Abstract
Purpose: Phyllospheric microorganisms are among the most vital factors that influence the flavor and taste of coffee (Coffea arabica). Little is known about the relationship between bean properties in C. arabica and phyllospheric microorganisms. The study was carried out to assess bean morphology and biochemical compositions in Coffea arabica cultivars and correlation analysis between them and phyllospheric microorganisms. Materials: Ten C. arabica accessions were collected to assess the factor affecting coffee quality. An extensive variation was determined in terms of the bean morphological and biochemical compositions traits examined between the ten C. arabica accessions. Results: Correlation analysis demonstrated that the hundred-grain weight had strong positive correlation with transverse diameter (r = 0.80***) and longitudinal diameter (r = 0.61***). Additionally, strong positive correlation was determined between chlorogenic acid and longitudinal diameter (r = 0.69***), between caffeine and neochlorogenic acid (r = 1.00***), and between isochlorogenic acid B and isochlorogenic acid C (r = 0.74***). Furthermore, among four C. arabica cultivars, highly significant differences for the alpha and beta diversity indices of the pyllospheric bacterial and fungal communities were observed. Besides, T test indicated that the relative abundance of top five phyllospheric bacterial and fungal phyla exhibited significant different enrichment among the four C. arabica varieties. Conclusion: The redundancy analysis revealed that Proteobacteria were the most correlated with transverse diameter, caffeine, and trigonelline for dominant fungal phylum, and strong correlations were detected between Ascomycota and two bean biochemical compositions (isochlorogenic acid C and crude oil). This study may be useful for promoting the quality and yield of C. arabica.
Similar content being viewed by others
Data Availability
Data will be made available on request.
References
Alkimim ER, Caixeta ET, Sousa TV, Resende MDV, Silva FLD, Sakiyama NS, Zambolim L (2020) Selective efficiency of genome-wide selection in Coffea canephora breeding. Tree Genet Genomes 16:41. https://doi.org/10.1007/s11295-020-01433-3
Anagbogu CF, Ilori CO, Bhattacharjee R, Olaniyi OO, Beckles DM (2019) Gas chromatography-mass spectrometry and single nucleotide polymorphism-genotype-by-sequencing analyses reveal the bean chemical profiles and relatedness of Coffea canephora genotypes in Nigeria. Plants 8:425. https://doi.org/10.3390/plants8100425
Belete Y (2014) Performance evaluations of hundred beans weights of indigenous Arabica coffee genotypes across different environments. Sky J Agri Res 3:120–127
Berlec A (2012) Novel techniques and findings in the study of plant microbiota: search for plant probiotics. Plant Sci 193–194:96–102. https://doi.org/10.1016/j.plantsci.2012.05.010
Bertrand B, Etienne H, Cilas C, Charrier A, Baradat P (2005) Coffea arabica hybrid performance for yield, fertility and bean weight. Euphytica 141:255–262. https://doi.org/10.1007/s10681-005-7681-7
Bringel F, Couee l (2015) Pivotal roles of phyllosphere microorganisms at the interface between plantfunctioning and atmospheric trace gas dynamics. Front Microbiol 6:486. https://doi.org/10.3389/fmicb.2015.00486
Delmotte N, Kniff C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Von mering C, Vorholt JA (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. P Natl Acad Sci USA 106:16428–16433. https://doi.org/10.1073/pnas.0905240106
Favoretto P, da Silva CC, Tavares AG, GiattI G, Moraes PF, Lobato MTV, Silvarolla MB, Oliveiro-Filho G, Maluf MP (2017) Assisted-selection of naturally caffeine-free coffee cultivars-characterization of SNPs from a methyltransferase gene. Mol Breed 37:31. https://doi.org/10.1007/s11032-017-0636-6
