Dynamic nitrogen fixation in an aerobic endophyte of Populus

Sher, Andrew W.; Aufrecht, Jayde A.; Herrera, Daisy; Zimmerman, Amy E.; Kim, Young-Mo; Munoz, Nathalie; Trejo, Jesse B.; Paurus, Vanessa L.; Cliff, John B.; Hu, Dehong; Chrisler, William B.; Tournay, Robert J.; Gomez-Rivas, Emma; Orr, Galya; Ahkami, Amir H.; Doty, Sharon L.

doi:10.1093/ismejo/wrad012

Dynamic nitrogen fixation in an aerobic endophyte of Populus

Journal Article · Wed Jan 10 00:00:00 EST 2024 · The ISME Journal

DOI:https://doi.org/10.1093/ismejo/wrad012· OSTI ID:2283588

Sher, Andrew W. ^[1]; Aufrecht, Jayde A. ^[2]; Herrera, Daisy ^[2]; Zimmerman, Amy E. ^[3]; ^[3]; Munoz, Nathalie ^[2]; Trejo, Jesse B. ^[3]; ^[3]; Cliff, John B. ^[2]; ^[2]; Chrisler, William B. ^[2]; Tournay, Robert J. ^[1]; Gomez-Rivas, Emma ^[1]; ^[2]; Ahkami, Amir H. ^[2]; Doty, Sharon L. ^[1]

University of Washington, Seattle, WA (United States)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Biological Sciences Division

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte–poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through ¹⁵N₂ enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant–endophyte interactions.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Univ. of Washington, Seattle, WA (United States); University of Washington, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830; SC0021137

OSTI ID:: 2283588

Alternate ID(s):: OSTI ID: 2336553
OSTI ID: 2507461
OSTI ID: 2337842

Report Number(s):: PNNL-SA--189611

Journal Information:: The ISME Journal, Journal Name: The ISME Journal Journal Issue: 1 Vol. 18; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (68)

