Eurasian Journal of Soil Science

Abstract

Soil bacterial communities are sensitive indicators of biological condition in tropical agroecosystems, yet field information from acidic maize soils in Ecuador remains scarce. This study provides an exploratory profile of soil bacterial communities and fertility indicators in maize amended with diatomaceous earth under field conditions. A randomized complete block field experiment was established with three treatments and five replications: untreated control without fertilization or diatomaceous earth (T1), conventional fertilization (T2), and conventional fertilization plus diatomaceous earth (T3). Grain yield was measured from replicated plots, whereas soil chemistry and 16S rRNA bacterial profiles were obtained from composite analytical profiles and interpreted descriptively. One composite baseline soil profile was obtained before treatment differentiation, and one composite profile per treatment was obtained at 60 and 120 days after sowing. Soil was sampled from the 0-30 cm layer in the inter-row zone. The diatomaceous earth product was applied edaphically at 12 kg ha-1 and contained 73.60% w/w SiO2 according to the product certificate. The 16S rRNA V3-V4 region was sequenced using an Illumina workflow, and raw FASTQ files were deposited in NCBI SRA. Grain yield differed among treatments (F = 18.18; P = 0.0011), with T2 and T3 statistically similar and both higher than T1. Bacterial profiles were dominated by Acidobacteria, Actinobacteria, Proteobacteria, Firmicutes and Verrucomicrobia. T3 at 120 DAS showed the highest numerical Shannon index and provider-reported species-level classifications among treatment-time profiles, but these patterns were not tested inferentially. The study offers a transparent baseline for future replicated microbiome work in tropical acidic maize soils.

Keywords

16S rRNA, acidic soil, diatomaceous earth, Ecuador, soil fertility, tropical maize.

References

<p>Akande, T., Adegoke, T.O., Wang, H., 2025. Biochar application enhances soil nutrient availability and microbial biomass in Chernozemic soil. <em>Eurasian Journal of Soil Science</em> 14(3): 280&ndash;289.</p>

<p>Bayadilova, G., Zhylkibayev, A., Yelibayeva, G., Yessenbayeva, J., Kazkeyev, D., Karasseva, V., 2022. Effect of different organic wastes on biological properties of clay-loam soil and rhizosphere soil of maize. <em>Eurasian Journal of Soil Science</em> 11(2): 141&ndash;150.</p>

<p>Berg, G., Smalla, K., 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. <em>FEMS Microbiology Ecology</em> 68: 1&ndash;13.</p>

<p>BioSequence S.A.S., 2024. Reporte de secuenciamiento BSRT_2414_007_UTEQ_CMESTANZA_16S. BioSequence S.A.S., Quito, Ecuador. Unpublished technical report.</p>

<p>Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-Gonz&aacute;lez, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. <em>Science</em> 359: 320&ndash;325.</p>

<p>Dimitrova, K., Kaiyrbekov, T., Balabanova, D., 2024. Assessing the impact of biofertilizer on soil microbial dynamics and metabolic activity in a controlled maize pot-grown experiment. <em>Eurasian Journal of Soil Science</em> 13(3): 202&ndash;209.</p>

<p>Etesami, H., 2024. Enhancing soil microbiome resilience: the mitigating role of silicon against environmental stresses. <em>Frontiers in Agronomy </em>6: 1465165.</p>

<p>Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. <em>Nature Reviews Microbiology</em> 15: 579&ndash;590.</p>

<p>Garbeva, P., van Veen, J.A., van Elsas, J.D., 2004. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. <em>Annual Review of Phytopathology</em> 42: 243&ndash;270.</p>

<p>Hartmann, M., Frey, B., Mayer, J., M&auml;der, P., Widmer, F., 2015. Distinct soil microbial diversity under long-term organic and conventional farming. <em>The ISME Journal</em> 9(5): 1177&ndash;1194.</p>

<p>Heiri, O., Lotter, A.F., Lemcke, G., 2001. Loss on ignition as a method for estimating organic and carbonate content in sediments: reproducibility and comparability of results. <em>Journal of Paleolimnology</em> 25: 101&ndash;110.</p>

<p>Herawati, A., Mujiyo, Dewi, W.S., Syamsiyah, J., Romadhon, M.R., 2024. Improving microbial properties in Psamments with mycorrhizal fungi, amendments, and fertilizer. <em>Eurasian Journal of Soil Science</em> 13(1): 59&ndash;69.</p>

