Bacterial microbiome and physicochemical properties of irrigation water and soil in Chonto type tomato from Boyaca, Colombia




Solanum lycopersicum L., Crop quality, Physicochemical variables, Microbione


Tomato cultivation ranks fourth in vegetable production in Boyaca. The largest production of Chonto tomato in greenhouses is supplied by the Alto Chicamocha irrigation and drainage district since it is the main agricultural production unit for the department. To investigate the physicochemical conditions of the soil and irrigation water in the crop and bacterial communities associated with the greenhouse Chonto tomato crop, a total of 15 crops of 50×50 m located within the irrigation and drainage district of Alto Chicamocha were analyzed. Soil and irrigation water samples were analyzed and the bacteriome associated with the crop rhizosphere was characterized. From the physicochemical results obtained, we observed a significant relationship between crop attributes, the physicochemical properties of soil, and irrigation water in the different study zones. On the other hand, in the bacterial composition associated with the crop (soil and irrigation water), a relationship was found between the genera Sphingomonas spp. and Sphingobium spp. with crop quality for the different crops evaluated.


Download data is not yet available.


Anzalone, A., A. Mosca, G. Dimaria, D. Nicotra, M. Tessitori, G.F. Privitera, A. Pulvirenti, C. Leonardi, and V. Catara. 2022. Soil and soilless tomato cultivation promote different microbial communities that provide new models for future crop interventions. Int. J. Mol. Sci. 23(15), 8820. Doi:

An, H., J. Zhang, L. Zhang, S. Li, B. Zhou, and X. Zhang. 2023. Effects of nutrition and light quality on the growth of southern highbush blueberry (Vaccinium corymbosum L.) in an advanced plant factory with artificial lighting (PFAL). Horticulturae 9(2), 287.

Alvarado, A., F. Bertsch, E. Bornemisza, G. Cabalceta, W. Forsythe, C. Henríquez, R. Mata, E. Molina, and R. Salas. 2001. Suelos derivados de cenizas volcánicas (Andisoles) de Costa Rica. Asociación Costarricense de la Ciencia del Suelo y Centro de Investigaciones Agronómicas/Universidad de Costa Rica. San José.

Alvarado, A. and W. Forsythe. 2005. Variación de la densidad aparente en órdenes de suelos de Costa Rica. Agron. Costarr. 29(1), 85-94.

Bonachela, S., M.D. Fernández, F.J. Cabrera, and M.R. Granados. 2018. Soil spatio-temporal distribution of water, salts and nutrients in greenhouse, drip-irrigated tomato crops using lysimetry and dielectric methods. Agric. Water Manage. 203, 151-161. Doi:

Bouksila, F., A. Bahri, R. Berndtsson, M. Persson, J. Rozema, and S.E.A.T.M. Van der Zee. 2013. Assessment of soil salinization risks under irrigation with brackish water in semiarid Tunisia. Environ. Exp. Bot. 92, 176-185. Doi:

Brissio, P.A. 2005. Evaluación preliminar del estado de contaminación en suelos de la provincia de Neuquén donde se efectúan actividades de explotación hidrocarburífera. Undergraduate thesis. Escuela Superior de Salud y Ambiente, Universidad Nacional de Comahue, Neuquén, Argentina.

Cabrera, F.J., S. Bonachela, M.D. Fernandez, M.R. Granados, and J.C. López. 2016. Lysimetry methods for monitoring soil solution electrical conductivity and nutrient concentration in greenhouse tomato crops. Agric. Water Manage. 178, 171-179. Doi:

Calderón-Medina, C.L., G.P. Bautista-Mantilla, and S. Rojas-González. 2018. Propiedades químicas, físicas y biológicas del suelo, indicadores del estado de diferentes ecosistemas en una terraza alta del departamento del Meta. Orinoquia 22(2), 141-157. Doi:

Caporaso, J.G., J. Kuczynski, J. Stombaugh, K. Bittinger, F.D. Bushman, E.K. Costello, N. Fierer, A. Gonzalez, J.K. Goodrich, J.I. Gordon, G.A. Huttley, S.T. Kelley, D. Knights, J.E. Koenig, R.E. Ley, C.A. Lozupone, D. McDonald, B.D. Muegge, M. Pirrung, J. Reeder, J.R. Sevinsky, P.J. Turnbaugh, W.A. Walters, J. Widmann, T. Yatsunenko, J. Zaneveld, and R. Knight. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336. Doi:

Chandel, A., R. Mann, J. Kaur, S. Norton, D. Auer, J. Edwards, G. Spangenberg, and T. Sawbridge. 2022. The role of soil microbial diversity in the conservation of native seed bacterial microbiotas. Microorganisms 10(4), 750. Doi:

Colombia IGAC, Instituto Geográfico Agustín Codazzi. 2006. Métodos analíticos del laboratorio de suelos. 6th ed. Bogota.

Dadhwal, M., S. Jit, H. Kumari, and R. Lal. 2009. Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite. Int. J. Syst. Evol. Microbiol. 59(12), 3140-3144. Doi:

Davis, J.F. 1959. Organic soils, their formation, distribution, utilization and management. Sp. Bull. 425 Agricultural Experiment Station, Michigan State University, .

De Pascale, S., A. Maggio, C. Ruggiero, and G. Barbieri. 2003. Growth, water relations, and ion content of field-grown celery [Apium graveolens L. var. dulce (Mill.) Pers.] under saline irrigation. J. Am. Soc. Hortic. Sci. 128(1), 136-143. Doi:

Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19), 2460-2461. Doi:

Edgar, R.C., B.J. Haas, J.C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16), 2194-2200. Doi:

Etesami, H., S. Emami, and H.A. Alikhani. 2017. Potassium solubilizing bacteria (KSB): Mechanisms, promotion of plant growth, and future prospects - A review. J. Soil Sci. Plant Nutr. 17(4), 897-911. Doi:

FAO. 2016. Propiedades físicas del suelo. In:; consulted: March, 2022.

Ferreras, L.A., S.M.I. Toresani, V.S. Faggioli, and C.M. Galarza. 2015. Sensibilidad de indicadores biológicos edáficos en un Argiudol de la Región Pampeana Argentina. Span. J. Soil Sci. 5(3), 220-235.

Foyer, C.H., B. Rasool, J.W. Davey, and R.D. Hancock. 2016. Cross-tolerance to biotic and abiotic stresses in plants: A focus on resistance to aphid infestation. J. Exp. Bot. 67(7), 2025-2037. Doi:

GISSAT-UPTC, Grupo Interinstitucional de Investigación en Suelos Sulfatados Ácidos Tropicales. 2012. Evaluación de impacto y plan de manejo de los suelos afectados por las inundaciones en los valles de Tundama y Sugamuxi (Boyacá). Universidad Pedagógica y Tecnológica de Colombia, Tunja.

Gobernación de Boyacá. 2020. Plan Departamental de Extensión Agropecuaria-PDEA 2020-2023.

González, I. and S. Déjean. 2021. CCA: Canonical correlation analysis. R package version 1.2.1. In:; consulted: March, 2022.

Gouda, S., R.G. Kerry, G. Das, S. Paramithiotis, H.-S. Shin, and J.K. Patra. 2018. Revitalization of plant growth promoting rhizobacteria for sustainable development in agriculture. Microbiol. Res. 206, 131-140. Doi:

Harrell, F.E. and C. Dupont. 2023. Hmisc: Harrell miscellaneous. R package version 5.1-0. In:; consulted: March, 2022.

Husson, F., J. Josse, S. Le, and J. Mazet. 2014. FactoMineR: Multivariate exploratory data analysis and data mining with R. R package version 1.34. In:; consulted: March,2022.

Jaurixje, M., D. Torres, B. Mendoza, M. Henríquez, and J. Contreras. 2013. Propiedades físicas y químicas del suelo y su relación con la actividad biológica bajo diferentes manejos en la zona de Quíbor, estado Lara. Bioagro 25(1), 47-56.

