1
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Cleere MM, Novodvorska M, Geib E, Whittaker J, Dalton H, Salih N, Hewitt S, Kokolski M, Brock M, Dyer PS. New colours for old in the blue-cheese fungus Penicillium roqueforti. NPJ Sci Food 2024; 8:3. [PMID: 38191473 PMCID: PMC10774375 DOI: 10.1038/s41538-023-00244-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/10/2024] Open
Abstract
Penicillium roqueforti is used worldwide in the production of blue-veined cheese. The blue-green colour derives from pigmented spores formed by fungal growth. Using a combination of bioinformatics, targeted gene deletions, and heterologous gene expression we discovered that pigment formation was due to a DHN-melanin biosynthesis pathway. Systematic deletion of pathway genes altered the arising spore colour, yielding white to yellow-green to red-pink-brown phenotypes, demonstrating the potential to generate new coloured strains. There was no consistent impact on mycophenolic acid production as a result of pathway interruption although levels of roquefortine C were altered in some deletants. Importantly, levels of methyl-ketones associated with blue-cheese flavour were not impacted. UV-induced colour mutants, allowed in food production, were then generated. A range of colours were obtained and certain phenotypes were successfully mapped to pathway gene mutations. Selected colour mutants were subsequently used in cheese production and generated expected new colourations with no elevated mycotoxins, offering the exciting prospect of use in future cheese manufacture.
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Affiliation(s)
- Matthew M Cleere
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- PhD Program in Biology, The Graduate Center; Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY10031, USA
| | - Michaela Novodvorska
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Elena Geib
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Jack Whittaker
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Heather Dalton
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Nadhira Salih
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
- Department of Biology, College of Education, University of Sulaimani, Sulaymaniyah, Iraq
| | - Sarah Hewitt
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthew Kokolski
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Matthias Brock
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Paul S Dyer
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom.
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2
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Crequer E, Ropars J, Jany J, Caron T, Coton M, Snirc A, Vernadet J, Branca A, Giraud T, Coton E. A new cheese population in Penicillium roqueforti and adaptation of the five populations to their ecological niche. Evol Appl 2023; 16:1438-1457. [PMID: 37622099 PMCID: PMC10445096 DOI: 10.1111/eva.13578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/26/2023] [Accepted: 06/22/2023] [Indexed: 08/26/2023] Open
Abstract
Domestication is an excellent case study for understanding adaptation and multiple fungal lineages have been domesticated for fermenting food products. Studying domestication in fungi has thus both fundamental and applied interest. Genomic studies have revealed the existence of four populations within the blue-cheese-making fungus Penicillium roqueforti. The two cheese populations show footprints of domestication, but the adaptation of the two non-cheese populations to their ecological niches (i.e., silage/spoiled food and lumber/spoiled food) has not been investigated yet. Here, we reveal the existence of a new P. roqueforti population, specific to French Termignon cheeses, produced using small-scale traditional practices, with spontaneous blue mould colonisation. This Termignon population is genetically differentiated from the four previously identified populations, providing a novel source of genetic diversity for cheese making. The Termignon population indeed displayed substantial genetic diversity, both mating types, horizontally transferred regions previously detected in the non-Roquefort population, and intermediate phenotypes between cheese and non-cheese populations. Phenotypically, the non-Roquefort cheese population was the most differentiated, with specific traits beneficial for cheese making, in particular higher tolerance to salt, to acidic pH and to lactic acid. Our results support the view that this clonal population, used for many cheese types in multiple countries, is a domesticated lineage on which humans exerted strong selection. The lumber/spoiled food and silage/spoiled food populations were not more tolerant to crop fungicides but showed faster growth in various carbon sources (e.g., dextrose, pectin, sucrose, xylose and/or lactose), which can be beneficial in their ecological niches. Such contrasted phenotypes between P. roqueforti populations, with beneficial traits for cheese-making in the cheese populations and enhanced ability to metabolise sugars in the lumber/spoiled food population, support the inference of domestication in cheese fungi and more generally of adaptation to anthropized environments.
