Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Beals, Delaney G.; Carper, Dana L.; Hochanadel, Leah H.; Jawdy, Sara S.; Klingeman, Dawn M.; Piatkowski, Bryan T.; Weston, David J.; Doktycz, Mitchel John; Pelletier, Dale A.

doi:10.1128/msystems.01605-25

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Journal Article · Mon Feb 16 00:00:00 EST 2026 · mSystems

DOI:https://doi.org/10.1128/msystems.01605-25· OSTI ID:3020916

^[1]; ^[1]; ^[1]; ^[1]; ^[1]; ^[2]; ^[1]; ^[1]; ^[1]

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Mayo Clinic, Rochester, MN (United States)

Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 3020916

Journal Information:: mSystems, Journal Name: mSystems Journal Issue: 2 Vol. 11; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (69)

Metabolic potential of endophytic bacteria Brader, Günter; Compant, Stéphane; Mitter, Birgit Current Opinion in Biotechnology, Vol. 27 https://doi.org/10.1016/j.copbio.2013.09.012	journal	June 2014
Formation, characterization and modeling of emergent synthetic microbial communities Wang, Jia; Carper, Dana L.; Burdick, Leah H. Computational and Structural Biotechnology Journal, Vol. 19 https://doi.org/10.1016/j.csbj.2021.03.034	journal	January 2021
An allelic exchange system for compliant genetic manipulation of the select agents Burkholderia pseudomallei and Burkholderia mallei Hamad, Mohamad A.; Zajdowicz, Sheryl L.; Holmes, Randall K. Gene, Vol. 430, Issue 1-2 https://doi.org/10.1016/j.gene.2008.10.011	journal	February 2009
Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.) Belimov, A. A.; Hontzeas, N.; Safronova, V. I. Soil Biology and Biochemistry, Vol. 37, Issue 2 https://doi.org/10.1016/j.soilbio.2004.07.033	journal	February 2005
The rhizosphere microbiome and plant health Berendsen, Roeland L.; Pieterse, Corné M. J.; Bakker, Peter A. H. M. Trends in Plant Science, Vol. 17, Issue 8 https://doi.org/10.1016/j.tplants.2012.04.001	journal	August 2012
Feed Your Friends: Do Plant Exudates Shape the Root Microbiome? Sasse, Joelle; Martinoia, Enrico; Northen, Trent Trends in Plant Science, Vol. 23, Issue 1 https://doi.org/10.1016/j.tplants.2017.09.003	journal	January 2018
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11336	journal	August 2012
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
Differential abundance analysis for microbial marker-gene surveys Paulson, Joseph N.; Stine, O. Colin; Bravo, Héctor Corrada Nature Methods, Vol. 10, Issue 12 https://doi.org/10.1038/nmeth.2658	journal	September 2013
ModelFinder: fast model selection for accurate phylogenetic estimates Kalyaanamoorthy, Subha; Minh, Bui Quang; Wong, Thomas K. F. Nature Methods, Vol. 14, Issue 6 https://doi.org/10.1038/nmeth.4285	journal	May 2017
Going back to the roots: the microbial ecology of the rhizosphere Philippot, Laurent; Raaijmakers, Jos M.; Lemanceau, Philippe Nature Reviews Microbiology, Vol. 11, Issue 11 https://doi.org/10.1038/nrmicro3109	journal	September 2013
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Jain, Chirag; Rodriguez-R, Luis M.; Phillippy, Adam M. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07641-9	journal	November 2018
A single bacterial genus maintains root growth in a complex microbiome Finkel, Omri M.; Salas-González, Isai; Castrillo, Gabriel Nature, Vol. 587, Issue 7832 https://doi.org/10.1038/s41586-020-2778-7	journal	September 2020
Genomic features of bacterial adaptation to plants Levy, Asaf; Salas Gonzalez, Isai; Mittelviefhaus, Maximilian Nature Genetics, Vol. 50, Issue 1 https://doi.org/10.1038/s41588-017-0012-9	journal	December 2017
Defining the root endosphere and rhizosphere microbiomes from the World Olive Germplasm Collection Fernández-González, Antonio J.; Villadas, Pablo J.; Gómez-Lama Cabanás, Carmen Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-56977-9	journal	December 2019
What makes Pseudomonas bacteria rhizosphere competent? Lugtenberg, Ben J. J.; Dekkers, Linda C. Environmental Microbiology, Vol. 1, Issue 1 https://doi.org/10.1046/j.1462-2920.1999.00005.x	journal	February 1999
