{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T11:13:49Z","timestamp":1789038829624,"version":"build-2803163510"},"reference-count":84,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:00:00Z","timestamp":1788998400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    Coffee (\n                    <jats:italic>Coffea arabica<\/jats:italic>\n                    L. and\n                    <jats:italic>Coffea canephora<\/jats:italic>\n                    Pierre ex A. Froehner) is a globally important perennial plantation crop that sustains the livelihoods of millions of smallholder farmers while making substantial contributions to agricultural economies worldwide global agricultural economies. Nevertheless, sustainable coffee production is increasingly constrained by climate change, declining soil fertility, emerging pests and diseases and the environmental costs associated with intensive use of synthetic agrochemicals. Recent advances in plant microbiome research have transformed the understanding of coffee from an individual organism to a holobiont, where the host plant and its associated microorganisms operate as an integrated biological system. The coffee phytobiome encompasses diverse microbial communities inhabiting the rhizosphere, rhizoplane, endosphere, phyllosphere, anthosphere, carposphere and spermosphere, together with complex multitrophic interactions involving shade trees, soil fauna, insects and the surrounding environment. These interactions collectively regulate nutrient acquisition, carbon assimilation, water-use efficiency, hormonal balance, stress tolerance, immune responses and overall plant productivity. This review critically examines current advances in multitrophic plant\u2013microbe interactions that influence physiological adaptation in coffee, with particular emphasis on sustainable production under Indian agroecological conditions. It highlights the functional functions of plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF), endophytic microorganisms and other beneficial microbes in enhancing root development, nutrient cycling, and resilience to biotic and abiotic stresses. Furthermore, the review evaluates recent progress in metagenomics, metatranscriptomics, metabolomics and microbiome engineering for harnessing indigenous microbial resources. Finally, it outlines future research priorities integrating plant physiology, microbial ecology, systems biology, and precision agriculture to develop climate-resilient, resource-efficient, and environmentally sustainable coffee production systems.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1951767","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:59:25Z","timestamp":1789037965000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Coffee phytobiome dynamics: integrating multitrophic interactions and plant physiology for climate-resilient production"],"prefix":"10.3389","volume":"17","author":[{"given":"Somashekhargouda","family":"Patil","sequence":"first","affiliation":[{"name":"Division of Plant Physiology, Central Coffee Research Institute, Coffee Research Station Post, Balehonnur","place":["Chikkamagaluru, Karnataka, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. S.","family":"Rudragouda","sequence":"additional","affiliation":[{"name":"Division of Agronomy, Central Coffee Research Institute, Coffee Research Station Post, Balehonnur","place":["Chikkamagaluru, Karnataka, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1038\/nature03608","article-title":"Plant sesquiterpenes induce hyphal branching in arbuscular mycorrhizal fungi","volume":"435","author":"Akiyama","year":"2005","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"911","DOI":"10.3390\/biology12070911","article-title":"Coffee-associated endophytes: plant growth promotion and crop protection","volume":"12","author":"Asad","year":"2023","journal-title":"Biology"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1007\/s12571-015-0446-9","article-title":"The coffee rust crises in Colombia and Central America (2008\u20132013): impacts, plausible causes and proposed solutions","volume":"7","author":"Avelino","year":"2015","journal-title":"Food Secur."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1111\/j.1365-3040.2009.01926.x","article-title":"Regulation and function of root exudates","volume":"32","author":"Badri","year":"2009","journal-title":"Plant Cell Environ."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1146\/annurev.arplant.57.032905.105159","article-title":"The role of root exudates in rhizosphere interactions with plants and other organisms","volume":"57","author":"Bais","year":"2006","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1007\/s11104-014-2186-6","article-title":"The art of isolating nitrogen-fixing bacteria associated with non-leguminous plants using N-free semi-solid media: a practical guide for microbiologists","volume":"384","author":"Baldani","year":"2014","journal-title":"Plant Soil"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"7246","DOI":"10.1128\/AEM.01047-06","article-title":"Enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, Burkholderia phytofirmans PsJn","volume":"72","author":"Barka","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"ref8","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1023\/A:1005956528316","article-title":"Shade management in coffee and cacao plantations","volume":"38","author":"Beer","year":"1998","journal-title":"Agrofor. Syst."