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Caldara M, Gullì M, Graziano S, Riboni N, Maestri E, Mattarozzi M, Bianchi F, Careri M, Marmiroli N. Microbial consortia and biochar as sustainable biofertilisers: Analysis of their impact on wheat growth and production. Sci Total Environ 2024; 917:170168. [PMID: 38244628 DOI: 10.1016/j.scitotenv.2024.170168] [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: 09/05/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024]
Abstract
The European Union is among the top wheat producers in the world, but its productivity relies on adequate soil fertilisation. Biofertilisers, either alone or in combination with biochar, can be a preferable alternative to chemical fertilisers. However, the addition of biofertilisers, specifically plant growth promoting microbes (PGPM), could modify grain composition, and/or deteriorate the soil composition. In this study, the two wheat cultivars Triticum aestivum (Bramante) and T. durum (Svevo) were cultivated in open fields for two consecutive years in the presence of a commercial PGPM mix supplied alone or in combination with biochar. An in-depth analysis was conducted by collecting physiological and agronomic data throughout the growth period. The effects of PGPM and biochar were investigated in detail; specifically, soil chemistry and rhizosphere microbial composition were characterized, along with the treatment effects on seed storage proteins. The results demonstrated that the addition of commercial microbial consortia and biochar, alone or in combination, did not modify the rhizospheric microbial community; however, it increased grain yield, especially in the cultivar Svevo (increase of 6.8 %-13.6 %), even though the factors driving the most variations were associated with both climate and cultivar. The total gluten content of the flours was not affected, whereas the main effect of the treatments was a variation in gliadins and low-molecular-weight-glutenin subunits in both cultivars when treated with PGPM and biochar. This suggested improved grain quality, especially regarding the viscoelastic properties of the dough, when the filling period occurred in a dry climate. The results indicate that the application of biofertilisers and biochar may aid the effective management of sustainable wheat cultivation, to support environmental health without altering the biodiversity of the resident microbiome.
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Affiliation(s)
- Marina Caldara
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Sara Graziano
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Nicolò Riboni
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Federica Bianchi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze, 43124 Parma, Italy.
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2
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Riboni N, Bianchi F, Mattarozzi M, Caldara M, Gullì M, Graziano S, Maestri E, Marmiroli N, Careri M. Ultra-high Performance Liquid Chromatography-Ion Mobility-High-Resolution Mass Spectrometry to Evaluate the Metabolomic Response of Durum Wheat to Sustainable Treatments. J Agric Food Chem 2023; 71:15407-15416. [PMID: 37796632 PMCID: PMC10591464 DOI: 10.1021/acs.jafc.3c04532] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/07/2023]
Abstract
Sustainable agriculture aims at achieving a healthy food production while reducing the use of fertilizers and greenhouse gas emissions using biostimulants and soil amendments. Untargeted metabolomics by ultra-high performance liquid chromatography-ion mobility-high-resolution mass spectrometry, operating in a high-definition MSE mode, was applied to investigate the metabolome of durum wheat in response to sustainable treatments, i.e., the addition of biochar, commercial plant growth promoting microbes, and their combination. Partial least squares-discriminant analysis provided a good discrimination among treatments with sensitivity, specificity, and a non-error rate close to 1. A total of 88 and 45 discriminant compounds having biological, nutritional, and technological implications were tentatively identified in samples grown in 2020 and 2021. The addition of biochar-biostimulants produced the highest up-regulation of lipids and flavonoids, with the glycolipid desaturation being the most impacted pathway, whereas carbohydrates were mostly down-regulated. The findings achieved suggest the safe use of the combined biochar-biostimulant treatment for sustainable wheat cultivation.
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Affiliation(s)
- Nicolò Riboni
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
| | - Federica Bianchi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Center
for Energy and Environment (CIDEA), Centro Santa Elisabetta, University of Parma, Parco Area delle Scienze 95, 43124 Parma, Italy
| | - Monica Mattarozzi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Marina Caldara
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
| | - Mariolina Gullì
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Sara Graziano
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Elena Maestri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Centro
Santa Elisabetta, National Interuniversity
Center for Environmental Sciences (CINSA), Parco Area delle Scienze 95, 43124 Parma, Italy
| | - Maria Careri
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A-17/A, 43124 Parma, Italy
- Interdepartmental
Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
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3
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Pavlicevic M, Elmer W, Zuverza-Mena N, Abdelraheem W, Patel R, Dimkpa C, O'Keefe T, Haynes CL, Pagano L, Caldara M, Marmiroli M, Maestri E, Marmiroli N, White JC. Nanoparticles and biochar with adsorbed plant growth-promoting rhizobacteria alleviate Fusarium wilt damage on tomato and watermelon. Plant Physiology and Biochemistry 2023; 203:108052. [PMID: 37778113 DOI: 10.1016/j.plaphy.2023.108052] [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: 06/10/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/03/2023]
Abstract
The addition of biochars and nanoparticles with adsorbed Azotobacter vinelandii and Bacillus megaterium alleviated damage from Fusarium infection in both tomato (Solanum lycopersicum) and watermelon (Citrullus lanatus) plants. Tomato and watermelon plants were grown in greenhouse for 28 and 30 days (respectively) and were treated with either nanoparticles (chitosan-coated mesoporous silica or nanoclay) or varying biochars (biochar produced by pyrolysis, gasification and pyrogasification). Treatments with nanoparticles and biochars were applied in two variants - with or without adsorbed plant-growth promoting bacteria (PGPR). Chitosan-coated mesoporous silica nanoparticles with adsorbed bacteria increased chlorophyll content in infected tomato and watermelon plants (1.12 times and 1.63 times, respectively) to a greater extent than nanoclay with adsorbed bacteria (1.10 times and 1.38 times, respectively). However, the impact on other endpoints (viability of plant cells, phosphorus and nitrogen content, as well antioxidative status) was species-specific. In all cases, plants treated with adsorbed bacteria responded better than plants without bacteria. For example, the content of antioxidative compounds in diseased watermelon plants increased nearly 46% upon addition of Aries biochar and by approximately 52% upon addition of Aries biochar with adsorbed bacteria. The overall effect on disease suppression was due to combination of the antifungal effects of both nanoparticles (and biochars) and plant-growth promoting bacteria. These findings suggest that nanoparticles or biochars with adsorbed PGPR could be viewed as a novel and sustainable solution for management of Fusarium wilt.