<p>Hu, L., Xia, M., Lin, X., Xu, C., Li, W., Wang, J., Zeng, R., Song, Y., 2018. Earthworm gut bacteria increase silicon bioavailability and acquisition by maize. <em>Soil Biology and Biochemistry </em>125: 215&ndash;221.</p>

<p>Illumina, 2021. 16S Metagenomic Sequencing Library Preparation. Illumina, Inc. Available at [Access date: 16.06.2026]: https://support.illumina.com/downloads/16s_metagenomic_sequencing_library_preparation.html</p>

<p>Illumina, 2024. BaseSpace Sequence Support Resources. Illumina, Inc. Available at [Access date: 16.06.2026]: https://support.illumina.com/sequencing/sequencing_software/basespace-apps.html</p>

<p>ISO 10390:2021. Soil, treated biowaste and sludge &ndash; Determination of pH. International Organization for Standardization, Geneva, Switzerland. Available at [Access date: 16.06.2026]: &nbsp;https://www.iso.org/standard/75243.html</p>

<p>Lauber, C.L., Hamady, M., Knight, R., Fierer, N., 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. <em>Applied and Environmental Microbiology</em> 75: 5111&ndash;5120.</p>

<p>Leite, M.R.L., de Alcantara Neto, F., Dutra, A.F., Mendes, L.W., de Souza Miranda, R., Melo, V.M.M., Oliveira, F.A.S., de Figueiredo, M.V.B., Sousa, T.K.S.A., Costa, R.M., Rocha, S.M.B., de Araujo Pereira, A.P., de Mello Prado, R., Araujo, A.S.F., 2024. Distinct sources of silicon shape differently the rhizospheric microbial community in sugarcane. <em>Applied Soil Ecology</em> 193: 105131.</p>

<p>Megyes, M., Borsodi, A.K., Arendas, T., Marialigeti, K., 2021. Variations in the diversity of soil bacterial and archaeal communities in response to different long-term fertilization regimes in maize fields. <em>Applied Soil Ecology</em> 168: 104120.</p>

<p>Mestanza Uquillas, C.A., Santana Ch&aacute;vez, J.R., V&eacute;liz Zamora, D.V., Merch&aacute;n S&aacute;nchez, B.R., 2026. Tierra de diatomeas como enmienda sil&iacute;cea en ma&iacute;z (Zea mays L.): respuesta agron&oacute;mica, suelo y rentabilidad en Los R&iacute;os, Ecuador. <em>Arandu UTIC</em> 13: 771&ndash;785.</p>

<p>Murphy, J., Riley, J.P., 1962. A modified single solution method for the determination of phosphate in natural waters. <em>Analytica Chimica Acta</em> 27: 31&ndash;36.</p>

<p>Namli, A., Mahmood, A., Sevilir, B., &Ouml;zkır, E., 2017. Effect of phosphorus solubilizing bacteria on some soil properties, wheat yield and nutrient contents. <em>Eurasian Journal of Soil Science</em> 6(3): 249&ndash;258.</p>

<p>Nannipieri, P., Ascher, J., Ceccherini, M.T., Landi, L., Pietramellara, G., Renella, G., 2003. Microbial diversity and soil functions. <em>European Journal of Soil Science</em> 54(4): 655&ndash;670.</p>

<p>Oburger, E., Schmidt, H., 2016. New methods to unravel rhizosphere processes. <em>Trends in Plant Science</em> 21: 243&ndash;255.</p>

<p>Olsen, S.R., Cole, C.V., Watanabe, F.S., Dean, L.A., 1954. Estimation of available phosphorus in soils by extraction with sodium bicarbonate. USDA Circular No. 939. U.S. Department of Agriculture, Washington, DC, USA.</p>

<p>Philippot, L., Raaijmakers, J.M., Lemanceau, P., van der Putten, W.H., 2013. Going back to the roots: the microbial ecology of the rhizosphere. <em>Nature Reviews Microbiology</em> 11: 789&ndash;799.</p>

<p>Rousk, J., B&aring;&aring;th, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N., 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. <em>The ISME Journal</em> 4: 1340&ndash;1351.</p>

<p>Sparks, D.L., Page, A.L., Helmke, P.A., Loeppert, R.H., Soltanpour, P.N., Tabatabai, M.A., Johnston, C.T., Sumner, M.E., 1996. Methods of Soil Analysis: Part 3 Chemical Methods. Soil Science Society of America and American Society of Agronomy, Madison, WI, USA.</p>