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Affiliation(s)
- Ewen Crequer
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jeanne Ropars
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Luc Jany
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Thibault Caron
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Monika Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
| | - Alodie Snirc
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Jean‐Philippe Vernadet
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Antoine Branca
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Tatiana Giraud
- Université Paris‐SaclayCNRS, AgroParisTech, Laboratoire Ecologie Systématique et Evolution, UMR 8079Gif‐sur‐YvetteFrance
| | - Emmanuel Coton
- Univ BrestINRAE, Laboratoire Universitaire de Biodiversité et Ecologie MicrobiennePlouzanéFrance
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3
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Çakır Y, Çakmakçı S, Hayaloğlu AA. Proteolysis and lipolysis in Tulum cheeses ripened in plastic barrels and goat skin bags made using Penicillium roqueforti 41 strain. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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4
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Anastasiou R, Kazou M, Georgalaki M, Aktypis A, Zoumpopoulou G, Tsakalidou E. Omics Approaches to Assess Flavor Development in Cheese. Foods 2022; 11:188. [PMID: 35053920 PMCID: PMC8775153 DOI: 10.3390/foods11020188] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/03/2022] [Accepted: 01/09/2022] [Indexed: 12/27/2022] Open
Abstract
Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.
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Affiliation(s)
- Rania Anastasiou
- Laboratory of Dairy Research, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece; (M.K.); (M.G.); (A.A.); (G.Z.); (E.T.)
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5
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Differentiation of Penicillium roqueforti from Closely Related Species Contaminating Cheeses and Dairy Environment. FERMENTATION 2021. [DOI: 10.3390/fermentation7040222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Currently, Penicillium roqueforti and the closely related P. carneum and P. paneum are identified based on their macromorphology, micromorphology, and molecular properties, the determination of which involves time-consuming procedures. Culture collections focused on dairy isolates of P. roqueforti require quick and efficient tools for routine applications to identify the (a) taxonomy affiliation and (b) morphological properties of strains that influence the sensory properties of blue-veined cheeses. Here, we assessed the morphological variability of P. roqueforti, P. carneum, P. paneum, and P.crustosum on artificial, Edam-like, and Roquefort-like media. Molecular tools were used to test P. roqueforti strains and clones effectively. A novel primer, PrsF, was tested for specificity within strains and isolates of P. roqueforti compared to P. carneum, P. paneum, and P. crustosum. The results reveal that PrsF was specific to the P. roqueforti samples and did not amplify the other tested Penicillium species. Identification based simultaneously on the specificity of the PrsF primer pair and cultivation of P. roqueforti strains on Roquefort-like medium represents an effective method for expanding the collections and practical use of P. roqueforti in the dairy industry.
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6
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Doğan M, Tekiner İH. Evaluating starter culture potential of wild Penicillium roqueforti strains from moldy cheeses of artisanal origin. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Nguyen Van Long N, Rigalma K, Jany JL, Mounier J, Vasseur V. Intraspecific variability in cardinal growth temperatures and water activities within a large diversity of Penicillium roqueforti strains. Food Res Int 2021; 148:110610. [PMID: 34507754 DOI: 10.1016/j.foodres.2021.110610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/01/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022]
Abstract
Different strains of a given fungal species may display heterogeneous growth behavior in response to environmental factors. In predictive mycology, the consideration of such variability during data collection could improve the robustness of predictive models. Among food-borne fungi, Penicillium roqueforti is a major food spoiler species which is also used as a ripening culture for blue cheese manufacturing. In the present study, we investigated the intraspecific variability of cardinal temperatures and water activities (aw), namely, minimal (Tmin and awmin), optimal (Topt and awopt) and maximal (Tmax) temperatures and/or aw estimated with the cardinal model for radial growth, of 29 Penicillium roqueforti strains belonging to 3 genetically distinct populations. The mean values of cardinal temperatures and aw for radial growth varied significantly across the tested strains, except for Tmax which was constant. In addition, the relationship between the intraspecific variability of the biological response to temperature and aw and putative genetic populations (based on microsatellite markers) within the selected P. roqueforti strains was investigated. Even though no clear relationship was identified between growth parameters and ecological characteristics, PCA confirmed that certain strains had marginal growth response to temperature or aw. Overall, the present data support the idea that a better knowledge of the response to abiotic factors such as temperature and aw at an intraspecific level would be useful to model fungal growth in predictive mycology approaches.