Counting mRNA Copies in Intact Bacterial Cells by Fluctuation Localization Imaging-Based Fluorescence In Situ Hybridization (fliFISH) Hu, Dehong; Cui, Yi; Markillie, Lye M. Methods in Molecular Biology https://doi.org/10.1007/978-1-0716-1115-9_15	book	February 2021
The ability of amino compounds and conditioned medium to alleviate the reduced nitrogen requirement of soybean cells grown in suspension cultures Bayley, J. M.; King, J.; Gamborg, O. L. Planta, Vol. 105, Issue 1 https://doi.org/10.1007/BF00385160	journal	January 1972
Biological nitrogen fixation associated with sugar cane Boddey, R. M.; Urquiaga, S.; Reis, V. Plant and Soil, Vol. 137, Issue 1 https://doi.org/10.1007/BF02187441	journal	November 1991
Diazotrophic endophytes of native black cottonwood and willow Doty, Sharon L.; Oakley, Brian; Xin, Gang Symbiosis, Vol. 47, Issue 1 https://doi.org/10.1007/BF03179967	journal	February 2009
Effects of the Inoculation of Burkholderia vietnamensis and Related Endophytic Diazotrophic Bacteria on Grain Yield of Rice Govindarajan, Munusamy; Balandreau, Jacques; Kwon, Soon-Wo Microbial Ecology, Vol. 55, Issue 1 https://doi.org/10.1007/s00248-007-9247-9	journal	April 2007
Do Endophytes Promote Growth of Host Plants Under Stress? A Meta-Analysis on Plant Stress Mitigation by Endophytes Rho, Hyungmin; Hsieh, Marian; Kandel, Shyam L. Microbial Ecology, Vol. 75, Issue 2 https://doi.org/10.1007/s00248-017-1054-3	journal	August 2017
A diazotrophic, indole-3-acetic acid-producing endophyte from wild cottonwood Xin, Gang; Zhang, Gengyun; Kang, Jun Won Biology and Fertility of Soils, Vol. 45, Issue 6 https://doi.org/10.1007/s00374-009-0377-8	journal	April 2009
The "oxygen paradox" of dinitrogen-fixing bacteria Marchal, K.; Vanderleyden, J. Biology and Fertility of Soils, Vol. 30, Issue 5-6 https://doi.org/10.1007/s003740050017	journal	March 2000
Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria do Amaral, Fernanda P.; Pankievicz, Vânia C. S.; Arisi, Ana Carolina M. Plant Molecular Biology, Vol. 90, Issue 6 https://doi.org/10.1007/s11103-016-0449-8	journal	February 2016
Strategies for enhancement of switchgrass (Panicum virgatum L.) performance under limited nitrogen supply based on utilization of N-fixing bacterial endophytes Lowman, Scott; Kim-Dura, Seonhwa; Mei, Chuansheng Plant and Soil, Vol. 405, Issue 1-2 https://doi.org/10.1007/s11104-015-2640-0	journal	August 2015
Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0 The, Matthew; MacCoss, Michael J.; Noble, William S. Journal of The American Society for Mass Spectrometry, Vol. 27, Issue 11 https://doi.org/10.1007/s13361-016-1460-7	journal	August 2016
[18] Genetic Analysis of Agrobacterium Angelosi, Gerard A.; Abest, Elaine; Martinetti, Gladys Methods in Enzymology https://doi.org/10.1016/0076-6879(91)04020-O	book	January 1991
Response of traditional upland rice varieties to inoculation with selected diazotrophic bacteria isolated from rice cropped at the Northeast region of Brazil Araújo, Antonio Edilson da Silva; Baldani, Vera Lúcia Divan; Galisa, Péricles de Souza Applied Soil Ecology, Vol. 64 https://doi.org/10.1016/j.apsoil.2012.10.004	journal	February 2013
Plant-Microbe Interactions Facing Environmental Challenge Cheng, Yu Ti; Zhang, Li; He, Sheng Yang Cell Host & Microbe, Vol. 26, Issue 2 https://doi.org/10.1016/j.chom.2019.07.009	journal	August 2019
Isolation, partial identification and application of diazotrophic rhizobacteria from traditional Indian rice cultivars Jha, Bhavanath; Thakur, Mukund C.; Gontia, Iti European Journal of Soil Biology, Vol. 45, Issue 1 https://doi.org/10.1016/j.ejsobi.2008.06.007	journal	January 2009
Polyamines: Α bioenergetic smart switch for plant protection and development Navakoudis, Eleni; Kotzabasis, Kiriakos Journal of Plant Physiology, Vol. 270, p. 153618 https://doi.org/10.1016/j.jplph.2022.153618	journal	January 2022
Causes and consequences of a conserved bacterial root microbiome response to drought stress Xu, Ling; Coleman-Derr, Devin Current Opinion in Microbiology, Vol. 49 https://doi.org/10.1016/j.mib.2019.07.003	journal	June 2019
