{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T07:59:17Z","timestamp":1790409557210,"version":"4.1.0"},"reference-count":72,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB\u20102153410"],"award-info":[{"award-number":["MCB\u20102153410"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Microbiology"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>Burkholderia thailandensis<\/jats:italic>\n                    <\/jats:styled-content>\n                    is a commonly used surrogate for pathogenic\n                    <jats:italic>Burkholderia<\/jats:italic>\n                    species, yet how it adapts to changes in extracellular pH remains poorly characterized. Using quantitative mass spectrometry, we report here the relative proteomes for cells exposed to a change in pH from 7.0 to either 6.0 or 8.0, conditions that may be encountered in the rhizosphere. Acute exposure to mildly acidic conditions resulted in four proteins being depleted while four accumulated based on an absolute log\n                    <jats:sub>2<\/jats:sub>\n                    \u2010fold change of 0.4. By comparison, a transition to mildly alkaline conditions resulted in accumulation of 13 proteins and depletion of 14. Exposure to both pH\u20096.0 and pH\u20098.0 resulted in an overall reduction in the pathways linked to ribosome, flagellar assembly, and \u03b2\u2010lactam resistance. Consistent with the observed pathway changes, both surface motility and resistance to certain \u03b2\u2010lactams were greatly reduced at pH\u20096.0 and 8.0 compared to pH\u20097.0. Transcriptome changes at pH\u20098.0 primarily included global downregulation of genes associated with flagellar motility and chemotaxis, while genes encoding secondary metabolite biosynthetic enzymes were markedly upregulated. Taken together, our data afford insight into how\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>B. thailandensis<\/jats:italic>\n                    <\/jats:styled-content>\n                    responds to physiologically relevant pH changes to achieve optimal niche adaptation, survival, and competitive fitness.\n                  <\/jats:p>","DOI":"10.1111\/mmi.70120","type":"journal-article","created":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T07:18:30Z","timestamp":1790407110000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Modest Changes in Extracellular\n                    <scp>pH<\/scp>\n                    Impose Metabolic and Envelope Remodeling in\n                    <i>Burkholderia thailandensis<\/i>"],"prefix":"10.1111","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6142-3304","authenticated-orcid":false,"given":"Ahmed","family":"Al\u2010Tohamy","sequence":"first","affiliation":[{"name":"Department of Biological Sciences Louisiana State University  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3282-5009","authenticated-orcid":false,"given":"Sarmin","family":"Akter","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Louisiana State University  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1397-9919","authenticated-orcid":false,"given":"Fabrizio","family":"Donnarumma","sequence":"additional","affiliation":[{"name":"Department of Chemistry Louisiana State University  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4390-0354","authenticated-orcid":false,"given":"Anne","family":"Grove","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences Louisiana State University  Baton Rouge Louisiana USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,26]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2024.1346813","article-title":"Untargeted Metabolomics Unveiled the Role of Butanoate Metabolism in the Development of \n                     Pseudomonas aeruginosa\n                   Hypoxic Biofilm","volume":"14","author":"Abdelhamid A. G.","year":"2024","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"key":"e_1_2_9_3_1","doi-asserted-by":"crossref","first-page":"4082","DOI":"10.1021\/acs.jproteome.5c00223","article-title":"Transcriptome\u2010Proteome Profiling in \n                     Burkholderia thailandensis\n                   During the Transition From Exponential to Stationary