Published July 6, 2022
| Version Version 1.0
Dataset
Open
A georeferenced rRNA amplicon database of aquatic microbiomes from South America
Creators
- Sebastian Metz1
- Paula Huber2
- Erick Mateus-Barros3
- Pedro C. Junger3
- Michaela de Melo4
- Inessa Lacativa Bagatini5
- Irina Izaguirre6
- Mariana Câmara dos Reis7
- Maria E. Llames8
- Victoria Accattatis9
- María Victoria Quiroga8
- Melina Devercelli9
- María Romina Schiaffino10
- Juan Pablo Niño-García11
- Marcela Bastidas Navarro12
- Beatriz Modenutti12
- Helena Vieira13
- Martin Saraceno6
- Carmen Sabio y García6
- Emiliano Pereira14
- Alvaro González-Revello15
- Claudia Piccini16
- Fernando Unrein8
- Cecilia Alonso14
- Hugo Sarmento17
- 1. Laboratorio de Ecología Acuática, Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina., 2. University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France.
- 2. Laboratorio de Plancton Instituto Nacional de Limnología (INALI), CONICET-UNL. Ciudad Universitaria, Paraje El Pozo, C. P. 3000 Santa Fe, Argentina. Laboratory of Microbial Processes & Biodiversity, Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil
- 3. Laboratory of Microbial Processes & Biodiversity, Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil
- 4. Laboratory of Microbial Processes & Biodiversity, Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil. 5. University of Quebec at Montreal, Department of Biological Science. Centre-Ville, C.P. 8888, Montreal (Quebec), Canada.
- 5. Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil.
- 6. Depto. de Ecología, Genética y Evolución, IEGEBA (UBA-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA). Intendente Güiraldes 2160, C1428EHA, Buenos Aires, Argentina.
- 7. Laboratory of Microbial Processes & Biodiversity, Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil. 8. Sorbonne Université/Centre National de la Recherche Scientifique, UMR 7144, Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff. Place Georges Teissier, Roscoff, France.
- 8. Laboratorio de Ecología Acuática, Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET. Av. Intendente Marino Km 8.200, (7130) Chascomús, Buenos Aires, Argentina.
- 9. Laboratorio de Plancton Instituto Nacional de Limnología (INALI), CONICET-UNL. Ciudad Universitaria, Paraje El Pozo, C. P. 3000 Santa Fe, Argentina.
- 10. Departamento de Ciencias Básicas y Experimentales, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA). Roque Sáenz Peña 456, 6000, Junín, Argentina. 10. Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) – UNNOBA-UNSAdA-CONICET. Monteagudo 2772, 2700, Buenos Aires, Argentina.
- 11. Escuela de Microbiología, Universidad de Antioquia. Cl. 67 ##53-108, Medellín, Antioquia, Colombia.
- 12. Instituto de Investigaciones en Biodiversidad y Medio Ambiente (INIBIOMA), CONICET-Universidad Nacional del Comahue. Quintral 1250, R8400 San Carlos de Bariloche, Río Negro, Argentina.
- 13. Laboratório de Ficologia, Departamento de Botânica, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil. 13. Czech Academy of Sciences, Biology Centre, Hydrobiology Institute. Na Sádkách 702/7, 370 05, Ceske Budejovice, Czech.
- 14. Centro Universitario Regional del Este. Universidad de la República. Ruta nacional Nº 9 intersección con ruta Nº15, CP 270000, Rocha, Uruguay.
- 15. Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Veterinaria, UDELAR. Alberto Lasplaces 1620, CP 11600, Montevideo, Uruguay. Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, MEC. Av. Italia 3318, 11600 Montevideo, Departamento de Montevideo, Uruguay.
- 16. Laboratorio de Ecología Microbiana Acuática, Departamento de Microbiología, Instituto de Investigaciones Biológicas Clemente Estable, MEC. Av. Italia 3318, 11600 Montevideo, Departamento de Montevideo, Uruguay.
- 17. Laboratory of Microbial Processes & Biodiversity, Departamento de Hydrobiologia, Universidade Federal de São Carlos (UFSCar). Rodovia Washington Luiz, São Carlos, São Paulo 13565-905, Brazil.
Description
Here we present the samples and data used in Metz & Huber et al. (2022) to construct µSudAqua[db].
µSudAqua[db] contains over 866 georeferenced samples with contextual environmental information manually revised. For its integration and validation, we constructed a curated database (µSudAqua[db.sp]) using the DADA2 pipeline (https://github.com/microsudaqua/usudaquadb). It comprised ~60% of the total georeferenced samples of the µSudAqua[db].
Here we provide five files compressed in a zip file (microsudaqua_data_V1.0_July2022.zip).
- The microsudaqua_metadata_V1.0_July2022.tsv presents the metadata associated with the samples used to build the µSudAqua[db] database. For samples included in the µSudAqua[db.sp] database, the number of high-quality reads and Amplicon Sequences Variants (ASVs) defined is also indicated.
- The archive microsudaqua_rawtable_V1.0_July2022.tsv harvests the number of reads in each sample (µSudAqua[db.sp]).
- The archive microsudaqua_rawseqs_V1.0_July2022.fasta harvests the nucleotide sequences of each ASV (µSudAqua[db.sp]).
- The archive microsudaqua_rawtaxonomy_blast_silva132_nr99_V1.0_July2022.tsv harvests taxonomic classification of each ASV (µSudAqua[db.sp]).
- The archive microsudaqua_bacteria_filtered_50reads_with_taxonomy_V1.0_July2022.tsv harvests the Bacterial filtered ASVs, with more than 50 reads in at least three samples (µSudAqua[db.sp]).
Further information regarding data usage and processing is available in the @microsudaqua GitHub (https://github.com/microsudaqua/usudaquadb)
Notes
This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.
This work was funded by the São Paulo Research Foundation (Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP process: 20/03716-0). We would like to acknowledge to the technician of the Pirayu Cluster. The samples from the µSudAqua project were analyzed using computational resurce of the Pirayu cluster, which was funded by Agencia Santafesina de Ciencia, Tecnología e Innovación (ASACTEI), Gobierno de la Provincia de Santa Fe, through the project AC-00010-18, Resolución No117/14. This cluster is part of the Sistema Nacional de Computación de Alto Desempeño del Min. Ciencia y Tecnología de la Rep. Argentina.
Files
microsudaqua_data_V1.0_July2022.zip
Files
(22.2 MB)
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Additional details
Related works
- Cites
- Workflow: https://github.com/microsudaqua/usudaquadb (URL)