Metabolic click-labeling with a fucose analog reveals pectin delivery, architecture, and dynamics in Arabidopsis cell walls Anderson, C. T.; Wallace, I. S.; Somerville, C. R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 4 https://doi.org/10.1073/pnas.1120429109	journal	January 2012
Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments Burghardt, Liana T.; Epstein, Brendan; Guhlin, Joseph Proceedings of the National Academy of Sciences, Vol. 115, Issue 10 https://doi.org/10.1073/pnas.1714246115	journal	February 2018
Trehalose and bacterial virulence Vanaporn, Muthita; Titball, Richard W. Virulence, Vol. 11, Issue 1 https://doi.org/10.1080/21505594.2020.1809326	journal	August 2020
Detection of Root Mucilage Using an Anti-fucose Antibody Sinha Roy, S. Annals of Botany, Vol. 89, Issue 3 https://doi.org/10.1093/aob/mcf040	journal	March 2002
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Robinson, M. D.; McCarthy, D. J.; Smyth, G. K. Bioinformatics, Vol. 26, Issue 1 https://doi.org/10.1093/bioinformatics/btp616	journal	November 2009
Drivers of bacterial and fungal root endophyte communities: understanding the relative influence of host plant, environment, and space Brigham, Laurel M.; Bueno de Mesquita, Clifton P.; Spasojevic, Marko J. FEMS Microbiology Ecology, Vol. 99, Issue 5 https://doi.org/10.1093/femsec/fiad034	journal	March 2023
Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum Jiang, F.; Chen, L.; Belimov, A. A. Journal of Experimental Botany, Vol. 63, Issue 18 https://doi.org/10.1093/jxb/ers301	journal	November 2012
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era Minh, Bui Quang; Schmidt, Heiko A.; Chernomor, Olga Molecular Biology and Evolution, Vol. 37, Issue 5 https://doi.org/10.1093/molbev/msaa015	journal	February 2020
Broccoli: Combining Phylogenetic and Network Analyses for Orthology Assignment Derelle, Romain; Philippe, Hervé; Colbourne, John K. Molecular Biology and Evolution, Vol. 37, Issue 11 https://doi.org/10.1093/molbev/msaa159	journal	June 2020
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Cantalapiedra, Carlos P.; Hernández-Plaza, Ana; Letunic, Ivica Molecular Biology and Evolution, Vol. 38, Issue 12 https://doi.org/10.1093/molbev/msab293	journal	October 2021
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
UFBoot2: Improving the Ultrafast Bootstrap Approximation Hoang, Diep Thi; Chernomor, Olga; von Haeseler, Arndt Molecular Biology and Evolution, Vol. 35, Issue 2 https://doi.org/10.1093/molbev/msx281	journal	October 2017
The IMG/M data management and analysis system v.7: content updates and new features Chen, I-Min A.; Chu, Ken; Palaniappan, Krishnaveni Nucleic Acids Research, Vol. 51, Issue D1 https://doi.org/10.1093/nar/gkac976	journal	November 2022
JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom Sreedasyam, Avinash; Plott, Christopher; Hossain, Md Shakhawat Nucleic Acids Research, Vol. 51, Issue 16 https://doi.org/10.1093/nar/gkad616	journal	August 2023
TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations Abascal, Federico; Zardoya, Rafael; Telford, Maximilian J. Nucleic Acids Research, Vol. 38, Issue suppl_2 https://doi.org/10.1093/nar/gkq291	journal	April 2010
limma powers differential expression analyses for RNA-sequencing and microarray studies Ritchie, Matthew E.; Phipson, Belinda; Wu, Di Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv007	journal	January 2015
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1085	journal	November 2018
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads Liao, Yang; Smyth, Gordon K.; Shi, Wei Nucleic Acids Research, Vol. 47, Issue 8 https://doi.org/10.1093/nar/gkz114	journal	February 2019
A Select and Resequence Approach Reveals Strain-Specific Effects of Medicago Nodule-Specific PLAT-Domain Genes Burghardt, Liana T.; Trujillo, Diana I.; Epstein, Brendan Plant Physiology, Vol. 182, Issue 1 https://doi.org/10.1104/pp.19.00831	journal	October 2019
