Mostrar el registro sencillo del documento

dc.rights.licenseAtribución-NoComercial-SinDerivadas 4.0 Internacional
dc.contributor.advisorUribe Vélez, Daniel
dc.contributor.advisorBarreto Hernández, Emiliano
dc.contributor.authorOtero Jiménez, Vanessa
dc.date.accessioned2022-03-22T12:15:56Z
dc.date.available2022-03-22T12:15:56Z
dc.date.issued2021-08-26
dc.identifier.urihttps://repositorio.unal.edu.co/handle/unal/81291
dc.descriptionilustraciones, gráficas, tablas
dc.description.abstractLos residuos agrícolas son precursores de la materia orgánica del suelo. Su descomposición en campo permite el ingreso de carbono y otros nutrientes al sistema, sin embargo, también puede favorecer la proliferación de patógenos. Entre las alternativas al manejo de los residuos se encuentran la quema, y su incorporación al suelo. Sin embargo, el impacto de las consecuencias de estas estrategias sobre la comunidad microbiana y su potencial funcional, es limitado. En este estudio se buscó determinar el efecto de la aplicación de cuatro estrategias de manejo de residuos sobre la estructura y función de las comunidades microbianas asociadas a los ciclos biogeoquímicos de carbono, nitrógeno y fósforo. Se implementó un ensayo en campo con un diseño de bloques incompletos al azar, haciendo toma de muestras de suelo en cuatro tiempos, durante un ciclo de cultivo, incluso desde la preparación del terreno previo a la siembra. Se caracterizó el suelo mediante análisis físico-químicos y enzimáticos, se describieron las comunidades microbianas usando secuenciación NGS, y se determinaron parámetros biológicos (productividad y el estado fitosanitario) del cultivo de arroz. Se identificó un efecto del manejo del tamo del arroz y el tiempo de muestreo sobre la estructura y función de la comunidad microbiana especialmente en los tiempos de degradación y floración. Este estudio evidenció que las estrategias del uso del tamo ya sea en cobertura o incorporado con o sin la ayuda de microorganismos, son una opción adecuada para la disposición final del tamo de arroz. (Texto tomado de la fuente)
dc.description.abstractAgricultural residues are precursors of soil organic matter. Its decomposition in the field allows the entry of carbon and other nutrients into the system; however, it can also favor the proliferation of pathogens. Among the alternatives to waste management are, burning and, its incorporation into the soil. However, the impact of the consequences of these strategies on the microbial community and their functional potential is limited. This study sought to determine the effect of the application of four rice straw management strategies on the structure and function of the microbial communities associated with the biogeochemical cycles of carbon, nitrogen, and phosphorus. A field trial was implemented with a random incomplete block design, taking soil samples four times, during a cultivation cycle, even from the preparation of the land prior to sowing. The soil was characterized by physicochemical and enzymatic analyzes, the microbial communities were described using NGS sequencing. Also, biological parameters (productivity and phytosanitary status) of the rice crop were determined. An effect of rice straw management and sampling time on the structure and function of the microbial community was identified, especially in degradation and flowering times. This study showed that the strategies of using the straw, either in mulch or incorporated in the soil with or without microorganisms, are an adequate option for the final disposal of the rice straw.
dc.format.extentxx, 198 páginas
dc.format.mimetypeapplication/pdf
dc.language.isospa
dc.publisherUniversidad Nacional de Colombia
dc.rightsDerechos reservados al autor, 2021
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject.ddc630 - Agricultura y tecnologías relacionadas
dc.titleDeterminación del efecto del manejo del tamo de arroz sobre la estructura y función de la comunidad microbiana en suelos de cultivo de arroz
dc.typeTrabajo de grado - Doctorado
dc.type.driverinfo:eu-repo/semantics/doctoralThesis
dc.type.versioninfo:eu-repo/semantics/acceptedVersion
dc.publisher.programBogotá - Ciencias - Doctorado en Ciencias - Biología
dc.contributor.researchgroupMicrobiología Agrícola
dc.contributor.researchgroupCentro de Bioinformática
dc.description.degreelevelDoctorado
dc.description.degreenameDoctor en Ciencias - Biología
dc.description.researchareaEcología Microbiana
dc.identifier.instnameUniversidad Nacional de Colombia
dc.identifier.reponameRepositorio Institucional Universidad Nacional de Colombia
dc.identifier.repourlhttps://repositorio.unal.edu.co/
dc.publisher.departmentDepartamento de Biología
dc.publisher.facultyFacultad de Ciencias
dc.publisher.placeBogotá, Colombia
dc.publisher.branchUniversidad Nacional de Colombia - Sede Bogotá
dc.relation.referencesAbarca, C., Martinez, A., Caro, M., & Quintero, R. (1992). Optimización del proceso de fermentación para producir Bacillus thuringiensis Var. Aisawai. Universidad: Ciencia y Tecnología, 2(3), 51–56. http://www.ibt.unam.mx/alfredo/OptimizacionBthuringiensis.pdf
dc.relation.referencesAbarenkov, K., Henrik Nilsson, R., Larsson, K., Alexander, I. J., Eberhardt, U., Erland, S., Høiland, K., Kjøller, R., Larsson, E., Pennanen, T., Sen, R., Taylor, A. F. S., Tedersoo, L., Ursing, B. M., Vrålstad, T., Liimatainen, K., Peintner, U., & Kõljalg, U. (2010). The UNITE database for molecular identification of fungi – recent updates and future perspectives. New Phytologist, 186(2), 281–285. https://doi.org/10.1111/j.1469-8137.2009.03160.x
dc.relation.referencesAbin, C. A., & Hollibaugh, J. T. (2016). Draft genome sequence for the type strain Vulcanibacillus modesticaldus BR, a strictly anaerobic, moderately thermophilic, and nitratereducing bacterium isolated from deep-sea hydrothermal vents of the Mid-Atlantic Ridge. Genome Announcements, 4(6), 6–7. https://doi.org/10.1128/genomeA.01246-16
dc.relation.referencesAbril, D., Navarro, E. A., & Abril, A. J. (2009). La paja de arroz, consecuencias de su manejo y alternativas de aprovechamiento. Revista de La Facultad de Agronomía, 17(January), 69–79.
dc.relation.referencesAcosta-Martínez, V., Cruz, L., Sotomayor-Ramírez, D., & Pérez-Alegría, L. (2007). Enzyme activities as affected by soil properties and land use in a tropical watershed. Applied Soil Ecology, 35(1), 35–45. https://doi.org/10.1016/j.apsoil.2006.05.012
dc.relation.referencesAdeolu, M., Alnajar, S., Naushad, S., & Gupta, R. S. (2016). Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: Proposal for enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morgane. International Journal of Systematic and Evolutionary Microbiology, 66(12), 5575–5599. https://doi.org/10.1099/ijsem.0.001485
dc.relation.referencesAgronet. (2019, August 2). Estadísticas home. https://www.agronet.gov.co/estadistica/Paginas/home.aspx?cod=1
dc.relation.referencesAhmed, A. I., Omer, A. M., Ibrahim, A. I., & Agha, M. K. (2018). Brevibacillus Spp. in Agroecology: The Beneficial Impacts in Biocontrol of Plant Pathogens and Soil Bioremediation. Fungal Genomics & Biology, 08(02). https://doi.org/10.4172/2165-8056.1000157
dc.relation.referencesAlam, S. . (1981). S . M . Alam Atomic Energy Agricultural Research Centre , Tandojam , Rice plants were grown in solution culture for a period of five weeks at pH ’ s ranging from 3 . 5 to 8 . 5 . Maximum dry matter was obtained at pH 5 . 5 , but substantial reductions in. 4, 247–260.
dc.relation.referencesAlberto, M. C. R., Wassmann, R., Gummert, M., Buresh, R. J., Quilty, J. R., Correa, T. Q., Centeno, C. A. R., & Oca, G. M. (2015). Straw incorporated after mechanized harvesting of irrigated rice affects net emissions of CH4 and CO2 based on eddy covariance measurements. Field Crops Research, 184, 162–175. https://doi.org/10.1016/j.fcr.2015.10.004
dc.relation.referencesAlef, K., & Nannipieri, P. (1995). Enzyme activities. In Methods in Applied Soil Microbiology and Biochemistry (pp. 311–373). Elsevier. https://doi.org/10.1016/B978-012513840-6/50022-7
dc.relation.referencesAllison, S. D., & Martiny, J. B. H. (2009). Resistance, resilience, and redundancy in microbial communities. In the Light of Evolution, 2, 149–166. https://doi.org/10.17226/12501
dc.relation.referencesAlvira, P., Negro, M., & Ballesteros, M. (2011). Effect of endoxylanase and α-L-arabinofuranosidase supplementation on the enzymatic hydrolysis of steam exploded wheat straw.
dc.relation.referencesAmbavaram, M. M. R., Krishnan, A., Trijatmiko, K. R., & Pereira, A. (2011). Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice. Plant Physiology, 155(2), 916–931. https://doi.org/10.1104/pp.110.168641
dc.relation.referencesAnasontzis, G. E., Thuy, N. T., Hang, D. T. M., Huong, H. T., Thanh, D. T., Hien, D. D., Thanh, V. N., & Olsson, L. (2017). Rice straw hydrolysis using secretomes from novel fungal isolates from Vietnam. Biomass and Bioenergy, 99, 11–20. https://doi.org/10.1016/j.biombioe.2017.02.008
dc.relation.referencesAulakh, M. S., Wassmann, R., Bueno, C., Kreuzwieser, J., & Rennenberg, H. (2001). Characterization of root exudates at different growth stages of ten rice (Oryza sativa L.) cultivars. Plant Biology, 3(2), 139–148. https://doi.org/10.1055/s-2001-12905
dc.relation.referencesBacilio-jiménez, M., Aguilar-flores, S., Ventura-zapata, E., Pérez, E., Bouquelet, S., & Zenteno, E. (2003). Chemical characterization of root exudates from rice (Oryza sativa) and their effects on the chemotactic response of endophytic bacteria. Plant and Soil, 249(2), 271–277.