Figueiredo LP, Borém FM, Ribeiro FC, Giomo GS, Taveira JHS, Malta MR (2015) Fatty acid profiles and parameters of quality of specialty coffees produced in different Brazilian regions. Afr J Agr Res 10:3484–3493. https://doi.org/10.5897/AJAR2015.9697
Ge Y, Zhang F, Xie C, Qu P, Jiang KL, Du HB, Zhao M, Lu Y, Wang BT, Shi XD (2023) Effects of different altitudes on Coffea arabica rhizospheric soil chemical properties and soil microbiota. Agronomy 13:471. https://doi.org/10.3390/agronomy13020471
Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E (2017) Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 109:351–361. https://doi.org/10.1016/j.ympev.2017.02.009
Hunter PJ, Pink DAC, Bending GD (2015) Cultivar-level genotype differences influence diversity and composition of lettuce (Lactuca sp.) phyllosphere fungal communities. Fungal Ecol 17:183–186. https://doi.org/10.1016/j.funeco.2015.05.007
International Coffee Organization (ICO) (2023) Available online: http://www.ico.org/prices/po-production.pdf (accessed on 18 December 2023)
Kishore GK, Pande S, Podile AR (2005) Biological control of late leaf spot of peanut (Arachis hypogaea) with chitinolytic bacteria. Phytopathology 95:1157–1165. https://doi.org/10.1094/PHYTO-95-1157
Kitzberger CSG, Scholz MBDS, Pereira LFP, Silva JBGDD, Benassi MDT (2016) Profile of the diterpenes, lipid and protein content of different coffee cultivars of three consecutive harvests. AIMS Agric Food 1:254–264. https://doi.org/10.3934/agrfood.2016.3.254
Lebot V, Melteras M, Pilecki A, Labouisse J-P (2020) Chemometric evaluation of cocoa (Theobroma cacao L.) and coffee (Coffea spp.) germplasm using HPTLC. Genet Resour Crop Ev 67:895–911. https://doi.org/10.1007/s10722-020-00888-6
Leroy T, Ribeyre F, Bertrand B, Charmetant P, Dufour M, Montagnon C, Marraccini P, Pot D (2006) Genetics of coffee quality. Braz J Plant Physiol 18:229–242. https://doi.org/10.1590/S1677-04202006000100016
Li L (2019) Genetie diversity of coffee leaf rust pathogen Hemileia vastatrix and coffee phyllosphere microorganisms in China. Master’s thesis, pp 15–16 (in Chinese)
Lindow SE, Brandl MT (2003) Microbiology of the phyllosphere. Appl Environ Microb 69:1875. https://doi.org/10.1128/AEM.69.4.1875-1883.2003
Lindow SE, Leveau JHJ (2002) Phyllosphere microbiology. Curr Opin Biotech 13:238–243
Liu H, Brettell L E, Singh B (2020) Linking the phyllosphere microbiome to plant health. Trends Plant Sci 5:841–844. https://doi.org/10.1016/j.tplants.2020.06.003
Martinez SJ, Simão JBP, Pylro VS, Schwan RF (2021) The altitude of coffee cultivation causes shifts in the microbial community assembly and biochemical compounds in natural induced anaerobic fermentations. Front Microbiol 12:671395. https://doi.org/10.3389/fmicb.2021.671395
Montagnon C, Bouharmont P (1996) Multivariate analysis of phenotypic diversity of Coffea arabica. Genet Resour Crop Ev 43:221–227. https://doi.org/10.1007/BF00123274
Oliveira LS, Franca AS, Mendonça JCF, Barros-Junior MC (2006) Proximate composition and fatty acids profile of green and roasted defective coffee beans. LWT Food Sci Technol 39:235–239. https://doi.org/10.1016/j.lwt.2005.01.011
Peters BA, Wu J, Hayes RB, Ahn JY (2017) The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study. BMC Microbiol 17:157. https://link.springer.com/article/https://doi.org/10.1186/s12866-017-1064-9
Rastogi G, Coaker GL, Leveau JHJ (2013) New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 348:1–10. https://doi.org/10.1111/1574-6968.12225