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Affiliation(s)
- Milica Pavlicevic
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Wade Elmer
- Connecticut Agricultural Experimental Station, New Haven, CT, USA.
| | | | - Wael Abdelraheem
- Connecticut Agricultural Experimental Station, New Haven, CT, USA; Chemistry Department, Faculty of Science, Sohag University, Sohag 82524, Egypt.
| | - Ravikumar Patel
- Connecticut Agricultural Experimental Station, New Haven, CT, USA.
| | - Christian Dimkpa
- Connecticut Agricultural Experimental Station, New Haven, CT, USA.
| | - Tana O'Keefe
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
| | - Christy L Haynes
- Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
| | - Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy.
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy; Interdepartmental Center SITEIA.PARMA, University of Parma, Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parma, Italy.
| | - Jason C White
- Connecticut Agricultural Experimental Station, New Haven, CT, USA.
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Pavlicevic M, Abdelraheem W, Zuverza-Mena N, O’Keefe T, Mukhtar S, Ridge G, Ranciato J, Haynes C, Elmer W, Pignatello J, Pagano L, Caldara M, Marmiroli M, Maestri E, Marmiroli N, White JC. Engineered Nanoparticles, Natural Nanoclay and Biochar, as Carriers of Plant-Growth Promoting Bacteria. Nanomaterials (Basel) 2022; 12:4474. [PMID: 36558327 PMCID: PMC9783841 DOI: 10.3390/nano12244474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The potential of biochar and nanoparticles to serve as effective delivery agents for beneficial bacteria to crops was investigated. Application of nanoparticles and biochar as carriers for beneficial bacteria improved not only the amount of nitrogen-fixing and phosphorus-solubilizing bacteria in soil, but also improved chlorophyll content (1.2-1.3 times), cell viability (1.1-1.5 times), and antioxidative properties (1.1-1.4 times) compared to control plants. Treatments also improved content of phosphorus (P) (1.1-1.6 times) and nitrogen (N) (1.1-1.4 times higher) in both tomato and watermelon plants. However, the effect of biochars and nanoparticles were species-specific. For example, chitosan-coated mesoporous silica nanoparticles with adsorbed bacteria increased the phosphorus content in tomato by 1.2 times compared to a 1.1-fold increase when nanoclay with adsorbed bacteria was applied. In watermelon, the situation was reversed: 1.1-fold increase in the case of chitosan-coated mesoporous silica nanoparticles and 1.2 times in case of nanoclay with adsorbed bacteria. Our findings demonstrate that use of nanoparticles and biochar as carriers for beneficial bacteria significantly improved plant growth and health. These findings are useful for design and synthesis of novel and sustainable biofertilizer formulations.
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Affiliation(s)
- Milica Pavlicevic
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Wael Abdelraheem
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
- Chemistry Department, Faculty of Science, Sohag University, Sohag 82524, Egypt
| | | | - Tana O’Keefe
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Salma Mukhtar
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
| | - Gale Ridge
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
| | - John Ranciato
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
| | - Christy Haynes
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wade Elmer
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
| | - Joseph Pignatello
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
| | - Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Center SITEIA.PARMA, University of Parma, 43124 Parma, Italy
- National Interuniversity Consortium for Environmental Sciences (CINSA), 43124 Parma, Italy
| | - Jason C. White
- Connecticut Agricultural Experimental Station, New Haven, CT 06511, USA
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5
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Marmiroli M, Caldara M, Pantalone S, Malcevschi A, Maestri E, Keller AA, Marmiroli N. Building a risk matrix for the safety assessment of wood derived biochars. Sci Total Environ 2022; 839:156265. [PMID: 35643132 DOI: 10.1016/j.scitotenv.2022.156265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/04/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Biochar is recognized as an efficient amendment and soil improver. However, environmental and quality assessments are needed to ensure the sustainability of its use in agriculture. This work considers the biochar's chemical-physical characterization and its potential phyto- and geno-toxicity, assessed with germination and Ames tests, obtaining valuable information for a safe field application. Three biochar types, obtained from gasification at different temperatures of green biomasses from the Tuscan-Emilian Apennines (in Italy), were compared through a broad chemical, physical and biological evaluation. The results obtained showed the relevance of temperature in determining the chemical and morphological properties of biochar, which was shown with several analytical techniques such as the elemental composition, water holding capacity, ash content, but also with FTIR and X-ray spectroscopies. These techniques showed the presence of different relevant surface aliphatic and aromatic groups. The procedures for evaluating the potential toxicity using seeds germination and Ames genotoxicity assay highlights that biochar does not cause detrimental effects when it enters in contact with soil, micro- and macro-organisms, and plants. The genotoxicity test provided a new highlight in evaluating biochar environmental safety.