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.3389\/fpls.2019.01068","article-title":"Role of arbuscular mycorrhizal fungi in plant growth regulation: implications in abiotic stress tolerance","volume":"10","author":"Begum","year":"2019","journal-title":"Front. Plant Sci."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.tplants.2012.04.001","article-title":"The rhizosphere microbiome and plant health","volume":"17","author":"Berendsen","year":"2012","journal-title":"Trends Plant Sci."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/j.tree.2008.01.005","article-title":"Agroforestry: a refuge for tropical biodiversity","volume":"23","author":"Bhagwat","year":"2008","journal-title":"Trends Ecol. Evol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"1327","DOI":"10.1007\/s11274-011-0979-9","article-title":"Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture","volume":"28","author":"Bhattacharyya","year":"2012","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1146\/annurev.arplant.57.032905.105346","article-title":"A renaissance of elicitors: perception of microbe-associated molecular patterns and danger signals by pattern-recognition receptors","volume":"60","author":"Boller","year":"2009","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1146\/annurev-arplant-050312-120106","article-title":"Structure and functions of the bacterial microbiota of plants","volume":"64","author":"Bulgarelli","year":"2013","journal-title":"Annu. Rev. Plant Biol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s10584-014-1306-x","article-title":"A bitter cup: climate change profile of global coffee production","volume":"129","author":"Bunn","year":"2015","journal-title":"Clim. Chang."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e2001793","DOI":"10.1371\/journal.pbio.2001793","article-title":"Research priorities for harnessing plant microbiomes in sustainable agriculture","volume":"15","author":"Busby","year":"2017","journal-title":"PLoS Biol."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e0106355","DOI":"10.1371\/journal.pone.0106355","article-title":"Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil","volume":"10","author":"Caldwell","year":"2015","journal-title":"PLoS One"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/j.apsoil.2010.08.001","article-title":"Microbial community structure of vineyard soils with different pH and copper content","volume":"46","author":"Calvino","year":"2010","journal-title":"Appl. Soil Ecol."},{"key":"ref19","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1007\/978-1-4615-6657-1_5","volume-title":"Coffee: Botany, Biochemistry and Production of Beans and Beverage","author":"Cannell","year":"1985"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1126\/science.aaw9285","article-title":"Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome","volume":"366","author":"Carrion","year":"2019","journal-title":"Science"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/ismej.2013.196","article-title":"Rhizosphere microbiome assemblage is affected by plant development","volume":"8","author":"Chaparro","year":"2014","journal-title":"ISME J."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"828","DOI":"10.3390\/plants13060828","article-title":"Drought stress responses in Arabica coffee genotypes: physiological and metabolic insights","volume":"13","author":"Chekol","year":"2024","journal-title":"Plants"},{"key":"ref23","volume-title":"Coffee Guide 2024","year":"2024"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.jare.2019.03.004","article-title":"A review on the plant microbiome: ecology, functions and emerging trends in microbial application","volume":"19","author":"Compant","year":"2019","journal-title":"J. Adv. Res."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1146\/annurev-micro-090817-062524","article-title":"Ecology and evolution of plant microbiomes","volume":"73","author":"Cordovez","year":"2019","journal-title":"Ann. Rev. Microbiol."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1007\/s10584-018-2346-4","article-title":"Why could the coffee crop endure climate change and global warming to a greater extent than previously estimated?","volume":"152","author":"DaMatta","year":"2019","journal-title":"Clim. Chang."