Rastogi G, Sbodio A, Tech JJ, Suslow TV, Coaker GL, Leveau JHJ (2012) Leaf Microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J 6:1812. https://doi.org/10.1038/ismej.2012.32
Silva BSRD, Santana GC, Chaves CL, Androcioli LG, Ferreira RV, Sera GH, Charmetant P, Leroy T, Pot D, Domingues DS et al (2019) Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers. Genetica 147:205–216. https://doi.org/10.1007/s10709-019-00064-4
Silvarolla MB, Mazzafera P, Lima MMAD (2000) Caffeine content of Ethiopian Coffea arabica beans. Genet Mol Biol 23:213–215. https://doi.org/10.1590/S1415-47572000000100036
Sousa LP, Silva MJ, Costa Mondego JM (2018) Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves. Genet Mol Biol 41:455–465. https://doi.org/10.1590/1678-4685-GMB-2017-0255
Sunarharum WB, Williams DJ, Smyth HE (2014) Complexity of coffee flavor: a compositional and sensory perspective. Food Res Int 62:315–325. https://doi.org/10.1016/j.foodres.2014.02.030
Su Z, Jia H, Sun M, Cai Z, Shen Z, Zhao B, Li J, Ma R, Yu M, Yan J (2022) Integrative analysis of the metabolome and transcriptome reveals the molecular mechanism of chlorogenic acid synthesis in peach fruit. Front Nutr 9:961626. https://doi.org/10.3389/fnut.2022.961626
Tran HTM, Vargas CAC, Lee LS, Furtado A, Smyth H, Henry R (2017) Variation in bean morphology and biochemical composition measured in different genetic groups of Arabica coffee (Coffea arabica L). Tree Genet Genomes 13:54. https://doi.org/10.1007/s11295-017-1138-8
Vorholt JA (2012) Microbial life in the phyllosphere. Nat Rev Microbiol 10:828–840. https://doi.org/10.1038/nrmicro2910
Wang XY, Zhou H, Chen JH, Li JH, Long YZ, Dong YP (2019) Genetic diversity of coffee germplasms by ISSR markers. Chin J Trop Crops 40:300–307 (in Chinese). https://doi.org/10.3969/j.issn.1000-2561.2019.02.013
Watanabe K, Kohzu A, Suda W, Yamamura S, Takamatsu T, Takenaka A, Koshikawa MK, Hayashi S, Watanabe M (2016) Microbial nitrification in throughfall of a Japanese cedar associated with archaea from the tree canopy. Springer plus 5:1596. https://doi.org/10.1186/s40064-016-3286-y
Weisburg WG, Barns SM, Pelletier DA (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–730. https://doi.org/10.1128/jb.173.2.697-703.1991
Whipps JM, Hand P, Pink D, Bending GD (2008) Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 105:1744–1755. https://doi.org/10.1111/j.1365-2672.2008.03906.x
Funding
This research was funded by Young Talents of “Xingdian Talent Support Program” of Yunnan Province (grant number XDYC-QNRC-2022-0711), Basic Research Project of Yunnan Province (grant number 202301AT070493), Key R&D Plan of Yunnan Province: Yunnan International Joint R&D Center for Green Development of Coffee Industry (grant number 202303AP140010), Yunnan Provincial Expert Basic Scientific Research Station (grant number 2021RYZJGZZ002), Start-up Fund for High-level Talents of Yunnan Agricultural University (grant number 2022RYKY001).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Additional information
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic Supplementary Material
Below is the link to the electronic supplementary material.
42729_2024_1757_MOESM1_ESM.xls
Supplementary Material 1: Table S1: Correlation coefficients among bean morphological and biochemical compositions characters of C. arabica cultivars investigated.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Wang, B., Shi, X., Shi, M. et al. Phyllospheric Microorganisms and Bean Characteristics Influence Quality of Ten Genotypes of Coffea Arabica. J Soil Sci Plant Nutr (2024). https://doi.org/10.1007/s42729-024-01757-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s42729-024-01757-2