The University of Southern Mississippi The Aquila Digital Community Faculty Publications 4-14-2021 Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes In Rhizosphere Pseudomonas Olga V. Mavrodi University of Southern Mississippi Janiece R. McWilliams University of Southern Mississippi Jacob O. Peter University of Southern Mississippi Anna Berim Washington State University Karl A. Hassan University of Newcastle FSeeollow next this page and for additional additional works authors at: https:/ /aquila.usm.edu/fac_pubs Part of the Microbiology Commons Recommended Citation Mavrodi, O. V., McWilliams, J. R., Peter, J. O., Berim, A., Hassan, K. A., Elbourne, L. D., LeTourneau, M. K., Gang, D. R., Paulsen, I. T., Weller, D. M., Thomashow, L. S., Flynt, A. S., Mavrodi, D. V. (2021). Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes In Rhizosphere Pseudomonas. Frontiers In Microbiology, 12. Available at: https://aquila.usm.edu/fac_pubs/18474 This Article is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Faculty Publications by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. Authors Olga V. Mavrodi, Janiece R. McWilliams, Jacob O. Peter, Anna Berim, Karl A. Hassan, Liam D.H. Elbourne, Melissa K. LeTourneau, David R. Gang, Ian T. Paulsen, David M. Weller, Linda S. Thomashow, Alex S. Flynt, and Dmitri V. Mavrodi This article is available at The Aquila Digital Community: https://aquila.usm.edu/fac_pubs/18474 fmicb-12-651282 April 8, 2021 Time: 20:20 # 1 ORIGINAL RESEARCH published: 14 April 2021 doi: 10.3389/fmicb.2021.651282 Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas Edited by: Olga V. Mavrodi1†, Janiece R. McWilliams1†, Jacob O. Peter1, Anna Berim2, Barbara Pivato, Karl A. Hassan3, Liam D. H. Elbourne4, Melissa K. LeTourneau5, David R. Gang2, Institut National de Recherche pour Ian T. Paulsen4, David M. Weller5, Linda S. Thomashow5, Alex S. Flynt1* and l’agriculture, l’alimentation et Dmitri V. Mavrodi1* l’environnement (INRAE), France 1 Reviewed by: School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, 2 3 Cara Helene Haney, United States, Institute of Biological Chemistry, Washington State University, Pullman, WA, United States, School 4 The University of British Columbia, of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia, Department of Molecular 5 Canada Sciences, Macquarie University, Sydney, NSW, Australia, USDA Agricultural Research Service, Wheat Health, Genetics Xingang Zhou, and Quality Research Unit, Pullman, WA, United States Northeast Agricultural University, China Plants live in association with microorganisms that positively influence plant *Correspondence: development, vigor, and fitness in response to pathogens and abiotic stressors. Dmitri V. Mavrodi [email protected] The bulk of the plant microbiome is concentrated belowground at the plant root- Alex S. Flynt soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and alex.fl[email protected] secondary low molecular weight metabolites, lysates, and mucilages. These exudates †These authors have contributed equally to this work provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by Specialty section: focusing on the molecular dialog between eight well-characterized beneficial strains This article was submitted to Microbe and Virus Interactions with of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for Plants, economically important food, feed, forage, and biomass crops of the grass family. We a section of the journal collected and analyzed root exudates of B. distachyon and demonstrated the presence Frontiers in Microbiology of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The Received: 09 January 2021 Accepted: 08 March 2021 subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many Published: 14 April 2021 of these metabolites provide carbon and energy for the Pseudomonas strains. RNA- Citation: seq profiling of bacterial cultures amended with root exudates revealed changes in the Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, expression of genes encoding numerous catabolic and anabolic enzymes, transporters, Elbourne LDH, LeTourneau MK, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost Gang DR, Paulsen IT, Weller DM, half of the differentially expressed genes mapped to the variable part of the strains’ Thomashow LS, Flynt AS and Mavrodi DV (2021) Root Exudates pangenome, reflecting the importance of the variable gene content in the adaptation of Alter the Expression of Diverse P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity Metabolic, Transport, Regulatory, and Stress Response Genes of cellular pathways and physiological responses underlying the establishment of in Rhizosphere Pseudomonas. mutualistic interactions between these beneficial rhizobacteria and their plant hosts. Front. Microbiol. 