Khan, N., R.H. Kazmi, L.A.J. Willems, A.W. van Heusden, W. Ligterink, and H.W.M. Hilhorst. 2012. Exploring the natural variation for seedling traits and their link with seed dimensions in tomato. PLoS One 7(8), e43991. Doi:

Klindworth, A., E. Pruesse, T. Schweer, J. Peplies, C. Quast, M. Horn, and F.O. Glöckner. 2013. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 41(1), e1. Doi:

Lahti, L. and S. Shetty. 2019. Microbiota R package. Bioconductor version 3.18. In:; consulted: March, 2022.

Lal, R., C. Dogra, S. Malhotra, P. Sharma, and R. Pal. 2006. Diversity, distribution and divergence of lin genes in hexachlorocyclohexane-degrading sphingomonads. Trends Biotechnol. 24(3), 121-130. Doi:

Li, L, M, Ding, Z. Lan, Y. Zhao, and J. Chen. 2019. Light availability and patterns of allocation to reproductive and vegetative biomass in the sexes of the dioecious macrophyte Vallisneria spinulosa. Front. Plant Sci. 10, 572. Doi:

Ma, G., J. Kang, J. Wang, Y. Chen, H. Lu, L. Wang, C. Wang, Y. Xie, D. Ma, and G. Kang. 2020. Bacterial community structure and predicted function in wheat soil from the north China plain are closely linked with soil and plant characteristics after seven years of irrigation and nitrogen application. Front. Microbiol. 11, 506. Doi:

Maggio, A., S. De Pascale, G. Angelino, C. Ruggiero, and G. Barbieri. 2004. Physiological response of tomato to saline irrigation in long-term salinized soils. Eur. J. Agron. 21(2), 149-159. Doi:

Manzotti, A., A. Bergna, M. Burow, H.J.L. Jørgensen, T. Cernava, G. Berg, D.B. Collinge, and B. Jensen. 2020. Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling. FEMS Microbiol. Ecol. 96(5), fiaa052. Doi:

Martínez, E., L.F. Rodríguez, and N. Medina. 2014. Estudio de factibilidad de una planta empacadora (packing house) para cebolla de bulbo (Allium cepa L.) en el Distrito de Riego del Alto Chicamocha (Boyacá). Rev. Colomb. Cienc. Hortic. 8(2), 287-301. Doi:

Monsalve-C., O.I., J.S. Gutiérrez-D., and W.A. Cardona. 2017. Factores que intervienen en el proceso de mineralización de nitrógeno cuando son aplicadas enmiendas orgánicas al suelo. Una revisión. Rev. Colomb. Cienc. Hortic. 11(1), 200-209. Doi:

Nakayasu, M., K. Takamatsu, K. Yazaki, and A. Sugiyama. 2022. Plant specialized metabolites in the rhizosphere of tomatoes: secretion and effects on microorganisms. Biosci. Biotechnol. Biochem. 87(1), 13-20. Doi:

Oksanen, J., G.L. Simpson, F.G. Blanchet, R. Kindt, P. Legendre, P.R. Minchin, R.B. O’Hara, P. Solymos, M.HH. Stevens, E. Szoecs, H. Wagner, M. Barbour, M. Bedward, B. Bolker, D. Borcard, G. Carvalho, M. Chirico, M. De Caceres, S. Durand, H.B.A. Evangelis-ta, R. FitzJohn, M. Friendly, B. Furneaux, G. Hanni-gan, M.O. Hill, L. Lahti, D. McGlinn, M.-H. Ouellette, E.R. Cunha, T. Smith, A. Stier, C.J.F. Ter Braak, and J. Weedon. 2022. Vegan: Community ecology package. R package version 3.4.0 In:; consulted: March, 2022.

Pacheco, M.C., L.F. Rodríguez, and L.T. Bermúdez. 2006. Plan estratégico de mercadeo para la cadena hortícola en el Distrito de riego del Alto Chicamocha. Agron. Colomb. 24(1),

Parmar, P. and S.S. Sindhu. 2013. Potassium solubilisation by rhizosphere bacteria: Influence of nutritional and environmental conditions. J. Microbiol. Res. 3(1), 25-31.

