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Plant & Rhizosphere Microbiome Research
The intricate interplay between plants and their microbiome is a fascinating research topic that has gained increasing attention in recent years. Microbes living inside and around plants contribute to shaping the host's ecological niche, affecting its survival and fitness in various ways. Plant and soil/rhizosphere microbiomes play a critical role in providing essential traits and functions such as nutrient uptake and growth regulation. Moreover, the microbiome can confer abiotic stress tolerance and protect against pathogens, providing a natural defense mechanism for the host. To understand the complex interactions between plants and their microbiome, we employ various approaches to unraveling the mechanisms underlying plant-microbe interactions, aimming to harness the power of the microbiome for sustainable agriculture.
Program Back to Roots using microorganisms to protect crops.
Papers
Selected
Mendes R, Kruijt M, Bruijn Id, Dekkers E, Voort Mvd, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011. DOI
Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, De Hollander M, Ruiz-Buck D, Mendes LW, Van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, Van Der Oost J, Paulson JN, Mendes R, Van Wezel GP, Medema MH, Raaijmakers JM. Pathogen-induced activation of disease-auppressive functions in the endophytic root microbiome. Science 2019. DOI
Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews 2013. DOI
Van der Voort M, Kempenaar M, Van Driel M, Raaijmakers JM, Mendes R. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecology Letters 2016. DOI
Pérez-Jaramillo JE, De Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome 2019. DOI
Mendes LW, Mendes R, Raaijmakers JM, Tsai SM. Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. The ISME Journal 2018. DOI
Full list
47. NISHISAKA CS, VENTURA JP, BAIS HP, MENDES R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. Environmental Microbiome 2024. DOI
46. Nishisaka CS, Ventura JP, Quevedo HD, Godoy FA, Rossmann M, Mendes R. Draft genome sequences of strain CMAA1738, strain CMAA1739 and strain CMAA1741, isolated from rhizosphere of wheat landraces. Microbiology Resource Announcements 2024. DOI
45. Cunha ICM, Silva AVR, Boleta EHM, Pellegrinetti TA, Zagatto LFG, Zagatto SSS, Chaves MG, Mendes R, Patreze CM, Tsai SM, Mendes LW. The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype. Microbiological Research 2024. DOI
44. Mendes R, Barros I, DAndrea PA, DAndrea-Kuhl MSC, Rodrigues GS. A multi-attribute approach to evaluating the impact of biostimulants on crop performance. Frontiers in Plant Science 2023. DOI
43. Mendes LW, Raaijmakers JM, Hollander M, Sepo E, Gomez-Exposito R, Chiorato AF, Mendes R, Tsai SM, Carrión VJ. Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome. Environmental Microbiome 2023. DOI
42. Costa LSAS, De Faria MR, Chiaramonte JB, Mendes LW, Sepo E, De Hollander M, Fernandes JMC, Carrión VJ, Bettiol W, Mauchline TH, Raaijmakers JM, Mendes R. Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness. Environmental Microbiome 2023. DOI
41. Braga LPP, Tanentzap AJ, Lee B, Tsai SM, Raaijmakers JM, Mendes R, Mendes LW. Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum. Applied Soil Ecology 2023. DOI
40. Soares MP, Cardoso IL, Araújo FE, De Angelis CF, Mendes R, Mendes LW, Fernandes MN, Jonsson CM, Queiroz SCN, Duarte MCT, Rantin FT, Sampaio FG. Influences of the alcoholic extract of Artemisia annua on gastrointestinal microbiota and performance of Nile tilapia. Aquaculture 2022. DOI
39. Kavamura VN, Mendes R, Bargaz A, Mauchline TH. Defining the wheat microbiome: towards microbiome-facilitated crop production. Computational and Strutural Biotechnology Journal 2021. DOI