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1590\/S1677-04202006000100006","article-title":"Impacts of drought and temperature stress on coffee physiology and production","volume":"18","author":"DaMatta","year":"2006","journal-title":"Braz. J. Plant Physiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1590\/S1677-04202007000400014","article-title":"Ecophysiology of coffee growth and production","volume":"19","author":"DaMatta","year":"2007","journal-title":"Braz. J. Plant Physiol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"eaav3473","DOI":"10.1126\/sciadv.aav3473","article-title":"High extinction risk for wild coffee species and implications for coffee sector sustainability","volume":"5","author":"Davis","year":"2019","journal-title":"Sci. Adv."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e02398","DOI":"10.1128\/AEM.02398-16","article-title":"Exploring the impacts of postharvest processing on the microbiota and metabolite profiles during coffee bean production","volume":"83","author":"De Bruyn","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e004442","DOI":"10.1128\/spectrum.00444-22","article-title":"The rhizosphere microbiomes of five species of coffee trees","volume":"10","author":"de Sousa","year":"2022","journal-title":"Microbiol. Spectrum"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"3033","DOI":"10.1038\/s41467-018-05516-7","article-title":"Soil bacterial networks are less stable under drought than fungal networks","volume":"9","author":"de Vries","year":"2018","journal-title":"Nat. Commun."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"2405","DOI":"10.1007\/s10531-019-01760-5","article-title":"Soil microbiome: a key player for conservation of soil health under changing climate","volume":"28","author":"Dubey","year":"2019","journal-title":"Biodivers. Conserv."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"126613","DOI":"10.1016\/j.micres.2020.126613","article-title":"Identification and characterization of Vietnamese coffee bacterial endophytes displaying in vitro antifungal and nematicidal activities","volume":"242","author":"Duong","year":"2021","journal-title":"Microbiol. Res."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1146\/annurev.phyto.42.040803.140421","article-title":"Systemic acquired resistance","volume":"42","author":"Durrant","year":"2004","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"110771","DOI":"10.1016\/j.plaphy.2025.110771","article-title":"Gene coexpression network analysis of galactomannan biosynthesis and endosperm maturation in species of the genus Coffea","volume":"229","author":"Dussert","year":"2025","journal-title":"Plant Physiol. Biochem."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1038\/nrmicro.2017.87","article-title":"Embracing the unknown: disentangling the complexities of the soil microbiome","volume":"15","author":"Fierer","year":"2017","journal-title":"Nat. Rev. Microbiol."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1111\/j.1574-6976.2011.00301.x","article-title":"Metabolic adaptation of human pathogenic and related nonpathogenic bacteria to extra and intracellular habitats","volume":"36","author":"Fuchs","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.micres.2013.09.009","article-title":"Bacteria with ACC deaminase can promote plant growth and help feed the world","volume":"169","author":"Glick","year":"2014","journal-title":"Microbiol. Res."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1007\/s005720050027","article-title":"Dependency of cassava (Manihot esculanta Crantz) on vesicular arbuscular mycorrhizal fungi","volume":"4","author":"Habte","year":"1994","journal-title":"Mycorrhiza"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1128\/MMBR.00050-14","article-title":"The hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes","volume":"79","author":"Hardoim","year":"2015","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"681","DOI":"10.3390\/antiox9080681","article-title":"Reactive oxygen species and antioxidant defense in plants under abiotic stress: revisiting the crucial role of a universal defence regulator","volume":"9","author":"Hasanuzzaman","year":"2020","journal-title":"Antioxidants"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"225","DOI":"10.3389\/fpls.2020.00225","article-title":"High resolution mapping of a Hordeum bulbosum derived powdery mildew resistance locus in barley using distinct homologous introgression lines","volume":"11","author":"Hoseinzadeh","year":"2020","journal-title":"Front. Plant Sci."},{"key":"ref44","volume-title":"Coffee Development Report 2024","year":"2024"},{"key":"ref45","volume-title":"Climate Change 2023: Synthesis Report","year":"2023"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e12119","DOI":"10.1002\/sae2.12119","article-title":"Linking biodiversity and biotic interactions to ecosystem functioning","volume":"3","author":"Jayaramaiah","year":"2024","journal-title":"J. Sustain. Agric. Environ."