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Affiliation(s)
- Marta Marmiroli
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Marina Caldara
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Serena Pantalone
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Alessio Malcevschi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Arturo A Keller
- Bren School of Environmental Science & Management, University of California Center for Environmental Implications of Nanotechnology, University of California, Santa Barbara, CA 93106-5131, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; Interdepartmental Centers SITEIA.PARMA and CIDEA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy; National Interuniversity Consortium for Environmental Sciences (CINSA), Parco Area delle Scienze, 43124 Parma, Italy.
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Graziano S, Caldara M, Gullì M, Bevivino A, Maestri E, Marmiroli N. A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar. Int J Mol Sci 2022; 23:ijms231810376. [PMID: 36142289 PMCID: PMC9499264 DOI: 10.3390/ijms231810376] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.
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Affiliation(s)
- Sara Graziano
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
| | - Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Mariolina Gullì
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA Casaccia Research Center, 00123 Rome, Italy
| | - Elena Maestri
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Nelson Marmiroli
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze, 43124 Parma, Italy
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
- National Interuniversity Consortium for Environmental Sciences (CINSA), 30123 Venice, Italy
- Correspondence:
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Caldara M, Belgiovine C, Secchi E, Rusconi R. Environmental, Microbiological, and Immunological Features of Bacterial Biofilms Associated with Implanted Medical Devices. Clin Microbiol Rev 2022; 35:e0022120. [PMID: 35044203 PMCID: PMC8768833 DOI: 10.1128/cmr.00221-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The spread of biofilms on medical implants represents one of the principal triggers of persistent and chronic infections in clinical settings, and it has been the subject of many studies in the past few years, with most of them focused on prosthetic joint infections. We review here recent works on biofilm formation and microbial colonization on a large variety of indwelling devices, ranging from heart valves and pacemakers to urological and breast implants and from biliary stents and endoscopic tubes to contact lenses and neurosurgical implants. We focus on bacterial abundance and distribution across different devices and body sites and on the role of environmental features, such as the presence of fluid flow and properties of the implant surface, as well as on the interplay between bacterial colonization and the response of the human immune system.
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Affiliation(s)
- Marina Caldara
- Interdepartmental Center on Safety, Technologies, and Agri-food Innovation (SITEIA.PARMA), University of Parma, Parma, Italy
| | - Cristina Belgiovine
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Scuola di Specializzazione in Microbiologia e Virologia, Università degli Studi di Pavia, Pavia, Italy
| | - Eleonora Secchi
- Institute of Environmental Engineering, ETH Zürich, Zürich, Switzerland
| | - Roberto Rusconi
- IRCCS Humanitas Research Hospital, Rozzano–Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele–Milan, Italy
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8
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Caldara M, Marmiroli N. Antimicrobial Properties of Antidepressants and Antipsychotics-Possibilities and Implications. Pharmaceuticals (Basel) 2021; 14:ph14090915. [PMID: 34577614 PMCID: PMC8470654 DOI: 10.3390/ph14090915] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
The spreading of antibiotic resistance is responsible annually for over 700,000 deaths worldwide, and the prevision is that this number will increase exponentially. The identification of new antimicrobial treatments is a challenge that requires scientists all over the world to collaborate. Developing new drugs is an extremely long and costly process, but it could be paralleled by drug repositioning. The latter aims at identifying new clinical targets of an “old” drug that has already been tested, approved, and even marketed. This approach is very intriguing as it could reduce costs and speed up approval timelines, since data from preclinical studies and on pharmacokinetics, pharmacodynamics, and toxicity are already available. Antidepressants and antipsychotics have been described to inhibit planktonic and sessile growth of different yeasts and bacteria. The main findings in the field are discussed in this critical review, along with the description of the possible microbial targets of these molecules. Considering their antimicrobial activity, the manuscript highlights important implications that the administration of antidepressants and antipsychotics may have on the gut microbiome.