Effect of Arsenic on EPS Synthesis, Biofilm Formation, and Plant Growth-Promoting Abilities of the Endophytes Pseudomonas PD9R and Rahnella laticis PD12R Tournay, Robert J.; Firrincieli, Andrea; Parikh, Shruti S. Environmental Science & Technology, Vol. 57, Issue 23 https://doi.org/10.1021/acs.est.2c08586	journal	May 2023
Identification of a novel cyanobacterial group as active diazotrophs in a coastal microbial mat using NanoSIMS analysis Woebken, Dagmar; Burow, Luke C.; Prufert-Bebout, Leslie The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.200	journal	January 2012
Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions Wang, Di; Xu, Anming; Elmerich, Claudine The ISME Journal, Vol. 11, Issue 7 https://doi.org/10.1038/ismej.2017.30	journal	March 2017
A cross-platform toolkit for mass spectrometry and proteomics Chambers, Matthew C.; Maclean, Brendan; Burke, Robert Nature Biotechnology, Vol. 30, Issue 10 https://doi.org/10.1038/nbt.2377	journal	October 2012
MS-GF+ makes progress towards a universal database search tool for proteomics Kim, Sangtae; Pevzner, Pavel A. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6277	journal	October 2014
Genetic regulation of biological nitrogen fixation Dixon, Ray; Kahn, Daniel Nature Reviews Microbiology, Vol. 2, Issue 8 https://doi.org/10.1038/nrmicro954	journal	August 2004
Fungal community assembly in drought-stressed sorghum shows stochasticity, selection, and universal ecological dynamics Gao, Cheng; Montoya, Liliam; Xu, Ling Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-019-13913-9	journal	January 2020
Tracking nitrogen allocation to proteome biosynthesis in a marine microbial community Zimmerman, Amy E.; Podowski, Justin C.; Gallagher, Gwendolyn E. Nature Microbiology, Vol. 8, Issue 3 https://doi.org/10.1038/s41564-022-01303-9	journal	January 2023
Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip Aufrecht, Jayde; Khalid, Muneeba; Walton, Courtney L. Lab on a Chip, Vol. 22, Issue 5 https://doi.org/10.1039/D1LC00705J	journal	January 2022
Interactions between plants and soil shaping the root microbiome under abiotic stress Hartman, Kyle; Tringe, Susannah G. Biochemical Journal, Vol. 476, Issue 19 https://doi.org/10.1042/BCJ20180615	journal	October 2019
Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria Xu, Ling; Naylor, Dan; Dong, Zhaobin Proceedings of the National Academy of Sciences, Vol. 115, Issue 18 https://doi.org/10.1073/pnas.1717308115	journal	April 2018
The versatile GABA in plants Li, Li; Dou, Na; Zhang, Hui Plant Signaling & Behavior, Vol. 16, Issue 3 https://doi.org/10.1080/15592324.2020.1862565	journal	January 2021
MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification Dudek, Christian-Alexander; Reuse, Carsten; Fuchs, Regine Bioinformatics, Vol. 36, Issue 12 https://doi.org/10.1093/bioinformatics/btaa251	journal	April 2020
MIA: non-targeted mass isotopolome analysis Weindl, Daniel; Wegner, Andre; Hiller, Karsten Bioinformatics, Vol. 32, Issue 18 https://doi.org/10.1093/bioinformatics/btw317	journal	June 2016
DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS Dagley, Michael J.; McConville, Malcolm J. Bioinformatics, Vol. 34, Issue 11 https://doi.org/10.1093/bioinformatics/bty025	journal	January 2018
New insights on trehalose: a multifunctional molecule Elbein, A. D. Glycobiology, Vol. 13, Issue 4 https://doi.org/10.1093/glycob/cwg047	journal	January 2003
More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis Rodriguez, R.; Redman, R. Journal of Experimental Botany, Vol. 59, Issue 5 https://doi.org/10.1093/jxb/erm342	journal	February 2008
Nitrogen signalling in plant interactions with associative and endophytic diazotrophic bacteria Carvalho, T. L. G.; Balsemao-Pires, E.; Saraiva, R. M. Journal of Experimental Botany, Vol. 65, Issue 19 https://doi.org/10.1093/jxb/eru319	journal	August 2014