},{"key":"ref111","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1093\/biosci\/biu038","article-title":"Shade coffee: update on a disappearing refuge for biodiversity","volume":"64","author":"Jha","year":"2014","journal-title":"BioScience,"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/nature05286","article-title":"The plant immune system","volume":"444","author":"Jones","year":"2006","journal-title":"Nature"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10457-009-9229-7","article-title":"Agroforestry for ecosystem services and environmental benefits: an overview","volume":"76","author":"Jose","year":"2009","journal-title":"Agrofor. Syst."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"S3","DOI":"10.1016\/j.ejsobi.2006.10.002","article-title":"Soil invertebrates and ecosystem services","volume":"42","author":"Lavelle","year":"2006","journal-title":"Eur. J. Soil Biol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1016\/j.cell.2017.04.025","article-title":"Communication in the phytobiome","volume":"169","author":"Leach","year":"2017","journal-title":"Cell"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1875","DOI":"10.1128\/AEM.69.4.1875-1883.2003","article-title":"Microbiology of the phyllosphere","volume":"69","author":"Lindow","year":"2003","journal-title":"Appl. Environ. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1094\/PDIS-03-15-0340-FE","article-title":"Plant disease detection by imaging sensors- parallels and specific demands for precision agriculture and plant phenotyping","volume":"100","author":"Mahlein","year":"2016","journal-title":"Plant Dis."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"4309","DOI":"10.1093\/jxb\/erx211","article-title":"Photosynthetic and metabolic acclimation to repeated drought events play key roles in drought tolerance in coffee","volume":"68","author":"Menezes-Silva","year":"2017","journal-title":"J. Exp. Bot."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1128\/MMBR.00012-07","article-title":"Siderophore-based iron acquisition and pathogen control","volume":"71","author":"Miethke","year":"2007","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"126861","DOI":"10.1016\/j.micres.2021.126861","article-title":"Plant growth promoting bacteria for combating salinity stress in plants- recent developments and prospects: a review","volume":"252","author":"Mishra","year":"2021","journal-title":"Microbiol. Res."},{"key":"ref56","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1016\/j.tim.2015.07.009","article-title":"Engineering microbiomes to improve plant and animal health","volume":"23","author":"Mueller","year":"2015","journal-title":"Trends Microbiol."},{"key":"ref222","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/j.jssas.2012.07.002","article-title":"Phosphate-solubilising rhizobacteria associated with Coffea arabica L. in natural coffee forests of southwestern Ethiopia","volume":"12","author":"Muleta","year":"2013","journal-title":"J. Saudi Soc. Agric. Sci."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.agee.2017.06.024","article-title":"Shade tree diversity enhances coffee production and quality in agroforestry systems in Western Ghats","volume":"247","author":"Nesper","year":"2017","journal-title":"Agric. Ecosyst. Environ."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/nrmicro.2016.89","article-title":"Quorum sensing signal\u2013response systems in gram-negative bacteria","volume":"14","author":"Papenfort","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"4575","DOI":"10.1093\/jxb\/ert271","article-title":"Overexpressed TPX2 causes ectonopic formation of microtubular arrays in the nuclei of acemtrosomal plant cell","volume":"64","author":"Petrovska","year":"2013","journal-title":"J. Exp. Bot."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1146\/annurev-phyto-082712-102340","article-title":"Induced systemic resistance by beneficial microbes","volume":"52","author":"Pieterse","year":"2014","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"2567","DOI":"10.3390\/microorganisms13112567","article-title":"Rhizospheric and endophytic plant growth-promoting bacteria associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner: a review of their agronomic potential","volume":"13","author":"Ramirez-Lopez","year":"2025","journal-title":"Microorganisms"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1007\/s11104-009-9895-2","article-title":"Acquisition of phosphorus and nitrogen in the rhizosphere and plant growth promotion by microorganisms","volume":"321","author":"Richardson","year":"2009","journal-title":"Plant Soil"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1104\/pp.111.175448","article-title":"Soil microorganisms mediating phosphorus availability update on microbial phosphorus","volume":"156","author":"Richardson","year":"2011","journal-title":"Plant Physiol."},{"key":"ref64","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1111\/j.1461-0248.2004.00620.x","article-title":"Arbuscular mycorrhizae and terrestrial ecosystem processes","volume":"7","author":"Rillig","year":"2004","journal-title":"Ecol. Lett."