Discovery of an operon that participates in agmatine metabolism and regulates biofilm formation in Pseudomonas aeruginosa Williams, Bryan J.; Du, Rui-Hong; Calcutt, M. Wade Molecular Microbiology, Vol. 76, Issue 1 https://doi.org/10.1111/j.1365-2958.2010.07083.x	journal	April 2010
Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling Belimov, Andrey A.; Dodd, Ian C.; Hontzeas, Nikos New Phytologist, Vol. 181, Issue 2 https://doi.org/10.1111/j.1469-8137.2008.02657.x	journal	October 2008
Climate change effects on beneficial plant-microorganism interactions: Climate change and beneficial plant-microorganism interactions Compant, Stéphane; Van Der Heijden, Marcel G. A.; Sessitsch, Angela FEMS Microbiology Ecology https://doi.org/10.1111/j.1574-6941.2010.00900.x	journal	May 2010
An important role of l ‐fucose biosynthesis and protein fucosylation genes in Arabidopsis immunity Zhang, Li; Paasch, Bradley C.; Chen, Jin New Phytologist, Vol. 222, Issue 2 https://doi.org/10.1111/nph.15639	journal	January 2019
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
The Plant Growth-Promoting Rhizobacterium Variovorax boronicumulans CGMCC 4969 Regulates the Level of Indole-3-Acetic Acid Synthesized from Indole-3-Acetonitrile Sun, Shi-Lei; Yang, Wen-Long; Fang, Wen-Wan Applied and Environmental Microbiology, Vol. 84, Issue 16 https://doi.org/10.1128/AEM.00298-18	journal	August 2018
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis Utturkar, Sagar M.; Cude, W. Nathan; Robeson, Michael S. Applied and Environmental Microbiology, Vol. 82, Issue 18 https://doi.org/10.1128/AEM.01285-16	journal	July 2016
Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types Gottel, Neil R.; Castro, Hector F.; Kerley, Marilyn Applied and Environmental Microbiology, Vol. 77, Issue 17 https://doi.org/10.1128/AEM.05255-11	journal	July 2011
Regulation and Physiologic Significance of the Agmatine Deiminase System of Streptococcus mutans UA159 Griswold, Ann R.; Jameson-Lee, Max; Burne, Robert A. Journal of Bacteriology, Vol. 188, Issue 3 https://doi.org/10.1128/JB.188.3.834-841.2006	journal	February 2006
The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes Hardoim, Pablo R.; van Overbeek, Leonard S.; Berg, Gabriele Microbiology and Molecular Biology Reviews, Vol. 79, Issue 3 https://doi.org/10.1128/MMBR.00050-14	journal	July 2015
A new medium for the enumeration and subculture of bacteria from potable water. Reasoner, D. J.; Geldreich, E. E. Applied and Environmental Microbiology, Vol. 49, Issue 1 https://doi.org/10.1128/aem.49.1.1-7.1985	journal	January 1985
Maintenance of broad-host-range incompatibility group P and group Q plasmids and transposition of Tn5 in Bartonella henselae following conjugal plasmid transfer from Escherichia coli. Dehio, C.; Meyer, M. Journal of Bacteriology, Vol. 179, Issue 2 https://doi.org/10.1128/jb.179.2.538-540.1997	journal	January 1997
Cultivating the Bacterial Microbiota of Populus Roots Carper, Dana L.; Weston, David J.; Barde, Aditya mSystems, Vol. 6, Issue 3 https://doi.org/10.1128/mSystems.01306-20	journal	June 2021
Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition Wang, Jia; Appidi, Manasa R.; Burdick, Leah H. mSystems, Vol. 9, Issue 4 https://doi.org/10.1128/msystems.00006-24	journal	April 2024
Structure and Functions of the Bacterial Microbiota of Plants Bulgarelli, Davide; Schlaeppi, Klaus; Spaepen, Stijn Annual Review of Plant Biology, Vol. 64, Issue 1 https://doi.org/10.1146/annurev-arplant-050312-120106	journal	April 2013
Plant-Growth-Promoting Rhizobacteria Lugtenberg, Ben; Kamilova, Faina Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.62.081307.162918	journal	October 2009
M OLECULAR D ETERMINANTS OF R HIZOSPHERE C OLONIZATION BY P SEUDOMONAS Lugtenberg, Ben J. J.; Dekkers, Linda; Bloemberg, Guido V. Annual Review of Phytopathology, Vol. 39, Issue 1 https://doi.org/10.1146/annurev.phyto.39.1.461	journal	September 2001
The plant microbiome Turner, Thomas R.; James, Euan K.; Poole, Philip S. Genome Biology, Vol. 14, Issue 6 https://doi.org/10.1186/gb-2013-14-6-209	journal	June 2013