dc.relation.referencesBailey, K. L., & Lazarovits, G. (2003). Suppressing soil-borne diseases with residue management and organic amendments. Soil and Tillage Research, 72(2), 169–180. https://doi.org/10.1016/S0167-1987(03)00086-2
dc.relation.referencesBanerjee, S., Kirkby, C. A., Schmutter, D., Bissett, A., Kirkegaard, J. A., & Richardson, A. E. (2016). Network analysis reveals functional redundancy and keystone taxa amongst bacterial and fungal communities during organic matter decomposition in an arable soil. Soil Biology and Biochemistry, 97, 188–198. https://doi.org/10.1016/j.soilbio.2016.03.017
dc.relation.referencesBanning, N. C., Maccarone, L. D., Fisk, L. M., & Murphy, D. V. (2015). Ammonia-oxidising bacteria not archaea dominate nitrification activity in semi-arid agricultural soil. Scientific Reports, 5(March), 1–8. https://doi.org/10.1038/srep11146
dc.relation.referencesBao, Y., Feng, Y., Stegen, J. C., Wu, M., Chen, R., Liu, W., Zhang, J., Li, Z., & Lin, X. (2020). Straw chemistry links the assembly of bacterial communities to decomposition in paddy soils. Soil Biology and Biochemistry, 148(September 2019), 107866. https://doi.org/10.1016/j.soilbio.2020.107866
dc.relation.referencesBarrera, S. E., Sarango-Flóres, S.-W., & Montenegro-Gómez, S.-P. (2019). The phyllosphere microbiome and its potential application in horticultural crops. A review. Revista Colombiana de Ciencias Hortícolas, 13(3), 384–396. https://doi.org/10.17584/rcch.2019v13i3.8405
dc.relation.referencesBastida, F., Torres, I. F., Hernández, T., & García, C. (2017). The impacts of organic amendments: Do they confer stability against drought on the soil microbial community? Soil Biology and Biochemistry, 113, 173–183. https://doi.org/10.1016/j.soilbio.2017.06.012
dc.relation.referencesBerendsen, R. L., Pieterse, C. M. J., & Bakker, P. A. H. M. (2012). The rhizosphere microbiome and plant health. Trends in Plant Science, 17(8), 478–486. https://doi.org/10.1016/j.tplants.2012.04.001
dc.relation.referencesBernaola, L., Cange, G., Way, M. O., Gore, J., Hardke, J., & Stout, M. (2018). Natural Colonization of Rice by Arbuscular Mycorrhizal Fungi in Different Production Areas. Rice Science, 25(3), 169–174. https://doi.org/10.1016/j.rsci.2018.02.006
dc.relation.referencesBerry, D., & Widder, S. (2014). Deciphering microbial interactions and detecting keystone species with co-occurrence networks. Frontiers in Microbiology, 5(MAY), 1–14. https://doi.org/10.3389/fmicb.2014.00219
dc.relation.referencesBhattacharyya, P., & Barman, D. (2018). Crop Residue Management and Greenhouse Gases Emissions in Tropical Rice Lands. Soil Management and Climate Change: Effects on Organic Carbon, Nitrogen Dynamics, and Greenhouse Gas Emissions, 323–335. https://doi.org/10.1016/B978-0-12-812128-3.00021-5
dc.relation.referencesBinod, P., Sindhu, R., Singhania, R. R., Vikram, S., Devi, L., Nagalakshmi, S., Kurien, N., Sukumaran, R. K., & Pandey, A. (2010). Bioethanol production from rice straw: An overview. Bioresource Technology, 101(13), 4767–4774. https://doi.org/10.1016/j.biortech.2009.10.079
dc.relation.referencesBissett, A., Brown, M. V., Siciliano, S. D., & Thrall, P. H. (2013). Microbial community responses to anthropogenically induced environmental change: Towards a systems approach. Ecology Letters, 16(SUPPL.1), 128–139. https://doi.org/10.1111/ele.12109
dc.relation.referencesBlaud, A., Menon, M., van der Zaan, B., Lair, G. J., & Banwart, S. A. (2017). Effects of Dry and Wet Sieving of Soil on Identification and Interpretation of Microbial Community Composition. In Advances in Agronomy (1st ed., Vol. 142). Elsevier Inc. https://doi.org/10.1016/bs.agron.2016.10.006
dc.relation.referencesBlin, K., Shaw, S., Steinke, K., Villebro, R., Ziemert, N., Lee, S. Y., Medema, M. H., & Weber, T. (2019). AntiSMASH 5.0: Updates to the secondary metabolite genome mining pipeline. Nucleic Acids Research, 47(W1), W81–W87. https://doi.org/10.1093/nar/gkz310
dc.relation.referencesBöhme, L., Langer, U., & Böhme, F. (2005). Microbial biomass, enzyme activities and microbial community structure in two European long-term field experiments. Agriculture, Ecosystems and Environment, 109(1–2), 141–152. https://doi.org/10.1016/j.agee.2005.01.017
dc.relation.referencesBolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., … Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8), 852–857. https://doi.org/10.1038/s41587-019-0209-9
dc.relation.referencesBorsetto, C., Amos, G. C. A., Da Rocha, U. N., Mitchell, A. L., Finn, R. D., Laidi, R. F., Vallin, C., Pearce, D. A., Newsham, K. K., & Wellington, E. M. H. (2019). Microbial community drivers of PK/NRP gene diversity in selected global soils. Microbiome, 7(1), 1–11. https://doi.org/10.1186/s40168-019-0692-8
dc.relation.referencesBowles, T. M., Acosta-Martínez, V., Calderón, F., & Jackson, L. E. (2014). Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively-managed agricultural landscape. Soil Biology and Biochemistry, 68, 252–262. https://doi.org/10.1016/j.soilbio.2013.10.004
dc.relation.referencesBoyce, R., Chilana, P., & Rose, T. M. (2009). iCODEHOP: A new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Research, 37(SUPPL. 2). https://doi.org/10.1093/nar/gkp379
dc.relation.referencesBreidenbach, B., & Conrad, R. (2015). Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage. Frontiers in Microbiology, 5(DEC), 1–16. https://doi.org/10.3389/fmicb.2014.00752
dc.relation.referencesBreton, C., Šnajdrová, L., Jeanneau, C., Koča, J., & Imberty, A. (2006). Structures and mechanisms of glycosyltransferases. Glycobiology, 16(2), 29–37. https://doi.org/10.1093/glycob/cwj016
dc.relation.referencesBrown, M. V., Philip, G. K., Bunge, J. A., Smith, M. C., Bissett, A., Lauro, F. M., Fuhrman, J. A., & Donachie, S. P. (2009). Microbial community structure in the North Pacific ocean. ISME Journal, 3(12), 1374–1386. https://doi.org/10.1038/ismej.2009.86
dc.relation.referencesBukin, Y. S., Galachyants, Y. P., Morozov, I. V., Bukin, S. V., Zakharenko, A. S., & Zemskaya, T. I. (2019). The effect of 16s rRNA region choice on bacterial community metabarcoding results. Scientific Data, 6, 1–14. https://doi.org/10.1038/sdata.2019.7
dc.relation.referencesBurns, R. G., DeForest, J. L., Marxsen, J., Sinsabaugh, R. L., Stromberger, M. E., Wallenstein, M. D., Weintraub, M. N., & Zoppini, A. (2013). Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biology and Biochemistry, 58, 216–234. https://doi.org/10.1016/j.soilbio.2012.11.009
dc.relation.referencesBustin, S. A. (2000). Absolute quantification of mrna using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology, 25(2), 169–193. https://doi.org/10.1677/jme.0.0250169
dc.relation.referencesCallahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7), 581–583. https://doi.org/10.1038/nmeth.3869
dc.relation.referencesCarreño-Carreño, J. del P. (2019). Evaluación de la diversidad taxonómica y funcional de la comunidad microbiana relacionada con el ciclo del nitrógeno en suelos de cultivo de arroz con diferentes manejos del tamo [Universidad Nacional de Colombia]. https://repositorio.unal.edu.co/bitstream/handle/unal/76023/1018449897.2019.pdf?sequence=1&isAllowed=y
dc.relation.referencesCarrión, V. J., Perez-Jaramillo, J., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz-Buck, D., Mendes, L. W., van Ijcken, W. F. J., Gomez-Exposito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G. P., Medema, M. H., & Raaijmakers, J. M. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366(6465), 606–612. https://doi.org/10.1126/science.aaw9285
dc.relation.referencesCassán, F., Coniglio, A., López, G., Molina, R., Nievas, S., de Carlan, C. L. N., Donadio, F., Torres, D., Rosas, S., Pedrosa, F. O., de Souza, E., Zorita, M. D., de-Bashan, L., & Mora, V. (2020). Everything you must know about Azospirillum and its impact on agriculture and beyond. Biology and Fertility of Soils, 56(4), 461–479. https://doi.org/10.1007/s00374-020-01463-y
dc.relation.referencesCastilla, A. (2012). Manejo productivo de los residuos de la cosecha de arroz. Revista Arroz, 60(500), 10–17.
dc.relation.referencesCharacterization, S., & Turbe-doan, A. (2019). crossm Quinone-Dependent Member of Auxiliary Activity Family 12 of the Carbohydrate-Active Enzymes Database : Functional and. 85(24), 1–15.
dc.relation.referencesChaudhari, P. R., Ahire, D. V, Ahire, V. D., Chkravarty, M., & Maity, S. (2013). Soil Bulk Density as related to Soil Texture, Organic Matter Content and available total Nutrients of Coimbatore Soil. International Journal of Scientific and Research Publications, 3(1), 2250–3153. www.ijsrp.org
dc.relation.referencesChen, S., Zheng, X., Wang, D., Chen, L., Xu, C., & Zhang, X. (2012). Effect of Long-Term Paddy-Upland Yearly Rotations on Rice ( Oryza sativa ) Yield , Soil Properties , and Bacteria Community Diversity. 2012. https://doi.org/10.1100/2012/279641
dc.relation.referencesChen, X., Jiang, N., Chen, Z., Tian, J., Sun, N., Xu, M., & Chen, L. (2017). Response of soil phoD phosphatase gene to long-term combined applications of chemical fertilizers and organic materials. Applied Soil Ecology, 119. https://doi.org/10.1016/j.apsoil.2017.06.019
dc.relation.referencesChhabra, V., & Mehta, C. M. (2019). Rice straw management for sustainable agriculture-a review. Plant Archives, 19, 47–49.
dc.relation.referencesChialva, M., Ghignone, S., Cozzi, P., Lazzari, B., Bonfante, P., Abbruscato, P., & Lumini, E. (2020). Water management and phenology influence the root-associated rice field microbiota. FEMS Microbiology Ecology, 96(9), 1–16. https://doi.org/10.1093/femsec/fiaa146
dc.relation.referencesChivenge, P., Rubianes, F., Chin, D. Van, & Thach, T. Van. (2020). Sustainable Rice Straw Management. In M. Gummert, N. Van Hung, P. Chivenge, & B. Douthwaite (Eds.), Sustainable Rice Straw Management. Springer International Publishing. https://doi.org/10.1007/978-3-030-32373-8
dc.relation.referencesChoi, J., Bach, E., Lee, J., Flater, J., Dooley, S., Howe, A., & Hofmockel, K. S. (2018). Spatial structuring of cellulase gene abundance and activity in soil. Frontiers in Environmental Science, 6(OCT), 1–10. https://doi.org/10.3389/fenvs.2018.00107
dc.relation.referencesCimermancic, P., Medema, M. H., Claesen, J., Kurita, K., Wieland Brown, L. C., Mavrommatis, K., Pati, A., Godfrey, P. A., Koehrsen, M., Clardy, J., Birren, B. W., Takano, E., Sali, A., Linington, R. G., & Fischbach, M. A. (2014). Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell, 158(2), 412–421. https://doi.org/10.1016/j.cell.2014.06.034
dc.relation.referencesCleveland, C. C., Nemergut, D. R., Schmidt, S. K., & Townsend, A. R. (2007). Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition. Biogeochemistry, 82(3), 229–240. https://doi.org/10.1007/s10533-006-9065-z
dc.relation.referencesConrad, R. (2007). Microbial Ecology of Methanogens and Methanotrophs. Advances in Agronomy, 96(07), 1–63. https://doi.org/10.1016/S0065-2113(07)96005-8
dc.relation.referencesConrad, R. (2009). The global methane cycle: Recent advances in understanding the microbial processes involved. Environmental Microbiology Reports, 1(5), 285–292. https://doi.org/10.1111/j.1758-2229.2009.00038.x
dc.relation.referencesCruz-Ramírez, C. A., Gómez-Ramírez, L. F., & Uribe-Vélez, D. (2017). Manejo biológico del tamo de arroz bajo diferentes relaciones C:N empleando co-inóculos microbianos y promotores de crecimiento vegetal. Revista Colombiana de Biotecnología, 19(2), 47–62. https://doi.org/10.15446/rev.colomb.biote.v19n2.70168
dc.relation.referencesD’haeseleer, P., Gladden, J. M., Allgaier, M., Chain, P. S. G., Tringe, S. G., Malfatti, S. A., T., J., & Singer, S. W. (2013). Proteogenomic Analysis of a Thermophilic BacterialConsortium Adapted to Deconstruct Switchgrass.
dc.relation.referencesDai, Z., Liu, G., Chen, H., Chen, C., Wang, J., Ai, S., Wei, D., Li, D., Ma, B., Tang, C., Brookes, P. C., & Xu, J. (2020). Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems. ISME Journal, 14(3), 757–770. https://doi.org/10.1038/s41396-019-0567-9
dc.relation.referencesDas, A. C. (1963). Ecology of soil fungi of rice fields 1. Succession of fungi on rice roots 2. Association of soil fungi with organic matter. Transactions of the British Mycological Society, 46(3), 431–443. https://doi.org/10.1016/s0007-1536(63)80037-6
dc.relation.referencesDas, S., Bhattacharyya, P., & Adhya, T. K. (2011). Impact of elevated CO2, flooding, and temperature interaction on heterotrophic nitrogen fixation in tropical rice soils. Biology and Fertility of Soils, 47(1), 25–30. https://doi.org/10.1007/s00374-010-0496-2
dc.relation.referencesde Souza, W. R. (2013). Microbial Degradation of Lignocellulosic Biomass. Sustainable Degradation of Lignocellulosic Biomass - Techniques, Applications and Commercialization. https://doi.org/10.5772/54325
dc.relation.referencesde Vries, M. (2018). Functional and phylogenetic diversity of cellulase genes in agricultural soil under two different tillage treatments. 1–166. https://mediatum.ub.tum.de/doc/1437155/file.pdf
dc.relation.referencesDebode, J., De Tender, C., Cremelie, P., Lee, A. S., Kyndt, T., Muylle, H., De Swaef, T., & Vandecasteele, B. (2018). Trichoderma-inoculated miscanthus straw can replace peat in strawberry cultivation, with beneficial effects on disease control. Frontiers in Plant Science, 9(February). https://doi.org/10.3389/fpls.2018.00213
dc.relation.referencesDeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., & Andersen, G. L. (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Applied and Environmental Microbiology, 72(7), 5069–5072. https://doi.org/10.1128/AEM.03006-05
dc.relation.referencesDhariwal, A., Chong, J., Habib, S., King, I. L., Agellon, L. B., & Xia, J. (2017). MicrobiomeAnalyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Research, 45(W1), W180–W188. https://doi.org/10.1093/nar/gkx295
dc.relation.referencesDing, L. J., Cui, H. L., Nie, S. A., Long, X. E., Duan, G. L., & Zhu, Y. G. (2019). Microbiomes inhabiting rice roots and rhizosphere. FEMS Microbiology Ecology, 95(5), 1–13. https://doi.org/10.1093/femsec/fiz040
dc.relation.referencesDobermann, A., & Fairhurst, T. H. (2002). Rice straw management. Better Crops International, 16(January), 7–11.
dc.relation.referencesDobermann, Achim, & Fairhurst, T. (2000). Arroz: Desórdenes Nutricionales y Manejo de Nutrientes. 214.
