The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils

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 sti...

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Autores principales:	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.
Formato:	JOUR
Materias:	Amplicon sequencing Argentina Land use Pampas Shotgun metagenome sequencing Soil microbial communities complementary DNA DNA 16S RNA 16S agricultural procedures 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
Acceso en línea:	http://hdl.handle.net/20.500.12110/paper_20492618_v1_n1_p_Rascovan
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

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spelling	todo:paper_20492618_v1_n1_p_Rascovan2023-10-03T16:38:43Z The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils 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. 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 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. Fil:Godeas, A.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Novas, M.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Iannone, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Zelada, A.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Pardo, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Mentaberry, A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Vazquez, M.P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. JOUR info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar http://hdl.handle.net/20.500.12110/paper_20492618_v1_n1_p_Rascovan
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	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
spellingShingle	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 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
topic_facet	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
description	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.
format	JOUR
author	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.
author_facet	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.
author_sort	Rascovan, N.
title	The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
title_short	The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
title_full	The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
title_fullStr	The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
title_full_unstemmed	The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils
title_sort	pampa datasets: a metagenomic survey of microbial communities in argentinean pampean soils
url	http://hdl.handle.net/20.500.12110/paper_20492618_v1_n1_p_Rascovan
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The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils

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