Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Processing, and Physicochemical Analyses
2.2. Microbiome DNA Extraction, PCR Amplification, and High-Throughput Sequencing
2.3. Sequence Analysis and Taxonomical Assignation
2.4. Alpha Diversity of Samples
2.5. Principal Components (PCA)
2.6. Co-Occurrence Networks Based on Co-Presence and Mutual Exclusion
2.7. Yeast Isolation and Molecular Identification
2.8. Microcultivation Assay
2.9. Fermentations and HPLC Analysis
2.10. Competition Experiments
3. Results
3.1. Fungal Composition in Unfermented and Fermented Musts from Two Consecutive Seasons of Wine Production
3.2. Identification of Yeast Species of Unfermented Grape Musts
3.3. Fermentation Performance of Natural yYeasts Isolates on Synthetic Wine Must MS300
3.4. Determination of Organic Acid Composition in Synthetic Wine
3.5. Competitive Performance of Native Strains in Co-Cultures Systems
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
- Fleet, G.H. Wine yeasts for the future. FEMS Yeast Res. 2008, 8, 979–995. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Steensels, J.; Snoek, T.; Meersman, E.; Nicolino, M.P.; Voordeckers, K.; Verstrepen, K.J. Improving industrial yeast strains: Exploiting natural and artificial diversity. FEMS Microbiol. Rev. 2014, 38, 947–995. [Google Scholar] [CrossRef] [Green Version]
- Cubillos, F.A. Exploiting budding yeast natural variation for industrial processes. Curr. Genet. 2016, 62, 745–751. [Google Scholar] [CrossRef] [PubMed]
- Matallana, E.; Aranda, A. Biotechnological impact of stress response on wine yeast. Lett. Appl. Microbiol. 2017, 64, 103–110. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Curiel, J.A.; Morales, P.; Gonzalez, R.; Tronchoni, J. Different non-Saccharomyces yeast species stimulate nutrient consumption in S. cerevisiae mixed cultures. Front. Microbiol. 2017, 8. [Google Scholar] [CrossRef]
- Morales, P.; Rojas, V.; Quirós, M.; Gonzalez, R. The impact of oxygen on the final alcohol content of wine fermented by a mixed starter culture. Appl. Microbiol. Biotechnol. 2015, 99, 3993–4003. [Google Scholar] [CrossRef] [Green Version]
- Bokulich, N.A.; Ohta, M.; Richardson, P.M.; Mills, D.A. Monitoring Seasonal Changes in Winery-Resident Microbiota. PLoS ONE 2013, 8, e0066437. [Google Scholar] [CrossRef]
- Bokulich, N.A.; Thorngate, J.H.; Richardson, P.M.; Mills, D.A. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc. Natl. Acad. Sci. USA 2014, 111. [Google Scholar] [CrossRef] [Green Version]
- Pinto, C.; Pinho, D.; Cardoso, R.; Custódio, V.; Fernandes, J.; Sousa, S.; Pinheiro, M.; Egas, C.; Gomes, A.C. Wine fermentation microbiome: A landscape from different Portuguese wine appellations. Front. Microbiol. 2015, 6. [Google Scholar] [CrossRef] [Green Version]
- Wei, Y.J.; Wu, Y.; Yan, Y.Z.; Zou, W.; Xue, J.; Ma, W.R.; Wang, W.; Tian, G.; Wang, L.Y. High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China. PLoS ONE 2018, 13, e0193097. [Google Scholar] [CrossRef] [Green Version]
- Drumonde-Neves, J.; Franco-Duarte, R.; Lima, T.; Schuller, D.; Pais, C. Association between Grape Yeast Communities and the Vineyard Ecosystems. PLoS ONE 2017, 12, e0169883. [Google Scholar] [CrossRef] [PubMed]
- Varela, C.; Borneman, A.R. Yeasts found in vineyards and wineries. Yeast 2017, 34, 111–128. [Google Scholar] [CrossRef] [PubMed]
- Eder, M.L.R.; Conti, F.; Rosa, A.L. Differences between indigenous yeast populations in spontaneously fermenting musts from V. vinifera L. and V. labrusca L. Grapes harvested in the same geographic location. Front. Microbiol. 2018, 9. [Google Scholar] [CrossRef]