Phase","volume":"24","author":"Al\u2010Tohamy A.","year":"2025","journal-title":"Journal of Proteome Research"},{"key":"e_1_2_9_4_1","doi-asserted-by":"crossref","DOI":"10.3390\/microorganisms9061290","article-title":"Genome\u2010Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates From Sugars and Fatty Acids by Burkholderia Sensu Lato Species","volume":"9","author":"Alvarez\u2010Santullano N.","year":"2021","journal-title":"Microorganisms"},{"key":"e_1_2_9_5_1","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.jmb.2014.12.018","article-title":"Bactobolin A Binds to a Site on the 70S Ribosome Distinct From Previously Seen Antibiotics","volume":"427","author":"Amunts A.","year":"2015","journal-title":"Journal of Molecular Biology"},{"key":"e_1_2_9_6_1","unstructured":"Andrews S.2010.\u201cFastQC: A Quality Control Tool for High Throughput Sequence Data.\u201d"},{"key":"e_1_2_9_7_1","doi-asserted-by":"crossref","first-page":"1425","DOI":"10.1093\/nar\/9.6.1425","article-title":"Basepairing Potential of the 3\u2032 Terminus of 16S RNA: Dependence on the Functional State of the 30S Subunit and the Presence of Protein S21","volume":"9","author":"Backendorf C.","year":"1981","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_9_8_1","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.sbi.2014.01.002","article-title":"A New System for Naming Ribosomal Proteins","volume":"24","author":"Ban N.","year":"2014","journal-title":"Current Opinion in Structural Biology"},{"key":"e_1_2_9_9_1","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/S0166-4328(01)00297-2","article-title":"Controlling the False Discovery Rate in Behavior Genetics Research","volume":"125","author":"Benjamini Y.","year":"2001","journal-title":"Behavioural Brain Research"},{"key":"e_1_2_9_10_1","doi-asserted-by":"crossref","first-page":"2878","DOI":"10.1016\/j.cub.2023.06.010","article-title":"Positive Interactions Between Mycorrhizal Fungi and Bacteria Are Widespread and Benefit Plant Growth","volume":"33","author":"Berrios L.","year":"2023","journal-title":"Current Biology"},{"key":"e_1_2_9_11_1","doi-asserted-by":"crossref","first-page":"3048","DOI":"10.1021\/ol200922s","article-title":"Sources of Diversity in Bactobolin Biosynthesis by \n                     Burkholderia thailandensis\n                   E264","volume":"13","author":"Carr G.","year":"2011","journal-title":"Organic Letters"},{"key":"e_1_2_9_12_1","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/nrmicro.2017.15","article-title":"Metal Homeostasis and Resistance in Bacteria","volume":"15","author":"Chandrangsu P.","year":"2017","journal-title":"Nature Reviews. Microbiology"},{"key":"e_1_2_9_13_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.biotechadv.2020.107553","article-title":"Glycoside Hydrolase Family 18 Chitinases: The Known and the Unknown","volume":"43","author":"Chen W.","year":"2020","journal-title":"Biotechnology Advances"},{"key":"e_1_2_9_14_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.geoderma.2020.114314","article-title":"How Root Nutrient Uptake Affects Rhizosphere pH: A Modelling Study","volume":"369","author":"Custos J.\u2010M.","year":"2020","journal-title":"Geoderma"},{"key":"e_1_2_9_15_1","doi-asserted-by":"crossref","first-page":"1230","DOI":"10.1590\/S1517-83822012000400001","article-title":"Production of Gaba (Gamma \u2010 Aminobutyric Acid) by Microorganisms: A Review","volume":"43","author":"Dhakal R.","year":"2012","journal-title":"Brazilian Journal of Microbiology"},{"key":"e_1_2_9_16_1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI Gene Expression and Hybridization Array Data Repository","volume":"30","author":"Edgar R.","year":"2002","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_9_17_1","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1111\/nph.20080","article-title":"Transcriptomics Reveal a Mechanism of Niche Defense: Two Beneficial Root Endophytes Deploy an Antimicrobial GH18\u2010CBM5 Chitinase to Protect Their Hosts","volume":"244","author":"Eichfeld R.","year":"2024","journal-title":"New Phytologist"},{"key":"e_1_2_9_18_1","doi-asserted-by":"crossref","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","article-title":"MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report","volume":"32","author":"Ewels