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Affiliation(s)
- Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy;
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
- Correspondence:
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy;
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
- Italian National Interuniversity Consortium for Environmental Sciences (CINSA), University of Parma, 43124 Parma, Italy
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Farr J, Kolano A, Aumon S, Degiovanni A, Caldara M, Valloni A. Proton LINAC Transverse Beam Scanning Performance Implications for Therapeutic Quality Improvement. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Caldara M, Marmiroli N. Known Antimicrobials Versus Nortriptyline in Candida albicans: Repositioning an Old Drug for New Targets. Microorganisms 2020; 8:microorganisms8050742. [PMID: 32429222 PMCID: PMC7284794 DOI: 10.3390/microorganisms8050742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 02/07/2023] Open
Abstract
Candida albicans has the capacity to develop resistance to commonly used antimicrobials, and to solve this problem, drug repositioning and new drug combinations are being studied. Nortriptyline, a tricyclic antidepressant, was shown to have the capacity to inhibit biofilm and hyphae formation, along with the ability to efficiently kill cells in a mature biofilm. To use nortriptyline as a new antimicrobial, or in combination with known drugs to increase their actions, it is important to characterize in more detail the effects of this drug on the target species. In this study, the Candida albicans GRACE™ collection and a Haplo insufficiency profiling were employed to identify the potential targets of nortriptyline, and to classify, in a parallel screening with amphotericin B, caspofungin, and fluconazole, general multi-drug resistance genes. The results identified mutants that, during biofilm formation and upon treatment of a mature biofilm, are sensitive or tolerant to nortriptyline, or to general drug treatments. Gene ontology analysis recognized the categories of ribosome biogenesis and spliceosome as enriched upon treatment with the tricyclic antidepressant, while mutants in oxidative stress response and general stress response were commonly retrieved upon treatment with any other drug. The data presented suggest that nortriptyline can be considered a “new” antimicrobial drug with large potential for application to in vivo infection models.
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Affiliation(s)
- Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy;
- Correspondence: ; Tel.: +39-0521-905658
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy;
- Interdepartmental Center SITEIA.PARMA, University of Parma, Parco Area delle Scienze 181/A, 43124 Parma, Italy
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Pagano L, Caldara M, Villani M, Zappettini A, Marmiroli N, Marmiroli M. In Vivo-In Vitro Comparative Toxicology of Cadmium Sulphide Quantum Dots in the Model Organism Saccharomyces cerevisiae. Nanomaterials (Basel) 2019; 9:nano9040512. [PMID: 30986968 PMCID: PMC6523553 DOI: 10.3390/nano9040512] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 12/22/2022]
Abstract
The aim of this work was to use the yeast Saccharomyces cerevisiae as a tool for toxicogenomic studies of Engineered Nanomaterials (ENMs) risk assessment, in particular focusing on cadmium based quantum dots (CdS QDs). This model has been exploited for its peculiar features: a short replication time, growth on both fermentable and oxidizable carbon sources, and for the contextual availability of genome wide information in the form of genetic maps, DNA microarray, and collections of barcoded mutants. The comparison of the whole genome analysis with the microarray experiments (99.9% coverage) and with the phenotypic analysis of 4688 barcoded haploid mutants (80.2% coverage), shed light on the genes involved in the response to CdS QDs, both in vivo and in vitro. The results have clarified the mechanisms involved in the exposure to CdS QDs, and whether these ENMs and Cd2+ exploited different pathways of response, in particular related to oxidative stress and to the maintenance of mitochondrial integrity and function. Saccharomyces cerevisiae remains a versatile and robust alternative for organismal toxicological studies, with a high level of heuristic insights into the toxicology of more complex eukaryotes, including mammals.
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Affiliation(s)
- Luca Pagano
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
| | - Marina Caldara
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
| | | | | | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
- Consorzio Interuniversitario Nazionale per le Scienze Ambientali (CINSA), University of Parma, 43123 Parma, Italy.
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy.
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Caldara M, Marmiroli N. Tricyclic antidepressants inhibit Candida albicans growth and biofilm formation. Int J Antimicrob Agents 2018; 52:500-505. [DOI: 10.1016/j.ijantimicag.2018.06.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/19/2018] [Accepted: 06/30/2018] [Indexed: 12/25/2022]
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Caldara M, Graziano S, Gullì M, Cadonici S, Marmiroli N. Editor's Highlight: Off-Target Effects of Neuroleptics and Antidepressants on Saccharomyces cerevisiae. Toxicol Sci 2017; 156:538-548. [PMID: 28087837 DOI: 10.1093/toxsci/kfx007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Over the past years, the use of antidepressants and neuroleptics has steadily increased. Although incredibly useful to treat disorders like depression, schizophrenia, epilepsy, or mental retardation, these drugs display many side effects. Toxicogenomic studies aim to limit this problem by trying to identify cellular targets and off-targets of medical compounds. The baker yeast Saccharomyces cerevisiae has been shown to be a key player in this approach, as it represents an incredible toolbox for the dissection of complex biological processes. Moreover, the evolutionary conservation of many pathways allows the translation of yeast data to the human system. In this paper, a better attention was paid to chlorpromazine, as it still is one of the most widely used drug in therapy. The results of a toxicogenomic screening performed on a yeast mutants collection treated with chlorpromazine were instrumental to identify a set of genes for further analyses. For this purpose, a multidisciplinary approach was used based on growth phenotypes identification, Gene Ontology search, and network analysis. Then, the impacts of three antidepressants (imipramine, doxepin, and nortriptyline) and three neuroleptics (promazine, chlorpromazine, and promethazine) on S. cerevisiae were compared through physiological analyses, microscopy characterization, and transcriptomic studies. Data highlight key differences between neuroleptics and antidepressants, but also between the individual molecules. By performing a network analysis on the human homologous genes, it emerged that genes and proteins involved in the Notch pathway are possible off-targets of these molecules, along with key regulatory proteins.
