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Perez-Bou L, Gonzalez-Martinez A, Cabrera JJ, Juarez-Jimenez B, Rodelas B, Gonzalez-Lopez J, Correa-Galeote D. Design and Validation of Primer Sets for the Detection and Quantification of Antibiotic Resistance Genes in Environmental Samples by Quantitative PCR. MICROBIAL ECOLOGY 2024; 87:71. [PMID: 38748252 PMCID: PMC11096201 DOI: 10.1007/s00248-024-02385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024]
Abstract
The high prevalence of antibiotic resistant bacteria (ARB) in several environments is a great concern threatening human health. Particularly, wastewater treatment plants (WWTP) become important contributors to the dissemination of ARB to receiving water bodies, due to the inefficient management or treatment of highly antibiotic-concentrated wastewaters. Hence, it is vital to develop molecular tools that allow proper monitoring of the genes encoding resistances to these important therapeutic compounds (antibiotic resistant genes, ARGs). For an accurate quantification of ARGs, there is a need for sensitive and robust qPCR assays supported by a good design of primers and validated protocols. In this study, eleven relevant ARGs were selected as targets, including aadA and aadB (conferring resistance to aminoglycosides); ampC, blaTEM, blaSHV, and mecA (resistance to beta-lactams); dfrA1 (resistance to trimethoprim); ermB (resistance to macrolides); fosA (resistance to fosfomycin); qnrS (resistance to quinolones); and tetA(A) (resistance to tetracyclines). The in silico design of the new primer sets was performed based on the alignment of all the sequences of the target ARGs (orthology grade > 70%) deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, allowing higher coverages of the ARGs' biodiversity than those of several primers described to date. The adequate design and performance of the new molecular tools were validated in six samples, retrieved from both natural and engineered environments related to wastewater treatment. The hallmarks of the optimized qPCR assays were high amplification efficiency (> 90%), good linearity of the standard curve (R2 > 0.980), repeatability and reproducibility across experiments, and a wide linear dynamic range. The new primer sets and methodology described here are valuable tools to upgrade the monitorization of the abundance and emergence of the targeted ARGs by qPCR in WWTPs and related environments.
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Affiliation(s)
- Lizandra Perez-Bou
- Environmental Microbiology Group, Department of Microbiology and Virology, Faculty of Biology, University of Havana, Havana, Cuba
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
| | - Alejandro Gonzalez-Martinez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan J Cabrera
- Nitrogen Metabolism Group, Zaidín Experimental Station, Spanish National Research Council, EEZ-CSIC, Granada, Spain
| | - Belen Juarez-Jimenez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Belen Rodelas
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jesus Gonzalez-Lopez
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - David Correa-Galeote
- Microbiology and Environmental Technologies Section, Water Research Institute, University of Granada, Granada, Spain.
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain.
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Chen T, Zhang Y, Xia M, Wang Q. Soil properties and functional genes in nitrogen removal process of bioretention. ENVIRONMENTAL TECHNOLOGY 2024; 45:2268-2283. [PMID: 36779295 DOI: 10.1080/09593330.2023.2172616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/09/2022] [Indexed: 06/18/2023]
Abstract
The effects of different soil properties on hydrology and nitrogen removal were studied in a simulated bioretention system. Soil capacity of permeability and water retention, changes in the soil environment, leachate concentrations at the surface and bottom layers, quantification of N removal from soil, microorganism and plant by 15N isotope tracer technique, and functional genes abundance at different depths were evaluated. The results showed that shallow root plants, soil compaction, and low organic matter content were not conducive to the infiltration of bioretention systems. In the 72 h experiment, compaction (especially surface compaction) and planting of herbaceous plants (Ophiopogon japonicus) were not beneficial to the removal of TN, TP, and COD. Adding an appropriate amount of organic matter also affects nitrogen and phosphorus removal. In the process of denitrification, the order of the ability to remove nitrogen is soil adsorption > microbial assimilation > plant uptake. The contribution of soil denitrification is affected by soil compaction, compaction location, plant species and organic matter content. The abundance of 16S rRNA, nitrifying, denitrifying and nrfA genes decreased with soil depth. More copies of genes in topsoil were thought to be due to sufficient nutrients, aerobic condition, anaerobic microsites and submerged state. Soil compaction, organic matter content and plant species affected nitrification, denitrification and DNRA gene characteristics.
