I.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 1
Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus.
journal, January 2001
- Weber, O. B.; Stoffels, M.; Hartmann, A.
- International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 1
Contribution of biological nitrogen fixation to Elephant grass (Pennisetum purpureum Schum.)
journal, September 2011
- de Morais, Rafael F.; Quesada, Diego M.; Reis, Veronica M.
- Plant and Soil, Vol. 356, Issue 1-2
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
journal, June 2009
- Lauber, C. L.; Hamady, M.; Knight, R.
- Applied and Environmental Microbiology, Vol. 75, Issue 15
Microbial Communities and Their Interactions in Soil and Rhizosphere Ecosystems
journal, October 2002
- Kent, Angela D.; Triplett, Eric W.
- Annual Review of Microbiology, Vol. 56, Issue 1
Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil
journal, January 2001
- Poly, Franck; Monrozier, Lucile Jocteur; Bally, René
- Research in Microbiology, Vol. 152, Issue 1
Improved methodology for isolation of Acetobacter diazotrophicus and confirmation of its endophytic habitat
journal, July 1994
- Reis, V. M.; Olivares, F. L.; D�bereiner, J.
- World Journal of Microbiology & Biotechnology, Vol. 10, Issue 4
Large-scale distribution of Atlantic nitrogen fixation controlled by iron availability
journal, November 2009
- Mark Moore, C.; Mills, Matthew M.; Achterberg, Eric P.
- Nature Geoscience, Vol. 2, Issue 12
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
journal, January 2011
- Chen, Hanbo; Boutros, Paul C.
- BMC Bioinformatics, Vol. 12, Issue 1
Seasonal dynamics of above- and below-ground biomass and nitrogen partitioning in Miscanthus × giganteus and Panicum virgatum across three growing seasons
journal, January 2012
- Dohleman, Frank G.; Heaton, Emily A.; Arundale, Rebecca A.
- GCB Bioenergy, Vol. 4, Issue 5
Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization
journal, May 2010
- Compant, Stéphane; Clément, Christophe; Sessitsch, Angela
- Soil Biology and Biochemistry, Vol. 42, Issue 5
Association Between Composition of the Human Gastrointestinal Microbiome and Development of Fatty Liver With Choline Deficiency
journal, March 2011
- Spencer, Melanie D.; Hamp, Timothy J.; Reid, Robert W.
- Gastroenterology, Vol. 140, Issue 3
Use of nitrogen-fixing bacteria as biofertiliser for non-legumes: prospects and challenges
journal, July 2008
- Bhattacharjee, Rumpa Biswas; Singh, Aqbal; Mukhopadhyay, S. N.
- Applied Microbiology and Biotechnology, Vol. 80, Issue 2
Novel Endophytic Nitrogen-Fixing Clostridia from the Grass Miscanthus sinensis as Revealed by Terminal Restriction Fragment Length Polymorphism Analysis
journal, November 2004
- Miyamoto, T.; Kawahara, M.; Minamisawa, K.
- Applied and Environmental Microbiology, Vol. 70, Issue 11
Nitrogen fixation in endophytic and associative symbiosis
journal, March 2000
- James, E. K.
- Field Crops Research, Vol. 65, Issue 2-3
Nutrient requirements of Miscanthus x giganteus: Conclusions from a review of published studies
journal, March 2012
- Cadoux, Stéphane; Riche, Andrew B.; Yates, Nicola E.
- Biomass and Bioenergy, Vol. 38
Regional and local factors affecting diversity, abundance and activity of free-living, N2-fixing bacteria in Australian agricultural soils
journal, October 2010
- Wakelin, S. A.; Gupta, V. V. S. R.; Forrester, S. T.
- Pedobiologia, Vol. 53, Issue 6
The role of root Exudates in Rhizosphere Interactions with Plants and Other Organisms
journal, June 2006
- Bais, Harsh P.; Weir, Tiffany L.; Perry, Laura G.
- Annual Review of Plant Biology, Vol. 57, Issue 1
Meta-analysis of the effects of management factors on Miscanthus×giganteus growth and biomass production
journal, July 2008
- Miguez, Fernando E.; Villamil, María Bonita; Long, Stephen P.
- Agricultural and Forest Meteorology, Vol. 148, Issue 8-9
Growth, yield and mineral content of Miscanthus×giganteus grown as a biofuel for 14 successive harvests
journal, November 2008
- Christian, D. G.; Riche, A. B.; Yates, N. E.
- Industrial Crops and Products, Vol. 28, Issue 3
The contribution of nitrogen fixation to sugarcane (Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial community
journal, October 2011
- Taulé, Cecilia; Mareque, Cintia; Barlocco, Claudia
- Plant and Soil, Vol. 356, Issue 1-2
Community Succession and Assembly: Comparing, Contrasting and Combining Paradigms in the Context of Ecological Restoration
journal, January 2001
- Young, Truman P.; Chase, Jonathan M.; Huddleston, Russell T.