<p>Usman, S., Muhammad, Y., Chiroman, A.M., 2016. Roles of soil biota and biodiversity in soil environment &ndash; A concise communication. <em>Eurasian Journal of Soil Science</em> 5(4): 255&ndash;265.</p>

<p>Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. <em>Applied and Environmental Microbiology</em> 73: 5261&ndash;5267.</p>

<p>Wang, Q., Jiang, X., Guan, D., Wei, D., Zhao, B., Ma, M., Chen, S., Li, L., Cao, F., Li, J., 2018. Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere. <em>Applied Soil Ecology</em> 125: 88&ndash;96.</p>

Abstract

Soil bacterial communities are sensitive indicators of biological condition in tropical agroecosystems, yet field information from acidic maize soils in Ecuador remains scarce. This study provides an exploratory profile of soil bacterial communities and fertility indicators in maize amended with diatomaceous earth under field conditions. A randomized complete block field experiment was established with three treatments and five replications: untreated control without fertilization or diatomaceous earth (T1), conventional fertilization (T2), and conventional fertilization plus diatomaceous earth (T3). Grain yield was measured from replicated plots, whereas soil chemistry and 16S rRNA bacterial profiles were obtained from composite analytical profiles and interpreted descriptively. One composite baseline soil profile was obtained before treatment differentiation, and one composite profile per treatment was obtained at 60 and 120 days after sowing. Soil was sampled from the 0-30 cm layer in the inter-row zone. The diatomaceous earth product was applied edaphically at 12 kg ha-1 and contained 73.60% w/w SiO2 according to the product certificate. The 16S rRNA V3-V4 region was sequenced using an Illumina workflow, and raw FASTQ files were deposited in NCBI SRA. Grain yield differed among treatments (F = 18.18; P = 0.0011), with T2 and T3 statistically similar and both higher than T1. Bacterial profiles were dominated by Acidobacteria, Actinobacteria, Proteobacteria, Firmicutes and Verrucomicrobia. T3 at 120 DAS showed the highest numerical Shannon index and provider-reported species-level classifications among treatment-time profiles, but these patterns were not tested inferentially. The study offers a transparent baseline for future replicated microbiome work in tropical acidic maize soils.

Keywords: 16S rRNA, acidic soil, diatomaceous earth, Ecuador, soil fertility, tropical maize.

References

Akande, T., Adegoke, T.O., Wang, H., 2025. Biochar application enhances soil nutrient availability and microbial biomass in Chernozemic soil. Eurasian Journal of Soil Science 14(3): 280–289.

Bayadilova, G., Zhylkibayev, A., Yelibayeva, G., Yessenbayeva, J., Kazkeyev, D., Karasseva, V., 2022. Effect of different organic wastes on biological properties of clay-loam soil and rhizosphere soil of maize. Eurasian Journal of Soil Science 11(2): 141–150.

Berg, G., Smalla, K., 2009. Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere. FEMS Microbiology Ecology 68: 1–13.

BioSequence S.A.S., 2024. Reporte de secuenciamiento BSRT_2414_007_UTEQ_CMESTANZA_16S. BioSequence S.A.S., Quito, Ecuador. Unpublished technical report.

Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. Science 359: 320–325.

Dimitrova, K., Kaiyrbekov, T., Balabanova, D., 2024. Assessing the impact of biofertilizer on soil microbial dynamics and metabolic activity in a controlled maize pot-grown experiment. Eurasian Journal of Soil Science 13(3): 202–209.

Etesami, H., 2024. Enhancing soil microbiome resilience: the mitigating role of silicon against environmental stresses. Frontiers in Agronomy 6: 1465165.

Fierer, N., 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology 15: 579–590.

Garbeva, P., van Veen, J.A., van Elsas, J.D., 2004. Microbial diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology 42: 243–270.

Hartmann, M., Frey, B., Mayer, J., Mäder, P., Widmer, F., 2015. Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal 9(5): 1177–1194.

Heiri, O., Lotter, A.F., Lemcke, G., 2001. Loss on ignition as a method for estimating organic and carbonate content in sediments: reproducibility and comparability of results. Journal of Paleolimnology 25: 101–110.

Herawati, A., Mujiyo, Dewi, W.S., Syamsiyah, J., Romadhon, M.R., 2024. Improving microbial properties in Psamments with mycorrhizal fungi, amendments, and fertilizer. Eurasian Journal of Soil Science 13(1): 59–69.