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Affiliation(s)
- Nicolas Nguyen Van Long
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
| | - Karim Rigalma
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jérôme Mounier
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Valérie Vasseur
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, IBSAM, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
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8
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Caron T, Piver ML, Péron AC, Lieben P, Lavigne R, Brunel S, Roueyre D, Place M, Bonnarme P, Giraud T, Branca A, Landaud S, Chassard C. Strong effect of Penicillium roqueforti populations on volatile and metabolic compounds responsible for aromas, flavor and texture in blue cheeses. Int J Food Microbiol 2021; 354:109174. [PMID: 34103155 DOI: 10.1016/j.ijfoodmicro.2021.109174] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023]
Abstract
Studies of food microorganism domestication can provide important insight into adaptation mechanisms and lead to commercial applications. Penicillium roqueforti is a fungus with four genetically differentiated populations, two of which were independently domesticated for blue cheese-making, with the other two populations thriving in other environments. Most blue cheeses are made with strains from a single P. roqueforti population, whereas Roquefort cheeses are inoculated with strains from a second population. We made blue cheeses in accordance with the production specifications for Roquefort-type cheeses, inoculating each cheese with a single P. roqueforti strain, using a total of three strains from each of the four populations. We investigated differences between the cheeses made with the strains from the four P. roqueforti populations, in terms of the induced flora, the proportion of blue color, water activity and the identity and abundance of aqueous and organic metabolites as proxies for proteolysis and lipolysis as well as volatile compounds responsible for flavor and aroma. We found that the population-of-origin of the P. roqueforti strains used for inoculation had a minor impact on bacterial diversity and no effect on the abundance of the main microorganism. The cheeses produced with P. roqueforti strains from cheese populations had a higher percentage of blue area and a higher abundance of the volatile compounds typical of blue cheeses, such as methyl ketones and secondary alcohols. In particular, the Roquefort strains produced higher amounts of these aromatic compounds, partly due to more efficient proteolysis and lipolysis. The Roquefort strains also led to cheeses with a lower water availability, an important feature for preventing spoilage in blue cheeses, which is subject to controls for the sale of Roquefort cheese. The typical appearance and flavors of blue cheeses thus result from human selection on P. roqueforti, leading to the acquisition of specific features by the two cheese populations. These findings have important implications for our understanding of adaptation and domestication, and for cheese improvement.
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Affiliation(s)
- Thibault Caron
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France; Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France.
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Anne-Claire Péron
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Pascale Lieben
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - René Lavigne
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
| | - Sammy Brunel
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Michel Place
- Laboratoire Interprofessionnel de Production - SAS L.I.P., 34 rue de Salers, 15 000 Aurillac, France
| | - Pascal Bonnarme
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Antoine Branca
- Ecologie Systematique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, 91400 Orsay, France
| | - Sophie Landaud
- Université Paris-Saclay, INRAE, AgroParisTech, UMR SayFood, 78850 Thiverval-Grignon, France
| | - Christophe Chassard
- Université Clermont Auvergne, INRAE, Vetagro Sup, UMRF, 20 Côte de Reyne, 15000 Aurillac, France
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9
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Domestication of the Emblematic White Cheese-Making Fungus Penicillium camemberti and Its Diversification into Two Varieties. Curr Biol 2020; 30:4441-4453.e4. [PMID: 32976806 DOI: 10.1016/j.cub.2020.08.082] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/02/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022]
Abstract
Domestication involves recent adaptation under strong human selection and rapid diversification and therefore constitutes a good model for studies of these processes. We studied the domestication of the emblematic white mold Penicillium camemberti, used for the maturation of soft cheeses, such as Camembert and Brie, about which surprisingly little was known, despite its economic and cultural importance. Whole-genome-based analyses of genetic relationships and diversity revealed that an ancient domestication event led to the emergence of the gray-green P. biforme mold used in cheese making, by divergence from the blue-green wild P. fuscoglaucum fungus. Another much more recent domestication event led to the generation of the P. camemberti clonal lineage as a sister group to P. biforme. Penicillium biforme displayed signs of phenotypic adaptation to cheese making relative to P. fuscoglaucum, in terms of whiter color, faster growth on cheese medium under cave conditions, lower amounts of toxin production, and greater ability to prevent the growth of other fungi. The P. camemberti lineage displayed even stronger signs of domestication for all these phenotypic features. We also identified two differentiated P. camemberti varieties, apparently associated with different kinds of cheeses and with contrasted phenotypic features in terms of color, growth, toxin production, and competitive ability. We have thus identified footprints of domestication in these fungi, with genetic differentiation between cheese and wild populations, bottlenecks, and specific phenotypic traits beneficial for cheese making. This study has not only fundamental implications for our understanding of domestication but can also have important effects on cheese making.