- Ecological Restoration, Vol. 19, Issue 1
Life in grasses: diazotrophic endophytes
journal, April 1998
- Reinhold-Hurek, Barbara; Hurek, Thomas
- Trends in Microbiology, Vol. 6, Issue 4
Development of specific rhizosphere bacterial communities in relation to plant species, nutrition and soil type
journal, April 2004
- Marschner, Petra; Crowley, David; Yang, Ching Hong
- Plant and Soil, Vol. 261, Issue 1/2
The iron-molybdenum cofactor of nitrogenase
journal, December 1990
- Burgess, Barbara K.
- Chemical Reviews, Vol. 90, Issue 8
Biological Nitrogen Fixation in Sugar Cane: A Key to Energetically Viable Biofuel Production
journal, January 1995
- Boddey, Robert M.
- Critical Reviews in Plant Sciences, Vol. 14, Issue 3
A quantitative review comparing the yields of two candidate C4 perennial biomass crops in relation to nitrogen, temperature and water
journal, July 2004
- Heaton, E.
- Biomass and Bioenergy, Vol. 27, Issue 1
Evidence of variability in the structure and recruitment of rhizospheric and endophytic bacterial communities associated with arable sweet sorghum (Sorghum bicolor (L) Moench)
journal, May 2013
- Ramond, Jean-Baptiste; Tshabuse, Freedom; Bopda, Cyprien W.
- Plant and Soil, Vol. 372, Issue 1-2
Two seasons’ study on nifH gene expression and nitrogen fixation by diazotrophic endophytes in sugarcane (Saccharum spp. hybrids): expression of nifH genes similar to those of rhizobia
journal, September 2010
- Thaweenut, Nisarat; Hachisuka, Yusuke; Ando, Shotaro
- Plant and Soil, Vol. 338, Issue 1-2
Fitting Multivariate Models to Community Data: a Comment on Distance-Based Redundancy Analysis
journal, January 2001
- McArdle, Brian H.; Anderson, Marti J.
- Ecology, Vol. 82, Issue 1
Bacterial endophytes in agricultural crops
journal, October 1997
- Hallmann, J.; Quadt-Hallmann, A.; Mahaffee, W. F.
- Canadian Journal of Microbiology, Vol. 43, Issue 10
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72
journal, October 2006
- Krause, Andrea; Ramakumar, Adarsh; Bartels, Daniela
- Nature Biotechnology, Vol. 24, Issue 11
Seasonal variations in the diversity and abundance of diazotrophic communities across soils: Dynamics of soil diazotrophic communities
journal, April 2011
- Pereira e. Silva, Michele C.; Semenov, Alexander V.; van Elsas, Jan Dirk
- FEMS Microbiology Ecology, Vol. 77, Issue 1
Evidence for the functional significance of diazotroph community structure in soil
journal, September 2008
- Hsu, Shi-Fang; Buckley, Daniel H.
- The ISME Journal, Vol. 3, Issue 1
Survival of endophytic bacteria in polymer-based inoculants and efficiency of their application to sugarcane
journal, May 2012
- da Silva, Marinete Flores; de Souza Antônio, Cecília; de Oliveira, Paulo Jansen
- Plant and Soil, Vol. 356, Issue 1-2
Molecular diversity of nitrogen-fixing bacteria from the Tibetan Plateau, China: Nitrogen-fixing bacteria from Tibet
journal, July 2006
- Zhang, Yuguang; Li, Diqiang; Wang, Huimin
- FEMS Microbiology Letters, Vol. 260, Issue 2
Contribution of nitrogen fixation to first year Miscanthus × giganteus
journal, July 2013
- Keymer, Daniel P.; Kent, Angela D.
- GCB Bioenergy, Vol. 6, Issue 5
Bacterial Endophytes and Their Interactions with Hosts
journal, August 2006
- Rosenblueth, Mónica; Martínez-Romero, Esperanza
- Molecular Plant-Microbe Interactions, Vol. 19, Issue 8
Community fingerprinting in a sequencing world
journal, March 2014
- van Dorst, Josie; Bissett, Andrew; Palmer, Anne S.
- FEMS Microbiology Ecology, Vol. 89, Issue 2
Evidence from field nitrogen balance and 15N natural abundance data for the contribution of biological N2 fixation to Brazilian sugarcane varieties
journal, October 2011
- Urquiaga, Segundo; Xavier, Rogério P.; de Morais, Rafael F.