dc.relation.referencesDotaniya, M. L., Aparna, K., Dotaniya, C. K., Singh, M., & Regar, K. L. (2018). Role of soil enzymes in sustainable crop production. In Enzymes in Food Biotechnology: Production, Applications, and Future Prospects. Elsevier Inc. https://doi.org/10.1016/B978-0-12-813280-7.00033-5
dc.relation.referencesDouglas, G., Maffei, V., Zaneveld, J., Yurgel, S., Brown, J., Taylor, C., Huttenhower, C., & Langille, M. (2019). PICRUSt2: An improved and customizable approach for metagenome inference. PICRUSt2: An Improved and Extensible Approach for Metagenome Inference, June, 672295. https://doi.org/10.1101/672295
dc.relation.referencesDraganova, D., Valcheva, I., & Kuzmanova, Y. (2019). Effect of wheat straw and cellulose degrading fungi of genus Trichoderma on soil respiration and cellulase, betaglucosidase and soil carbon content. January. https://doi.org/10.15547/ast.2018.04.064
dc.relation.referencesDror, B., Jurkevitch, E., & Cytryn, E. (2020). State-of-the-art methodologies to identify antimicrobial secondary metabolites in soil bacterial communities-A review. Soil Biology and Biochemistry, 147(April). https://doi.org/10.1016/j.soilbio.2020.107838
dc.relation.referencesEdgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16), 2194–2200. https://doi.org/10.1093/bioinformatics/btr381
dc.relation.referencesEdwards, J. A., Santos-Medellín, C. M., Liechty, Z. S., Nguyen, B., Lurie, E., Eason, S., Phillips, G., & Sundaresan, V. (2018). Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. PLoS Biology, 16(2), 1–28. https://doi.org/10.1371/journal.pbio.2003862
dc.relation.referencesEdwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N. K., Bhatnagar, S., Eisen, J. A., & Sundaresan, V. (2015). Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences, 112(8), E911–E920. https://doi.org/10.1073/PNAS.1414592112
dc.relation.referencesEdwards, J., Johnson, C., Santos-Medellín, C., Lurie, E., Podishetty, N. K., Bhatnagar, S., Eisen, J. A., Sundaresan, V., & Jeffery, L. D. (2015). Structure, variation, and assembly of the root-associated microbiomes of rice. Proceedings of the National Academy of Sciences of the United States of America, 112(8), E911–E920. https://doi.org/10.1073/pnas.1414592112
dc.relation.referencesEdwards, J., Santos-Medellín, C., Nguyen, B., Kilmer, J., Liechty, Z., Veliz, E., Ni, J., Phillips, G., & Sundaresan, V. (2019). Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota. Genome Biology, 20(1), 1–14. https://doi.org/10.1186/s13059-019-1825-x
dc.relation.referencesEichorst, S. A., & Kuske, C. R. (2012). Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing. Applied and Environmental Microbiology, 78(7), 2316–2327. https://doi.org/10.1128/AEM.07313-11
dc.relation.referencesEichorst, S. A., Trojan, D., Roux, S., Herbold, C., Rattei, T., & Woebken, D. (2018). Genomic insights into the Acidobacteria reveal strategies for their success in terrestrial environments. Environmental Microbiology, 20(3), 1041–1063. https://doi.org/10.1111/1462-2920.14043
dc.relation.referencesEiland, F., Klamer, M., Lind, A. M., Leth, M., & Bååth, E. (2001). Influence of initial C/N ratio on chemical and microbial composition during long term composting of straw. Microbial Ecology, 41(3), 272–280. https://doi.org/10.1007/s002480000071
dc.relation.referencesEivazi, F., & Tabatabai, M. A. (1977). Phosphates in soils. Soil Biology and Biochemistry, 9(1969), 167–172.
dc.relation.referencesEivazi, F., & Tabatabai, M. A. (1988). Glucosidases and galactosidases in soils. Soil Biology and Biochemistry, 20(5), 601–606. https://doi.org/10.1016/0038-0717(88)90141-1
dc.relation.referencesEivazi, F., & Tabatabai, M. A. (1990). Factors affecting glucosidase and galactosidase activities in soils. Soil Biology and Biochemistry, 22(7), 891–897. https://doi.org/10.1016/0038-0717(90)90126-K
dc.relation.referencesEkenler, M., & Tabatabai, M. A. (2003). Effects of liming and tillage systems on microbial biomass and glycosidases in soils. Biology and Fertility of Soils. https://doi.org/10.1007/s00374-003-0664-8
dc.relation.referencesEkwue, E. I. (1990). Organic-matter effects on soil strength properties. Soil and Tillage Research, 16(3), 289–297. https://doi.org/10.1016/0167-1987(90)90102-J
dc.relation.referencesEl-Sobky, E. S. E. A. (2017). Effect of burned rice straw, phosphorus and nitrogen fertilization on wheat (Triticum aestivum L.). Annals of Agricultural Sciences, 62(1), 113–120. https://doi.org/10.1016/j.aoas.2017.05.007
dc.relation.referencesElsas, J. D. van, Trevors, J. T., Jansson, J. K., & Nannipieri, P. (2006). Modern Soil Microbiology. In J. D. van Elsas, J. T. Trevors, J. K. Jansson, & P. Nannipieri (Eds.), Modern Soil Microbiology, Second Edition (3rd Editio). CRC Press. https://doi.org/10.1201/9781420015201
dc.relation.referencesEyre, A. W., Wang, M., Oh, Y., & Dean, R. A. (2019). Identification and characterization of the core rice seed microbiome. In Phytobiomes Journal (Vol. 3, Issue 2). https://doi.org/10.1094/PBIOMES-01-19-0009-R
dc.relation.referencesFAOSTAT. (2020). FAOSTAT. http://www.fao.org/faostat/es/#data/QI
dc.relation.referencesFedearroz. (2020). Fedearroz. http://www.fedearroz.com.co/new/apr_public.php
dc.relation.referencesFerrando, L., & Fernández Scavino, A. (2015). Strong shift in the diazotrophic endophytic bacterial community inhabiting rice (Oryza sativa) plants after flooding. FEMS Microbiology Ecology, 91(9), 1–12. https://doi.org/10.1093/femsec/fiv104
dc.relation.referencesFierer, N., A.Bradford, M., & B.Jackson, R. (2007). TOWARD AN ECOLOGICAL CLASSIFICATION OF SOIL BACTERIA Edited by Foxit Reader. Ecology, 88(6), 1354–1364.
dc.relation.referencesFierer, N., Lauber, C. L., Ramirez, K. S., Zaneveld, J., Bradford, M. A., & Knight, R. (2012). Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients. ISME Journal, 6(5), 1007–1017. https://doi.org/10.1038/ismej.2011.159
dc.relation.referencesFontaine, S., Mariotti, A., & Abbadie, L. (2003). The priming effect of organic matter: A question of microbial competition? Soil Biology and Biochemistry, 35(6), 837–843. https://doi.org/10.1016/S0038-0717(03)00123-8
dc.relation.referencesFrankenberger, W. T., & Bingham, F. T. (1982). Influence of Salinity on Soil Enzyme Activities. Soil Science Society of America Journal, 46(6), 1173–1177. https://doi.org/10.2136/sssaj1982.03615995004600060011x
dc.relation.referencesFraser, T. D., Lynch, D. H., Bent, E., Entz, M. H., & Dunfield, K. E. (2015). Soil bacterial phoD gene abundance and expression in response toapplied phosphorus and long-term management. Soil Biology and Biochemistry, 88(May), 137–147. https://doi.org/10.1016/j.soilbio.2015.04.014
dc.relation.referencesGadde, B., Bonnet, S., Menke, C., & Garivait, S. (2009). Air pollutant emissions from rice straw open field burning in India, Thailand and the Philippines. Environmental Pollution, 157(5), 1554–1558. https://doi.org/10.1016/j.envpol.2009.01.004
dc.relation.referencesGallardo, C. A., Baldrian, P., & López-mondéjar, R. (2020). Litter-inhabiting fungi show high level of specialization towards biopolymers composing plant and fungal biomass.
dc.relation.referencesGallego, V., García, M. T., & Ventosa, A. (2005). Methylobacterium hispanicum sp. nov. and Methylobacterium aquaticum sp. nov., isolated from drinking water. International Journal of Systematic and Evolutionary Microbiology, 55(1), 281–287. https://doi.org/10.1099/ijs.0.63319-0
dc.relation.referencesGarbeva, P., Van Elsas, J. D., & Van Veen, J. A. (2008). Rhizosphere microbial community and its response to plant species and soil history. Plant and Soil, 302(1–2), 19–32. https://doi.org/10.1007/s11104-007-9432-0
dc.relation.referencesGarbeva, 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(29), 243–270. https://doi.org/10.1146/annurev.phyto.42.012604.135455
dc.relation.referencesGianfreda, L. (2015). Enzymes of importance to rhizosphere processes. Journal of Soil Science and Plant Nutrition, 15(2), 283–306. https://doi.org/10.4067/s0718-95162015005000022
dc.relation.referencesGianfreda, Liliana, Rao, M. A., Piotrowska, A., Palumbo, G., & Colombo, C. (2005). Soil enzyme activities as affected by anthropogenic alterations: Intensive agricultural practices and organic pollution. Science of the Total Environment, 341(1–3), 265–279. https://doi.org/10.1016/j.scitotenv.2004.10.005
dc.relation.referencesGood, A. I. J. (1953). Biometrika Trust The Population Frequencies of Species and the Estimation of Population Parameters THE POPULATION FREQUENCIES OF SPECIES AND THE ESTIMATION OF POPULATION PARAMETERS. Biometrika, 40(3), 237–264.
dc.relation.referencesGrant, C., Bittman, S., Montreal, M., Plenchette, C., & Morel, C. (2005). Soil and fertilizer phosphorus: Effects on plant P supply and mycorrhizal development. Canadian Journal of Plant Science, 85(1), 3–14. https://doi.org/10.4141/P03-182
dc.relation.referencesGredner, B. (2010). Effect of rice straw application on hydrolytic enzyme activities in Chinese paddy soils. World, August, 13–16.
dc.relation.referencesGrum-Grzhimaylo, A. A., Georgieva, M. L., Bondarenko, S. A., Debets, A. J. M., & Bilanenko, E. N. (2016). On the diversity of fungi from soda soils. Fungal Diversity, 76(1), 27–74. https://doi.org/10.1007/s13225-015-0320-2
dc.relation.referencesGuillén, D., Sánchez, S., & Rodríguez-Sanoja, R. (2010). Carbohydrate-binding domains: Multiplicity of biological roles. Applied Microbiology and Biotechnology, 85(5), 1241–1249. https://doi.org/10.1007/s00253-009-2331-y
dc.relation.referencesGuo, B., Liang, Y., Li, Z., & Han, F. (2009). Phosphorus adsorption and bioavailability in a paddy soil amended with pig manure compost and decaying rice straw. Communications in Soil Science and Plant Analysis, 40(13–14), 2185–2199. https://doi.org/10.1080/00103620902960666
dc.relation.referencesGuo, T., Zhang, Q., Ai, C., Liang, G., He, P., Lei, Q., & Zhou, W. (2020). Analysis of microbial utilization of rice straw in paddy soil using a DNA-SIP approach. Soil Science Society of America Journal, 84(1), 99–114. https://doi.org/10.1002/saj2.20019
dc.relation.referencesGuo, T., Zhang, Q., Ai, C., Liang, G., He, P., & Zhou, W. (2018). Nitrogen enrichment regulates straw decomposition and its associated microbial community in a double-rice cropping system. Scientific Reports, 12, 1–12. https://doi.org/10.1038/s41598-018-20293-5
dc.relation.referencesGupta, P. K., Sahai, S., Singh, N., Dixit, C. K., Singh, D. P., Sharma, C., Tiwari, M. K., Gupta, R. K., & Garg, S. C. (2004). Residue burning in rice-wheat cropping system: Causes and implications. Current Science, 87(12), 1713–1717.
dc.relation.referencesGweon, H. S., Oliver, A., Taylor, J., Booth, T., Gibbs, M., Read, D. S., Griffiths, R. I., & Schonrogge, K. (2015). PIPITS: An automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform. Methods in Ecology and Evolution, 6(8), 973–980. https://doi.org/10.1111/2041-210X.12399
dc.relation.referencesHallmann, J., Quadt-Hallmann, A., Mahaffee, W. F., & Kloepper, J. W. (1997). Bacterial endophytes in agricultural crops. NRC Canada Can. J. Microbiol, 43, 895–914. www.nrcresearchpress.com
dc.relation.referencesHam, J. H., Melanson, R. A., & Rush, M. C. (2011). Burkholderia glumae: Next major pathogen of rice? Molecular Plant Pathology, 12(4), 329–339. https://doi.org/10.1111/j.1364-3703.2010.00676.x
dc.relation.referencesHan, Q., Ma, Q., Chen, Y., Tian, B., Xu, L., Bai, Y., Chen, W., & Li, X. (2020). Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean. ISME Journal, 14(8), 1915–1928. https://doi.org/10.1038/s41396-020-0648-9
dc.relation.referencesHardoim, P. R., Andreote, F. D., Reinhold-Hurek, B., Sessitsch, A., van Overbeek, L. S., & van Elsas, J. D. (2011). Rice root-associated bacteria: Insights into community structures across10 cultivars. FEMS Microbiology Ecology, 77(1), 154–164. https://doi.org/10.1111/j.1574-6941.2011.01092.x
dc.relation.referencesHe, J. Z., Liu, X. Z., Zheng, Y., Shen, J. P., & Zhang, L. M. (2010). Dynamics of sulfate reduction and sulfate-reducing prokaryotes in anaerobic paddy soil amended with rice straw. Biology and Fertility of Soils, 46(3), 283–291. https://doi.org/10.1007/s00374-009-0426-3
dc.relation.referencesHermans, S. M., Buckley, H. L., Case, B. S., Curran-cournane, F., & Taylor, M. (2017). crossm Condition. Applied and Environmental Microbiology, 83(1), 1–13.