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10
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Niccum BA, Kastman EK, Kfoury N, Robbat A, Wolfe BE. Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function. mSystems 2020; 5:e00149-20. [PMID: 32546667 PMCID: PMC7300356 DOI: 10.1128/msystems.00149-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/28/2020] [Indexed: 12/23/2022] Open
Abstract
Diversification can generate genomic and phenotypic strain-level diversity within microbial species. This microdiversity is widely recognized in populations, but the community-level consequences of microbial strain-level diversity are poorly characterized. Using the cheese rind model system, we tested whether strain diversity across microbiomes from distinct geographic regions impacts assembly dynamics and functional outputs. We first isolated the same three bacterial species (Staphylococcus equorum, Brevibacterium auranticum, and Brachybacterium alimentarium) from nine cheeses produced in different regions of the United States and Europe to construct nine synthetic microbial communities consisting of distinct strains of the same three bacterial species. Comparative genomics identified distinct phylogenetic clusters and significant variation in genome content across the nine synthetic communities. When we assembled each synthetic community with initially identical compositions, community structure diverged over time, resulting in communities with different dominant taxa. The taxonomically identical communities showed differing responses to abiotic (high salt) and biotic (the fungus Penicillium) perturbations, with some communities showing no response and others substantially shifting in composition. Functional differences were also observed across the nine communities, with significant variation in pigment production (light yellow to orange) and in composition of volatile organic compound profiles emitted from the rinds (nutty to sulfury).IMPORTANCE Our work demonstrated that the specific microbial strains used to construct a microbiome could impact the species composition, perturbation responses, and functional outputs of that system. These findings suggest that 16S rRNA gene taxonomic profiles alone may have limited potential to predict the dynamics of microbial communities because they usually do not capture strain-level diversity. Observations from our synthetic communities also suggest that strain-level diversity has the potential to drive variability in the aesthetics and quality of surface-ripened cheeses.
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Affiliation(s)
- Brittany A Niccum
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Erik K Kastman
- Tufts University, Department of Biology, Medford, Massachusetts, USA
| | - Nicole Kfoury
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Albert Robbat
- Tufts University, Department of Chemistry, Medford, Massachusetts, USA
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, Massachusetts, USA
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11
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Penicillium roqueforti: an overview of its genetics, physiology, metabolism and biotechnological applications. FUNGAL BIOL REV 2020. [DOI: 10.1016/j.fbr.2020.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Dumas E, Feurtey A, Rodríguez de la Vega RC, Le Prieur S, Snirc A, Coton M, Thierry A, Coton E, Le Piver M, Roueyre D, Ropars J, Branca A, Giraud T. Independent domestication events in the blue-cheese fungus Penicillium roqueforti. Mol Ecol 2020; 29:2639-2660. [PMID: 31960565 PMCID: PMC7497015 DOI: 10.1111/mec.15359] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/02/2020] [Accepted: 01/04/2020] [Indexed: 12/13/2022]
Abstract
Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre‐industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation. see also the Perspective by Brigida Gallone, Jan Steensels and Kevin J. Verstrepen.
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Affiliation(s)
- Emilie Dumas
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Laboratory for Molecular Immunology and Inflammation, Department of Rheumatology, University Hospital Ghent, The Vlaams Instituut voor Biotechnologie (VIB) Center for Inflammation Research (IRC), Ghent, Belgium
| | - Alice Feurtey
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France.,Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Stéphanie Le Prieur
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Monika Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Anne Thierry
- Science et Technologie du Lait et de l'Œuf (STLO), UMR1253, Agrocampus Ouest, INRAE, Rennes, France
| | - Emmanuel Coton
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, Plouzané, France
| | - Mélanie Le Piver
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Daniel Roueyre
- Laboratoire Interprofessionnel de Production - SAS L.I.P, Aurillac, France
| | - Jeanne Ropars
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Antoine Branca
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
| | - Tatiana Giraud
- Ecologie Systématique et Evolution, CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, Orsay, France
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13
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Quéro L, Courault P, Cellière B, Lorber S, Jany JL, Puel O, Girard V, Vasseur V, Nodet P, Mounier J. Application of MALDI-TOF MS to species complex differentiation and strain typing of food related fungi: Case studies with Aspergillus section Flavi species and Penicillium roqueforti isolates. Food Microbiol 2019; 86:103311. [PMID: 31703856 DOI: 10.1016/j.fm.2019.103311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 05/29/2019] [Accepted: 08/20/2019] [Indexed: 11/26/2022]
Abstract
Filamentous fungi are one of the main causes of food losses worldwide and their ability to produce mycotoxins represents a hazard for human health. Their correct and rapid identification is thus crucial to manage food safety. In recent years, MALDI-TOF emerged as a rapid and reliable tool for fungi identification and was applied to typing of bacteria and yeasts, but few studies focused on filamentous fungal species complex differentiation and typing. Therefore, the aim of this study was to evaluate the use of MALDI-TOF to identify species of the Aspergillus section Flavi, and to differentiate Penicillium roqueforti isolates from three distinct genetic populations. Spectra were acquired from 23 Aspergillus species and integrated into a database for which cross-validation led to more than 99% of correctly attributed spectra. For P. roqueforti, spectra were acquired from 63 strains and a two-step calibration procedure was applied before database construction. Cross-validation and external validation respectively led to 94% and 95% of spectra attributed to the right population. Results obtained here suggested very good agreement between spectral and genetic data analysis for both Aspergillus species and P. roqueforti, demonstrating MALDI-TOF applicability as a fast and easy alternative to molecular techniques for species complex differentiation and strain typing of filamentous fungi.