Exogenous GABA promotes adaptation and growth by altering the carbon and nitrogen metabolic flux in poplar seedlings under low nitrogen conditions Chen, Wei; Meng, Chen; Ji, Jing Tree Physiology, Vol. 40, Issue 12 https://doi.org/10.1093/treephys/tpaa101	journal	August 2020
Biological Nitrogen Fixation in the Context of Global Change Olivares, José; Bedmar, Eulogio J.; Sanjuán, Juan Molecular Plant-Microbe Interactions®, Vol. 26, Issue 5 https://doi.org/10.1094/MPMI-12-12-0293-CR	journal	May 2013
A Metabolic Signature of the Beneficial Interaction of the Endophyte Paenibacillus sp. Isolate and In Vitro–Grown Poplar Plants Revealed by Metabolomics Scherling, Christian; Ulrich, Kristina; Ewald, Dietrich Molecular Plant-Microbe Interactions, Vol. 22, Issue 8 https://doi.org/10.1094/MPMI-22-8-1032	journal	August 2009
Improved gfp and inaZ Broad-Host-Range Promoter-Probe Vectors Miller, William G.; Leveau, Johan H. J.; Lindow, Steven E. Molecular Plant-Microbe Interactions, Vol. 13, Issue 11 https://doi.org/10.1094/MPMI.2000.13.11.1243	journal	November 2000
Comparison of Benefit to Sugarcane Plant Growth and ¹⁵ N ₂ Incorporation Following Inoculation of Sterile Plants with Acetobacter diazotrophicus Wild-Type and Nif¯ Mutant Strains Sevilla, Myrna; Burris, Robert H.; Gunapala, Nirmala Molecular Plant-Microbe Interactions, Vol. 14, Issue 3 https://doi.org/10.1094/MPMI.2001.14.3.358	journal	March 2001
Azoarcus Grass Endophytes Contribute Fixed Nitrogen to the Plant in an Unculturable State Hurek, Thomas; Handley, Linda L.; Reinhold-Hurek, Barbara Molecular Plant-Microbe Interactions, Vol. 15, Issue 3 https://doi.org/10.1094/MPMI.2002.15.3.233	journal	March 2002
Nitrogen Fixation in Wheat Provided by Klebsiella pneumoniae 342 Iniguez, A. Leonardo; Dong, Yuemei; Triplett, Eric W. Molecular Plant-Microbe Interactions, Vol. 17, Issue 10 https://doi.org/10.1094/MPMI.2004.17.10.1078	journal	October 2004
Polyphasic Taxonomy in the Genus Burkholderia Leading to an Emended Description of the Genus and Proposition of Burkholderia vietnamiensis sp. nov. for N2-Fixing Isolates from Rice in Vietnam Gillis, M.; Van Van, T.; Bardin, R. International Journal of Systematic Bacteriology, Vol. 45, Issue 2 https://doi.org/10.1099/00207713-45-2-274	journal	April 1995
POLYAMINES AS SOLE NITROGEN SOURCES FOR HELIANTHUS TUBEROSUS EXPLANTS IN VITRO Bagni, N.; Calzoni, G. L.; Speranza, A. New Phytologist, Vol. 80, Issue 2 https://doi.org/10.1111/j.1469-8137.1978.tb01564.x	journal	March 1978
Reconciling the incompatible: N2 fixation And O2 Gallon, J. R. New Phytologist, Vol. 122, Issue 4 https://doi.org/10.1111/j.1469-8137.1992.tb00087.x	journal	December 1992
Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia Knoth, Jenny L.; Kim, Soo-Hyung; Ettl, Gregory J. New Phytologist, Vol. 201, Issue 2 https://doi.org/10.1111/nph.12536	journal	October 2013
An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing Roux, Brice; Rodde, Nathalie; Jardinaud, Marie-Françoise The Plant Journal, Vol. 77, Issue 6 https://doi.org/10.1111/tpj.12442	journal	February 2014
Robust biological nitrogen fixation in a model grass-bacterial association Pankievicz, Vânia C. S.; do Amaral, Fernanda P.; Santos, Karina F. D. N. The Plant Journal, Vol. 81, Issue 6 https://doi.org/10.1111/tpj.12777	journal	March 2015
The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) Tuskan, G. A.; DiFazio, S.; Jansson, S. Science, Vol. 313, Issue 5793, p. 1596-1604 https://doi.org/10.1126/science.1128691	journal	September 2006
Nitrogen stewardship in the Anthropocene Seitzinger, Sybil P.; Phillips, Leigh Science, Vol. 357, Issue 6349 https://doi.org/10.1126/science.aao0812	journal	July 2017
LuxR- and LuxI-Type Quorum-Sensing Circuits Are Prevalent in Members of the Populus deltoides Microbiome Schaefer, Amy L.; Lappala, Colin R.; Morlen, Ryan P. Applied and Environmental Microbiology, Vol. 79, Issue 18 https://doi.org/10.1128/AEM.01417-13	journal	July 2013