dc.relation.referencesHernández León, F. A. (2016). VARIEDAD FL - FEDEARROZ 68 EN LA ZONA ABSORCIÓN DE NUTRIENTES DE LA DEL ARIARI-META. REVISTA ARROZ, 64(521), 4–12. http://www.fedearroz.com.co/revistanew/arroz521.pdf
dc.relation.referencesHernández, M., Dumont, M. G., Yuan, Q., & Conrad, R. (2015). Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon. Applied and Environmental Microbiology, 81(6), 2244–2253. https://doi.org/10.1128/AEM.03209-14
dc.relation.referencesHesse, C. N., Mueller, R. C., Vuyisich, M., Gallegos-Graves, L. V., Gleasner, C. D., Zak, D. R., & Kuske, C. R. (2015). Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. Frontiers in Microbiology, 6(APR), 1–15. https://doi.org/10.3389/fmicb.2015.00337
dc.relation.referencesHilleRisLambers, J., Adler, P. B., Harpole, W. S., Levine, J. M., & Mayfield, M. M. (2012). Rethinking community assembly through the lens of coexistence theory. Annual Review of Ecology, Evolution, and Systematics, 43, 227–248. https://doi.org/10.1146/annurev-ecolsys-110411-160411
dc.relation.referencesHoltsmark, I., Eijsink, V. G. H., & Brurberg, M. B. (2008). Bacteriocins from plant pathogenic bacteria. FEMS Microbiology Letters, 280(1), 1–7. https://doi.org/10.1111/j.1574-6968.2007.01010.x
dc.relation.referencesHong, S.-B., Kim, D.-H., Park, I.-C., Samson, R. A., & Shin, H.-D. (2010). Isolation and Identification of Aspergillus Section Fumigati Strains from Arable Soil in Korea . Mycobiology, 38(1), 1. https://doi.org/10.4489/myco.2010.38.1.001
dc.relation.referencesHori, T., Müller, A., Igarashi, Y., Conrad, R., & Friedrich, M. W. (2010). Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13 C-acetate probing. ISME Journal, 4(2), 267–278. https://doi.org/10.1038/ismej.2009.100
dc.relation.referencesHuang, L., Zhang, H., Wu, P., Entwistle, S., Li, X., Yohe, T., Yi, H., Yang, Z., & Yin, Y. (2018). dbCAN-seq: a database of carbohydrate-active enzyme (CAZyme) sequence and annotation. Nucleic Acids Research, 46(D1), D516–D521. https://doi.org/10.1093/nar/gkx894
dc.relation.referencesHubell, S. (2006). Neutral theory and the evolution of ecological equivalence. Ecology, 87(6), 1387–1398.
dc.relation.referencesHuhndorf, S. M., Miller, A. N., & Fernández, F. A. (2004). Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined. Mycologia, 96(2), 368–387. https://doi.org/10.1080/15572536.2005.11832982
dc.relation.referencesHung, D. T., Hughes, H. J., Keck, M., & Sauer, D. (2019). Rice-residue management practices of smallholder farms in Vietnam and their effects on nutrient fluxes in the soil-plant system. Sustainability (Switzerland), 11(6). https://doi.org/10.3390/su11061641
dc.relation.referencesHung, N. Van, Maguyon-Detras, M. C., Migo, M. V., Quilloy, R., Balingbing, C., Chivenge, P., & Gummert, M. (2020). Rice Straw Overview: Availability, Properties, and Management Practices. Sustainable Rice Straw Management, 1–13. https://doi.org/10.1007/978-3-030-32373-8_1
dc.relation.referencesHuson, D. H., Auch, A. F., Qi, J., & Schuster, S. C. (2007). MEGAN analysis of metagenomic data. Genome Research, 17(3), 377–386. https://doi.org/10.1101/gr.5969107
dc.relation.referencesHussain, Q., Pan, G. X., Liu, Y. Z., Zhang, A., Li, L. Q., Zhang, X. H., & Jin, Z. J. (2012). Microbial community dynamics and function associatedwith rhizosphere over periods of rice growth. Plant, Soil and Environment, 58(2), 55–61. https://doi.org/10.17221/390/2010-pse
dc.relation.referencesHyatt, D., Chen, G. L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11. https://doi.org/10.1186/1471-2105-11-119
dc.relation.referencesIchikawa, S., Nishida, A., Yasui, S., & Karita, S. (2017). Characterization of lignocellulose particles during lignocellulose solubilization by Clostridium thermocellum. Bioscience, Biotechnology and Biochemistry, 81(10), 2028–2033. https://doi.org/10.1080/09168451.2017.1364619
dc.relation.referencesImchen, M., Kumavath, R., Vaz, A. B. M., Góes-Neto, A., Barh, D., Ghosh, P., Kozyrovska, N., Podolich, O., & Azevedo, V. (2019). 16S rRNA Gene Amplicon Based Metagenomic Signatures of Rhizobiome Community in Rice Field During Various Growth Stages. Frontiers in Microbiology, 10(September), 1–15. https://doi.org/10.3389/fmicb.2019.02103
dc.relation.referencesIto, O., Ella, E., & Kawano, N. (1999). Physiological basis of submergence tolerance in rainfed lowland rice ecosystem. Field Crops Research, 64(1–2), 75–90. https://doi.org/10.1016/S0378-4290(99)00052-0
dc.relation.referencesIvanova, A. A., Zhelezova, A. D., Chernov, T. I., & Dedysh, S. N. (2020). Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils. PLoS ONE, 15(3), 1–19. https://doi.org/10.1371/journal.pone.0230157
dc.relation.referencesJenkins M., B., Bexter L., L., Miles R. Jr., T., & Miles R., T. (1998). Combustion Properties of Biomass Flash. Fuel Processing Technology, 54, 17–46.
dc.relation.referencesJia, Z., & Conrad, R. (2009). Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environmental Microbiology, 11(7), 1658–1671. https://doi.org/10.1111/j.1462-2920.2009.01891.x
dc.relation.referencesJiang, X., Hou, X., Zhou, X., Xin, X., Wright, A., & Jia, Z. (2015). pH regulates key players of nitrification in paddy soils. Soil Biology and Biochemistry, 81(November), 9–16. https://doi.org/10.1016/j.soilbio.2014.10.025
dc.relation.referencesJiao, S., Xu, Y., Zhang, J., Hao, X., & Lu, Y. (2019). Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling. MSystems, 4(2), 1–16. https://doi.org/10.1128/msystems.00313-18
dc.relation.referencesJiménez, D. J., Chaves-Moreno, D., & Van Elsas, J. D. (2015). Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw. Scientific Reports, 5, 1–16. https://doi.org/10.1038/srep13845
dc.relation.referencesJiménez, D. J., de Lima Brossi, M. J., Schückel, J., Kračun, S. K., Willats, W. G. T., & van Elsas, J. D. (2016). Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches. Applied Microbiology and Biotechnology, 100(24), 10463–10477. https://doi.org/10.1007/s00253-016-7713-3
dc.relation.referencesJiménez, D. J., Dini-Andreote, F., & Van Elsas, J. D. (2014). Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia. Biotechnology for Biofuels, 7(1). https://doi.org/10.1186/1754-6834-7-92
dc.relation.referencesJiménez, D. J., Korenblum, E., & Van Elsas, J. D. (2014). Novel multispecies microbial consortia involved in lignocellulose and 5-hydroxymethylfurfural bioconversion. Applied Microbiology and Biotechnology, 98(6), 2789–2803. https://doi.org/10.1007/s00253-013-5253-7
dc.relation.referencesJin, Z., Shah, T., Zhang, L., Liu, H., Peng, S., & Nie, L. (2020). Effect of straw returning on soil organic carbon in rice – wheat rotation system : A review. December 2019, 1–13. https://doi.org/10.1002/fes3.200
dc.relation.referencesKanasugi, M., Sarkodee-Addo, E., Omari, R. A., Dastogeer, K. M. G., Fujii, Y., Abebrese, S. O., Bam, R., Asuming-Brempong, S., & Okazaki, S. (2020). Exploring rice root microbiome; The variation, specialization and interaction of bacteria and fungi in six tropic Savanna Regions in Ghana. Sustainability (Switzerland), 12(14). https://doi.org/10.3390/su12145835
dc.relation.referencesKandeler, E., & Gerber, H. (1988). Short-term assay of soil urease activity using colorimetric determination of ammonium. Biology and Fertility of Soils, 6(1), 68–72. https://doi.org/10.1007/BF00257924
dc.relation.referencesKato, H., Mori, H., Maruyama, F., Toyoda, A., Oshima, K., Endo, R., Fuchu, G., Miyakoshi, M., Dozono, A., Ohtsubo, Y., Nagata, Y., Hattori, M., Fujiyama, A., Kurokawa, K., & Tsuda, M. (2015). Time-series metagenomic analysis reveals robustness of soil microbiome against chemical disturbance. DNA Research, 22(6), 413–424. https://doi.org/10.1093/dnares/dsv023
dc.relation.referencesKielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A., & Kuramae, E. E. (2016). The Ecology of Acidobacteria: Moving beyond Genes and Genomes. Frontiers in Microbiology, 7(MAY), 1–16. https://doi.org/10.3389/fmicb.2016.00744
dc.relation.referencesKielak, A. M., Cipriano, M. A. P., & Kuramae, E. E. (2016). Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Archives of Microbiology, 198(10), 987–993. https://doi.org/10.1007/s00203-016-1260-2
dc.relation.referencesKim, H., & Lee, Y. H. (2020). The rice microbiome: A model platform for crop holobiome. Phytobiomes Journal, 4(1), 5–18. https://doi.org/10.1094/PBIOMES-07-19-0035-RVW
dc.relation.referencesKnief, C., Delmotte, N., Chaffron, S., Stark, M., Innerebner, G., Wassmann, R., Von Mering, C., & Vorholt, J. A. (2012). Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME Journal, 6(7), 1378–1390. https://doi.org/10.1038/ismej.2011.192
dc.relation.referencesKnoblauch R, Ernani PR, Deschamps FC, Gatiboni LC, Walker TW, Lourenço KS, A. A. & M. A. (2014). RICE STRAW INCORPORATED JUST BEFORE SOIL FLOODING INCREASES ACETIC ACID FORMATION AND DECREASES AVAILABLE NITROGEN. 38, 177–184.