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Affiliation(s)
- Laura Quéro
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France; BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Priscillia Courault
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Beatrice Cellière
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Sophie Lorber
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Jean-Luc Jany
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Olivier Puel
- Toxalim (Research Center in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Victoria Girard
- BioMérieux, R&D Microbiologie, Route de Port Michaud, 38390, La Balme les Grottes, France.
| | - Valérie Vasseur
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Patrice Nodet
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
| | - Jérôme Mounier
- Univ Brest, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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de Almeida Antunes Ferraz JL, Oliveira Souza L, Gustavo de Araújo Fernandes A, Luiz Ferreira Oliveira M, de Oliveira JR, Franco M. Optimization of the solid-state fermentation conditions and characterization of xylanase produced by Penicillium roqueforti ATCC 10110 using yellow mombin residue (Spondias mombin L.). CHEM ENG COMMUN 2019. [DOI: 10.1080/00986445.2019.1572000] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Lucas Oliveira Souza
- Department of Exact Sciences and Natural, State University of Southwest Bahia (UESB), Itapetinga, Brazil
| | | | | | | | - Marcelo Franco
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Ilhéus, Brazil
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15
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Rico-Munoz E, Samson RA, Houbraken J. Mould spoilage of foods and beverages: Using the right methodology. Food Microbiol 2018; 81:51-62. [PMID: 30910088 DOI: 10.1016/j.fm.2018.03.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/19/2022]
Abstract
Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.
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Affiliation(s)
- Emilia Rico-Munoz
- BCN Research Laboratories, Inc., 2491 Stock Creek Blvd., Rockford, TN 37853, USA.
| | - Robert A Samson
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Dept. Applied and Industrial Mycology, Uppsalalaan 8, Utrecht, CT 3584, The Netherlands
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16
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Dubey MK, Aamir M, Kaushik MS, Khare S, Meena M, Singh S, Upadhyay RS. PR Toxin - Biosynthesis, Genetic Regulation, Toxicological Potential, Prevention and Control Measures: Overview and Challenges. Front Pharmacol 2018; 9:288. [PMID: 29651243 PMCID: PMC5885497 DOI: 10.3389/fphar.2018.00288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/13/2018] [Indexed: 01/28/2023] Open
Abstract
Out of the various mycotoxigenic food and feed contaminant, the fungal species belonging to Penicillium genera, particularly Penicillium roqueforti is of great economic importance, and well known for its crucial role in the manufacturing of Roquefort and Gorgonzola cheese. The mycotoxicosis effect of this mold is due to secretion of several metabolites, of which PR toxin is of considerable importance, with regard to food quality and safety challenges issues. The food products and silages enriched with PR toxin could lead into damage to vital internal organs, gastrointestinal perturbations, carcinogenicity, immunotoxicity, necrosis, and enzyme inhibition. Moreover, it also has the significant mutagenic potential to disrupt/alter the crucial processes like DNA replication, transcription, and translation at the molecular level. The high genetic diversities in between the various strains of P. roqueforti persuaded their nominations with Protected Geographical Indication (PGI), accordingly to the cheese type, they have been employed. Recently, the biosynthetic mechanism and toxicogenetic studies unraveled the role of ari1 and prx gene clusters that cross-talk with the synthesis of other metabolites or involve other cross-regulatory pathways to negatively regulate/inhibit the other biosynthetic route targeted for production of a strain-specific metabolites. Interestingly, the chemical conversion that imparts toxic properties to PR toxin is the substitution/oxidation of functional hydroxyl group (-OH) to aldehyde group (-CHO). The rapid conversion of PR toxin to the other derivatives such as PR imine, PR amide, and PR acid, based on conditions available reflects their unstability and degradative aspects. Since the PR toxin-induced toxicity could not be eliminated safely, the assessment of dose-response and other pharmacological aspects for its safe consumption is indispensable. The present review describes the natural occurrences, diversity, biosynthesis, genetics, toxicological aspects, control and prevention strategies, and other management aspects of PR toxin with paying special attention on economic impacts with intended legislations for avoiding PR toxin contamination with respect to food security and other biosafety purposes.