38. May A, Coelho LF, Pedrinho A, Batista BD, Mendes LW, Mendes R, Morandi MAB, Barth G, Viana RS, Vilela ESD. The use of indigenous bacterial community as inoculant for plant growth promotion in soybean cultivation. Archives of Agronomy and Soil Science 2021. DOI
37. Poudel M, Mousami, Mendes R, Costa LAS, Bueno CG, Meng Y, Folimonova SY, Garret KA, Martins SJ. The role of plant-associated bacteria, fungi, and viruses in drought stress mitigation. Frontiers in Microbiology 2021. DOI
36. De Faria MR, Costa LSAS, Chiaramonte JB, Bettiol W, Mendes R. The rhizosphere microbiome: functions, dynamics, and role in plant protection. Tropical Plant Pathology 2020. DOI
35. Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo ISDe, Hirsch PR, Mendes R, Mauchline TH. Wheat dwarfing influences selection of the rhizosphere microbiome. Scientific Reports 2020. DOI
34. Rossmann M., Pérez-Jaramillo JE, Kavamura VN, Chiaramonte JB, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira MMC, Bonkowski M, Raaijmakers JM, Mauchline TH, Mendes R, Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiology Ecology 2020. DOI
33. Pérez-Jaramillo JE, De Hollander M, Ramírez CA, Mendes R, Raaijmakers JM, Carrión VJ. Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome 2019. DOI
32. Mendes LW, De Chaves MG, Fonseca MDeC, Mendes R, Raaijmakers JM, Tsai SM. Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome. Frontiers in Microbiology 2019. DOI
31. Carrión VJ, Perez-Jaramillo J, Cordovez V, Tracanna V, De Hollander M, Ruiz-Buck D, Mendes LW, Van Ijcken WFJ, Gomez-Exposito R, Elsayed SS, Mohanraju P, Arifah A, Van Der Oost J, Paulson JN, Mendes R, Van Wezel GP, Medema MH, Raaijmakers JM. Pathogen-induced activation of disease-auppressive functions in the endophytic root microbiome. Science 2019. DOI
30. Kavamura VN, Robinson RJ, Hayat R, Clark IM, Hughes D, Rossmann, M, Hirsch PR, Mendes R, Mauchiline TH. Land management and microbial seed load effect on rhizosphere and endosphere bacterial community ssembly in Wheat. Frontiers in Microbiology 2019. DOI
29. Kavamura VN, Hayat R, Clark IM, Rossmann M, Mendes R, Hirsch PR, Mauchiline TH. Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities. Frontiers in Microbiology 2018. DOI
28. Mendes LW, Mendes R, Raaijmakers JM, Tsai SM. Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. The ISME Journal 2018. DOI
27. Kavamura VN, Hayat R, Clark IM, Rossmann M, Mendes R, Hirsch PR, Mauchline TH. Inorganic nitrogen application affects both taxonomical and predicted functional structure of wheat rhizosphere bacterial communities. Frontiers in Microbiology 2018. DOI
26. Kavamura VN, Taketani RG, Ferreira C, Melo IS, Mendes R. The role of species turnover in structuring bacterial communities in a local scale in the cactus rhizosphere. Plant and Soil 2018. DOI
25. Mendes LW, Raaijmakers JM, De Hollander M, Mendes R, Tsai SM. Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. The ISME Journal 2017. DOI
24. Perez-Jaramillo JE, Carrión VJ, Bosse M, Ferrão LFV, De Hollander M, Garcia AAF, Ramírez CA, Mendes R, Raaijmakers JM. Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. The ISME Journal 2017. DOI
23. Cavalett A, SILVA MAC, Toyofuku T, Mendes R, Taketani RG, Pedrini J, Freitas RC, Sumida PYG, Yamanaka T, Nagano Y, Pellizari VH, Perez JAA, Kitazato H, Lima AOS. Dominance of Epsilonproteobacteria associated with a whale fall at a 4204 m depth - South Atlantic Ocean. Deep-Sea Research 2017. DOI
22. Van der Voort M, Kempenaar M, Van Driel M, Raaijmakers JM, Mendes R. Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecology Letters 2016. DOI
21. Romão-Dumaresq AS, Dourado MN, Fávaro LCL, Mendes R, Ferreira A, Araújo WL. Diversity of cultivated fungi associated with conventional and transgenic sugarcane and the interaction between endophytic Trichoderma virens and the host plant. Plos One 2016. DOI
20. Berg G, Krause R, Mendes R. Cross-kingdom similarities in microbiome ecology and biocontrol of pathogens. Frontiers in Microbiology 2015. DOI