dc.relation.referencesKont, R., Kurašin, M., Teugjas, H., & Väljamäe, P. (2013). Strong cellulase inhibitors from the hydrothermal pretreatment of wheat straw. Biotechnology for Biofuels, 6(1), 1–14. https://doi.org/10.1186/1754-6834-6-135
dc.relation.referencesKotur, Z., Siddiqi, Y. M., & Glass, A. D. M. (2013). Characterization of nitrite uptake in Arabidopsis thaliana: Evidence for a nitrite-specific transporter. New Phytologist, 200(1), 201–210. https://doi.org/10.1111/nph.12358
dc.relation.referencesKovaleva, O. L., Merkel, A. Y., Novikov, A. A., Baslerov, R. V., Toshchakov, S. V., & Bonch-Osmolovskaya, E. A. (2015). Tepidisphaera mucosa gen. Nov., sp. nov., a moderately thermophilic member of the class phycisphaerae in the phylum Planctomycetes, and proposal of a new family, tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov. International Journal of Systematic and Evolutionary Microbiology, 65(2), 549–555. https://doi.org/10.1099/ijs.0.070151-0
dc.relation.referencesKozera, B., & Rapacz, M. (2013). Reference genes in real-time PCR. Journal of Applied Genetics, 54(4), 391–406. https://doi.org/10.1007/s13353-013-0173-x
dc.relation.referencesKulichevskaya, I. S., Suzina, N. E., Liesack, W., & Dedysh, S. N. (2010). Bryobacter aggregatus gen. nov., sp. nov., a peat-inhabiting, aerobic chemo-organotroph from subdivision 3 of the acidobacteria. International Journal of Systematic and Evolutionary Microbiology, 60(2), 301–306. https://doi.org/10.1099/ijs.0.013250-0
dc.relation.referencesKumar, M., Kour, D., Yadav, A. N., Saxena, R., Rai, P. K., Jyoti, A., & Tomar, R. S. (2019). Biodiversity of methylotrophic microbial communities and their potential role in mitigation of abiotic stresses in plants. Biologia, 74(3), 287–308. https://doi.org/10.2478/s11756-019-00190-6
dc.relation.referencesKumari, A., Kapoor, K. K., Kundu, B. S., & Mehta, R. K. (2008). Identification of organic acids produced during rice straw decomposition and their role in rock phosphate solubilization. Plant, Soil and Environment, 54(2), 72–77. https://doi.org/10.17221/2783-pse
dc.relation.referencesKuramae, E. E., Hillekens, R. H. E., de Hollander, M., van der Heijden, M. G. A., van den Berg, M., van Straalen, N. M., & Kowalchuk, G. A. (2013). Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf. FEMS Microbiology Ecology, 84(3), 519–531. https://doi.org/10.1111/1574-6941.12080
dc.relation.referencesKuypers, M. M. M., Marchant, H. K., & Kartal, B. (2018). The microbial nitrogen-cycling network. Nature Reviews Microbiology, 16(5), 263–276. https://doi.org/10.1038/nrmicro.2018.9
dc.relation.referencesKuzyakov, Y., & Blagodatskaya, E. (2015). Microbial hotspots and hot moments in soil: Concept & review. Soil Biology and Biochemistry, 83(February), 184–199. https://doi.org/10.1016/j.soilbio.2015.01.025
dc.relation.referencesLadd, J. N., & Butler, J. H. A. (1972). Short-term assays of soil proteolytic enzyme activities using proteins and dipeptide derivatives as substrates. Soil Biology and Biochemistry, 4(1), 19–30. https://doi.org/10.1016/0038-0717(72)90038-7
dc.relation.referencesLanoiselet, V. M., Cother, E. J., Ash, G. J., Hind-Lanoiselet, T. L., Murray, G. M., & Harper, J. D. I. (2005). Prevalence and survival, with emphasis on stubble burning, of Rhizoctonia spp., causal agents of sheath diseases of rice in Australia. Australasian Plant Pathology, 34(2), 135–142. https://doi.org/10.1071/AP05010
dc.relation.referencesLe Cocq, K., Gurr, S. J., Hirsch, P. R., & Mauchline, T. H. (2017). Exploitation of endophytes for sustainable agricultural intensification. Molecular Plant Pathology, 18(3), 469–473. https://doi.org/10.1111/mpp.12483
dc.relation.referencesLe Roux, X., Poly, F., Currey, P., Commeaux, C., Hai, B., Nicol, G. W., Prosser, J. I., Schloter, M., Attard, E., & Klumpp, K. (2008). Effects of aboveground grazing on coupling among nitrifier activity, abundance and community structure. ISME Journal, 2(2), 221–232. https://doi.org/10.1038/ismej.2007.109
dc.relation.referencesLee, J., & Cho, K. (2004). Relationships between methane production and sulfate reduction in reclaimed rice field soils. Korean Journal of Biological Sciences, 8(4), 281–288. https://doi.org/10.1080/12265071.2004.9647761
dc.relation.referencesLee, Y. H., Ko, S. J., Cha, K. H., & Park, E. W. (2015). BGRcast: A disease forecast model to support decision-making for chemical sprays to control bacterial grain rot of rice. Plant Pathology Journal, 31(4), 350–362. https://doi.org/10.5423/PPJ.OA.07.2015.0136
dc.relation.referencesLi, H. Y., Wang, H., Wang, H. T., Xin, P. Y., Xu, X. H., Ma, Y., Liu, W. P., Teng, C. Y., Jiang, C. L., Lou, L. P., Arnold, W., Cralle, L., Zhu, Y. G., Chu, J. F., Gilbert, J. A., & Zhang, Z. J. (2018). The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome, 6(1), 1–16. https://doi.org/10.1186/s40168-018-0561-x
dc.relation.referencesLi, S., Wang, Z. hui, Miao, Y. fang, & Li, S. qing. (2014). Soil Organic Nitrogen and Its Contribution to Crop Production. Journal of Integrative Agriculture, 13(10), 2061–2080. https://doi.org/10.1016/S2095-3119(14)60847-9
dc.relation.referencesLi, X., Wang, H., Li, X., Li, X., & Zhang, H. (2019). Shifts in bacterial community composition increase with depth in three soil types from paddy fields in China. Pedobiologia, 77(February). https://doi.org/10.1016/j.pedobi.2019.150589
dc.relation.referencesLi, Y., Chapman, S. J., Nicol, G. W., & Yao, H. (2018). Nitrification and nitrifiers in acidic soils. Soil Biology and Biochemistry, 116(January), 290–301. https://doi.org/10.1016/j.soilbio.2017.10.023
dc.relation.referencesLiesack, W., Schnell, S., & Revsbech, N. P. (2000). Microbiology of flooded rice paddies. FEMS Microbiology Reviews, 24(5), 625–645. https://doi.org/10.1016/S0168-6445(00)00050-4
dc.relation.referencesLima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Cesar Ignacio-Espinosa, J., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., … Raes, J. (2015). 24 Silvia G. Acinas, 12 Shinichi Sunagawa, 17 Peer Bork. Science, 10(6237), 1–10. www.sciencemag.org
dc.relation.referencesLimmer, C., & Drake, H. L. (1996). Non-symbiotic N2-fixation in acidic and pH-neutral forest soils: Aerobic and anaerobic differentials. Soil Biology and Biochemistry, 28(2), 177–183. https://doi.org/10.1016/0038-0717(95)00118-2
dc.relation.referencesLin, H. C., & Fukushima, Y. (2016). Rice cultivation methods and their sustainability aspects: Organic and conventional rice production in industrialized tropical monsoon Asia with a dual cropping system. Sustainability (Switzerland), 8(6). https://doi.org/10.3390/su8060529
dc.relation.referencesLin, J. T., Goldman, B. S., & Stewart, V. (1993). Structures of genes nasA and nasB, encoding assimilatory nitrate and nitrite reductases in Klebsiella pneumoniae M5al. Journal of Bacteriology, 175(8), 2370–2378. https://doi.org/10.1128/jb.175.8.2370-2378.1993
dc.relation.referencesLinhardt, R. J., Galliher, P. M., & Cooney, C. L. (1987). Polysaccharide lyases. Applied Biochemistry and Biotechnology, 12(2), 135–176. https://doi.org/10.1007/BF02798420
dc.relation.referencesLou, Y., Xu, M., Wang, W., Sun, X., & Zhao, K. (2011). Return rate of straw residue affects soil organic C sequestration by chemical fertilization. Soil and Tillage Research, 113(1), 70–73. https://doi.org/10.1016/j.still.2011.01.007
dc.relation.referencesLouca, S., Polz, M. F., Mazel, F., Albright, M. B. N., Huber, J. A., O’Connor, M. I., Ackermann, M., Hahn, A. S., Srivastava, D. S., Crowe, S. A., Doebeli, M., & Parfrey, L. W. (2018). Function and functional redundancy in microbial systems. Nature Ecology and Evolution, 2(6), 936–943. https://doi.org/10.1038/s41559-018-0519-1
dc.relation.referencesLove, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 1–21. https://doi.org/10.1186/s13059-014-0550-8
dc.relation.referencesLozupone, C., Faust, K., Raes, J., Faith, J. J., Frank, D. N., Zaneveld, J., Gordon, J. I., & Knight, R. (2012). Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. Genome Research, 22(10), 1974–1984. https://doi.org/10.1101/gr.138198.112
dc.relation.referencesLundberg, D. S., Lebeis, S. L., Paredes, S. H., Yourstone, S., Gehring, J., Malfatti, S., Tremblay, J., Engelbrektson, A., Kunin, V., Rio, T. G. Del, Edgar, R. C., Eickhorst, T., Ley, R. E., Hugenholtz, P., Tringe, S. G., & Dangl, J. L. (2012). Defining the core Arabidopsis thaliana root microbiome. Nature, 488(7409), 86–90. https://doi.org/10.1038/nature11237
dc.relation.referencesLuo, G., Ling, N., Nannipieri, P., Chen, H., Raza, W., Wang, M., Guo, S., & Shen, Q. (2017). Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions. Biology and Fertility of Soils, 53(4), 375–388. https://doi.org/10.1007/s00374-017-1183-3
dc.relation.referencesLuo, X., Fu, X., Yang, Y., Cai, P., Peng, S., Chen, W., & Huang, Q. (2016). Microbial communities play important roles in modulating paddy soil fertility. Scientific Reports, 6(February), 1–12. https://doi.org/10.1038/srep20326
dc.relation.referencesLupatini, M., Suleiman, A. K. A., Jacques, R. J. S., Antoniolli, Z. I., de Siqueira Ferreira, A., Kuramae, E. E., & Roesch, L. F. W. (2014). Network topology reveals high connectance levels and few key microbial genera within soils. Frontiers in Environmental Science, 2(MAY), 1–11. https://doi.org/10.3389/fenvs.2014.00010
dc.relation.referencesMa, B., Wang, Y., Ye, S., Liu, S., Stirling, E., Gilbert, J. A., Faust, K., Knight, R., Jansson, J. K., Cardona, C., Röttjers, L., & Xu, J. (2020). Earth microbial co-occurrence network reveals interconnection pattern across microbiomes. Microbiome, 8(1), 1–12. https://doi.org/10.1186/s40168-020-00857-2
dc.relation.referencesMaarastawi, S. A., Frindte, K., Geer, R., Kröber, E., & Knief, C. (2018). Temporal dynamics and compartment specific rice straw degradation in bulk soil and the rhizosphere of maize. Soil Biology and Biochemistry, 127, 200–212. https://doi.org/10.1016/j.soilbio.2018.09.028
dc.relation.referencesMaarastawi, S. A., Frindte, K., Linnartz, M., & Knief, C. (2018). Crop rotation and straw application impact microbial communities in Italian and Philippine Soils and the rhizosphere of Zea mays. Frontiers in Microbiology, 9(JUN), 1–17. https://doi.org/10.3389/fmicb.2018.01295
dc.relation.referencesMarentes, F., Vanegas, J., Luna, J. N., & Uribe-Vélez, D. (2011). Ecología de microorganismos rizosféricos asociados a cultivos de arroz de Tolima y Meta (D. Uribe-Vélez & L. M. Melgarejo (eds.); Primera ed). Editorial Universidad Nacional de Colombia. https://www.uneditorial.com/ecologia-de-microorganismos-rizosfericos-asociados-a-cultivos-de-arroz-de-tolima-y-meta-agropecuario.html
dc.relation.referencesMargalef, O., Sardans, J., Fernández-Martínez, M., Molowny-Horas, R., Janssens, I. A., Ciais, P., Goll, D., Richter, A., Obersteiner, M., Asensio, D., & Peñuelas, J. (2017). Global patterns of phosphatase activity in natural soils. Scientific Reports, 7(1), 1–13. https://doi.org/10.1038/s41598-017-01418-8
dc.relation.referencesMartínez-Hidalgo, P., & Hirsch, A. M. (2017). The nodule microbiome: N2fixing rhizobia do not live alone. Phytobiomes Journal, 1(2), 70–82. https://doi.org/10.1094/PBIOMES-12-16-0019-RVW
dc.relation.referencesMašínová, T., Yurkov, A., & Baldrian, P. (2018). Forest soil yeasts: Decomposition potential and the utilization of carbon sources. Fungal Ecology, 34, 10–19. https://doi.org/10.1016/j.funeco.2018.03.005
dc.relation.referencesMedema, M. H., Blin, K., Cimermancic, P., De Jager, V., Zakrzewski, P., Fischbach, M. A., Weber, T., Takano, E., & Breitling, R. (2011). AntiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Research, 39(SUPPL. 2), 339–346. https://doi.org/10.1093/nar/gkr466
dc.relation.referencesMekasha, S., Tuveng, T. R., Askarian, F., Choudhary, S., Schmidt-Dannert, C., Niebisch, A., Modregger, J., Vaaje-Kolstad, G., & Eijsink, V. G. H. (2020). A trimodular bacterial enzyme combining hydrolytic activity with oxidative glycosidic bond cleavage efficiently degrades chitin. Journal of Biological Chemistry, 295(27), 9134–9146. https://doi.org/10.1074/jbc.ra120.013040
dc.relation.referencesMendes, R., Garbeva, P., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: Significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews, 37(5), 634–663. https://doi.org/10.1111/1574-6976.12028
dc.relation.referencesMendes, R., Kruijt, M., De Bruijn, I., Dekkers, E., Van Der Voort, M., Schneider, J. H. M., Piceno, Y. M., DeSantis, T. Z., Andersen, G. L., Bakker, P. A. H. M., & Raaijmakers, J. M. (2011). Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science, 332(6033), 1097–1100. https://doi.org/10.1126/science.1203980
dc.relation.referencesMerlin, C., Besaury, L., Niepceron, M., Mchergui, C., Riah, W., Bureau, F., Gattin, I., & Bodilis, J. (2014). Real-time PCR for quantification in soil of glycoside hydrolase family 6 cellulase genes. Letters in Applied Microbiology, 59(3), 284–291. https://doi.org/10.1111/lam.12273
dc.relation.referencesMidha, S., Bansal, K., Sharma, S., Kumar, N., Patil, P. P., Chaudhry, V., & Patil, P. B. (2016). Genomic resource of rice seed associated bacteria. Frontiers in Microbiology, 6(JAN), 1–8. https://doi.org/10.3389/fmicb.2015.01551
dc.relation.referencesMinamisawa, K., Imaizumi-Anraku, H., Bao, Z., Shinoda, R., Okubo, T., & Ikeda, S. (2016). Are symbiotic methanotrophs key microbes for N acquisition in paddy rice root? Microbes and Environments, 31(1), 4–10. https://doi.org/10.1264/jsme2.ME15180
dc.relation.referencesMueller, G. M., & Schmit, J. P. (2007). Fungal biodiversity: What do we know? What can we predict? Biodiversity and Conservation, 16(1), 1–5. https://doi.org/10.1007/s10531-006-9117-7
dc.relation.referencesMüller, T., & Ruppel, S. (2014). Progress in cultivation-independent phyllosphere microbiology. FEMS Microbiology Ecology, 87(1), 2–17. https://doi.org/10.1111/1574-6941.12198
dc.relation.referencesMurase, J., Shibata, M., Lee, C. G., Watanabe, T., Asakawa, S., & Kimura, M. (2012). Incorporation of plant residue-derived carbon into the microeukaryotic community in a rice field soil revealed by DNA stable-isotope probing. FEMS Microbiology Ecology, 79(2), 371–379. https://doi.org/10.1111/j.1574-6941.2011.01224.x
dc.relation.referencesMurillo-Antolinez, L. M. (2018). 2018_Tesis final_Laura Murillo. UNiversidad El Bosque.