Hu, L., Xia, M., Lin, X., Xu, C., Li, W., Wang, J., Zeng, R., Song, Y., 2018. Earthworm gut bacteria increase silicon bioavailability and acquisition by maize. Soil Biology and Biochemistry 125: 215–221.

Illumina, 2021. 16S Metagenomic Sequencing Library Preparation. Illumina, Inc. Available at [Access date: 16.06.2026]: https://support.illumina.com/downloads/16s_metagenomic_sequencing_library_preparation.html

Illumina, 2024. BaseSpace Sequence Support Resources. Illumina, Inc. Available at [Access date: 16.06.2026]: https://support.illumina.com/sequencing/sequencing_software/basespace-apps.html

ISO 10390:2021. Soil, treated biowaste and sludge – Determination of pH. International Organization for Standardization, Geneva, Switzerland. Available at [Access date: 16.06.2026]:  https://www.iso.org/standard/75243.html

Lauber, C.L., Hamady, M., Knight, R., Fierer, N., 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Applied and Environmental Microbiology 75: 5111–5120.

Leite, M.R.L., de Alcantara Neto, F., Dutra, A.F., Mendes, L.W., de Souza Miranda, R., Melo, V.M.M., Oliveira, F.A.S., de Figueiredo, M.V.B., Sousa, T.K.S.A., Costa, R.M., Rocha, S.M.B., de Araujo Pereira, A.P., de Mello Prado, R., Araujo, A.S.F., 2024. Distinct sources of silicon shape differently the rhizospheric microbial community in sugarcane. Applied Soil Ecology 193: 105131.

Megyes, M., Borsodi, A.K., Arendas, T., Marialigeti, K., 2021. Variations in the diversity of soil bacterial and archaeal communities in response to different long-term fertilization regimes in maize fields. Applied Soil Ecology 168: 104120.

Mestanza Uquillas, C.A., Santana Chávez, J.R., Véliz Zamora, D.V., Merchán Sánchez, B.R., 2026. Tierra de diatomeas como enmienda silícea en maíz (Zea mays L.): respuesta agronómica, suelo y rentabilidad en Los Ríos, Ecuador. Arandu UTIC 13: 771–785.

Murphy, J., Riley, J.P., 1962. A modified single solution method for the determination of phosphate in natural waters. Analytica Chimica Acta 27: 31–36.

Namli, A., Mahmood, A., Sevilir, B., Özkır, E., 2017. Effect of phosphorus solubilizing bacteria on some soil properties, wheat yield and nutrient contents. Eurasian Journal of Soil Science 6(3): 249–258.

Nannipieri, P., Ascher, J., Ceccherini, M.T., Landi, L., Pietramellara, G., Renella, G., 2003. Microbial diversity and soil functions. European Journal of Soil Science 54(4): 655–670.

Oburger, E., Schmidt, H., 2016. New methods to unravel rhizosphere processes. Trends in Plant Science 21: 243–255.

Olsen, S.R., Cole, C.V., Watanabe, F.S., Dean, L.A., 1954. Estimation of available phosphorus in soils by extraction with sodium bicarbonate. USDA Circular No. 939. U.S. Department of Agriculture, Washington, DC, USA.

Philippot, L., Raaijmakers, J.M., Lemanceau, P., van der Putten, W.H., 2013. Going back to the roots: the microbial ecology of the rhizosphere. Nature Reviews Microbiology 11: 789–799.

Rousk, J., Bååth, E., Brookes, P.C., Lauber, C.L., Lozupone, C., Caporaso, J.G., Knight, R., Fierer, N., 2010. Soil bacterial and fungal communities across a pH gradient in an arable soil. The ISME Journal 4: 1340–1351.

Sparks, D.L., Page, A.L., Helmke, P.A., Loeppert, R.H., Soltanpour, P.N., Tabatabai, M.A., Johnston, C.T., Sumner, M.E., 1996. Methods of Soil Analysis: Part 3 Chemical Methods. Soil Science Society of America and American Society of Agronomy, Madison, WI, USA.

Usman, S., Muhammad, Y., Chiroman, A.M., 2016. Roles of soil biota and biodiversity in soil environment – A concise communication. Eurasian Journal of Soil Science 5(4): 255–265.

Wang, Q., Garrity, G.M., Tiedje, J.M., Cole, J.R., 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology 73: 5261–5267.

Wang, Q., Jiang, X., Guan, D., Wei, D., Zhao, B., Ma, M., Chen, S., Li, L., Cao, F., Li, J., 2018. Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere. Applied Soil Ecology 125: 88–96.