- Bokulich, N.A.; Collins, T.S.; Masarweh, C.; Allen, G.; Heymann, H.; Ebeler, S.E.; Millsa, D.A. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. MBio 2016, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Liu, D.; Zhang, P.; Chen, D.; Howell, K. From the Vineyard to the Winery: How Microbial Ecology Drives Regional Distinctiveness of Wine. Front. Microbiol. 2019, 10, 1–13. [Google Scholar] [CrossRef] [PubMed]
- Padilla, B.; Gil, J.V.; Manzanares, P. Past and future of non-Saccharomyces yeasts: From spoilage microorganisms to biotechnological tools for improving wine aroma complexity. Front. Microbiol. 2016, 7, 411. [Google Scholar] [CrossRef] [Green Version]
- Zhang, B.Q.; Shen, J.Y.; Duan, C.Q.; Yan, G.L. Use of indigenous Hanseniaspora vineae and Metschnikowia pulcherrima Co-fermentation with Saccharomyces cerevisiae to improve the aroma diversity of Vidal blanc icewine. Front. Microbiol. 2018, 9. [Google Scholar] [CrossRef]
- Lombardi, S.J.; Pannella, G.; Iorizzo, M.; Moreno-Arribas, M.V.; Tremonte, P.; Succi, M.; Sorrentino, E.; Macciola, V.; Di Renzo, M.; Coppola, R. Sequential inoculum of Hanseniaspora guilliermondii and Saccharomyces cerevisiae for winemaking Campanino on an industrial scale. World J. Microbiol. Biotechnol. 2018, 34. [Google Scholar] [CrossRef]
- Chen, K.; Escott, C.; Loira, I.; del Fresno, J.M.; Morata, A.; Tesfaye, W.; Calderon, F.; Suárez-Lepe, J.A.; Han, S.; Benito, S. Use of non-Saccharomyces yeasts and oenological tannin in red winemaking: Influence on colour, aroma and sensorial properties of young wines. Food Microbiol. 2018, 69, 51–63. [Google Scholar] [CrossRef]
- Jara, C.; Laurie, V.F.; Mas, A.; Romero, J. Microbial terroir in chilean valleys: Diversity of non-conventional yeast. Front. Microbiol. 2016, 7. [Google Scholar] [CrossRef]
- Ganga, M.A.; Martínez, C. Effect of wine yeast monoculture practice on the biodiversity of non-Saccharomyces yeasts. Proc. J. Appl. Microbiol. 2004, 96, 76–83. [Google Scholar] [CrossRef] [PubMed]
- Horta, C.B.; Piccardo, C.C. Una Mirada al Mercado Vitivinícola Nacional e Internacional; Oficina de Estudios y Políticas Agrarias—Odepa: Santiago de Chile, Chile, 2018. [Google Scholar]
- Handl, S.; Dowd, S.E.; Garcia-Mazcorro, J.F.; Steiner, J.M.; Suchodolski, J.S. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiol. Ecol. 2011, 76, 301–310. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Dowd, S.E.; Callaway, T.R.; Wolcott, R.D.; Sun, Y.; McKeehan, T.; Hagevoort, R.G.; Edrington, T.S. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiol. 2008, 8. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Edgar, R.C.; Haas, B.J.; Clemente, J.C.; Quince, C.; Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27, 2194–2200. [Google Scholar] [CrossRef] [Green Version]
- Edgar, R.C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26, 2460–2461. [Google Scholar] [CrossRef] [Green Version]
- Schloss, P.D.; Westcott, S.L.; Ryabin, T.; Hall, J.R.; Hartmann, M.; Hollister, E.B.; Lesniewski, R.A.; Oakley, B.B.; Parks, D.H.; Robinson, C.J.; et al. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009, 75, 7537–7541. [Google Scholar] [CrossRef] [Green Version]
- Caporaso, J.G.; Kuczynski, J.; Stombaugh, J.; Bittinger, K.; Bushman, F.D.; Costello, E.K.; Fierer, N.; Pẽa, A.G.; Goodrich, J.K.; Gordon, J.I.; et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7, 335–336. [Google Scholar] [CrossRef] [Green Version]
- Nilsson, R.H.; Larsson, K.H.; Taylor, A.F.S.; Bengtsson-Palme, J.; Jeppesen, T.S.; Schigel, D.; Kennedy, P.; Picard, K.; Glöckner, F.O.; Tedersoo, L.; et al. The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res. 2019, 47, D259–D264. [Google Scholar] [CrossRef]
- Oksanen, J.; Blanchet, F.G.; Friendly, M.; Kindt, R.; Legendre, P.; Mcglinn, D.; Minchin, P.R.; O’hara, R.B.; Simpson, G.L.; Solymos, P.; et al. Package “Vegan”—Community Ecology Package Version 2.5-6. 2019. Available online: https://rdrr.io/cran/vegan/ (accessed on 15 January 2020).