P.","year":"2016","journal-title":"Bioinformatics"},{"key":"e_1_2_9_19_1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1111\/j.1365-2672.2012.05434.x","article-title":"Role of Glutamate Metabolism in Bacterial Responses Towards Acid and Other Stresses","volume":"114","author":"Feehily C.","year":"2013","journal-title":"Journal of Applied Microbiology"},{"key":"e_1_2_9_20_1","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1111\/j.1574-6968.2009.01726.x","article-title":"Copper Acquisition by the SenC Protein Regulates Aerobic Respiration in \n                     Pseudomonas aeruginosa\n                   PAO1","volume":"298","author":"Frangipani E.","year":"2009","journal-title":"FEMS Microbiology Letters"},{"key":"e_1_2_9_21_1","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.851011","article-title":"Extracytoplasmic Function Sigma Factors Governing Production of the Primary Siderophores in Pathogenic Burkholderia Species","volume":"13","author":"Grove A.","year":"2022","journal-title":"Frontiers in Microbiology"},{"key":"e_1_2_9_22_1","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex Heatmaps Reveal Patterns and Correlations in Multidimensional Genomic Data","volume":"32","author":"Gu Z.","year":"2016","journal-title":"Bioinformatics"},{"key":"e_1_2_9_23_1","doi-asserted-by":"crossref","first-page":"3012","DOI":"10.1021\/acschembio.7b00681","article-title":"Global Awakening of Cryptic Biosynthetic Gene Clusters in \n                     Burkholderia thailandensis","volume":"12","author":"Gupta A.","year":"2017","journal-title":"ACS Chemical Biology"},{"key":"e_1_2_9_24_1","doi-asserted-by":"crossref","first-page":"5402","DOI":"10.1128\/IAI.00626-08","article-title":"Burkholderia thailandensis\n                   As a Model System for the Study of the Virulence\u2010Associated Type III Secretion System of \n                     Burkholderia pseudomallei","volume":"76","author":"Haraga A.","year":"2008","journal-title":"Infection and Immunity"},{"key":"e_1_2_9_25_1","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00068-18","article-title":"Determinants of Extreme Beta\u2010Lactam Tolerance in the \n                     Burkholderia pseudomallei\n                   Complex","volume":"62","author":"Held K.","year":"2018","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"e_1_2_9_26_1","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph\u2010Based Genome Alignment and Genotyping With HISAT2 and HISAT\u2010Genotype","volume":"37","author":"Kim D.","year":"2019","journal-title":"Nature Biotechnology"},{"key":"e_1_2_9_27_1","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/1471-2180-10-81","article-title":"Mosaic Structure of Intragenic Repetitive Elements in Histone H1\u2010Like Protein Hc2 Varies Within Serovars of \n                     Chlamydia trachomatis","volume":"10","author":"Klint M.","year":"2010","journal-title":"BMC Microbiology"},{"key":"e_1_2_9_28_1","unstructured":"Korotkevich G. V.Sukhov N.Budin B.Shpak M. N.Artyomov andA.Sergushichev.2021.\u201cFast Gene Set Enrichment Analysis.\u201dbioRxiv: The Preprint Server for Biology."},{"key":"e_1_2_9_29_1","unstructured":"Krueger F. F.James P.Ewels et\u00a0al.2023.\u201cFelixKrueger\/TrimGalore: v0. 6.10\u2010add default decompression path.\u201dZenodo."},{"key":"e_1_2_9_30_1","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features","volume":"30","author":"Liao Y.","year":"2014","journal-title":"Bioinformatics"},{"key":"e_1_2_9_31_1","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated Estimation of Fold Change and Dispersion for RNA\u2010Seq Data With DESeq2","volume":"15","author":"Love M. I.","year":"2014","journal-title":"Genome Biology"},{"key":"e_1_2_9_32_1","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1111\/1751-7915.13283","article-title":"Engineering Sucrose Metabolism in \n                     Pseudomonas putida\n                   Highlights the Importance of Porins","volume":"13","author":"Lowe H.","year":"2020","journal-title":"Microbial Biotechnology"},{"key":"e_1_2_9_33_1","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2022.937940","article-title":"Root