dc.relation.referencesMurphy, B. (2015). Key soil functional properties affected by soil organic matter - Evidence from published literature. IOP Conference Series: Earth and Environmental Science, 25(1). https://doi.org/10.1088/1755-1315/25/1/012008
dc.relation.referencesNAAS. (2017). Innovative viable solution to rice residue burning in rice-wheat cropping system through concurrent use of super straw management system-fitted combines and turbo happy seeder. Policy Brief No. 2, 1–16. http://naasindia.org/documents/CropBurning.pdf
dc.relation.referencesNannipieri, 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. https://doi.org/10.1046/j.1351-0754.2003.0556.x
dc.relation.referencesNannipieri, P., Ascher, J., Ceccherini, M. T., Landi, L., Pietramellara, G., & Renella, G. (2017). Landmark Papers Microbial diversity and soil functions. European Journal of Soil Science, 68(1), 12–26. http://doi.wiley.com/10.1111/ejss.4_12398
dc.relation.referencesNannipieri, P., Giagnoni, L., Renella, G., Puglisi, E., Ceccanti, B., Masciandaro, G., Fornasier, F., Moscatelli, M. C., & Marinari, S. (2012). Soil enzymology: Classical and molecular approaches. Biology and Fertility of Soils, 48(7), 743–762. https://doi.org/10.1007/s00374-012-0723-0
dc.relation.referencesNannipieri, P, Giagnoni, L., Landi, L., & Renella, G. (2011). Phosphorus in Action. 26, 215–243. https://doi.org/10.1007/978-3-642-15271-9
dc.relation.referencesNannipieri, Paolo. (2006). Role of Stabilised Enzymes in Microbial Ecology and Enzyme Extraction from Soil with Potential Applications in Soil Proteomics. Nucleic Acids and Proteins in Soil, 8, 75–94. https://doi.org/10.1007/3-540-29449-x_4
dc.relation.referencesNavarrete, Acácio A., Kuramae, E. E., de Hollander, M., Pijl, A. S., van Veen, J. A., & Tsai, S. M. (2013). Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiology Ecology, 83(3), 607–621. https://doi.org/10.1111/1574-6941.12018
dc.relation.referencesNavarrete, Acacio A., Tsai, S. M., Mendes, L. W., Faust, K., De Hollander, M., Cassman, N. A., Raes, J., Van Veen, J. A., & Kuramae, E. E. (2015). Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology, 24(10), 2433–2448. https://doi.org/10.1111/mec.13172
dc.relation.referencesNelkner, J., Henke, C., Lin, T. W., Pätzold, W., Hassa, J., Jaenicke, S., Grosch, R., Pühler, A., Sczyrba, A., & Schlüter, A. (2019). Effect of long-term farming practices on agricultural soil microbiome members represented by metagenomically assembled genomes (MAGs) and their predicted plant-beneficial genes. Genes, 10(6). https://doi.org/10.3390/genes10060424
dc.relation.referencesNemergut, D. R., Townsend, A. R., Sattin, S. R., Freeman, K. R., Fierer, N., Neff, J. C., Bowman, W. D., Schadt, C. W., Weintraub, M. N., & Schmidt, S. K. (2008). The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: Implications for carbon and nitrogen cycling. Environmental Microbiology, 10(11), 3093–3105. https://doi.org/10.1111/j.1462-2920.2008.01735.x
dc.relation.referencesNguyen, N. H., Song, Z., Bates, S. T., Branco, S., Tedersoo, L., Menke, J., Schilling, J. S., & Kennedy, P. G. (2016). FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20, 241–248. https://doi.org/10.1016/j.funeco.2015.06.006
dc.relation.referencesNicol, G. W., Leininger, S., Schleper, C., & Prosser, J. I. (2008). The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology, 10(11), 2966–2978. https://doi.org/10.1111/j.1462-2920.2008.01701.x
dc.relation.referencesNie, San’an, Lei, X., Zhao, L., Brookes, P. C., Wang, F., Chen, C., Yang, W., & Xing, S. (2018). Fungal communities and functions response to long-term fertilization in paddy soils. Applied Soil Ecology, 130(August), 251–258. https://doi.org/10.1016/j.apsoil.2018.06.008
dc.relation.referencesNie, San’An, Li, H., Yang, X., Zhang, Z., Weng, B., Huang, F., Zhu, G. B., & Zhu, Y. G. (2015). Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere. ISME Journal, 9(9), 2059–2067. https://doi.org/10.1038/ismej.2015.25
dc.relation.referencesNilsson, R. Henrik, Wurzbacher, C., Bahram, M., Coimbra, V. R. M., Larsson, E., Tedersoo, L., Eriksson, J., Ritter, C. D., Svantesson, S., Sánchez-García, M., Ryberg, M., Kristiansson, E., & Abarenkov, K. (2016). Top 50 most wanted fungi. MycoKeys, 12, 29–40. https://doi.org/10.3897/mycokeys.12.7553
dc.relation.referencesNilsson, Rolf Henrik, Larsson, K. H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P., Picard, K., Glöckner, F. O., Tedersoo, L., Saar, I., Kõljalg, U., & Abarenkov, K. (2019). The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47(D1), D259–D264. https://doi.org/10.1093/nar/gky1022
dc.relation.referencesNsenga Kumwimba, M., & Meng, F. (2019). Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review. Science of the Total Environment, 659, 419–441. https://doi.org/10.1016/j.scitotenv.2018.12.236
dc.relation.referencesPandey, A. K., Gaind, S., Ali, A., & Nain, L. (2009). Effect of bioaugmentation and nitrogen supplementation on composting of paddy straw. Biodegradation, 20(3), 293–306. https://doi.org/10.1007/s10532-008-9221-3
dc.relation.referencesPandit, P. S., Ranade, D. R., Dhakephalkar, P. K., & Rahalkar, M. C. (2016). A pmoA-based study reveals dominance of yet uncultured Type I methanotrophs in rhizospheres of an organically fertilized rice field in India. 3 Biotech, 6(2), 1–6. https://doi.org/10.1007/s13205-016-0453-3
dc.relation.referencesPanhwar, Q. A., Naher, U. A., Shamshuddin, J., Othman, R., & Latif, M. A. (2014). Correction: Biochemical and molecular characterization of potential phosphate-solubilizing bacteria in acid sulfate soils and their beneficial effects on rice growth. PLoS ONE, 9(12). https://doi.org/10.1371/journal.pone.0097241
dc.relation.referencesPansu, M., & Gautheyrou, J. (2006). Handbook of Soil Analysis. In Handbook of Soil Analysis: Mineralogical, Organic and Inorganic Methods. Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-540-31211-6
dc.relation.referencesParks, D. H., Tyson, G. W., Hugenholtz, P., & Beiko, R. G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles. Bioinformatics, 30(21), 3123–3124. https://doi.org/10.1093/bioinformatics/btu494
dc.relation.referencesPascault, N., Ranjard, L., Kaisermann, A., Bachar, D., Christen, R., Terrat, S., Mathieu, O., Lévêque, J., Mougel, C., Henault, C., Lemanceau, P., Péan, M., Boiry, S., Fontaine, S., & Maron, P. A. (2013). Stimulation of Different Functional Groups of Bacteria by Various Plant Residues as a Driver of Soil Priming Effect. Ecosystems, 16(5), 810–822. https://doi.org/10.1007/s10021-013-9650-7
dc.relation.referencesPaul, Ε. Α., & Clark, F. E. (1989). Soil Microbiology and Biochemistry. Elsevier. https://doi.org/10.1016/C2009-0-02814-1
dc.relation.referencesPedregosa, F., Varoquaux, G., Buitinck, L., Louppe, G., Grisel, O., & Mueller, A. (2015). Scikit-learn. GetMobile: Mobile Computing and Communications, 19(1), 29–33. https://doi.org/10.1145/2786984.2786995
dc.relation.referencesPhy, C., Dejbhimon, K., Tulaphitak, D., Lawongsa, P., Thammasom, N., & Saenjan, P. (2014). Rice Straw Amendment and Sulfate Affecting Methane Production and Chemical Properties in Paddy Soils.
dc.relation.referencesPiotrowska, A., & Koper, J. (2010). Soil β-glucosidase activity under winter wheat cultivated in crop rotation systems depleting and enriching the soil in organic matter. Journal of Elementology, 15(3), 593–600. https://doi.org/10.5601/jelem.2010.15.3.593-600
dc.relation.referencesPiotrowska, A., & Koper, J. (2013). Soil β-glucosidase activity under winter wheat cultivated in crop rotation systems depleting and enriching the soil in organic matter. Journal of Elemntology, 15(3/2010), 593–600. https://doi.org/10.5601/jelem.2010.15.3.593-600
dc.relation.referencesPittol, M., Scully, E., Miller, D., Durso, L., Mariana Fiuza, L., & Valiati, V. H. (2018). Bacterial Community of the Rice Floodwater Using Cultivation-Independent Approaches. International Journal of Microbiology, 2018. https://doi.org/10.1155/2018/6280484
dc.relation.referencesPoly, F., Monrozier, L. J., & Bally, R. (2001). Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil. Research in Microbiology, 152(1), 95–103. https://doi.org/10.1016/S0923-2508(00)01172-4
dc.relation.referencesPower, M. E., Tilman, D., Estes, J. A., Menge, B. A., Bond, W. J., Mills, L. S., Daily, G., Castilla, J. C., Lubchenco, J., & Paine, R. T. (1996). Challenges in the Quest for Keystones. BioScience, 46(8), 609–620. https://doi.org/10.2307/1312990
dc.relation.referencesProsser, J. I., & Nicol, G. W. (2012). Archaeal and bacterial ammonia-oxidisers in soil: The quest for niche specialisation and differentiation. Trends in Microbiology, 20(11), 523–531. https://doi.org/10.1016/j.tim.2012.08.001
dc.relation.referencesQuast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), 590–596. https://doi.org/10.1093/nar/gks1219
dc.relation.referencesQuevedo Amaya, Y. M., Beltrán Medina, J. I., & Barragán Quijano, E. (2019). Identification of climatic and physiological variables associated with rice (Oryza sativa L.) yield under tropical conditions. Revista Facultad Nacional de Agronomia Medellin, 72(1), 8699–8706. https://doi.org/10.15446/rfnam.v72n1.72076
dc.relation.referencesR Core Team. (2019). R: The R Project for Statistical Computing. In R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https://www.r-project.org/
dc.relation.referencesRagot, S. A., Kertesz, M. A., & Bünemann, E. K. (2015). phoD alkaline phosphatase gene diversity in soil. Applied and Environmental Microbiology, 81(20), 7281–7289. https://doi.org/10.1128/AEM.01823-15
dc.relation.referencesRawat, S. R., Männistö, M. K., Bromberg, Y., & Häggblom, M. M. (2012). Comparative genomic and physiological analysis provides insights into the role of Acidobacteria in organic carbon utilization in Arctic tundra soils. FEMS Microbiology Ecology, 82(2), 341–355. https://doi.org/10.1111/j.1574-6941.2012.01381.x
dc.relation.referencesRawway, M., Ali, S. G., & Badawy, A. S. (2018). Isolation and Identification of Cellulose Degrading Bacteria from Different Sources at Assiut Governorate (Upper Egypt). Journal of Ecology of Health & Environment, 6(1), 15–24. https://doi.org/10.18576/jehe/060103
dc.relation.referencesReay, D. S., & Nedwell, D. B. (2004). Methane oxidation in temperate soils: Effects of inorganic N. Soil Biology and Biochemistry, 36(12), 2059–2065. https://doi.org/10.1016/j.soilbio.2004.06.002
dc.relation.referencesReicosky, D. C., & Wilts, A. R. (2005). CROP-RESIDUE MANAGEMENT. Encyclopedia of Soils in the Environment, 4, 334–338. https://doi.org/10.1016/B0-12-348530-4/00254-X
dc.relation.referencesRen, Z., You, W., Wu, S., Poetsch, A., & Xu, C. (2019). Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. Biotechnology for Biofuels, 12(1), 1–14. https://doi.org/10.1186/s13068-019-1522-8
dc.relation.referencesRho, M., Tang, H., & Ye, Y. (2010). FragGeneScan: Predicting genes in short and error-prone reads. Nucleic Acids Research, 38(20), 1–12. https://doi.org/10.1093/nar/gkq747
dc.relation.referencesRognes, T., Flouri, T., Nichols, B., Quince, C., & Mahé, F. (2016). VSEARCH: A versatile open source tool for metagenomics. PeerJ, 2016(10), 1–22. https://doi.org/10.7717/peerj.2584
dc.relation.referencesRoman-Reyna, V., Pinili, D., Borja, F. ., I.L., Q., & S.C., G. (2019). The rice leaf microbiome has a conserved community structure controlled by complex host-microbe interactions.
dc.relation.referencesRovira, P., & Ramón Vallejo, V. (2002). Mineralization of carbon and nitrogen from plant debris, as affected by debris size and depth of burial. Soil Biology and Biochemistry, 34(3), 327–339. https://doi.org/10.1016/S0038-0717(01)00186-9
dc.relation.referencesS. P. DENG and M. A. TABATABAI. (1994). Cellulase Activity. International Cenological Codex, 26(1990), 1–11.