- Mandakovic, D.; Rojas, C.; Maldonado, J.; Latorre, M.; Travisany, D.; Delage, E.; Bihouée, A.; Jean, G.; Díaz, F.P.; Fernández-Gómez, B.; et al. Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience. Sci. Rep. 2018, 8, 5875. [Google Scholar] [CrossRef]
- Faust, K.; Raes, J. CoNet app: Inference of biological association networks using Cytoscape. F1000Research 2016, 5, 1519. [Google Scholar] [CrossRef]
- Faust, K.; Raes, J. Microbial interactions: From networks to models. Nat. Rev. Microbiol. 2012, 10, 538–550. [Google Scholar] [CrossRef] [PubMed]
- Shannon, P.; Markiel, A.; Ozier, O.; Baliga, N.S.; Wang, J.T.; Ramage, D.; Amin, N.; Schwikowski, B.; Ideker, T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13, 2498–2504. [Google Scholar] [CrossRef] [PubMed]
- Kessi-Pérez, E.I.; Araos, S.; García, V.; Salinas, F.; Abarca, V.; Larrondo, L.F.; Martínez, C.; Cubillos, F.A. RIM15 antagonistic pleiotropy is responsible for differences in fermentation and stress response kinetics in budding yeast. FEMS Yeast Res. 2016, 16. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Hall, B.G.; Acar, H.; Nandipati, A.; Barlow, M. Growth rates made easy. Mol. Biol. Evol. 2014, 31, 232–238. [Google Scholar] [CrossRef] [Green Version]
- Tapia, S.M.; Cuevas, M.; Abarca, V.; Delgado, V.; Rojas, V.; García, V.; Brice, C.; Martínez, C.; Salinas, F.; Larrondo, L.F.; et al. GPD1 and ADH3 natural variants underlie glycerol yield differences in wine fermentation. Front. Microbiol. 2018, 9. [Google Scholar] [CrossRef] [Green Version]
- Rossignol, T.; Dulau, L.; Julien, A.; Blondin, B. Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation. Yeast 2003, 20, 1369–1385. [Google Scholar] [CrossRef]
- Salinas, F.; Cubillos, F.A.; Soto, D.; Garcia, V.; Bergström, A.; Warringer, J.; Ganga, M.A.; Louis, E.J.; Liti, G.; Martinez, C. The Genetic Basis of Natural Variation in Oenological Traits in Saccharomyces cerevisiae. PLoS ONE 2012, 7. [Google Scholar] [CrossRef] [Green Version]
- Tesnière, C.; Delobel, P.; Pradal, M.; Blondin, B. Impact of Nutrient Imbalance on Wine Alcoholic Fermentations: Nitrogen Excess Enhances Yeast Cell Death in Lipid-Limited Must. PLoS ONE 2013, 8. [Google Scholar] [CrossRef] [Green Version]
- García, V.; Rivera, J.; Contreras, A.; Ganga, M.A.; Martínez, C. Development and characterization of hybrids from native wine yeasts. Braz. J. Microbiol. 2012, 43, 482–489. [Google Scholar] [CrossRef] [Green Version]
- Freilich, M.A.; Wieters, E.; Broitman, B.R.; Marquet, P.A.; Navarrete, S.A. Species co-occurrence networks: Can they reveal trophic and non-trophic interactions in ecological communities? Ecology 2018, 99, 690–699. [Google Scholar] [CrossRef]