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Affiliation(s)
- Marina Caldara
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Sara Graziano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Mariolina Gullì
- Department of Life Sciences, University of Parma, 43124 Parma, Italy.,Interdepartmental Center SITEIA.PARMA, University of Parma, 43124 Parma, Italy
| | - Stefania Cadonici
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Nelson Marmiroli
- Department of Life Sciences, University of Parma, 43124 Parma, Italy.,Interdepartmental Center SITEIA.PARMA, University of Parma, 43124 Parma, Italy
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Rosseels J, Van den Brande J, Violet M, Jacobs D, Grognet P, Lopez J, Huvent I, Caldara M, Swinnen E, Papegaey A, Caillierez R, Buée-Scherrer V, Engelborghs S, Lippens G, Colin M, Buée L, Galas MC, Vanmechelen E, Winderickx J. Tau monoclonal antibody generation based on humanized yeast models: impact on Tau oligomerization and diagnostics. J Biol Chem 2014; 290:4059-74. [PMID: 25540200 DOI: 10.1074/jbc.m114.627919] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A link between Tau phosphorylation and aggregation has been shown in different models for Alzheimer disease, including yeast. We used human Tau purified from yeast models to generate new monoclonal antibodies, of which three were further characterized. The first antibody, ADx201, binds the Tau proline-rich region independently of the phosphorylation status, whereas the second, ADx215, detects an epitope formed by the Tau N terminus when Tau is not phosphorylated at Tyr(18). For the third antibody, ADx210, the binding site could not be determined because its epitope is probably conformational. All three antibodies stained tangle-like structures in different brain sections of THY-Tau22 transgenic mice and Alzheimer patients, and ADx201 and ADx210 also detected neuritic plaques in the cortex of the patient brains. In hippocampal homogenates from THY-Tau22 mice and cortex homogenates obtained from Alzheimer patients, ADx215 consistently stained specific low order Tau oligomers in diseased brain, which in size correspond to Tau dimers. ADx201 and ADx210 additionally reacted to higher order Tau oligomers and presumed prefibrillar structures in the patient samples. Our data further suggest that formation of the low order Tau oligomers marks an early disease stage that is initiated by Tau phosphorylation at N-terminal sites. Formation of higher order oligomers appears to require additional phosphorylation in the C terminus of Tau. When used to assess Tau levels in human cerebrospinal fluid, the antibodies permitted us to discriminate patients with Alzheimer disease or other dementia like vascular dementia, indicative that these antibodies hold promising diagnostic potential.
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Affiliation(s)
- Joëlle Rosseels
- From Functional Biology, KU Leuven, Kasteelpark Arenberg 31 Box 2433, 3001 Heverlee, Belgium
| | - Jeff Van den Brande
- From Functional Biology, KU Leuven, Kasteelpark Arenberg 31 Box 2433, 3001 Heverlee, Belgium, ADx NeuroSciences NV, Technologiepark Zwijnaarde 4, 9052 Ghent, Belgium, Fujirebio Europe, Technologiepark Zwijnaarde 6, 9052 Ghent, Belgium
| | - Marie Violet
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Dirk Jacobs
- ADx NeuroSciences NV, Technologiepark Zwijnaarde 4, 9052 Ghent, Belgium
| | - Pierre Grognet
- Fujirebio Europe, Technologiepark Zwijnaarde 6, 9052 Ghent, Belgium
| | - Juan Lopez
- Université Lille Nord de France, 59000 Lille, France, CNRS, UMR8576 Structural and Functional Glycobiology, 59650 Villeneuve d'Ascq, France
| | - Isabelle Huvent
- Université Lille Nord de France, 59000 Lille, France, CNRS, UMR8576 Structural and Functional Glycobiology, 59650 Villeneuve d'Ascq, France
| | - Marina Caldara
- From Functional Biology, KU Leuven, Kasteelpark Arenberg 31 Box 2433, 3001 Heverlee, Belgium
| | - Erwin Swinnen
- From Functional Biology, KU Leuven, Kasteelpark Arenberg 31 Box 2433, 3001 Heverlee, Belgium
| | - Anthony Papegaey
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Raphaëlle Caillierez
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Valerie Buée-Scherrer
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Sebastiaan Engelborghs
- the Reference Center for Biological Markers of Dementia (BIODEM), Institute Born-Bunge, University of Antwerp, 2610 Wilrijk, Belgium, and the Department of Neurology and Memory Clinic, Hospital Network Antwerp (ZNA) Middelheim and Hoge Beuken, 2660 Antwerp, Belgium
| | - Guy Lippens
- Université Lille Nord de France, 59000 Lille, France, CNRS, UMR8576 Structural and Functional Glycobiology, 59650 Villeneuve d'Ascq, France
| | - Morvane Colin
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Luc Buée
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Marie-Christine Galas
