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

Mostrar todas las versiones(2)

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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Godeas, Alicia Margarita, Novas, Maria Victoria, Iannone, Leopoldo Javier, Zelada, Alicia M., Pardo, Alejandro Guillermo, Mentaberry, Alejandro Néstor, Vazquez, Martín Pablo
Publicado:	2013
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:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20492618_v1_n1_p_Rascovan 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

id	paper:paper_20492618_v1_n1_p_Rascovan
record_format	dspace
spelling	paper:paper_20492618_v1_n1_p_Rascovan2023-06-08T16:33:49Z The PAMPA datasets: A metagenomic survey of microbial communities in Argentinean pampean soils Godeas, Alicia Margarita Novas, Maria Victoria Iannone, Leopoldo Javier Zelada, Alicia M. Pardo, Alejandro Guillermo Mentaberry, Alejandro Néstor Vazquez, Martín Pablo 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. 2013 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20492618_v1_n1_p_Rascovan 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 Godeas, Alicia Margarita Novas, Maria Victoria Iannone, Leopoldo Javier Zelada, Alicia M. Pardo, Alejandro Guillermo Mentaberry, Alejandro Néstor Vazquez, Martín Pablo 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.
author	Godeas, Alicia Margarita Novas, Maria Victoria Iannone, Leopoldo Javier Zelada, Alicia M. Pardo, Alejandro Guillermo Mentaberry, Alejandro Néstor Vazquez, Martín Pablo
author_facet	Godeas, Alicia Margarita Novas, Maria Victoria Iannone, Leopoldo Javier Zelada, Alicia M. Pardo, Alejandro Guillermo Mentaberry, Alejandro Néstor Vazquez, Martín Pablo
author_sort	Godeas, Alicia Margarita
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
publishDate	2013
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_20492618_v1_n1_p_Rascovan http://hdl.handle.net/20.500.12110/paper_20492618_v1_n1_p_Rascovan
work_keys_str_mv	AT godeasaliciamargarita thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT novasmariavictoria thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT iannoneleopoldojavier thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT zeladaaliciam thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT pardoalejandroguillermo thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT mentaberryalejandronestor thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT vazquezmartinpablo thepampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT godeasaliciamargarita pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT novasmariavictoria pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT iannoneleopoldojavier pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT zeladaaliciam pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT pardoalejandroguillermo pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT mentaberryalejandronestor pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils AT vazquezmartinpablo pampadatasetsametagenomicsurveyofmicrobialcommunitiesinargentineanpampeansoils
_version_	1768543346896142336

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

Ejemplares similares