Prakash, O. and R. Lal. 2006. Description of Sphingobium fuliginis sp. nov., a phenanthrene-degrading bacterium from a fly ash dumping site, and reclassification of Sphingomonas cloacae as Sphingobium cloacae comb. nov. Int. J. Syst. Evol. Microbiol. 56(9), 2147-2152. Doi:

Quast, C., E. Pruesse, P. Yilmaz, J. Gerken, T. Schweer, P. Yarza, J. Peplies, and F.O. Glöckner. 2013. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Opens external link in new window. Nucl. Acids Res. 41(D1), 590-596. Doi:

Quinteros, J.A., J. Gómez-García, M. Solano, G. Llumiquinga, C. Burgos, and D. Carrera-Villacrés. 2019. Evalua-ción de la calidad de agua para riego y aprovechamiento del recurso hídrico de la quebrada Togllahuayco. Siembra 6(2), 46-57. Doi:

Ren, Z., F. Wang, X. Qu, J.J. Elser, Y. Liu and L. Chu. 2017. Taxonomic and functional diferences between microbial communities in Qinghai Lake and its input streams. Front Microbiol. 8, 2319. Doi:

Rodriguez, P.A., M. Rothballer, S.P. Chowdhury, T. Nussbaumer, C. Gutjahr, and P. Falter-Braun. 2019. Systems biology of plant-microbiota interactions. Mol. Plant, 12(6), 804-821. Doi:

Schmitz, L., Z. Yan, M. Schneijderberg, M. de Roij, R. Pijnenburg, Q. Zheng, C. Franken, A. Dechesne, L.M. Trindade, R. van Velzen, T. Bisseling, R. Geurts, and X. Cheng. 2022. Synthetic bacterial community derived from a desert rhizosphere confers salt stress resilience to tomato in the presence of a soil microbiota. ISME J. 16(8), 1907-1920. Doi:

Shaheb, M.R., R. Venkatesh, and S.A. Shearer. 2021. A review on the effect of soil compaction and its management for sustainable crop production. J. Biosyst. Eng. 46, 417-439.

Singh, G., D.R. Biswas, and T.S. Marwaha. 2010. Mobilization of potassium from waste mica by plant growth promoting rhizobacteria and its assimilation by maize (Zea mays) and wheat (Triticum aestivum L.): A hydroponics study under phytotron growth chamber. J. Plant Nutr. 33(8), 1236-1251. Doi:

Suman, J., A. Rakshit, S.D. Ogireddy, S. Singh, C. Gupta, and J. Chandrakala. 2022. Microbiome as a key player in sustainable agriculture and human health. Front. Soil Sci. 2, 821589. Doi:

Toledo, D.M., J.A. Galantini, E. Ferreccio, S. Arzuaga, L. Gimenez, and S. Vázquez. 2013. Indicadores e índices de calidad en suelos rojos bajo sistemas naturales y cultivados. Cienc. Suelo 31(2), 201-212.

Usero, F.M., C. Armas, J.A. Morillo, M. Gallardo, R.B. Thompson, and F.I. Pugnaire. 2021. Effects of soil microbial communities associated to different soil fertilization practices on tomato growth in intensive greenhouse agriculture. Appl. Soil Ecol. 162, 103896. Doi:

Venturi, V. and C. Keel. 2016. Signaling in the rhizosphere. Trends Plant Sci. 21(3), 187-198. Doi:

Wickham, H. 2011 ggplot2. WIREs Comp. Statis. 3(2), 180-185. Doi:

Zhang, Z., Y.S. Xiao, Y. Zhan, Z. Zhang, Y. Liu, Y. Wei, T. Xu, and J. Li. 2022. Tomato microbiota under long-term organic and conventional farming. iMeta 1(3), e48. Doi:

Chonto tomato fuits. Photo: T.-A. Correa-Castro


Additional Files


  • Abstract
  • PDF
  • XLSX
  • PNG

How to Cite

Forero-Pineda, N, Correa-Castro, T-A, Serrano-Cely, P-A, Forero-Ulloa, F-E, & Cely-Reyes, G-E. (2023). Bacterial microbiome and physicochemical properties of irrigation water and soil in Chonto type tomato from Boyaca, Colombia. Revista Colombiana de Ciencias Hortícolas, 17(1), e15702.



Vegetable section