- INSERM, UMR1172, JPArc, Alzheimer & Tauopathies, Rue Polonovski, 59045 Lille, France, the Faculté de Médecine, Université de Lille, Place de Verdun, 59045 Lille, France, the Memory Clinic, Centre Hospitalier Régional Universitaire de Lille, 59037 Lille, France
| | - Eugeen Vanmechelen
- ADx NeuroSciences NV, Technologiepark Zwijnaarde 4, 9052 Ghent, Belgium,
| | - Joris Winderickx
- From Functional Biology, KU Leuven, Kasteelpark Arenberg 31 Box 2433, 3001 Heverlee, Belgium,
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Billings N, Ramirez Millan M, Caldara M, Rusconi R, Tarasova Y, Stocker R, Ribbeck K. The extracellular matrix Component Psl provides fast-acting antibiotic defense in Pseudomonas aeruginosa biofilms. PLoS Pathog 2013; 9:e1003526. [PMID: 23950711 PMCID: PMC3738486 DOI: 10.1371/journal.ppat.1003526] [Citation(s) in RCA: 199] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 06/14/2013] [Indexed: 02/01/2023] Open
Abstract
Bacteria within biofilms secrete and surround themselves with an extracellular matrix, which serves as a first line of defense against antibiotic attack. Polysaccharides constitute major elements of the biofilm matrix and are implied in surface adhesion and biofilm organization, but their contributions to the resistance properties of biofilms remain largely elusive. Using a combination of static and continuous-flow biofilm experiments we show that Psl, one major polysaccharide in the Pseudomonas aeruginosa biofilm matrix, provides a generic first line of defense toward antibiotics with diverse biochemical properties during the initial stages of biofilm development. Furthermore, we show with mixed-strain experiments that antibiotic-sensitive “non-producing” cells lacking Psl can gain tolerance by integrating into Psl-containing biofilms. However, non-producers dilute the protective capacity of the matrix and hence, excessive incorporation can result in the collapse of resistance of the entire community. Our data also reveal that Psl mediated protection is extendible to E. coli and S. aureus in co-culture biofilms. Together, our study shows that Psl represents a critical first bottleneck to the antibiotic attack of a biofilm community early in biofilm development. Many bacteria have the ability to form multicellular communities, termed biofilms. An important characteristic of a biofilm is the ability of cells to synthesize and secrete an extracellular matrix. This matrix offers structural support, community organization, and added protection, often making the cells impervious to desiccation, predation, and antimicrobials. In this study, we investigate the contributions of polysaccharide components found in the extracellular matrix of Pseudomonas aeruginosa at progressive stages in biofilm development. We first show that one specific polysaccharide, Psl, provides an added defense for P. aeruginosa biofilms against antimicrobials of different properties for young biofilms. Then, by cultivating biofilms that contain both Psl producing and Psl non-producing strains, we find that P. aeruginosa, E. coli, and S. aureus species that lack Psl take advantage of the protection offered by cells producing Psl. Collectively, the data indicate that Psl is likely to play a key protective role in early development of P. aeruginosa biofilm associated infections.
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Affiliation(s)
- Nicole Billings
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Maria Ramirez Millan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Marina Caldara
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roberto Rusconi
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Yekaterina Tarasova
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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Buccella M, Dorigato A, Caldara M, Pasqualini E, Fambri L. Thermo-mechanical behaviour of Polyamide 6 chain extended with 1,1′-Carbonyl-Bis-Caprolactam and 1,3-Phenylene-Bis-2-Oxazoline. J Polym Res 2013. [DOI: 10.1007/s10965-013-0225-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Buccella M, Dorigato A, Pasqualini E, Caldara M, Fambri L. Chain extension behavior and thermo-mechanical properties of polyamide 6 chemically modified with 1,1′-carbonyl-bis-caprolactam. POLYM ENG SCI 2013. [DOI: 10.1002/pen.23547] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- M. Buccella
- Department of Industrial Engineering and INSTM Research Unit; University of Trento; Via Mesiano 77 Trento 38123 Italy
| | - A. Dorigato
- Department of Industrial Engineering and INSTM Research Unit; University of Trento; Via Mesiano 77 Trento 38123 Italy
| | - E. Pasqualini
- Aquafil Spa; Via Linfano 9 Arco (Trento) 38062 Italy
| | - M. Caldara
- Aquafil Spa; Via Linfano 9 Arco (Trento) 38062 Italy
| | - L. Fambri