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Affiliation(s)
- Tao Chen
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Yafu Zhang
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Mengmeng Xia
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
| | - Qianpeng Wang
- Key Laboratory of Urban Stormwater System and Water Environment (Ministry of Education), Beijing University of Civil Engineering and Architecture, Beijing, People's Republic of China
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Revealing the bacterial abundance and diversity in brines from started Spanish-style green table olives. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Garibay-Valdez E, Martínez-Córdova LR, López-Torres MA, Almendariz-Tapia FJ, Martínez-Porchas M, Calderón K. The implication of metabolically active Vibrio spp. in the digestive tract of Litopenaeus vannamei for its post-larval development. Sci Rep 2020; 10:11428. [PMID: 32651435 PMCID: PMC7351783 DOI: 10.1038/s41598-020-68222-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/11/2020] [Indexed: 11/19/2022] Open
Abstract
This work aimed to evaluate the link between the occurrence/abundance of Vibrio populations and bacterial composition in shrimp’s intestine (Litopenaeus vannamei) during post-larval ontogenetic development and in its culture water, and the correlation of these with environmental parameters. The total and metabolically active populations of Vibrio in the digestive tract of shrimp during its post-larval development were analysed using quantitative PCR (qPCR) and reverse transcription qPCR targeting the 16S rRNA gene sequence. A lab-scale shrimp bioassay was performed for 80 days in a recirculating aquarium under strictly controlled conditions. The results indicate that the Vibrio population from shrimp’s gut is associated with its developmental stage and the environment. Multivariate analyses revealed that the presence of Vibrio spp. drove the studied system, but their metabolically active performance was related to earlier developmental stages in an aqueous environment. Also, the samples taken from water of culture units to compare the influence of the aquatic environment on the intestinal microbial community during shrimp’s ontogenetic development showed significant differences. Finally, our results revealed that Vibrio is an important member of shrimp’s gut microbiota; however, its metabolic activity seems to be highly regulated, possibly by the host and by the rest of the microbiota.
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Affiliation(s)
- Estefanía Garibay-Valdez
- Centro de Investigación en Alimentos y Desarrollo A.C (CIAD), Carretera a La Victoria S/N, CP. 83304, Hermosillo, Sonora, Mexico
| | - Luis Rafael Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N, CP. 83000, Hermosillo, Sonora, Mexico
| | - Marco A López-Torres
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N, CP. 83000, Hermosillo, Sonora, Mexico
| | - F Javier Almendariz-Tapia
- Departamento de Ingeniería Química y Metalurgia, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N, CP. 83000, Hermosillo, Sonora, Mexico
| | - Marcel Martínez-Porchas
- Centro de Investigación en Alimentos y Desarrollo A.C (CIAD), Carretera a La Victoria S/N, CP. 83304, Hermosillo, Sonora, Mexico
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas (DICTUS), Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N, CP. 83000, Hermosillo, Sonora, Mexico.
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Amberkar U, Khandeparker R, Parab P. Nitrate Reductase Gene Expression in Idiomarina Strain cos21 Obtained from Oxygen Minimum Zone of Arabian Sea. Curr Microbiol 2018; 76:63-69. [DOI: 10.1007/s00284-018-1585-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
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Correa-Galeote D, Bedmar EJ, Arone GJ. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History. Front Microbiol 2018; 9:484. [PMID: 29662471 PMCID: PMC5890191 DOI: 10.3389/fmicb.2018.00484] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/28/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterial endophytic communities residing within roots of maize (Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Gregorio J Arone
- Department of Agricultural Sciences, National University of Huancavelica, Huancavelica, Peru
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Torralbo F, Menéndez S, Barrena I, Estavillo JM, Marino D, González-Murua C. Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N 2O emission. Sci Rep 2017; 7:13810. [PMID: 29062007 PMCID: PMC5653738 DOI: 10.1038/s41598-017-14225-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/06/2017] [Indexed: 11/09/2022] Open
Abstract
Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2 by nitrous oxide reductase during the denitrification process.
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Affiliation(s)
- Fernando Torralbo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - Sergio Menéndez
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Iskander Barrena
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - José M Estavillo
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Carmen González-Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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Correa-Galeote D, Bedmar EJ, Fernández-González AJ, Fernández-López M, Arone GJ. Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:1016. [PMID: 27524985 PMCID: PMC4966391 DOI: 10.3389/fpls.2016.01016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/27/2016] [Indexed: 05/05/2023]
Abstract
Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize intercropped with bur clover, and Gp4, Subdivision3 genera incertae sedis of phylum Verrucomicrobia, Gp6 and Rhodoferax were the main genera in the rhizosphere of maize plants. Taken together, our results suggest that bur clover produces specific changes in rhizospheric bacterial diversity of amilaceous maize plants.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
- *Correspondence: David Correa-Galeote, Eulogio J. Bedmar,
| | - Eulogio J. Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
- *Correspondence: David Correa-Galeote, Eulogio J. Bedmar,
| | - Antonio J. Fernández-González
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Manuel Fernández-López
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones CientíficasGranada, Spain
| | - Gregorio J. Arone
- Department of Agricultural Sciences, National University of HuancavelicaHuancavelica, Peru
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Eggleston EM, Lee DY, Owens MS, Cornwell JC, Crump BC, Hewson I. Key respiratory genes elucidate bacterial community respiration in a seasonally anoxic estuary. Environ Microbiol 2015; 17:2306-18. [DOI: 10.1111/1462-2920.12690] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/03/2014] [Indexed: 11/29/2022]
Affiliation(s)
| | - Dong Y. Lee
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Michael S. Owens
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Jeffrey C. Cornwell
- Horn Point Laboratory; University of Maryland Center for Environmental Science; Cambridge MD USA
| | - Byron C. Crump
- College of Earth, Ocean and Atmospheric Sciences; Oregon State University; Corvallis OR USA
| | - Ian Hewson
- Department of Microbiology; Cornell University; Ithaca NY USA
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