Phenotypic Switching in Pseudomonas brassicacearum Involves GacS- and GacA-Dependent Rsm Small RNAs Lalaouna, David; Fochesato, Sylvain; Sanchez, Lisa Applied and Environmental Microbiology, Vol. 78, Issue 6 https://doi.org/10.1128/AEM.06769-11	journal	March 2012
Endophytic Colonization and In Planta Nitrogen Fixation by a Herbaspirillum sp. Isolated from Wild Rice Species Elbeltagy, A.; Nishioka, K.; Sato, T. Applied and Environmental Microbiology, Vol. 67, Issue 11 https://doi.org/10.1128/AEM.67.11.5285-5293.2001	journal	November 2001
Burkholderia, a Genus Rich in Plant-Associated Nitrogen Fixers with Wide Environmental and Geographic Distribution Estrada-De Los Santos, P.; Bustillos-Cristales, R.; Caballero-Mellado, J. Applied and Environmental Microbiology, Vol. 67, Issue 6 https://doi.org/10.1128/AEM.67.6.2790-2798.2001	journal	June 2001
Genome Sequence of Azotobacter vinelandii, an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes Setubal, J. C.; dos Santos, P.; Goldman, B. S. Journal of Bacteriology, Vol. 191, Issue 14 https://doi.org/10.1128/JB.00504-09	journal	May 2009
Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome Timm, Collin M.; Carter, Kelsey R.; Carrell, Alyssa A. mSystems, Vol. 3, Issue 1 https://doi.org/10.1128/mSystems.00070-17	journal	January 2018
A single medium for the isolation of acetylene-reducing (dinitrogen-fixing) bacteria from soils Rennie, R. J. Canadian Journal of Microbiology, Vol. 27, Issue 1 https://doi.org/10.1139/m81-002	journal	January 1981
Do Polyamines Have Roles in Plant Development? Evans, P. T.; Malmberg, R. L. Annual Review of Plant Physiology and Plant Molecular Biology, Vol. 40, Issue 1 https://doi.org/10.1146/annurev.pp.40.060189.001315	journal	June 1989
The wild side of plant microbiomes Pérez-Jaramillo, Juan E.; Carrión, Víctor J.; de Hollander, Mattias Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0519-z	journal	August 2018
Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota Van Deynze, Allen; Zamora, Pablo; Delaux, Pierre-Marc PLOS Biology, Vol. 16, Issue 8 https://doi.org/10.1371/journal.pbio.2006352	journal	August 2018
Symbiotic ß-Proteobacteria beyond Legumes: Burkholderia in Rubiaceae Verstraete, Brecht; Janssens, Steven; Smets, Erik PLoS ONE, Vol. 8, Issue 1 https://doi.org/10.1371/journal.pone.0055260	journal	January 2013
Variable Nitrogen Fixation in Wild Populus Doty, Sharon L.; Sher, Andrew W.; Fleck, Neil D. PLOS ONE, Vol. 11, Issue 5 https://doi.org/10.1371/journal.pone.0155979	journal	May 2016
Ammonia Assessment from Agriculture: U.S. Status and Needs Aneja, Viney P.; Blunden, Jessica; James, Kristen Journal of Environment Quality, Vol. 37, Issue 2 https://doi.org/10.2134/jeq2007.0002in	journal	January 2008
Symbiotic Nitrogen Fixation Mylona, Panagiota; Pawlowski, Katharina; Bisseling, Ton The Plant Cell, Vol. 7, Issue 7 https://doi.org/10.2307/3870043	journal	July 1995
Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms Kim, Young-Mo; Nowack, Shane; Olsen, Millie T. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00209	journal	April 2015
Closing the loop on the GABA shunt in plants: are GABA metabolism and signaling entwined? Michaeli, Simon; Fromm, Hillel Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00419	journal	June 2015
Plant Host-Associated Mechanisms for Microbial Selection Jones, Piet; Garcia, Benjamin J.; Furches, Anna Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00862	journal	July 2019
Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar Firrincieli, Andrea; Khorasani, Mahsa; Frank, A. Carolin Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.00203	journal	February 2020

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59 BASIC BIOLOGICAL SCIENCES
Burkholderia
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microbial ecology
nanoSIMS
nitrogen fixation
nitrogen fixation
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plant microbiome
nitrogenase expression
plant-microbe interactions
plant–microbe interactions
populus

Dynamic nitrogen fixation in an aerobic endophyte of Populus

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