1
|
Zambrano-Romero A, Ramirez-Villacis DX, Barriga-Medina N, Sierra-Alvarez R, Trueba G, Ochoa-Herrera V, Leon-Reyes A. Comparative Methods for Quantification of Sulfate-Reducing Bacteria in Environmental and Engineered Sludge Samples. Biology (Basel) 2023; 12:985. [PMID: 37508415 PMCID: PMC10375983 DOI: 10.3390/biology12070985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
This study aimed to compare microscopic counting, culture, and quantitative or real-time PCR (qPCR) to quantify sulfate-reducing bacteria in environmental and engineered sludge samples. Four sets of primers that amplified the dsrA and apsA gene encoding the two key enzymes of the sulfate-reduction pathway were initially tested. qPCR standard curves were constructed using genomic DNA from an SRB suspension and dilutions of an enriched sulfate-reducing sludge. According to specificity and reproducibility, the DSR1F/RH3-dsr-R primer set ensured a good quantification based on dsrA gene amplification; however, it exhibited inconsistencies at low and high levels of SRB concentrations in environmental and sulfate-reducing sludge samples. Ultimately, we conducted a qPCR method normalized to dsrA gene copies, using a synthetic double-stranded DNA fragment as a calibrator. This method fulfilled all validation criteria and proved to be specific, accurate, and precise. The enumeration of metabolically active SRB populations through culture methods differed from dsrA gene copies but showed a plausible positive correlation. Conversely, microscopic counting had limitations due to distinguishing densely clustered organisms, impacting precision. Hence, this study proves that a qPCR-based method optimized with dsrA gene copies as a calibrator is a sensitive molecular tool for the absolute enumeration of SRB populations in engineered and environmental sludge samples.
Collapse
Affiliation(s)
- Aracely Zambrano-Romero
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Dario X Ramirez-Villacis
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Noelia Barriga-Medina
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, The University of Arizona, P.O. Box 210011, Tucson, AZ 85721-0011, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Valeria Ochoa-Herrera
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles s/n y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
| |
Collapse
|
2
|
Ramirez-Villacis DX, Erazo-Garcia P, Quijia-Pillajo J, Llerena-Llerena S, Barriga-Medina N, Jones CD, Leon-Reyes A. Influence of Grafting on Rootstock Rhizosphere Microbiome Assembly in Rosa sp. 'Natal Brier'. Biology (Basel) 2023; 12:biology12050663. [PMID: 37237477 DOI: 10.3390/biology12050663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/18/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023]
Abstract
The root microbiome is vital in plant development and health and is highly influenced by crop cultural practices. Rose (Rosa sp.) is the most popular cut flower worldwide. Grafting in rose production is a standard practice to increase yield, improve flower quality, or reduce root-associated pests and diseases. 'Natal Brier' is a standard rootstock used in most commercial operations in Ecuador and Colombia, leading countries in producing and exporting ornamentals. It is known that the rose scion genotype affects root biomass and the root exudate profile of grafted plants. However, little is known about the influence of the rose scion genotype on the rhizosphere microbiome. We examined the influence of grafting and scion genotype on the rhizosphere microbiome of the rootstock 'Natal Brier'. The microbiomes of the non-grafted rootstock and the rootstock grafted with two red rose cultivars were assessed using 16S rRNA and ITS sequencing. Grafting changed microbial community structure and function. Further, analysis of grafted plant samples revealed that the scion genotype highly influences the rootstock microbiome. Under the presented experimental conditions, the rootstock 'Natal Brier' core microbiome consisted of 16 bacterial and 40 fungal taxa. Our results highlight that the scion genotype influences root microbe's recruitment, which might also influence the functionality of assembled microbiomes.
Collapse
Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Pablo Erazo-Garcia
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Juan Quijia-Pillajo
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH 43210, USA
| | - Sol Llerena-Llerena
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Noelia Barriga-Medina
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
| | - Corbin D Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito 170109, Ecuador
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| |
Collapse
|
3
|
Erazo-Garcia MP, Sotelo-Proaño AR, Ramirez-Villacis DX, Garcés-Carrera S, Leon-Reyes A. Methyl jasmonate-induced resistance to Delia platura (Diptera: Anthomyiidae) in Lupinus mutabilis. Pest Manag Sci 2021; 77:5382-5395. [PMID: 34313385 DOI: 10.1002/ps.6578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Andean lupin (Lupinus mutabilis Sweet) is an important leguminous crop from South America with a high protein content. In Ecuador, lupin yields are severely affected by the infestation of Delia platura larvae on germinating seeds. The application of elicitor molecules with activity against herbivorous insects to control D. platura infestation constitutes an unexplored and promising alternative for chemical insecticides. In this study, methyl jasmonate (MeJA), hexanoic acid, menadione sodium bisulfite, and DL-β-aminobutyric acid were evaluated for their ability to induce resistance against D. platura in three commercial lupin cultivars. RESULTS Only seeds pretreated with MeJA significantly impaired insect performance during choice and no-choice assays. Additionally, fitness indicators such as seed germination and growth were not affected by MeJA treatment. To investigate the molecular mechanisms behind the MeJA-mediated resistance, RT-qPCR assays were performed. First, RT-qPCR reference genes were validated, showing that LmUBC was the most stable reference gene. Next, expression analysis over time revealed that MeJA application up-regulated the activity of the jasmonic acid biosynthetic genes LmLOX2 and LmAOS, together with other jasmonate-related defense genes, such as LmTPS1, LmTPS4, LmPI2, LmMBL, LmL/ODC, LmCSD1, and LmPOD. CONCLUSION This study indicates that MeJA can be used as an environmentally friendly elicitor molecule to protect Andean lupin from D. platura attack without fitness cost. MeJA application induces plant defense responses to insects in Andean lupin that may be modulated by the onset of terpenoid biosynthesis, proteinase inhibitors, lectins, polyamines, and antioxidative enzymes. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Maria P Erazo-Garcia
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Adolfo R Sotelo-Proaño
- Laboratorio de Entomología, Departamento de Protección Vegetal, Estación Experimental Santa Catalina, Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sandra Garcés-Carrera
- Laboratorio de Entomología, Departamento de Protección Vegetal, Estación Experimental Santa Catalina, Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Colegio de Ciencias e Ingenierías-Ing. en Agronomía, Universidad San Francisco de Quito, Quito, Ecuador
| |
Collapse
|
4
|
Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:5/4/e00484-20. [PMID: 32817451 DOI: 10.46678/pb.20.1383160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
Collapse
Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
| |
Collapse
|
5
|
Ramirez-Villacis DX, Finkel OM, Salas-González I, Fitzpatrick CR, Dangl JL, Jones CD, Leon-Reyes A. Root Microbiome Modulates Plant Growth Promotion Induced by Low Doses of Glyphosate. mSphere 2020; 5:e00484-20. [PMID: 32817451 PMCID: PMC7426167 DOI: 10.1128/msphere.00484-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/23/2020] [Indexed: 01/22/2023] Open
Abstract
Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis We found that a dose of 3.6 × 10-6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains.IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
Collapse
Affiliation(s)
- Dario X Ramirez-Villacis
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos-Ingeniería en Agronomía, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Instituto de Microbiologia, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Galapagos Science Center, USFQ-UNC, San Cristobal, Galápagos, Ecuador
| |
Collapse
|