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1038\/ismej.2007.106","article-title":"Stress tolerance in plants via habitat-adapted symbiosis","volume":"2","author":"Rodriguez","year":"2008","journal-title":"ISME J."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"4927","DOI":"10.1073\/pnas.0730845100","article-title":"Bacterial volatiles promote growth in Arabidopsis","volume":"100","author":"Ryu","year":"2003","journal-title":"Proc. Natl Acad. Sci. U. S. A"},{"key":"ref67","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.tplants.2017.09.003","article-title":"Feed your friends: do plant exudates shape the root microbiome?","volume":"23","author":"Sasse","year":"2018","journal-title":"Trends Plant Sci."},{"key":"ref68","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/B978-0-443-13856-0.00017-8","volume-title":"Biodiversity, Bioengineering and Biotechnology of Fungi","author":"Saxena","year":"2025"},{"key":"ref69","volume-title":"Mycorrhizal Symbiosis","author":"Smith","year":"2008"},{"key":"ref70","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1111\/j.1574-6976.2007.00072.x","article-title":"Indole-3-acetic acid in microbial and microorganism\u2013plant signalling","volume":"31","author":"Spaepen","year":"2007","journal-title":"FEMS Microbiol. Rev."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"2041","DOI":"10.1128\/JB.06637-11","article-title":"Novel N-demethylases enable bacterial degradation of caffeine and related purine alkaloids","volume":"194","author":"Summers","year":"2012","journal-title":"J. Bacteriol."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"1602940","DOI":"10.3389\/fmicb.2025.1602940","article-title":"Rhizobacteria consortium improves growth, yield, and phytochemicals in Robusta coffee (Coffea canephora L.)","volume":"16","author":"Suriani","year":"2025","journal-title":"Front. Microbiol."},{"key":"ref73","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1038\/nature01014","article-title":"Agricultural sustainability and intensive production practices","volume":"418","author":"Tilman","year":"2002","journal-title":"Nature"},{"key":"ref74","doi-asserted-by":"publisher","first-page":"607","DOI":"10.1038\/s41579-020-0412-1","article-title":"Plant\u2013microbiome interactions: from community assembly to plant health","volume":"18","author":"Trivedi","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref75","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1111\/1758-2229.12181","article-title":"Bacterial seed endophytes: genera, vertical transmission and interaction with plants","volume":"7","author":"Truyens","year":"2014","journal-title":"Environ. Microbiol. Rep."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1007\/978-94-017-7462-8_16","article-title":"Coffee and cocoa production in agroforestry \u2013 a climate smart agriculture model","volume":"90","author":"Vaast","year":"2016","journal-title":"Clim. Chang. Agric. Worldw."},{"key":"ref77","doi-asserted-by":"publisher","first-page":"1196","DOI":"10.1111\/nph.13312","article-title":"The importance of the microbiome of the plant holobiont","volume":"206","author":"Vandenkoornhuyse","year":"2015","journal-title":"New Phytol."},{"key":"ref78","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1146\/annurev-ecolsys-011720-013401","article-title":"The floral microbiome: plant, pollinator and microbial perspectives","volume":"51","author":"Vannette","year":"2020","journal-title":"Annu. Rev. Ecol. Evol. Syst."},{"key":"ref79","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.funeco.2009.07.002","article-title":"Fungal endophyte diversity in coffee plants from Colombia, Hawai\u2019i, Mexico and Puerto Rico","volume":"3","author":"Vega","year":"2010","journal-title":"Fungal Ecol."},{"key":"ref80","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.chom.2017.07.004","article-title":"Establishing causality: opportunities of synthetic communities for plant microbiome research","volume":"22","author":"Vorholt","year":"2017","journal-title":"Cell Host Microbe"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/j.micres.2015.12.003","article-title":"Enhancement of drought stress tolerance in crops by plant growth-promoting rhizobacteria","volume":"184","author":"Vurukonda","year":"2016","journal-title":"Microbiol. Res."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"1884416","DOI":"10.3389\/fpls.2026.1884416","article-title":"Coffee endophytes: diversity, ecological functions, and application prospects in sustainable production","volume":"17","author":"Wei","year":"2026","journal-title":"Front. Plant Sci."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1951767\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T10:59:27Z","timestamp":1789037967000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1951767\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,10]]},"references-count":84,"alternative-id":["10.3389\/fmicb.2026.1951767"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1951767","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,10]]},"article-number":"1951767"}}