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Affiliation(s)
- Manish K. Dubey
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mohd Aamir
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Manish S. Kaushik
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Saumya Khare
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Mukesh Meena
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
- Centre for Transgenic Plant Development, Department of Biotechnology, Faculty of Science, Hamdard University, New Delhi, India
| | - Surendra Singh
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Ram S. Upadhyay
- Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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17
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Casquete R, Benito MJ, Córdoba MDG, Ruiz-Moyano S, Galván AI, Martín A. Physicochemical factors affecting the growth and mycotoxin production of Penicillium strains in a synthetic cheese medium. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2017.10.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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18
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de Almeida Antunes Ferraz JL, Souza LO, Soares GA, Coutinho JP, de Oliveira JR, Aguiar-Oliveira E, Franco M. Enzymatic saccharification of lignocellulosic residues using cellulolytic enzyme extract produced by Penicillium roqueforti ATCC 10110 cultivated on residue of yellow mombin fruit. BIORESOURCE TECHNOLOGY 2018; 248:214-220. [PMID: 28669572 DOI: 10.1016/j.biortech.2017.06.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/08/2017] [Accepted: 06/09/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to enzymatic saccharification of food waste was performed by crude enzymatic cellulolytic extract produced by P. roqueforti cultivated in yellow mombin residue. The best yield of reducing sugars (259.45mgg-1) was achieved with sugarcane bagasse after 4h; the hydrolysis of corn cob, rice husk and peanut hull resulted in yields around 128-180mgg-1. The addition of 10mmolL-1 of Mn2+ potentiated the saccharification of sugarcane bagasse, in about 86%. The temperature and substrate (sugarcane bagasse) concentration parameters were optimized using a Doehlert Design and, a maximum sugar yield of 662.34±26.72mgg-1 was achieved at 62.40°C, 0.22% (w/v) of substrate, with the addition of Mn2+. Sugar yield was significantly high when compared to previous studies available in scientific literature, suggesting the use of crude cellulolytic supplemented with Mn2+ an alternative and promising process for saccharification of sugarcane bagasse.
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Affiliation(s)
| | - Lucas Oliveira Souza
- Department of Exact Sciences and Natural, State University of Southwest Bahia (UESB), Postal Code: 45700-000 Itapetinga, Brazil
| | - Glêydison Amarante Soares
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Postal Code: 45654-370 Ilhéus, Brazil
| | - Janclei Pereira Coutinho
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Postal Code: 45654-370 Ilhéus, Brazil
| | - Julieta Rangel de Oliveira
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Postal Code: 45654-370 Ilhéus, Brazil
| | - Elizama Aguiar-Oliveira
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Postal Code: 45654-370 Ilhéus, Brazil
| | - Marcelo Franco
- Department of Exact Sciences and Technology, State University of Santa Cruz (UESC), Postal Code: 45654-370 Ilhéus, Brazil.
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19
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Abstract
ABSTRACT
In this article, we review some of the best-studied fungi used as food sources, in particular, the cheese fungi, the truffles, and the fungi used for drink fermentation such as beer, wine, and sake. We discuss their history of consumption by humans and the genomic mechanisms of adaptation during artificial selection.
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20
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 372] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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21
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Blue cheese-making has shaped the population genetic structure of the mould Penicillium roqueforti. PLoS One 2017; 12:e0171387. [PMID: 28248964 PMCID: PMC5331954 DOI: 10.1371/journal.pone.0171387] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/18/2017] [Indexed: 11/28/2022] Open
Abstract
Background Penicillium roqueforti is a filamentous fungus used for making blue cheeses worldwide. It also occurs as a food spoiler and in silage and wood. Previous studies have revealed a strong population genetic structure, with specific traits associated with the different populations. Here, we used a large strain collection from worldwide cheeses published recently to investigate the genetic structure of P. roqueforti. Principal findings We found a genetic population structure in P. roqueforti that was consistent with previous studies, with two main genetic clusters (W+C+ and W-C-, i.e., with and without horizontal gene transferred regions CheesyTer and Wallaby). In addition, we detected a finer genetic subdivision that corresponded to the environment and to protected designation of origin (PDO), namely the Roquefort PDO. We indeed found evidence for eight genetic clusters, one of the cluster including only strains from other environments than cheeses, and another cluster encompassing only strains from the Roquefort PDO. The W-C- and W+C+ cheese clusters were not the most closely related ones, suggesting that there may have been two independent domestication events of P. roqueforti for making blue cheeses. Significance The additional population structure revealed here may be relevant for cheese-makers and for understanding the history of domestication in P. roqueforti.