19. Mendes R, Raaijmakers JM. Cross-kingdom similarities in microbiome functions. The ISME Journal 2015. DOI
18. Chapelle E, Mendes R, Bakker PAHM, Raaijmakers JM. Fungal invasion of the rhizosphere microbiome. The ISME Journal 2015. DOI
17. Perez-Jaramillo JE, Mendes R, Raaijmakers JM. Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology 2015. DOI
16. VOORT Mvd, Meijer HJG, Schmidt Y, Watrous J, Dekkers E, Mendes R, Dorrestein PC, Gross H, Raaijmakers JM. Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Frontiers in Microbiology 2015. DOI
15. Lopes LD, Lima AOS, Taketani RG, Darias P, Silva LRF, Romagnoli EM, Louvandini H, Abdalla AL, Mendes R. Exploring the sheep rumen microbiome for carbohydrate-active enzymes. Antonie Van Leeuwenhoek 2015. DOI
14. Taketani RG, Kavamura VN, Mendes R, Melo IS. Functional congruence of rhizosphere microbial communities associated to leguminous tree from Brazilian semiarid region. Environmental Microbiology Reports 2014. DOI
13. Liu Y, de Bruijn I, Jack ALH, Drynan K, van den Berg AH, Thoen E, Sandoval-Sierra V, Skaar I, van West P, Diéguez-Uribeondo J, van der Voort M, Mendes R, Mazzola M, Raaijmakers JM. Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. The ISME Journal 2014. DOI
12. Vasconcellos RLF, Mendes R, Taketani RG, Zucchi TD, Melo IS. Draft Genome Sequence of Pseudomonas sp. CMAA 1215, a Plant-Growth Promoting Bacterium isolated from a Brazilian Mangrove. Genome Announcements 2013. DOI
11. Taketani RG, Zucchi TD, Melo IS, Mendes R. Whole-Genome Shotgun Sequencing of Rhodococcus erythropolis Strain P27, a Highly Radiation-Resistant Actinomycete from Antarctica. Genome Announcements 2013. DOI
10. Kavamura VN, Taketani RG, Lanconi MD, Andreote FD, Mendes R, Melo IS. Water regime influences bulk soil and rhizosphere of Cereus jamacaru bacterial communities in the Brazilian Caatinga biome. Plos One 2013. DOI
09. Mendes R, Garbeva P, Raaijmakers JM. The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews 2013. DOI
08. Le CN, Mendes R, Kruijt M, Raaijmakers JM. Genetic and phenotypic diversity of Sclerotium rolfsii in groundnut fields in central Vietnam. Plant Disease 2012. DOI
07. Mendes R, Kruijt M, Bruijn Id, Dekkers E, Voort Mvd, Schneider JHM, Piceno YM, DeSantis TZ, Andersen GL, Bakker PAHM, Raaijmakers JM. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science 2011. DOI
06. Andreote FD, Rossetto PB, Mendes R, Avila LA, Labate CA, Pizzirani-Kleiner AA, Azevedo JL, Araujo WL. Bacterial community in the rhizosphere and rhizoplan of wild type and transgenic eucalyptus. World Journal of Microbiology and Biotechnology 2009. DOI
05. Costa R, van Aarle IM, Mendes R, van Elsas JD. Genomics of pyrrolnitrin biosynthetic loci: evidence for conservation and whole-operon mobility within Gram-negative bacteria. Environmental Microbiology 2009. DOI
04. Andreote FD, Mendes R, Dini-Andreote F, Rossetto PB, Labate CA, Pizzirani-Kleiner AA, van Elsas JD, Azevedo JL, Araújo WL. Transgenic tobacco revealing altered bacterial diversity in the rhizosphere during early plant development. Antonie Van Leeuwenhoek 2008. DOI
03. Mendes R, Pizzirani-Kleiner AA, Araujo WL, Raaijmakers JM. Diversity of cultivated endophytic bacteria from sugarcane: genetic and biochemical characterization of Burkholderia cepacia complex isolates. Applied and Environmental Microbiology 2007. DOI
02. Kuklinsky-Sobral J, Araújo WL, Mendes R, Pizzirani-Kleiner AA, Azevedo JL. Isolation and characterization of endophytic bacteria from soybean (Glycine max) grown in soil treated with glyphosate herbicide. Plant and Soil 2005. DOI
01. Kuklinsky-Sobral J, Araújo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL. Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environmental Microbiology 2004. DOI
> Mendes R. Diversity and genetic characterization of endophytic microbial communities associated with sugarcane. PhD Thesis Full version (Portuguese)
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