- Department of Industrial Engineering and INSTM Research Unit; University of Trento; Via Mesiano 77 Trento 38123 Italy
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Van Rossom S, Op de Beeck K, Franssens V, Swinnen E, Schepers A, Ghillebert R, Caldara M, Van Camp G, Winderickx J. The splicing mutant of the human tumor suppressor protein DFNA5 induces programmed cell death when expressed in the yeast Saccharomyces cerevisiae. Front Oncol 2012; 2:77. [PMID: 22848872 PMCID: PMC3404532 DOI: 10.3389/fonc.2012.00077] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 07/05/2012] [Indexed: 12/12/2022] Open
Abstract
DFNA5 was first identified as a gene responsible for autosomal dominant deafness. Different mutations were found, but they all resulted in exon 8 skipping during splicing and premature termination of the protein. Later, it became clear that the protein also has a tumor suppression function and that it can induce apoptosis. Epigenetic silencing of the DFNA5 gene is associated with different types of cancers, including gastric and colorectal cancers as well as breast tumors. We introduced the wild-type and mutant DFNA5 allele in the yeast Saccharomyces cerevisiae. The expression of the wild-type protein was well tolerated by the yeast cells, although the protein was subject of degradation and often deposited in distinct foci when cells entered the diauxic shift. In contrast, cells had problems to cope with mutant DFNA5 and despite an apparent compensatory reduction in expression levels, the mutant protein still triggered a marked growth defect, which in part can be ascribed to its interaction with mitochondria. Consistently, cells with mutant DFNA5 displayed significantly increased levels of ROS and signs of programmed cell death. The latter occurred independently of the yeast caspase, Mca1, but involved the mitochondrial fission protein, Fis1, the voltage-dependent anion channel protein, Por1 and the mitochondrial adenine nucleotide translocators, Aac1 and Aac3. Recent data proposed DFNA5 toxicity to be associated to a globular domain encoded by exon 2–6. We confirmed these data by showing that expression of solely this domain confers a strong growth phenotype. In addition, we identified a point mutant in this domain that completely abrogated its cytotoxicity in yeast as well as human Human Embryonic Kidney 293T cells (HEK293T). Combined, our data underscore that the yeast system offers a valuable tool to further dissect the apoptotic properties of DFNA5.
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Affiliation(s)
- Sofie Van Rossom
- Department of Biology, Functional Biology, KU Leuven Leuven-Heverlee, Belgium
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Abstract
Biofilms grow on various surfaces and in many different environments, a phenomenon that constitutes major problems in industry and medicine. Despite their importance little is known about the viscoelastic properties of biofilms and how these depend on the chemical microenvironment. Here, we find that the mechanical properties of Pseudomonas aeruginosa (P.a.) biofilms are highly robust towards chemical perturbations. Specifically, we observe that P.a. biofilms are able to fully regain their initial stiffness after yielding is enforced, even in the presence of chemicals. Moreover, only trivalent ions and citric acid significantly affect the biofilm elasticity, the first of which also alter the texture of the material. Finally, our results indicate that biofilm mechanics and bacteria viability inside the biofilm are not necessarily linked which suggests that targeting bacteria alone might not be sufficient for biofilm removal strategies.
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Affiliation(s)
- Oliver Lieleg
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139
| | - Marina Caldara
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139
| | - Regina Baumgärtel
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139
| | - Katharina Ribbeck
- Department of Biological Engineering, Massachusetts Institute of Technology, 500 Technology Square, Cambridge, MA 02139
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Abstract
Relative to most regions of the genome, tandemly repeated DNA sequences display a greater propensity to mutate. A search for tandem repeats in the Saccharomyces cerevisiae genome revealed that the nucleosome-free region directly upstream of genes (the promoter region) is enriched in repeats. As many as 25% of all gene promoters contain tandem repeat sequences. Genes driven by these repeat-containing promoters show significantly higher rates of transcriptional divergence. Variations in repeat length result in changes in expression and local nucleosome positioning. Tandem repeats are variable elements in promoters that may facilitate evolutionary tuning of gene expression by affecting local chromatin structure.
