Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System

Appidi, Manasa R.; Bible, Amber N.; Carper, Dana L.; Jawdy, Sara S.; Giannone, Richard J.; Hettich, Robert L.; Morrell-Falvey, Jennifer; Abraham, Paul E.

doi:10.1094/mpmi-01-22-0011-ta

Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System

Journal Article · Wed Jul 06 00:00:00 EDT 2022 · Molecular Plant-Microbe Interactions

DOI:https://doi.org/10.1094/mpmi-01-22-0011-ta· OSTI ID:1878710

Appidi, Manasa R. ^[1]; ^[2]; Carper, Dana L. ^[2]; Jawdy, Sara S. ^[2]; ^[2]; ^[2]; ^[2]; ^[2]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Plant–microbe interactions in the rhizosphere play a vital role in plant health and productivity. The composition and function of root-associated microbiomes is strongly influenced by their surrounding environment, which is often customized by their host. How microbiomes change with respect to space and time across plant roots remains poorly understood, and methodologies that facilitate spatiotemporal metaproteomic studies of root-associated microbiomes are yet to be realized. Here, we developed a method that provides spatially resolved metaproteome measurements along plant roots embedded in agar-plate culture systems, which have long been used to study plants. Spatially defined agar “plugs” of interest were excised and subsequently processed using a novel peptide extraction method prior to metaproteomics, which was used to infer both microbial community composition and function. As a proof-of-principle, a previously studied 10-member community constructed from a Populus root system was grown in an agar plate with a 3-week-old Populus trichocarpa plant. Metaproteomics was performed across two time points (24 and 48 h) for three distinct locations (root base, root tip, and a region distant from the root). The spatial resolution of these measurements provides evidence that microbiome composition and expression changes across the plant root interface. Interrogation of the individual microbial proteomes revealed functional profiles related to their behavioral associations with the plant root, in which chemotaxis and augmented metabolism likely supported predominance of the most abundant member. This study demonstrated a novel peptide extraction method for studying plant agar-plate culture systems, which was previously unsuitable for (meta)proteomic measurements.

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:: 1878710

Journal Information:: Molecular Plant-Microbe Interactions, Journal Name: Molecular Plant-Microbe Interactions Journal Issue: 8 Vol. 35; ISSN 0894-0282

Publisher:: APS Press - International Society for Molecular Plant-Microbe InteractionsCopyright Statement

Country of Publication:: United States

Language:: English

References (55)