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22
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Functional diversity within the Penicillium roqueforti species. Int J Food Microbiol 2017; 241:141-150. [DOI: 10.1016/j.ijfoodmicro.2016.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/29/2016] [Accepted: 10/01/2016] [Indexed: 11/22/2022]
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23
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Gillot G, Jany JL, Dominguez-Santos R, Poirier E, Debaets S, Hidalgo PI, Ullán RV, Coton E, Coton M. Genetic basis for mycophenolic acid production and strain-dependent production variability in Penicillium roqueforti. Food Microbiol 2016; 62:239-250. [PMID: 27889155 DOI: 10.1016/j.fm.2016.10.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 08/29/2016] [Accepted: 10/03/2016] [Indexed: 11/16/2022]
Abstract
Mycophenolic acid (MPA) is a secondary metabolite produced by various Penicillium species including Penicillium roqueforti. The MPA biosynthetic pathway was recently described in Penicillium brevicompactum. In this study, an in silico analysis of the P. roqueforti FM164 genome sequence localized a 23.5-kb putative MPA gene cluster. The cluster contains seven genes putatively coding seven proteins (MpaA, MpaB, MpaC, MpaDE, MpaF, MpaG, MpaH) and is highly similar (i.e. gene synteny, sequence homology) to the P. brevicompactum cluster. To confirm the involvement of this gene cluster in MPA biosynthesis, gene silencing using RNA interference targeting mpaC, encoding a putative polyketide synthase, was performed in a high MPA-producing P. roqueforti strain (F43-1). In the obtained transformants, decreased MPA production (measured by LC-Q-TOF/MS) was correlated to reduced mpaC gene expression by Q-RT-PCR. In parallel, mycotoxin quantification on multiple P. roqueforti strains suggested strain-dependent MPA-production. Thus, the entire MPA cluster was sequenced for P. roqueforti strains with contrasted MPA production and a 174bp deletion in mpaC was observed in low MPA-producers. PCRs directed towards the deleted region among 55 strains showed an excellent correlation with MPA quantification. Our results indicated the clear involvement of mpaC gene as well as surrounding cluster in P. roqueforti MPA biosynthesis.
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Affiliation(s)
- Guillaume Gillot
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Jean-Luc Jany
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Rebeca Dominguez-Santos
- Área de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Instituto de Biotecnología de León (INBIOTEC), Avenida Real n°1, Parque Científico de León, 24006 León, Spain
| | - Elisabeth Poirier
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Stella Debaets
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Pedro I Hidalgo
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Ricardo V Ullán
- mAbxience, Upstream Production, Parque Tecnológico de León, Julia Morros s/n, Armunia, 24009, León, Spain
| | - Emmanuel Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France
| | - Monika Coton
- Université de Brest, EA 3882 Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, IBSAM ESIAB, Technopôle Brest-Iroise, 29280 Plouzané, France.
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24
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Ropars J, Lo YC, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López-Villavicencio M. Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution 2016; 70:2099-109. [PMID: 27470007 PMCID: PMC5129480 DOI: 10.1111/evo.13015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/20/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Genetic differentiation occurs when gene flow is prevented, due to reproductive barriers or asexuality. Investigating the early barriers to gene flow is important for understanding the process of speciation. Here, we therefore investigated reproductive isolation between different genetic clusters of the fungus Penicillium roqueforti, used for maturing blue cheeses, and also occurring as food spoiler or in silage. We investigated premating and postmating fertility between and within three genetic clusters (two from cheese and one from other substrates), and we observed sexual structures under scanning electron microscopy. All intercluster types of crosses showed some fertility, suggesting that no intersterility has evolved between domesticated and wild populations despite adaptation to different environments and lack of gene flow. However, much lower fertility was found in crosses within the cheese clusters than within the noncheese cluster, suggesting reduced fertility of cheese strains, which may constitute a barrier to gene flow. Such degeneration may be due to bottlenecks during domestication and/or to the exclusive clonal replication of the strains in industry. This study shows that degeneration has occurred rapidly and independently in two lineages of a domesticated species. Altogether, these results inform on the processes and tempo of degeneration and speciation.
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Affiliation(s)
- Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.,Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Ying-Chu Lo
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Emilie Dumas
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Dominik Begerow
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Tanja Rollnik
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Sandrine Lacoste
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.