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Affiliation(s)
- Marcelo D. Vinces
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- Laboratory for Systems Biology, Flanders Institute for Biotechnology (VIB), Katholieke Universiteit Leuven (K.U. Leuven), B-3001 Heverlee, Belgium
- Genetics and Genomics Group, Centre of Microbial and Plant Genetics (CMPG), K.U. Leuven, Gaston Geenslaan 1, B-3001 Leuven (Heverlee), Belgium
| | - Matthieu Legendre
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- Structural and Genomic Information Laboratory, CNRS-UPR 2589, IFR-88, Université de la Méditerranée Parc Scientifique de Luminy, Avenue de Luminy, FR-13288 Marseille, France
| | - Marina Caldara
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Masaki Hagihara
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Kevin J. Verstrepen
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
- Laboratory for Systems Biology, Flanders Institute for Biotechnology (VIB), Katholieke Universiteit Leuven (K.U. Leuven), B-3001 Heverlee, Belgium
- Genetics and Genomics Group, Centre of Microbial and Plant Genetics (CMPG), K.U. Leuven, Gaston Geenslaan 1, B-3001 Leuven (Heverlee), Belgium
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Smukalla S, Caldara M, Pochet N, Beauvais A, Guadagnini S, Yan C, Vinces MD, Jansen A, Prevost MC, Latgé JP, Fink GR, Foster KR, Verstrepen KJ. FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast. Cell 2008; 135:726-37. [PMID: 19013280 DOI: 10.1016/j.cell.2008.09.037] [Citation(s) in RCA: 304] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 08/21/2008] [Accepted: 09/16/2008] [Indexed: 11/27/2022]
Abstract
The budding yeast, Saccharomyces cerevisiae, has emerged as an archetype of eukaryotic cell biology. Here we show that S. cerevisiae is also a model for the evolution of cooperative behavior by revisiting flocculation, a self-adherence phenotype lacking in most laboratory strains. Expression of the gene FLO1 in the laboratory strain S288C restores flocculation, an altered physiological state, reminiscent of bacterial biofilms. Flocculation protects the FLO1 expressing cells from multiple stresses, including antimicrobials and ethanol. Furthermore, FLO1(+) cells avoid exploitation by nonexpressing flo1 cells by self/non-self recognition: FLO1(+) cells preferentially stick to one another, regardless of genetic relatedness across the rest of the genome. Flocculation, therefore, is driven by one of a few known "green beard genes," which direct cooperation toward other carriers of the same gene. Moreover, FLO1 is highly variable among strains both in expression and in sequence, suggesting that flocculation in S. cerevisiae is a dynamic, rapidly evolving social trait.
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Affiliation(s)
- Scott Smukalla
- FAS Center for Systems Biology, Harvard University, Northwest Labs, Cambridge, MA 02138, USA
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Caldara M, Minh PNL, Bostoen S, Massant J, Charlier D. ArgR-dependent repression of arginine and histidine transport genes in Escherichia coli K-12. J Mol Biol 2007; 373:251-67. [PMID: 17850814 DOI: 10.1016/j.jmb.2007.08.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 07/31/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
In Escherichia coli L-arginine is taken up by three periplasmic binding protein-dependent transport systems that are encoded by two genetic loci: the artPIQM-artJ and argT-hisJQMP gene clusters. The transcription of the artJ, artPIQM and hisJQMP genes and operons is repressed by liganded ArgR, whereas argT, encoding the LAO (lysine, arginine, ornithine) periplasmic binding protein, is insensitive to the repressor. Here we characterize the repressible Esigma70 P artJ, P artP and P hisJ promoters and demonstrate that the cognate operators consist of two 18 bp ARG boxes separated by 3 bp. Determination of the energy landscape of the ArgR-operator contacts by missing contact probing and mutant studies indicated that each box of a pair contributes to complex formation in vitro and to the repressibility in vivo, but to a different extent. The organization of the ARG boxes and promoter elements in the control regions of the uptake genes is distinct from that of the arginine biosynthetic genes. The hisJQMP operon is the first member of the E. coli ArgR regulon, directly repressed by liganded ArgR, where none of the core promoter elements overlaps the ARG boxes. Single round in vitro transcription assays and DNase I footprinting experiments indicate that liganded ArgR inhibits P artJ and P artP promoter activity by steric exclusion of the RNA polymerase. In contrast, ArgR-mediated repression of P hisJ by inhibition of RNA polymerase binding appears to occur through topological changes of the promoter region.
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Affiliation(s)
- Marina Caldara
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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Caldara M, Charlier D, Cunin R. The arginine regulon of Escherichia coli: whole-system transcriptome analysis discovers new genes and provides an integrated view of arginine regulation. Microbiology (Reading) 2007; 152:3343-3354. [PMID: 17074904 DOI: 10.1099/mic.0.29088-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the response to arginine of the Escherichia coli K-12 transcriptome by microarray hybridization and real-time quantitative PCR provides the first coherent quantitative picture of the ArgR-mediated repression of arginine biosynthesis and uptake genes. Transcriptional repression was shown to be the major control mechanism of the biosynthetic genes, leaving only limited room for additional transcriptional or post-transcriptional regulation. The art genes, encoding the specific arginine uptake system, are subject to ArgR-mediated repression, with strong repression of artJ, encoding the periplasmic binding protein of the system. The hisJQMP genes of the histidine transporter (part of the lysine-arginine-ornithine uptake system) were discovered to be a part of the arginine regulon. Analysis of their control region with reporter gene fusions and electrophoretic mobility shift in the presence of pure ArgR repressor showed the involvement in repression of the ArgR protein and an ARG box 120 bp upstream of hisJ. No repression of the genes of the third uptake system, arginine-ornithine, was observed. Finally, comparison of the time course of arginine repression of gene transcription with the evolution of the specific activities of the cognate enzymes showed that while full genetic repression was achieved 2 min after arginine addition, enzyme concentrations were diluted at the rate of cell division. This emphasizes the importance of feedback inhibition of the first enzymic step in the pathway in controlling the metabolic flow through biosynthesis in the period following the onset of repression.
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Affiliation(s)
- Marina Caldara
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Daniel Charlier
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Raymond Cunin
- Laboratorium voor Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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