A metaproteomic approach dissecting major bacterial functions in the rhizosphere of plants living in serpentine soil Mattarozzi, Monica; Manfredi, Marcello; Montanini, Barbara Analytical and Bioanalytical Chemistry, Vol. 409, Issue 9 https://doi.org/10.1007/s00216-016-0175-8	journal	January 2017
A simple cleanup method for the removal of humic substances from soil protein extracts using aluminum coagulation Mandalakis, Manolis; Panikov, Nicolai S.; Polymenakou, Paraskevi N. Environmental Science and Pollution Research, Vol. 25, Issue 24 https://doi.org/10.1007/s11356-018-2434-z	journal	June 2018
Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review Doornbos, Rogier F.; van Loon, Leendert Cornelis; Bakker, Peter A. H. M. Agronomy for Sustainable Development, Vol. 32, Issue 1 https://doi.org/10.1007/s13593-011-0028-y	journal	April 2011
An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database Eng, Jimmy K.; McCormack, Ashley L.; Yates, John R. Journal of the American Society for Mass Spectrometry, Vol. 5, Issue 11 https://doi.org/10.1016/1044-0305(94)80016-2	journal	November 1994
Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere Mattarozzi, Monica; Di Zinno, Jessica; Montanini, Barbara Applied Soil Ecology, Vol. 148 https://doi.org/10.1016/j.apsoil.2019.103480	journal	April 2020
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
Metaproteomic data of maize rhizosphere for deciphering functional diversity No authors listed Data in Brief, Vol. 27 https://doi.org/10.1016/j.dib.2019.104574	journal	December 2019
Improved protocol for the extraction of bacterial mRNA from soils Sharma, Shilpi; Mehta, Ravikumar; Gupta, Rashi Journal of Microbiological Methods, Vol. 91, Issue 1 https://doi.org/10.1016/j.mimet.2012.07.016	journal	October 2012
Optimized Extraction Method To Remove Humic Acid Interferences from Soil Samples Prior to Microbial Proteome Measurements Qian, Chen; Hettich, Robert L. Journal of Proteome Research, Vol. 16, Issue 7 https://doi.org/10.1021/acs.jproteome.7b00103	journal	June 2017
Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343 Estenson, Kasey; Hurst, Gregory B.; Standaert, Robert F. Journal of Proteome Research, Vol. 17, Issue 4 https://doi.org/10.1021/acs.jproteome.7b00708	journal	February 2018
Direct Cellular Lysis/Protein Extraction Protocol for Soil Metaproteomics Chourey, Karuna; Jansson, Janet; VerBerkmoes, Nathan Journal of Proteome Research, Vol. 9, Issue 12 https://doi.org/10.1021/pr100787q	journal	December 2010
Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis Masuda, Takeshi; Tomita, Masaru; Ishihama, Yasushi Journal of Proteome Research, Vol. 7, Issue 2 https://doi.org/10.1021/pr700658q	journal	February 2008
Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice Knief, Claudia; Delmotte, Nathanaël; Chaffron, Samuel The ISME Journal, Vol. 6, Issue 7 https://doi.org/10.1038/ismej.2011.192	journal	December 2011
Who's who in the plant root microbiome? Hirsch, Penny R.; Mauchline, Tim H. Nature Biotechnology, Vol. 30, Issue 10 https://doi.org/10.1038/nbt.2387	journal	October 2012
The Perseus computational platform for comprehensive analysis of (prote)omics data Tyanova, Stefka; Temu, Tikira; Sinitcyn, Pavel Nature Methods, Vol. 13, Issue 9 https://doi.org/10.1038/nmeth.3901	journal	June 2016
Semi-supervised learning for peptide identification from shotgun proteomics datasets Käll, Lukas; Canterbury, Jesse D.; Weston, Jason Nature Methods, Vol. 4, Issue 11 https://doi.org/10.1038/nmeth1113	journal	October 2007
Assessing species biomass contributions in microbial communities via metaproteomics Kleiner, Manuel; Thorson, Erin; Sharp, Christine E. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-01544-x	journal	November 2017
Multidimensional gene regulatory landscape of a bacterial pathogen in plants Nobori, Tatsuya; Wang, Yiming; Wu, Jingni Nature Plants, Vol. 6, Issue 7 https://doi.org/10.1038/s41477-020-0690-7	journal	June 2020