Exudates Contribute to Belowground Ecosystem Hotspots: A Review","volume":"13","author":"Ma W.","year":"2022","journal-title":"Frontiers in Microbiology"},{"key":"e_1_2_9_34_1","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.1128\/JB.01405-13","article-title":"Global Analysis of the \n                     Burkholderia thailandensis\n                   Quorum Sensing\u2010Controlled Regulon","volume":"196","author":"Majerczyk C.","year":"2014","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_9_35_1","first-page":"E2920","article-title":"Discovery of scmR as a Global Regulator of Secondary Metabolism and Virulence in \n                     Burkholderia thailandensis\n                   E264","volume":"114","author":"Mao D.","year":"2017","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"e_1_2_9_36_1","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1128\/JB.187.1.304-319.2005","article-title":"pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in \n                     Escherichia coli\n                   K\u201012","volume":"187","author":"Maurer L. M.","year":"2005","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_9_37_1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41579-023-00972-5","article-title":"Burkholderia pseudomallei and melioidosis","volume":"22","author":"Meumann E. M.","year":"2024","journal-title":"Nature Reviews. Microbiology"},{"key":"e_1_2_9_38_1","doi-asserted-by":"crossref","first-page":"5411","DOI":"10.1038\/s41467-024-49785-x","article-title":"Molecular Motor Tug\u2010Of\u2010War Regulates Elongasome Cell Wall Synthesis Dynamics in \n                     Bacillus subtilis","volume":"15","author":"Middlemiss S.","year":"2024","journal-title":"Nature Communications"},{"key":"e_1_2_9_39_1","article-title":"Preparation, Imaging, and Quantification of Bacterial Surface Motility Assays","volume":"98","author":"Morales\u2010Soto N.","year":"2015","journal-title":"Journal of Visualized Experiments"},{"key":"e_1_2_9_40_1","doi-asserted-by":"crossref","DOI":"10.1111\/ejss.70021","article-title":"Soil pH: Techniques, Challenges and Insights From a Global Dataset","volume":"75","author":"Mosley L. M.","year":"2024","journal-title":"European Journal of Soil Science"},{"key":"e_1_2_9_41_1","doi-asserted-by":"crossref","first-page":"914","DOI":"10.1007\/s00248-015-0574-y","article-title":"The Microbiome of \n                     Pinus muricata\n                   Ectomycorrhizae: Community Assemblages, Fungal Species Effects, and Burkholderia as Important Bacteria in Multipartnered Symbioses","volume":"69","author":"Nguyen N. H.","year":"2015","journal-title":"Microbial Ecology"},{"key":"e_1_2_9_42_1","doi-asserted-by":"crossref","first-page":"e0076124","DOI":"10.1128\/aac.00761-24","article-title":"The OprF Porin as a Potential Target for the Restoration of Carbapenem Susceptibility in \n                     Pseudomonas aeruginosa\n                   Expressing Acquired Carbapenemases","volume":"68","author":"Nordmann P.","year":"2024","journal-title":"Antimicrobial Agents and Chemotherapy"},{"key":"e_1_2_9_43_1","doi-asserted-by":"crossref","DOI":"10.3390\/proteomes9010015","article-title":"Proteome Discoverer\u2010A Community Enhanced Data Processing Suite for Protein Informatics","volume":"9","author":"Orsburn B. C.","year":"2021","journal-title":"Proteomes"},{"key":"e_1_2_9_44_1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1111\/j.1365-2958.1996.tb02618.x","article-title":"Purification of Recombinant \n                     Chlamydia trachomatis\n                   Histone H1\u2010Like Protein Hc2, and Comparative Functional Analysis of Hc2 and Hc1","volume":"20","author":"Pedersen L. B.","year":"1996","journal-title":"Molecular Microbiology"},{"key":"e_1_2_9_45_1","first-page":"2825","article-title":"Scikit\u2010Learn: Machine Learning in Python","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_2_9_46_1","doi-asserted-by":"crossref","first-page":"27468","DOI":"10.1074\/jbc.M109.095182","article-title":"Structural Insights Into the Catalytic Mechanism of Bacterial Guanosine\u2010Diphospho\u2010D\u2010Mannose Pyrophosphorylase and Its Regulation by Divalent