voom: precision weights unlock linear model analysis tools for RNA-seq read counts Law, Charity W.; Chen, Yunshun; Shi, Wei Genome Biology, Vol. 15, Issue 2 https://doi.org/10.1186/gb-2014-15-2-r29	journal	January 2014
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Love, Michael I.; Huber, Wolfgang; Anders, Simon Genome Biology, Vol. 15, Issue 12 https://doi.org/10.1186/s13059-014-0550-8	journal	December 2014
OrthoFinder: phylogenetic orthology inference for comparative genomics Emms, David M.; Kelly, Steven Genome Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s13059-019-1832-y	journal	November 2019
Microbial interactions within the plant holobiont Hassani, M. Amine; Durán, Paloma; Hacquard, Stéphane Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0445-0	journal	March 2018
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference Steenwyk, Jacob L.; Buida, Thomas J.; Li, Yuanning PLOS Biology, Vol. 18, Issue 12 https://doi.org/10.1371/journal.pbio.3001007	journal	December 2020
Seasonal variation of bacterial endophytes in urban trees Shen, Shu Yi; Fulthorpe, Roberta Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00427	journal	May 2015
Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment Timm, Collin M.; Campbell, Alisha G.; Utturkar, Sagar M. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01118	journal	October 2015
Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects Khare, Ekta; Mishra, Jitendra; Arora, Naveen Kumar Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02732	journal	November 2018
Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea Yamamoto, Kosuke; Shiwa, Yuh; Ishige, Taichiro Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02878	journal	November 2018
Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding Taye, Zelalem M.; Helgason, Bobbi L.; Bell, Jennifer K. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.03007	journal	January 2020
Comparative Study of the Rhizosphere and Root Endosphere Microbiomes of Cholistan Desert Plants Mukhtar, Salma; Mehnaz, Samina; Malik, Kauser Abdulla Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.618742	journal	March 2021
Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System Timm, Collin M.; Pelletier, Dale A.; Jawdy, Sara S. Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00497	journal	April 2016
Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli Canarini, Alberto; Kaiser, Christina; Merchant, Andrew Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.00157	journal	February 2019
Trehalose Metabolism: From Osmoprotection to Signaling Iturriaga, Gabriel; Suárez, Ramón; Nova-Franco, Barbara International Journal of Molecular Sciences, Vol. 10, Issue 9 https://doi.org/10.3390/ijms10093793	journal	September 2009
Inside the root microbiome: Bacterial root endophytes and plant growth promotion Gaiero, Jonathan R.; McCall, Crystal A.; Thompson, Karen A. American Journal of Botany, Vol. 100, Issue 9 https://doi.org/10.3732/ajb.1200572	journal	September 2013
Atropos: specific, sensitive, and speedy trimming of sequencing reads Didion, John P.; Martin, Marcel; Collins, Francis S. PeerJ, Vol. 5 https://doi.org/10.7717/peerj.3720	journal	January 2017

Similar Records

Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment

Journal Article · Tue Oct 13 20:00:00 EDT 2015 · Frontiers in Microbiology · OSTI ID:1234335

Complete genome sequences of five Variovorax strains isolated from the Populus rhizosphere and endosphere

Journal Article · Tue Jan 07 19:00:00 EST 2025 · Microbiology Resource Announcements · OSTI ID:3017012

Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides

Journal Article · Sat Dec 31 23:00:00 EST 2011 · Journal of Bacteriology · OSTI ID:1081976

Related Subjects

comparative genomics
endosphere colonization
functional trait enrichment
niche differentiation
strain-resolved metagenomics
synthetic community

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Citation Formats

References (69)

Similar Records

Related Subjects