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Rascovan, N.; Carbonetto, B.; Revale, S.; Reinert, M.D.; Alvarez, R.; Godeas, A.M.; Colombo, R.; Aguilar, M.; Novas, M.V.; Iannone, L.; Zelada, A.M.; Pardo, A.; Schrauf, G.; Mentaberry, A.; Vazquez, M.P. "The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils" (2013) Microbiome. 1(1)
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Abstract:

Background: Soil is among the most diverse and complex environments in the world. Soil microorganisms play an essential role in biogeochemical cycles and affect plant growth and crop production. However, our knowledge of the relationship between species-assemblies and soil ecosystem processes is still very limited. The aim of this study was to generate a comprehensive metagenomic survey to evaluate the effect of high-input agricultural practices on soil microbial communities. Results: We collected soil samples from three different areas in the Argentinean Pampean region under three different types of land uses and two soil sources (bulk and rhizospheric). We extracted total DNA from all samples and also synthetized cDNA from rhizospheric samples. Using 454-FLX technology, we generated 112 16S ribosomal DNA and 14 16S ribosomal RNA amplicon libraries totaling 1.3 M reads and 36 shotgun metagenome libraries totaling 17.8 million reads (7.7 GB). Our preliminary results suggested that water availability could be the primary driver that defined microbial assemblages over land use and soil source. However, when water was not a limiting resource (annual precipitation >800 mm) land use was a primary driver. Conclusion: This was the first metagenomic study of soil conducted in Argentina and our datasets are among the few large soil datasets publicly available. The detailed analysis of these data will provide a step forward in our understanding of how soil microbiomes respond to high-input agricultural systems, and they will serve as a useful comparison with other soil metagenomic studies worldwide. © 2013 Rascovan et al.; licensee BioMed Central Ltd.

Registro:

Documento: Artículo
Título:The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
Autor:Rascovan, N.; Carbonetto, B.; Revale, S.; Reinert, M.D.; Alvarez, R.; Godeas, A.M.; Colombo, R.; Aguilar, M.; Novas, M.V.; Iannone, L.; Zelada, A.M.; Pardo, A.; Schrauf, G.; Mentaberry, A.; Vazquez, M.P.
Filiación:Instituto de Agrobiotecnología de Rosario (INDEAR), Predio CCT Rosario, Ocampo 210 bis, Santa Fe 2000, Argentina
Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martin 4453, Buenos Aires 1417, Argentina
Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 4to Piso, Pabellón 2, Buenos Aires 1428, Argentina
Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-16 CONICET, La Plata, Argentina
Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 4to Piso, Pabellón 2, Buenos Aires 1428, Argentina
Laboratorio de Agrobiotecnología, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
Consejo Nacional de Investigaciones Cientificas y Técnicas (CONICET), Ciudad Universitaria, Intendente Güiraldes 2160, Buenos Aires 1428, Argentina
Laboratorio de Micología Molecular, Departmento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Consejo Nacional de Investigaciones Cientificas y Técnicas (CONICET), Roque Saenz Peña 352 Bernal, Buenos Aires B1876BXD, Argentina
Palabras clave:Amplicon sequencing; Argentina; Land use; Pampas; Shotgun metagenome sequencing; Soil microbial communities; complementary DNA; DNA 16S; RNA 16S; agricultural procedures; Argentina; article; data analysis; data base; DNA extraction; gene sequence; information processing; metagenomics; microbial community; nonhuman; polymerase chain reaction; principal component analysis; priority journal; quality control; soil analysis; soil microflora
Año:2013
Volumen:1
Número:1
DOI: http://dx.doi.org/10.1186/2049-2618-1-21
Título revista:Microbiome
Título revista abreviado:Microbiome
ISSN:20492618
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20492618_v1_n1_p_Rascovan

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Citas:

---------- APA ----------
Rascovan, N., Carbonetto, B., Revale, S., Reinert, M.D., Alvarez, R., Godeas, A.M., Colombo, R.,..., Vazquez, M.P. (2013) . The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils. Microbiome, 1(1).
http://dx.doi.org/10.1186/2049-2618-1-21
---------- CHICAGO ----------
Rascovan, N., Carbonetto, B., Revale, S., Reinert, M.D., Alvarez, R., Godeas, A.M., et al. "The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils" . Microbiome 1, no. 1 (2013).
http://dx.doi.org/10.1186/2049-2618-1-21
---------- MLA ----------
Rascovan, N., Carbonetto, B., Revale, S., Reinert, M.D., Alvarez, R., Godeas, A.M., et al. "The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils" . Microbiome, vol. 1, no. 1, 2013.
http://dx.doi.org/10.1186/2049-2618-1-21
---------- VANCOUVER ----------
Rascovan, N., Carbonetto, B., Revale, S., Reinert, M.D., Alvarez, R., Godeas, A.M., et al. The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils. Microbiome. 2013;1(1).
http://dx.doi.org/10.1186/2049-2618-1-21