dc.relation.referencesSakurai, M., Wasaki, J., Tomizawa, Y., Shinano, T., & Osaki, M. (2008). Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter. Soil Science and Plant Nutrition, 54(1), 62–71. https://doi.org/10.1111/j.1747-0765.2007.00210.x
dc.relation.referencesSalazar, S., Sánchez, L. E., Alvarez, J., Valverde, A., Galindo, P., Igual, J. M., Peix, A., & Santa-Regina, I. (2011). Correlation among soil enzyme activities under different forest system management practices. Ecological Engineering, 37(8), 1123–1131. https://doi.org/10.1016/j.ecoleng.2011.02.007
dc.relation.referencesSantos-Medellín, C., Edwards, J., Liechty, Z., Nguyen, B., & Sundaresan, V. (2017). Drought Stress Results in a Compartment-Specific Restructuring of. MBio, 8(4: 8:e00764-17), 1–15. http://www.ncbi.nlm.nih.gov/pubmed/28720730%0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5516253
dc.relation.referencesSarkodee-Addo, E., Yasuda, M., Lee, C. G., Kanasugi, M., Fujii, Y., Omari, R. A., Abebrese, S. O., Bam, R., Asuming-Brempong, S., Golam Dastogeer, K. M., & Okazaki, S. (2020). Arbuscular Mycorrhizal Fungi Associated with Rice (Oryza sativa L.) in Ghana: Effect of regional locations and soil factors on diversity and community assembly. Agronomy, 10(4). https://doi.org/10.3390/agronomy10040559
dc.relation.referencesSchimel, J. P., & Bennett, J. B. (2004). Nitrogen Mineralization: Challenges of a Changing Paradigm. Ecology, 85(3), 591–602. https://doi.org/10.1890/03-8024
dc.relation.referencesSchinner, F., & Mersi, W. V. O. N. (1990). and Invertase Activity in Soil : an Improved Method. 3–7.
dc.relation.referencesSchinner, F., & von Mersi, W. (1990). Xylanase-, CM-cellulase- and invertase activity in soil: An improved method. Soil Biology and Biochemistry, 22(4), 511–515. https://doi.org/10.1016/0038-0717(90)90187-5
dc.relation.referencesSchöner, T. A., Gassel, S., Osawa, A., Tobias, N. J., Okuno, Y., Sakakibara, Y., Shindo, K., Sandmann, G., & Bode, H. B. (2016). Aryl Polyenes, a Highly Abundant Class of Bacterial Natural Products, Are Functionally Related to Antioxidative Carotenoids. ChemBioChem, 17(3), 247–253. https://doi.org/10.1002/cbic.201500474
dc.relation.referencesSegata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011). Metagenomic biomarker discovery and explanation. Genome Biology, 12(6), R60. https://doi.org/10.1186/gb-2011-12-6-r60
dc.relation.referencesSerrano-Silva, N., Sarria-Guzmán, Y., Dendooven, L., & Luna-Guido, M. (2014). Methanogenesis and Methanotrophy in Soil: A Review. Pedosphere, 24(3), 291–307. https://doi.org/10.1016/S1002-0160(14)60016-3
dc.relation.referencesSessitsch, A., Hardoim, P., Döring, J., Weilharter, A., Krause, A., Woyke, T., Mitter, B., Hauberg-Lotte, L., Friedrich, F., Rahalkar, M., Hurek, T., Sarkar, A., Bodrossy, L., Van Overbeek, L., Brar, D., Van Elsas, J. D., & Reinhold-Hurek, B. (2012). Functional Characteristics of an Endophyte Community Colonizing Rice Roots as Revealed by Metagenomic Analysis. Molecular Plant-Microbe Interactions, 25(1), 28–36. https://doi.org/10.1094/MPMI-08-11-0204
dc.relation.referencesSethi, S., Datta, A., Gupta, B. L., & Gupta, S. (2013). Optimization of Cellulase Production from Bacteria Isolated from Soil. ISRN Biotechnology, 2013, 1–7. https://doi.org/10.5402/2013/985685
dc.relation.referencesShade, A., & Handelsman, J. (2012). Beyond the Venn diagram: The hunt for a core microbiome. Environmental Microbiology, 14(1), 4–12. https://doi.org/10.1111/j.1462-2920.2011.02585.x
dc.relation.referencesShade, A., Jacques, M. A., & Barret, M. (2017). Ecological patterns of seed microbiome diversity, transmission, and assembly. Current Opinion in Microbiology, 37, 15–22. https://doi.org/10.1016/j.mib.2017.03.010
dc.relation.referencesShade, A., Peter, H., Allison, S. D., Baho, D. L., Berga, M., Bürgmann, H., Huber, D. H., Langenheder, S., Lennon, J. T., Martiny, J. B. H., Matulich, K. L., Schmidt, T. M., & Handelsman, J. (2012). Fundamentals of microbial community resistance and resilience. Frontiers in Microbiology, 3(DEC), 1–19. https://doi.org/10.3389/fmicb.2012.00417
dc.relation.referencesShannon, C. E. (1948). A Mathematical Theory of Communication. Bell System Technical Journal, 27(4), 623–656. https://doi.org/10.1002/j.1538-7305.1948.tb00917.x
dc.relation.referencesShapiro, S. S., & Wilk, M. B. (1965). An Analysis of Variance Test for Normality (Complete Samples). Biometrika, 52(3/4), 591. https://doi.org/10.2307/2333709
dc.relation.referencesSharrar, A. M., Crits-Christoph, A., Méheust, R., Diamond, S., Starr, E. P., & Banfield, J. F. (2020). Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. MBio, 11(3), 1–17. https://doi.org/10.1128/mBio.00416-20
dc.relation.referencesShew, A. M., Durand-morat, A., Nalley, L. L., Zhou, X., Rojas, C., & Greg, T. (2019). Warming increases Bacterial Panicle Blight ( Burkholderia glumae ) occurrences and impacts on USA rice production. 1–18. https://doi.org/10.1371/journal.pone.0219199
dc.relation.referencesShiau, Y. J., Lin, C. W., Cai, Y., Jia, Z., Lin, Y. Te, & Chiu, C. Y. (2020). Niche differentiation of active methane-oxidizing bacteria in estuarine mangrove forest soils in taiwan. Microorganisms, 8(8), 1–15. https://doi.org/10.3390/microorganisms8081248
dc.relation.referencesSimonet, P., Grosjean, M. C., Misra, A. K., Nazaret, S., Cournoyer, B., & Normand, P. (1991). Frankia genus-specific characterization by polymerase chain reaction. Applied and Environmental Microbiology, 57(11), 3278–3286. https://doi.org/10.1128/aem.57.11.3278-3286.1991
dc.relation.referencesSinclair, L., Osman, O. A., Bertilsson, S., & Eiler, A. (2015). Microbial community composition and diversity via 16S rRNA gene amplicons: Evaluating the illumina platform. PLoS ONE, 10(2), 1–18. https://doi.org/10.1371/journal.pone.0116955
dc.relation.referencesSnedecor, G. W. (George W., & Cochran, W. G. (William G. (1989). Statistical methods. Iowa State University Press.
dc.relation.referencesSneh Goyal & S.S. Sindhu. (2011). Composting of rice straw using different inocula and analysi of compost quality (pp. 126–138).
dc.relation.referencesSong, N., Xu, H., Yan, Z., Yang, T., Wang, C., & Jiang, H. L. (2019). Improved lignin degradation through distinct microbial community in subsurface sediments of one eutrophic lake. Renewable Energy, 138(February), 861–869. https://doi.org/10.1016/j.renene.2019.01.121
dc.relation.referencesSood, M., Kapoor, D., Kumar, V., & Sheteiwy, M. S. (2020). Trichoderma : The “ Secrets ” of a Multitalented.
dc.relation.referencesSpence, C., Alff, E., Johnson, C., Ramos, C., Donofrio, N., Sundaresan, V., & Bais, H. (2014). Natural rice rhizospheric microbes suppress rice blast infections. BMC Plant Biology, 14(1), 1–17. https://doi.org/10.1186/1471-2229-14-130
dc.relation.referencesSterkenburg, E., Bahr, A., Brandström Durling, M., Clemmensen, K. E., & Lindahl, B. D. (2015). Changes in fungal communities along a boreal forest soil fertility gradient. New Phytologist, 207(4), 1145–1158. https://doi.org/10.1111/nph.13426
dc.relation.referencesSubramanian, S., & Smith, D. L. (2015). Bacteriocins from the rhizosphere microbiome – From an agriculture perspective. Frontiers in Plant Science, 6(OCTOBER), 1–7. https://doi.org/10.3389/fpls.2015.00909
dc.relation.referencesSugano, A., Tsuchimoto, H., Tun, C. C., Asakawa, S., & Kimura, M. (2005). Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: Estimation by PCR-DGGE and sequence analyses. Soil Science and Plant Nutrition, 53(5), 585–594. https://doi.org/10.1111/j.1747-0765.2007.00187.x
dc.relation.referencesSuleiman, A. K. A., Gonzatto, R., Aita, C., Lupatini, M., Jacques, R. J. S., Kuramae, E. E., Antoniolli, Z. I., & Roesch, L. F. W. (2016). Temporal variability of soil microbial communities after application of dicyandiamide-treated swine slurry and mineral fertilizers. Soil Biology and Biochemistry, 97, 71–82. https://doi.org/10.1016/j.soilbio.2016.03.002
dc.relation.referencesSutherland, I. W. (1995). Polysaccharide lyases. FEMS Microbiology Reviews, 16(4), 323–347. https://doi.org/10.1016/0168-6445(95)00020-D
dc.relation.referencesTabatabai, M. A., & Bremner, J. M. (1969). Use of p-nitrophenyl phosphate for assay of soil phosphatase activity. Soil Biology and Biochemistry, 1(4), 301–307. https://doi.org/10.1016/0038-0717(69)90012-1
dc.relation.referencesTAKEUCHI, S. (1987). Importance and problems of disposal of crop residues containing pathogens of plant diseases. JARQ. Japan Agricultural Research Quarterly, 21(2), 102–108.
dc.relation.referencesTarafdar, J. C., Yadav, R. S., & Meena, S. C. (2001). Comparative efficiency of acid phosphatase originated from plant and fungal sources. Journal of Plant Nutrition and Soil Science, 164(3), 279–282. https://doi.org/10.1002/1522-2624(200106)164:3<279::AID-JPLN279>3.0.CO;2-L
dc.relation.referencesThe Cazypedia Consortium, Davies, G., Gilbert, H., Henrissat, B., Svensson, B., Vocadlo, D., & Williams, S. (2018). Ten years of CAZypedia: A living encyclopedia of carbohydrate-active enzymes. Glycobiology, 28(1), 3–8. https://doi.org/10.1093/glycob/cwx089
dc.relation.referencesTian, J., Dippold, M., Pausch, J., Blagodatskaya, E., Fan, M., Li, X., & Kuzyakov, Y. (2013). Microbial response to rhizodeposition depending on water regimes in paddy soils. Soil Biology and Biochemistry, 65, 195–203. https://doi.org/10.1016/j.soilbio.2013.05.021
dc.relation.referencesTipayarom, D., & Oanh, N. T. K. (2007). Effects from open rice straw burning emission on air quality in the Bangkok metropolitan region. ScienceAsia, 33(3), 339–345. https://doi.org/10.2306/scienceasia1513-1874.2007.33.339
dc.relation.referencesTrivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant–microbiome interactions: from community assembly to plant health. Nature Reviews Microbiology, 18(11), 607–621. https://doi.org/10.1038/s41579-020-0412-1
dc.relation.referencesTrujillo, M. E., Riesco, R., Benito, P., & Carro, L. (2015). Endophytic actinobacteria and the interaction of Micromonospora and nitrogen fixing plants. Frontiers in Microbiology, 6(DEC), 1–15. https://doi.org/10.3389/fmicb.2015.01341
dc.relation.referencesTung, N. S., Cu, N. X., & Hai, N. X. (2016). ARPN Journal of Agricultural and Biological Science IMPACT OF RICE STRAW BURNING METHODS ON SOIL TEMPERATURE AND MICROORGANISM IMPACT OF RICE STRAW BURNING METHODS ON SOIL TEMPERATURE AND MICROORGANISM DISTRIBUTION. ARPN Journal of Agricultural and Biological Science I, 23(4), 157–160.