Ions","volume":"285","author":"Pelissier M. C.","year":"2010","journal-title":"Journal of Biological Chemistry"},{"key":"e_1_2_9_47_1","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE Database Resources in 2022: A Hub for Mass Spectrometry\u2010Based Proteomics Evidences","volume":"50","author":"Perez\u2010Riverol Y.","year":"2022","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_9_48_1","doi-asserted-by":"crossref","first-page":"2434","DOI":"10.1101\/gad.475808","article-title":"Inverse Regulatory Coordination of Motility and Curli\u2010Mediated Adhesion in \n                     Escherichia coli","volume":"22","author":"Pesavento C.","year":"2008","journal-title":"Genes & Development"},{"key":"e_1_2_9_49_1","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2022.e12137","article-title":"Characterization of Levansucrase Produced by Novel Bacillus siamensis and Optimization of Culture Condition for Levan Biosynthesis","volume":"8","author":"Phengnoi P.","year":"2022","journal-title":"Heliyon"},{"key":"e_1_2_9_50_1","volume-title":"Collaborative Data Science","author":"Plotly Technologies Inc","year":"2015"},{"key":"e_1_2_9_51_1","doi-asserted-by":"crossref","DOI":"10.1098\/rsob.190223","article-title":"The Architects of Bacterial DNA Bridges: A Structurally and Functionally Conserved Family of Proteins","volume":"9","author":"Qin L.","year":"2019","journal-title":"Open Biology"},{"key":"e_1_2_9_52_1","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.drup.2016.07.003","article-title":"Antibiotic Resistance in Burkholderia Species","volume":"28","author":"Rhodes K. A.","year":"2016","journal-title":"Drug Resistance Updates"},{"key":"e_1_2_9_53_1","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1128\/AEM.02775-08","article-title":"Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization","volume":"75","author":"Rousk J.","year":"2009","journal-title":"Applied and Environmental Microbiology"},{"key":"e_1_2_9_54_1","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/pr400098r","article-title":"Measuring and Managing Ratio Compression for Accurate iTRAQ\/TMT Quantification","volume":"12","author":"Savitski M. M.","year":"2013","journal-title":"Journal of Proteome Research"},{"key":"e_1_2_9_55_1","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.1213\/ANE.0000000000002864","article-title":"Correlation Coefficients: Appropriate Use and Interpretation","volume":"126","author":"Schober P.","year":"2018","journal-title":"Anesthesia and Analgesia"},{"key":"e_1_2_9_56_1","doi-asserted-by":"crossref","DOI":"10.1201\/9780429447273","volume-title":"Interactive Web\u2010Based Data Visualization With R, Plotly, and Shiny","author":"Sievert C.","year":"2020"},{"key":"e_1_2_9_57_1","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1042\/bj20031118","article-title":"Functional Reconstitution, Gene Isolation and Topology Modelling of Porins From Burkholderia pseudomallei and \n                     Burkholderia thailandensis","volume":"377","author":"Siritapetawee J.","year":"2004","journal-title":"Biochemical Journal"},{"key":"e_1_2_9_58_1","doi-asserted-by":"crossref","first-page":"19242","DOI":"10.1038\/s41598-020-76186-z","article-title":"Functional Redundancy of \n                     Burkholderia pseudomallei\n                   Phospholipase C Enzymes and Their Role in Virulence","volume":"10","author":"Srinon V.","year":"2020","journal-title":"Scientific Reports"},{"key":"e_1_2_9_59_1","doi-asserted-by":"crossref","first-page":"4246","DOI":"10.1128\/JB.184.15.4246-4258.2002","article-title":"pH\u2010Dependent Expression of Periplasmic Proteins and Amino Acid Catabolism in \n                     Escherichia coli","volume":"184","author":"Stancik L. M.","year":"2002","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_9_60_1","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1111\/1462-2920.12211","article-title":"Genus\u2010Wide Acid Tolerance Accounts for the Biogeographical Distribution of Soil Burkholderia Populations","volume":"16","author":"Stopnisek N.","year":"2014","journal-title":"Environmental Microbiology"},{"key":"e_1_2_9_61_1","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene Set Enrichment Analysis: A