- Plant and Soil, Vol. 356, Issue 1-2
A Nitrogen-Fixing Endophyte of Sugarcane Stems (A New Role for the Apoplast)
journal, August 1994
- Dong, Z.; Canny, M. J.; McCully, M. E.
- Plant Physiology, Vol. 105, Issue 4
Root ethylene signalling is involved in Miscanthus sinensis growth promotion by the bacterial endophyte Herbaspirillum frisingense GSF30T
journal, September 2013
- Straub, Daniel; Yang, Huaiyu; Liu, Yan
- Journal of Experimental Botany, Vol. 64, Issue 14
Structure and Functions of the Bacterial Microbiota of Plants
journal, April 2013
- Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn
- Annual Review of Plant Biology, Vol. 64, Issue 1
nifH pyrosequencing reveals the potential for location-specific soil chemistry to influence N 2 -fixing community dynamics : N
journal, March 2014
- Collavino, Mónica M.; Tripp, H. James; Frank, Ildiko E.
- Environmental Microbiology, Vol. 16, Issue 10
Iron and phosphorus co-limit nitrogen fixation in the eastern tropical North Atlantic
journal, May 2004
- Mills, Matthew M.; Ridame, Celine; Davey, Margaret
- Nature, Vol. 429, Issue 6989
Toward an Ecological Classification of soil Bacteria
journal, June 2007
- Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
- Ecology, Vol. 88, Issue 6
Automated Approach for Ribosomal Intergenic Spacer Analysis of Microbial Diversity and Its Application to Freshwater Bacterial Communities
journal, October 1999
- Fisher, Madeline M.; Triplett, Eric W.
- Applied and Environmental Microbiology, Vol. 65, Issue 10
Ordination and significance testing of microbial community composition derived from terminal restriction fragment length polymorphisms: application of multivariate statistics
journal, January 2005
- Rees, Gavin N.; Baldwin, Darren S.; Watson, Garth O.
- Antonie van Leeuwenhoek, Vol. 86, Issue 4
Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms
journal, March 2020
- Sun, Jian; Liao, Xiao-Ping; D’Souza, Alaric W.
- Nature Communications, Vol. 11, Issue 1
Biological Nitrogen Fixation in Sugar Cane: A Key to Energetically Viable Biofuel Production
journal, January 1995
- Boddey, R. M.
- Critical Reviews in Plant Sciences, Vol. 14, Issue 3
Works referencing / citing this record:
Plant growth promotion of Miscanthus × giganteus by endophytic bacteria and fungi on non-polluted and polluted soils
journal, March 2018
- Schmidt, Christoph Stephan; Mrnka, Libor; Frantík, Tomáš
- World Journal of Microbiology and Biotechnology, Vol. 34, Issue 3
Edaphic correlates of feedstock-associated diazotroph communities
journal, February 2018
- Soman, Chinmay; Keymer, Daniel P.; Kent, Angela D.
- GCB Bioenergy, Vol. 10, Issue 5
Nitrogen‐dependent bacterial community shifts in root, rhizome and rhizosphere of nutrient‐efficient Miscanthus x giganteus from long‐term field trials
journal, June 2019
- Liu, Yuan; Ludewig, Uwe
- GCB Bioenergy, Vol. 11, Issue 11
Research priorities for harnessing plant microbiomes in sustainable agriculture
journal, March 2017
- Busby, Posy E.; Soman, Chinmay; Wagner, Maggie R.
- PLOS Biology, Vol. 15, Issue 3
Mediterranean Native Leguminous Plants: A Reservoir of Endophytic Bacteria with Potential to Enhance Chickpea Growth under Stress Conditions
journal, September 2019
- Brígido, Clarisse; Menéndez, Esther; Paço, Ana
- Microorganisms, Vol. 7, Issue 10
Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants
journal, February 2019
- Brígido, Clarisse; Singh, Sakshi; Menéndez, Esther
- Plants, Vol. 8, Issue 2
Research priorities for harnessing plant microbiomes in sustainable agriculture
text, January 2017
- Alison, Bennett,; Mustafa, Morsy,; E., Leach, Jan
- The University of North Carolina at Chapel Hill University Libraries
Diazotroph Diversity and Nitrogen Fixation in Summer Active Perennial Grasses in a Mediterranean Region Agricultural Soil
journal, November 2019
- Gupta, Vadakattu V. S. R.; Zhang, Bangzhou; Penton, Christopher Ryan
- Frontiers in Molecular Biosciences, Vol. 6
Diversity and Functionality of Culturable Endophytic Bacterial Communities in Chickpea Plants
journal, February 2019
- Brígido, Clarisse; Singh, Sakshi; Menéndez, Esther
- Plants, Vol. 8, Issue 2