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Sánchez-Sánchez C, Aranda-Medina M, Rodríguez A, Hernández A, Córdoba MG, Cuadros-Blázquez F, Ruiz-Moyano S. Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion. J Microbiol Methods 2022; 199:106529. [PMID: 35772572 DOI: 10.1016/j.mimet.2022.106529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/18/2022] [Accepted: 06/22/2022] [Indexed: 12/27/2022]
Abstract
Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditions to detect Methanosarcina, Methanoculleus and Methanobacterium by real-time PCR based on the SYBR Green System. The functionality of the developed methods was demonstrated by the high linear relationship of the standard curves, and the specificity of each primer was empirically verified by testing DNA isolated from methane-producing and non-producing strains. These assays also exhibited good repeatability and reproducibility, which indicates the robustness of the methods. The described primers were successfully used to investigate the methanogenic communities of 10 samples from an anaerobic co-digestion. The genus Methanosarcina was the dominant methanogenic group.
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Affiliation(s)
- Consolación Sánchez-Sánchez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Mercedes Aranda-Medina
- Expresión Gráfica, Escuela de Ingenierías Industriales, Campus Universitario, Avda de Elvas sn, 06006 Badajoz, Spain
| | - Alicia Rodríguez
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain.
| | - Alejandro Hernández
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - María G Córdoba
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
| | - Francisco Cuadros-Blázquez
- Departamento de Física Aplicada, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda, de Adolfo Suárez S/n, 06007 Badajoz, Spain
| | - Santiago Ruiz-Moyano
- Instituto Universitario de Investigación de Recursos Agrarios (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, Avda. Adolfo Suarez, s/n, 06071 Badajoz, Spain
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Phylodynamics of Alagoas vesiculovirus in Brazil. Braz J Microbiol 2022; 53:1691-1699. [PMID: 35553417 PMCID: PMC9433616 DOI: 10.1007/s42770-022-00756-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/10/2022] [Indexed: 11/02/2022] Open
Abstract
The vesicular stomatitis virus belongs to the Rhabdoviridae family, genus Vesiculovirus. Four species (New Jersey, Indiana, Cocal, and Alagoas) are responsible for disease outbreaks in Western Hemisphere countries. In Brazil, the Alagoas virus is responsible for the main outbreaks of the disease, mainly in the states of the Northeast, Midwest, and Southeast regions of the country. The present study aimed to perform the genetic characterization of 41 vesicular stomatitis virus samples. RNA was extracted using Trizol and used to amplify part of gene P. Amplicons were sequenced using the Sanger method. The phylogenetic trees generated showed that Alagoas vesiculoviruses were positioned into three groups: group A formed by the first virus isolate; group B by isolates from states in the Northeast region; and group C by isolates from the states of Bahia, Goiás, and Tocantins. Their divergence to date has generated the formation of two genotypes evolving independently in regions that until the present study had little geographic overlap.
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de Oliveira Lopes GA, Ferreira LR, de Souza Trindade G, Fonseca AA, Dos Reis JKP. qPCR assay for the detection of pseudocowpox virus. Arch Virol 2020; 166:243-247. [PMID: 33159590 DOI: 10.1007/s00705-020-04872-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
Abstract
Pseudocowpox is a zoonosis caused by pseudocowpox virus (PCPV), which mainly affects cows but can be an occupational disease of humans. The aim of the study was to validate a quantitative polymerase chain reaction (qPCR) assay for the detection of PCPV. The assay was able to detect up to 1000 copies of PCPV per µL in field samples, with a sensitivity of 80% and a specificity of 100%. We did not observe any cross-reactivity between PCPV-positive samples and samples that were positive for other genetically similar viruses. The repeatability and reproducibility were adequate according to parameters preestablished in official test validation manuals.
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Affiliation(s)
- Gabriel Augusto de Oliveira Lopes
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Laboratório Federal de Defesa Agropecuária, Pedro Leopoldo, Brazil
| | | | - Giliane de Souza Trindade
- Departamento de Microbiologia, Instituto de Ciencias Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Jenner Karlisson Pimenta Dos Reis
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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