12:651282. doi: 10.3389/fmicb.2021.651282 Keywords: Pseudomonas, Brachypodium, rhizosphere, root exudates, transcriptome Frontiers in Microbiology | www.frontiersin.org 1 April 2021 | Volume 12 | Article 651282 fmicb-12-651282 April 8, 2021 Time: 20:20 # 2 Mavrodi et al. The Effect of Root Exudates on the Pseudomonas Transcriptome INTRODUCTION root exudates strongly affect the expression of diverse plant growth promotion and biocontrol genes (Vacheron et al., 2013). Plants are meta-organisms or holobionts that rely in part on Over the past decade, the genomes of numerous rhizosphere their microbiome for specific functions and traits. The ability strains have been sequenced and analyzed, but functional of the plant microbiome to influence plant development, vigor, genomics studies of rhizosphere competence lag behind the health, and fitness in response to abiotic stressors associated availability of sequence data. with global climate change is documented by numerous studies This study explored the molecular dialog between the (Lugtenberg and Kamilova, 2009). There is mounting evidence model host plant Brachypodium distachyon and several well- that plants actively recruit beneficial microbiomes, but many characterized rhizosphere strains of the Pseudomonas fluorescens aspects of this process are still very much a black box (Reinhold- group. Brachypodium is a small annual grass originating in semi- Hurek et al., 2015). The foundation for the differential affinity arid regions of the Middle East that has emerged as a prime model of rhizobacteria toward host plants is built upon complex for economically important food, feed, forage, and biomass crops chemical cross talk between microorganisms and plant roots. of the grass family (Bevan et al., 2010; Schwartz et al., 2010; Up to 40% of photosynthetically fixed carbon is released by Brkljacic et al., 2011; Hong et al., 2011; Tyler et al., 2014). The plant roots in the form of exudates and secretions, lysates, and biology, extensive collection of resources, and research tools mucilages (Curl and Truelove, 1986; Lynch, 1990; Whipps, 1990; make B. distachyon an attractive model to investigate interactions Badri and Vivanco, 2009). The release of these compounds is between plants and root-associated microbes. Pseudomonads actively controlled in response to environmental stimuli, and the are ubiquitous Gram-negative g-proteobacteria that colonize composition of root exudates varies greatly according to plant eukaryotic hosts and include both commensals and economically species and physiological condition (Lynch, 1990; Nguyen, 2003; important pathogens of plants and animals (Moore et al., Phillips et al., 2004; De-la-Pena et al., 2008). The presence and 2006; Schroth et al., 2006; Yahr and Parsek, 2006). The genus composition of exudates strongly impact soil microorganisms, Pseudomonas currently comprises > 100 named species that have which is consistent with the idea that plants actively select and been separated based on multilocus sequence analysis into 14 shape their root microbiota (Zolla et al., 2013). species groups (Garrido-Sanz et al., 2016; Hesse et al., 2018). Primary root exudates include simple and complex sugars, The P. fluorescens group is the most diverse regarding both amino acids, polypeptides and proteins, organic, aliphatic and the genetic distances within it, the number of species and the fatty acids, sterols, and phenolics (Nguyen, 2003; Badri and large pangenome that makes up > 50% of the pangenome Vivanco, 2009; Badri et al., 2009). These compounds serve as of the genus as a whole (Loper et al., 2012). The group also carbon and energy sources for rhizobacteria, and the presence encompasses an unusually high proportion of strains that inhabit of the intact corresponding catabolic pathways is essential the plant rhizosphere and possess plant growth promoting and for competitive colonization of roots and disease suppression biocontrol properties. Naylor et al. (2017) profiled bacterial (Lugtenberg et al., 2001; Kamilova et al., 2005; Lugtenberg and communities associated with root tissues and rhizosphere