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25
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Masneuf-Pomarede I, Salin F, Börlin M, Coton E, Coton M, Jeune CL, Legras JL. Microsatellite analysis of Saccharomyces uvarum diversity. FEMS Yeast Res 2016; 16:fow002. [PMID: 26772797 DOI: 10.1093/femsyr/fow002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2016] [Indexed: 01/02/2023] Open
Abstract
Considered as a sister species of Saccharomyces cerevisiae, S. uvarum is, to a lesser extent, an interesting species for fundamental and applied research studies. Despite its potential interest as a new gene pool for fermenting agents, the intraspecific molecular genetic diversity of this species is still poorly investigated. In this study, we report the use of nine microsatellite markers to describe S. uvarum genetic diversity and population structure among 108 isolates from various geographical and substrate origins (wine, cider and natural sources). Our combined microsatellite markers set allowed differentiating 89 genotypes. In contrast to S. cerevisiae genetic diversity, wild and human origin isolates were intertwined. A total of 75% of strains were proven to be homozygotes and estimated heterozygosity suggests a selfing rate above 0.95 for the different population tested here. From this point of view, the S. uvarum life cycle appears to be more closely related to S. paradoxus or S. cerevisiae of natural resources than S. cerevisiae wine isolates. Population structure could not be correlated to distinct geographic or technological origins, suggesting lower differentiation that may result from a large exchange between human and natural populations mediated by insects or human activities.
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Affiliation(s)
- Isabelle Masneuf-Pomarede
- Université de Bordeaux, Unité de recherche Œnologie, ISVV, EA 4577, USC 1366 INRA, Villenave d'Ornon, France Bordeaux Sciences Agro, 1 cours du Général de Gaulle, 33170 Gradignan, France
| | - Franck Salin
- INRA, UMR1202 Biodiversité Gènes et Ecosystèmes, PlateForme Génomique, Cestas 33610, France
| | - Marine Börlin
- Université de Bordeaux, Unité de recherche Œnologie, ISVV, EA 4577, USC 1366 INRA, Villenave d'Ornon, France
| | - Emmanuel Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané
| | - Monika Coton
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, 29280 Plouzané
| | - Christine Le Jeune
- Université de Haute Alsace, Laboratoire Vigne Biotechnologie et Environnement, 68000 Colmar, France
| | - Jean-Luc Legras
- INRA, UMR1083 Science pour l'Œnologie, Montpellier, F-34060, France SupAgro, UMR1083, Montpellier, F-34060, France Université Montpellier, UMR1083, Montpellier, F-34060, France
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Ropars J, Rodríguez de la Vega RC, López-Villavicencio M, Gouzy J, Sallet E, Dumas É, Lacoste S, Debuchy R, Dupont J, Branca A, Giraud T. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi. Curr Biol 2015; 25:2562-9. [PMID: 26412136 PMCID: PMC4598740 DOI: 10.1016/j.cub.2015.08.025] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/09/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
Abstract
Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1–5]. Few studies have focused on the domestication of fungi, with notable exceptions [6–11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making—P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13–15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. New HTRs are found in cheese fungi HTRs are flanked by specific transposable elements HTRs have spread in cheese-associated fungi through recent selective sweeps Experiments link two HTRs to growth and competitive advantages on cheese
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Affiliation(s)
- Jeanne Ropars
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Manuela López-Villavicencio
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, INRA, Castanet-Tolosan 31326, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, CNRS, Castanet-Tolosan 31326, France
| | - Émilie Dumas
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France
| | - Sandrine Lacoste
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Robert Debuchy
- Institut de Génétique et Microbiologie, UMR8621, Univ. Paris-Sud, 91405 Orsay, France; Institut de Génétique et Microbiologie, UMR8621, CNRS, 91405 Orsay, France
| | - Joëlle Dupont
- Institut de Systématique, Evolution, Biodiversité, UMR 7205 CNRS-MNHN-UPMC-EPHE, Muséum national d'Histoire naturelle, Sorbonne Université, CP39, 57 Rue Cuvier, 75231 Paris Cedex 05, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, UMR8079, Univ. Paris-Sud, 91405 Orsay, France; Ecologie, Systématique et Evolution, UMR8079, CNRS, 91405 Orsay, France.
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Gibbons JG, Rinker DC. The genomics of microbial domestication in the fermented food environment. Curr Opin Genet Dev 2015; 35:1-8. [PMID: 26338497 DOI: 10.1016/j.gde.2015.07.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/10/2015] [Accepted: 07/16/2015] [Indexed: 02/07/2023]
Abstract
Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.
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Affiliation(s)
- John G Gibbons
- Biology Department, Clark University, 950 Main Street, Worcester, MA, USA.
| | - David C Rinker
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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