dc.relation.referencesUtobo, E. B., & Tewari, L. (2015). Soil enzymes as bioindicators of soil ecosystem status. Applied Ecology and Environmental Research, 13(1), 147–169. https://doi.org/10.15666/aeer/1301_147169
dc.relation.referencesVaksmaa, A., van Alen, T. A., Ettwig, K. F., Lupotto, E., Valè, G., Jetten, M. S. M., & Lüke, C. (2017). Stratification of diversity and activity of methanogenic and methanotrophic microorganisms in a nitrogen-fertilized Italian paddy soil. Frontiers in Microbiology, 8(NOV), 1–15. https://doi.org/10.3389/fmicb.2017.02127
dc.relation.referencesVan Bruggen, A. H. C., & Semenov, A. M. (2000). In search of biological indicators for soil health and disease suppression. Applied Soil Ecology, 15(1), 13–24. https://doi.org/10.1016/S0929-1393(00)00068-8
dc.relation.referencesvan der Lelie, D., Taghavi, S., McCorkle, S. M., Li, L. L., Malfatti, S. A., Monteleone, D., Donohoe, B. S., Ding, S. Y., Adney, W. S., Himmel, M. E., & Tringe, S. G. (2012). The metagenome of an anaerobic microbial community decomposing poplar wood chips. PLoS ONE, 7(5). https://doi.org/10.1371/journal.pone.0036740
dc.relation.referencesVan Groenigen, K. J., Osenberg, C. W., & Hungate, B. A. (2011). Increased soil emissions of potent greenhouse gases under increased atmospheric CO 2. Nature, 475(7355), 214–216. https://doi.org/10.1038/nature10176
dc.relation.referencesVanegas, J., Landazabal, G., Melgarejo, L. M., Beltran, M., & Uribe-Vélez, D. (2013). Structural and functional characterization of the microbial communities associated with the upland and irrigated rice rhizospheres in a neotropical Colombian savannah. European Journal of Soil Biology, 55, 1–8. https://doi.org/10.1016/j.ejsobi.2012.10.008
dc.relation.referencesVeres, Z., Kotroczó, Z., Fekete, I., Tóth, J. A., Lajtha, K., Townsend, K., & Tóthmérész, B. (2015). Soil extracellular enzyme activities are sensitive indicators of detrital inputs and carbon availability. Applied Soil Ecology, 92, 18–23. https://doi.org/10.1016/j.apsoil.2015.03.006
dc.relation.referencesViborg, A. H., Terrapon, N., Lombard, V., Michel, G., Czjzek, M., Henrissat, B., & Brumer, H. (2019). A subfamily roadmap of the evolutionarily diverse glycoside hydrolase family 16 (GH16). Journal of Biological Chemistry, 294(44), 15973–15986. https://doi.org/10.1074/jbc.RA119.010619
dc.relation.referencesVranova, V., Rejsek, K., & Formanek, P. (2013). Proteolytic activity in soil: A review. Applied Soil Ecology, 70, 23–32. https://doi.org/10.1016/j.apsoil.2013.04.003
dc.relation.referencesWalsh, E., & McDonnell, K. P. (2012). The influence of added organic matter on soil physical, chemical, and biological properties: A small-scale and short-time experiment using straw. Archives of Agronomy and Soil Science, 58(SUPPL.), 17–20. https://doi.org/10.1080/03650340.2012.697999
dc.relation.referencesWang, M., Eyre, A. W., Thon, M. R., Oh, Y., & Dean, R. A. (2020). Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. Frontiers in Microbiology, 11(September), 1–21. https://doi.org/10.3389/fmicb.2020.559728
dc.relation.referencesWang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007). Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16), 5261–5267. https://doi.org/10.1128/AEM.00062-07
dc.relation.referencesWang, W., Luo, X., Chen, Y., Ye, X., Wang, H., Cao, Z., Ran, W., & Cui, Z. (2019). Succession of composition and function of soil bacterial communities during key rice growth stages. Frontiers in Microbiology, 10(MAR). https://doi.org/10.3389/fmicb.2019.00421
dc.relation.referencesWang, Y., Xu, L., Gu, Y. Q., & Coleman-Derr, D. (2016). MetaCoMET: A web platform for discovery and visualization of the core microbiome. Bioinformatics, 32(22), 3469–3470. https://doi.org/10.1093/bioinformatics/btw507
dc.relation.referencesWaqas, M., Khan, A. L., & Lee, I. J. (2014). Bioactive chemical constituents produced by endophytes and effects on rice plant growth. Journal of Plant Interactions, 9(1), 478–487. https://doi.org/10.1080/17429145.2013.860562
dc.relation.referencesWatanabe, T., Luu, H. M., Nguyen, N. H., Ito, O., & Inubushi, K. (2013). Combined effects of the continual application of composted rice straw and chemical fertilizer on rice yield under a double rice cropping system in the Mekong Delta, Vietnam. Japan Agricultural Research Quarterly, 47(4), 397–404. https://doi.org/10.6090/jarq.47.397
dc.relation.referencesWeber, S., Stubner, S., & Conrad, R. (2001). Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil. Applied and Environmental Microbiology, 67(3), 1318–1327. https://doi.org/10.1128/AEM.67.3.1318-1327.2001
dc.relation.referencesWilliams, R. J., Howe, A., & Hofmockel, K. S. (2014). Demonstrating microbial co-occurrence pattern analyses within and between ecosystems. Frontiers in Microbiology, 5(JULY), 1–10. https://doi.org/10.3389/fmicb.2014.00358
dc.relation.referencesWilson, G. W. T., Rice, C. W., Rillig, M. C., Springer, A., & Hartnett, D. C. (2009). Soil aggregation and carbon sequestration are tightly correlated with the abundance of arbuscular mycorrhizal fungi: Results from long-term field experiments. Ecology Letters, 12(5), 452–461. https://doi.org/10.1111/j.1461-0248.2009.01303.x
dc.relation.referencesWongwilaiwalin, S., Laothanachareon, T., Mhuantong, W., Tangphatsornruang, S., Eurwilaichitr, L., Igarashi, Y., & Champreda, V. (2013). Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia. Applied Microbiology and Biotechnology, 97(20), 8941–8954. https://doi.org/10.1007/s00253-013-4699-y
dc.relation.referencesWu, Y., Zaiden, N., & Cao, B. (2018). The core- and pan-genomic analyses of the genus Comamonas: From environmental adaptation to potential virulence. Frontiers in Microbiology, 9(DEC), 1–12. https://doi.org/10.3389/fmicb.2018.03096
dc.relation.referencesYadav, R., & Tarafdar, J. (2001). Influence of organic and inorganic phosphorus supply on the maximum secretion of acid phosphatase by plants. Biology and Fertility of Soils, 34(3), 140–143. https://doi.org/10.1007/s003740100376
dc.relation.referencesYadvinder-Singh, Bijay-Singh, & Timsina, J. (2005). Crop Residue Management for Nutrient Cycling and Improving Soil Productivity in Rice-Based Cropping Systems in the Tropics. Advances in Agronomy, 85, 269–407. https://doi.org/10.1016/S0065-2113(04)85006-5
dc.relation.referencesYao, H., Chen, X., Yang, J., Li, J., Hong, J., Hu, Y., & Mao, X. (2020). Effects and mechanisms of phosphate activation in paddy soil by phosphorus activators. Sustainability (Switzerland), 12(9), 1–15. https://doi.org/10.3390/su12093917
dc.relation.referencesYin, Y., Mao, X., Yang, J., Chen, X., Mao, F., & Xu, Y. (2012). DbCAN: A web resource for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 40(W1), 445–451. https://doi.org/10.1093/nar/gks479
dc.relation.referencesYoshida, M., Ishii, S., Otsuka, S., & Senoo, K. (2009). Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biology and Biochemistry, 41(10), 2044–2051. https://doi.org/10.1016/j.soilbio.2009.07.012
dc.relation.referencesYoung and Crawford. (2004). Interactions and Self-Organization in the Soil-Microbe Complex Author ( s ): I . M . Young and J . W . Crawford Published by : American Association for the Advancement of Science Stable URL : https://www.jstor.org/stable/3837024. 304(5677), 1634–1637.
dc.relation.referencesYu, Y., Wu, M., Petropoulos, E., Zhang, J., Nie, J., Liao, Y., Li, Z., Lin, X., & Feng, Y. (2019). Responses of paddy soil bacterial community assembly to different long-term fertilizations in southeast China. Science of the Total Environment, 656, 625–633. https://doi.org/10.1016/j.scitotenv.2018.11.359
dc.relation.referencesYuan, C. L., Zhang, L. M., Wang, J. T., Hu, H. W., Shen, J. P., Cao, P., & He, J. Z. (2019). Distributions and environmental drivers of archaea and bacteria in paddy soils. Journal of Soils and Sediments, 19(1), 23–37. https://doi.org/10.1007/s11368-018-1997-0
dc.relation.referencesYuan, C., Zhang, L., Hu, H., Wang, J., Shen, J., & He, J. (2018). The biogeography of fungal communities in paddy soils is mainly driven by geographic distance. Journal of Soils and Sediments, 18(5), 1795–1805. https://doi.org/10.1007/s11368-018-1924-4
dc.relation.referencesZang, X., Liu, M., Fan, Y., Xu, J., Xu, X., & Li, H. (2018). The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting. Biotechnology for Biofuels, 11(1), 1–13. https://doi.org/10.1186/s13068-018-1045-8
dc.relation.referencesZhan, Y., Liu, W., Bao, Y., Zhang, J., Petropoulos, E., Li, Z., Lin, X., & Feng, Y. (2018). Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation. Scientific Reports, 8(1), 1–10. https://doi.org/10.1038/s41598-018-26375-8
dc.relation.referencesZhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., & Yin, Y. (2018). dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Research, 46(W1), W95–W101. https://doi.org/10.1093/nar/gky418
dc.relation.referencesZhang, L., Chen, W., Burger, M., Yang, L., Gong, P., & Wu, Z. (2015). Changes in soil carbon and enzyme activity as a result of different long-term fertilization regimes in a greenhouse field. PLoS ONE, 10(2), 1–13. https://doi.org/10.1371/journal.pone.0118371
dc.relation.referencesZhang, L. M., Offre, P. R., He, J. Z., Verhamme, D. T., Nicol, G. W., & Prosser, J. I. (2010). Autotrophic ammonia oxidation by soil thaumarchaea. Proceedings of the National Academy of Sciences of the United States of America, 107(40), 17240–17245. https://doi.org/10.1073/pnas.1004947107
dc.relation.referencesZhang, Y., Schoch, C. L., Fournier, J., Crous, P. W., de Gruyter, J., Woudenberg, J. H. C., Hirayama, K., Tanaka, K., Pointing, S. B., Spatafora, J. W., & Hyde, K. D. (2009). Multi-locus phylogeny of Pleosporales: A taxonomic, ecological and evolutionary re-evaluation. Studies in Mycology, 64, 85–102. https://doi.org/10.3114/sim.2009.64.04
dc.relation.referencesZhao, X., Yuan, G., Wang, H., Lu, D., Chen, X., & Zhou, J. (2019). Effects of full straw incorporation on soil fertility and crop yield in rice-wheat rotation for silty clay loamy cropland. Agronomy, 9(3). https://doi.org/10.3390/agronomy9030133
dc.relation.referencesZheng, Y., Huang, R., Wang, B. Z., Bodelier, P. L. E., & Jia, Z. J. (2014). Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil. Biogeosciences, 11(12), 3353–3368. https://doi.org/10.5194/bg-11-3353-2014
dc.relation.referencesZhou-qi, C., Bo, Z., Guan-lin, X., Bin, L., & Shi-wen, H. (2016). Research Status and Prospect of Burkholderia glumae, the Pathogen Causing Bacterial Panicle Blight. Rice Science, 23(3), 111–118. https://doi.org/10.1016/j.rsci.2016.01.007
dc.relation.referencesZhou, J., Xue, K., Xie, J., Deng, Y., Wu, L., Cheng, X., Fei, S., Deng, S., He, Z., Van Nostrand, J. D., & Luo, Y. (2012). Microbial mediation of carbon-cycle feedbacks to climate warming. Nature Climate Change, 2(2), 106–110. https://doi.org/10.1038/nclimate1331
dc.relation.referencesZhu, H., Wang, Z. X., Luo, X. M., Song, J. X., & Huang, B. (2014). Effects of straw incorporation on Rhizoctonia solani inoculum in paddy soil and rice sheath blight severity. Journal of Agricultural Science, 152(5), 741–748. https://doi.org/10.1017/S002185961300035X
dc.relation.referencesZhu, L., Hu, N., Zhang, Z., Xu, J., Tao, B., & Meng, Y. (2015). Short-term responses of soil organic carbon and carbon pool management index to different annual straw return rates in a rice-wheat cropping system. Catena, 135, 283–289. https://doi.org/10.1016/j.catena.2015.08.008
dc.relation.referencesŽifčáková, L., Větrovský, T., Lombard, V., Henrissat, B., Howe, A., & Baldrian, P. (2017). Feed in summer, rest in winter: microbial carbon utilization in forest topsoil. Microbiome, 5(1), 122. https://doi.org/10.1186/s40168-017-0340-0
dc.rights.accessrightsinfo:eu-repo/semantics/openAccess
dc.subject.agrovocCascarilla de arroz
dc.subject.agrovocRice husks
dc.subject.agrovocEnmiendas del suelo
dc.subject.agrovocSoil amendments
dc.subject.agrovocBiotecnología vegetal
dc.subject.agrovocPlant biotechnology
dc.subject.proposalResiduos agrícolas
dc.subject.proposalDegradación
dc.subject.proposalEnzimas
dc.subject.proposalMicroorganismos
dc.subject.proposalCiclos biogeoquímicos
dc.subject.proposalTamo de arroz
dc.subject.proposalNGS
dc.subject.proposalAgricultural residues
dc.subject.proposalDegradation
dc.subject.proposalEnzymes
dc.subject.proposalMicroorganisms
dc.subject.proposalBiogeochemical cycles
dc.subject.proposalRice straw
dc.subject.proposalNext generation sequencing
dc.title.translatedDetermination of the effect of using rice straw on the structure and function of microbial community in rice crop soils
dc.type.coarhttp://purl.org/coar/resource_type/c_db06
dc.type.coarversionhttp://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.contentText
dc.type.redcolhttp://purl.org/redcol/resource_type/TD
oaire.accessrightshttp://purl.org/coar/access_right/c_abf2
oaire.fundernameMinciencias/Colciencias
oaire.fundernameUniversidad Nacional de Colombia
dcterms.audience.professionaldevelopmentEstudiantes
dcterms.audience.professionaldevelopmentInvestigadores
dcterms.audience.professionaldevelopmentMaestros
dcterms.audience.professionaldevelopmentMedios de comunicación
dcterms.audience.professionaldevelopmentPúblico general
dcterms.audience.professionaldevelopmentReceptores de fondos federales y solicitantes
dcterms.audience.professionaldevelopmentResponsables políticos


Archivos en el documento

Thumbnail

Este documento aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del documento

Atribución-NoComercial-SinDerivadas 4.0 InternacionalEsta obra está bajo licencia internacional Creative Commons Reconocimiento-NoComercial 4.0.Este documento ha sido depositado por parte de el(los) autor(es) bajo la siguiente constancia de depósito