Metaproteomics characterizes human gut microbiome function in colorectal cancer Long, Shuping; Yang, Yi; Shen, Chengpin npj Biofilms and Microbiomes, Vol. 6, Issue 1 https://doi.org/10.1038/s41522-020-0123-4	journal	March 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
EcoFABs: advancing microbiome science through standardized fabricated ecosystems Zengler, Karsten; Hofmockel, Kirsten; Baliga, Nitin S. Nature Methods, Vol. 16, Issue 7 https://doi.org/10.1038/s41592-019-0465-0	journal	June 2019
A carotenoid-deficient mutant of the plant-associated microbe Pantoea sp. YR343 displays an altered membrane proteome Vijaya Kumar, Sushmitha; Abraham, Paul E.; Hurst, Gregory B. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-71672-w	journal	September 2020
Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia Mello, Bruno L.; Alessi, Anna M.; McQueen-Mason, Simon Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep38781	journal	December 2016
Sloughing of cap cells and carbon exudation from maize seedling roots in compacted sand Iijima, Morio; Griffiths, Bryan; Bengough, A. Glyn New Phytologist, Vol. 145, Issue 3 https://doi.org/10.1046/j.1469-8137.2000.00595.x	journal	March 2000
Shining a light on the dark world of plant root–microbe interactions Poole, Philip Proceedings of the National Academy of Sciences, Vol. 114, Issue 17 https://doi.org/10.1073/pnas.1703800114	journal	April 2017
Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation* Batth, Tanveer S.; Tollenaere, MaximA. X.; Rüther, Patrick Molecular & Cellular Proteomics, Vol. 18, Issue 5 https://doi.org/10.1074/mcp.TIR118.001270	journal	May 2019
Physical and chemical properties in rhizosphere and bulk soils of Tsuga and Yushania in a temperate rain forest Chiu, Chih-Yu; Wang, Ming Kuang; Hwong, Jeen-Lian Communications in Soil Science and Plant Analysis, Vol. 33, Issue 11-12 https://doi.org/10.1081/CSS-120004818	journal	July 2002
DAnTE: a statistical tool for quantitative analysis of -omics data Polpitiya, A. D.; Qian, W. -J.; Jaitly, N. Bioinformatics, Vol. 24, Issue 13 https://doi.org/10.1093/bioinformatics/btn217	journal	May 2008
Decoding molecular interactions in microbial communities Abreu, Nicole A.; Taga, Michiko E. FEMS Microbiology Reviews, Vol. 40, Issue 5 https://doi.org/10.1093/femsre/fuw019	journal	July 2016
Bridging the Gap Between Single-Strain and Community-Level Plant-Microbe Chemical Interactions O’Banion, Bridget S.; O’Neal, Lindsey; Alexandre, Gladys Molecular Plant-Microbe Interactions®, Vol. 33, Issue 2 https://doi.org/10.1094/MPMI-04-19-0115-CR	journal	February 2020
Root Mucilage from Pea and Its Utilization by Rhizosphere Bacteria as a Sole Carbon Source Knee, Emma M.; Gong, Fang-Chen; Gao, Mensheng Molecular Plant-Microbe Interactions®, Vol. 14, Issue 6 https://doi.org/10.1094/MPMI.2001.14.6.775	journal	June 2001
Root Exudation and Rhizosphere Biology: Fig. 1. Walker, Travis S.; Bais, Harsh Pal; Grotewold, Erich Plant Physiology, Vol. 132, Issue 1 https://doi.org/10.1104/pp.102.019661	journal	May 2003
Spatiotemporal patterns of rhizosphere microbiome assembly: From ecological theory to agricultural application Munoz‐Ucros, Juana; Zwetsloot, Marie J.; Cuellar‐Gempeler, Catalina Journal of Applied Ecology, Vol. 58, Issue 5 https://doi.org/10.1111/1365-2664.13850	journal	March 2021
Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particle size fractions Hemkemeyer, Michael; Pronk, Geertje J.; Heister, Katja FEMS Microbiology Ecology, Vol. 90, Issue 3 https://doi.org/10.1111/1574-6941.12436	journal	November 2014
Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?: Root exudates and rhizosphere bacteria Dennis, Paul G.; Miller, Anthony J.; Hirsch, Penny R. FEMS Microbiology Ecology, Vol. 72, Issue 3 https://doi.org/10.1111/j.1574-6941.2010.00860.x	journal	March 2010
The importance of the microbiome of the plant holobiont Vandenkoornhuyse, Philippe; Quaiser, Achim; Duhamel, Marie New Phytologist, Vol. 206, Issue 4 https://doi.org/10.1111/nph.13312	journal	February 2015
Emergent simplicity in microbial community assembly Goldford, Joshua E.; Lu, Nanxi; Bajić, Djordje Science, Vol. 361, Issue 6401 https://doi.org/10.1126/science.aat1168	journal	August 2018
Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants Bao, Zhihua; Okubo, Takashi; Kubota, Kengo Applied and Environmental Microbiology, Vol. 80, Issue 16 https://doi.org/10.1128/AEM.00969-14	journal	August 2014
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
Twenty-One Genome Sequences from Pseudomonas Species and 19 Genome Sequences from Diverse Bacteria Isolated from the Rhizosphere and Endosphere of Populus deltoides Brown, S. D.; Utturkar, S. M.; Klingeman, D. M. Journal of Bacteriology, Vol. 194, Issue 21 https://doi.org/10.1128/JB.01243-12	journal	October 2012
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
Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate Ramirez-Villacis, Dario X.; Finkel, Omri M.; Salas-González, Isai mSphere, Vol. 5, Issue 4 https://doi.org/10.1128/mSphere.00484-20	journal	August 2020
Exploration of the Biosynthetic Potential of the Populus Microbiome Blair, Patricia M.; Land, Miriam L.; Piatek, Marek J. mSystems, Vol. 3, Issue 5 https://doi.org/10.1128/mSystems.00045-18	journal	October 2018
Bridging the Holistic-Reductionist Divide in Microbial Ecology Tecon, Robin; Mitri, Sara; Ciccarese, Davide mSystems, Vol. 4, Issue 1 https://doi.org/10.1128/mSystems.00265-18	journal	February 2019
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
Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance Shrestha, Him K.; Appidi, Manasa R.; Villalobos Solis, Manuel I. BMC Microbiology, Vol. 21, Issue 1 https://doi.org/10.1186/s12866-021-02370-4	journal	November 2021
A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization Bible, Amber N.; Fletcher, Sarah J.; Pelletier, Dale A. Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00491	journal	April 2016
Identification of Nitrogen-Fixing Bradyrhizobium Associated With Roots of Field-Grown Sorghum by Metagenome and Proteome Analyses Hara, Shintaro; Morikawa, Takashi; Wasai, Sawa Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00407	journal	March 2019
Assembly Patterns of the Rhizosphere Microbiome Along the Longitudinal Root Axis of Maize (Zea mays L.) Rüger, Lioba; Feng, Kai; Dumack, Kenneth Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.614501	journal	February 2021
Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota Bonkowski, Michael; Tarkka, Mika; Razavi, Bahar S. Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.619499	journal	March 2021
Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions Yee, Mon Oo; Kim, Peter; Li, Yifan Frontiers in Microbiology, Vol. 12 https://doi.org/10.3389/fmicb.2021.625752	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
Plant–Microbe Interaction 2017—The Good, the Bad and the Diverse Schirawski, Jan; Perlin, Michael International Journal of Molecular Sciences, Vol. 19, Issue 5 https://doi.org/10.3390/ijms19051374	journal	May 2018
Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights Tartaglia, Maria; Bastida, Felipe; Sciarrillo, Rosaria International Journal of Molecular Sciences, Vol. 21, Issue 22 https://doi.org/10.3390/ijms21228455	journal	November 2020
Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics Orsburn, Benjamin C. Proteomes, Vol. 9, Issue 1 https://doi.org/10.3390/proteomes9010015	journal	March 2021

Similar Records

Shotgun Metaproteomics of the Human Distal Gut Microbiota

Journal Article · Wed Dec 31 23:00:00 EST 2008 · Nature Methods · OSTI ID:958920

Shotgun metaproteomics of the human distal gut microbiota

Journal Article · Wed Oct 15 00:00:00 EDT 2008 · International Society for Microbial Ecology Journal · OSTI ID:943452

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
agar removal
agar-plate system
constructed microbial community
metaproteomics
plant-associated microbes
reductionist approach
rhizosphere microbiome
spatially resolved microbiomes

Development of an Experimental Approach to Achieve Spatially Resolved Plant Root-Associated Metaproteomics Using an Agar-Plate System

Citation Formats

References (55)

Similar Records

Related Subjects