Knowledge\u2010Based Approach for Interpreting Genome\u2010Wide Expression Profiles","volume":"102","author":"Subramanian A.","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"e_1_2_9_62_1","doi-asserted-by":"crossref","first-page":"e0023722","DOI":"10.1128\/jb.00237-22","article-title":"The Global Regulator MftR Controls Virulence and Siderophore Production in \n                     Burkholderia thailandensis","volume":"204","author":"Thapa S. S.","year":"2022","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_9_63_1","doi-asserted-by":"crossref","DOI":"10.3390\/antibiotics8040160","article-title":"Do Global Regulators Hold the Key to Production of Bacterial Secondary Metabolites?","volume":"8","author":"Thapa S. S.","year":"2019","journal-title":"Antibiotics"},{"key":"e_1_2_9_64_1","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: The Universal Protein Knowledgebase in 2023","volume":"51","author":"The UniProt Consortium","year":"2023","journal-title":"Nucleic Acids Research"},{"key":"e_1_2_9_65_1","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/nmeth.1714","article-title":"MS3 Eliminates Ratio Distortion in Isobaric Multiplexed Quantitative Proteomics","volume":"8","author":"Ting L.","year":"2011","journal-title":"Nature Methods"},{"key":"e_1_2_9_66_1","doi-asserted-by":"crossref","first-page":"e0026822","DOI":"10.1128\/jb.00268-22","article-title":"A Ribosomal Protein Homolog Governs Gene Expression and Virulence in a Bacterial Pathogen","volume":"204","author":"Trautmann H. S.","year":"2022","journal-title":"Journal of Bacteriology"},{"key":"e_1_2_9_67_1","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python","volume":"17","author":"Virtanen P.","year":"2020","journal-title":"Nature Methods"},{"key":"e_1_2_9_68_1","doi-asserted-by":"crossref","DOI":"10.1093\/ismejo\/wrae073","article-title":"Mechanisms and Implications of Bacterial\u2010Fungal Competition for Soil Resources","volume":"18","author":"Wang C.","year":"2024","journal-title":"ISME Journal"},{"key":"e_1_2_9_69_1","doi-asserted-by":"crossref","first-page":"5052","DOI":"10.1093\/jxb\/erac202","article-title":"Natural Variation in Root Exudation of GABA and DIMBOA Impacts the Maize Root Endosphere and Rhizosphere Microbiomes","volume":"73","author":"Wang P.","year":"2022","journal-title":"Journal of Experimental Botany"},{"key":"e_1_2_9_70_1","first-page":"448","article-title":"Mechanisms of Bacterial Attachment to Roots","volume":"42","author":"Wheatley R. M.","year":"2018","journal-title":"FEMS Microbiology Reviews"},{"key":"e_1_2_9_71_1","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham H.","year":"2016"},{"key":"e_1_2_9_72_1","doi-asserted-by":"crossref","first-page":"2803","DOI":"10.1093\/bioinformatics\/btn524","article-title":"The Burkholderia Genome Database: Facilitating Flexible Queries and Comparative Analyses","volume":"24","author":"Winsor G. L.","year":"2008","journal-title":"Bioinformatics"},{"key":"e_1_2_9_73_1","doi-asserted-by":"crossref","first-page":"1006","DOI":"10.1002\/pmic.201300553","article-title":"Suspension Trapping (STrap) Sample Preparation Method for Bottom\u2010Up Proteomics Analysis","volume":"14","author":"Zougman A.","year":"2014","journal-title":"Proteomics"}],"container-title":["Molecular Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mmi.70120","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/mmi.70120","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/mmi.70120","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T07:18:40Z","timestamp":1790407120000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/mmi.70120"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,26]]},"references-count":72,"alternative-id":["10.1111\/mmi.70120"],"URL":"https:\/\/doi.org\/10.1111\/mmi.70120","archive":["Portico"],"relation":{},"ISSN":["0950-382X","1365-2958"],"issn-type":[{"value":"0950-382X","type":"print"},{"value":"1365-2958","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,26]]},"assertion":[{"value":"2026-07-02","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-21","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2026-09-26","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"mmi.70120"}}