- De Vries, F.T.; Griffiths, R.I.; Bailey, M.; Craig, H.; Girlanda, M.; Gweon, H.S.; Hallin, S.; Kaisermann, A.; Keith, A.M.; Kretzschmar, M.; et al. Soil bacterial networks are less stable under drought than fungal networks. Nat. Commun. 2018, 9. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Setati, M.E.; Jacobson, D.; Bauer, F.F. Sequence-based analysis of the Vitis vinifera L. cv cabernet sauvignon grape must mycobiome in three South African vineyards employing distinct agronomic systems. Front. Microbiol. 2015, 6. [Google Scholar] [CrossRef] [PubMed]
- Zhang, S.; Chen, X.; Zhong, Q.; Zhuang, X.; Bai, Z. Microbial community analyses associated with nine varieties of wine grape carposphere based on high-throughput sequencing. Microorganisms 2019, 7. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Duc, C.; Pradal, M.; Sanchez, I.; Noble, J.; Tesnière, C.; Blondin, B. A set of nutrient limitations trigger yeast cell death in a nitrogen-dependent manner during wine alcoholic fermentation. PLoS ONE 2017, 12. [Google Scholar] [CrossRef] [PubMed]
- Romano, P.; Ciani, M.; Fleet, G.H. Yeasts in the Production of Wine; Springer: Basel, Switzerland, 2019. [Google Scholar]
- Alsammar, H.F.; Naseeb, S.; Brancia, L.B.; Gilman, R.T.; Wang, P.; Delneri, D. Targeted metagenomics approach to capture the biodiversity of Saccharomyces genus in wild environments. Environ. Microbiol. Rep. 2019, 11, 206–214. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Li, J.; Hu, W.Z.; Xu, Y.P. Diversity and dynamics of yeasts during vidal blanc icewine fermentation: A strategy of the combination of culture-dependent and high-throughput sequencing approaches. Front. Microbiol. 2019, 10. [Google Scholar] [CrossRef] [PubMed]
- Röttjers, L.; Faust, K. From hairballs to hypotheses–biological insights from microbial networks. FEMS Microbiol. Rev. 2018, 42, 761–780. [Google Scholar] [CrossRef] [Green Version]
- Zhang, B.Q.; Luan, Y.; Duan, C.Q.; Yan, G.L. Use of Torulaspora delbrueckii Co-fermentation with two Saccharomyces cerevisiae Strains with different aromatic characteristic to improve the diversity of red wine aroma profile. Front. Microbiol. 2018, 9. [Google Scholar] [CrossRef]
- Bolton, M.D.; Thomma, B.P.H.J.; Nelson, B.D. Sclerotinia sclerotiorum (Lib.) de Bary: Biology and molecular traits of a cosmopolitan pathogen. Mol. Plant Pathol. 2006, 7, 1–16. [Google Scholar] [CrossRef]
- Williamson, B.; Tudzynski, B.; Tudzynski, P.; Van Kan, J.A.L. Botrytis cinerea: The cause of grey mould disease. Mol. Plant Pathol. 2007, 8, 561–580. [Google Scholar] [CrossRef]
- Barata, A.; Malfeito-Ferreira, M.; Loureiro, V. The microbial ecology of wine grape berries. Int. J. Food Microbiol. 2012, 153, 243–259. [Google Scholar] [CrossRef] [PubMed]
- Stefanini, I.; Cavalieri, D. Metagenomic approaches to investigate the contribution of the vineyard environment to the quality of wine fermentation: Potentials and difficulties. Front. Microbiol. 2018, 9, 991. [Google Scholar] [CrossRef] [PubMed]
- Auld, R.R.; Myre, M.; Mykytczuk, N.C.S.; Leduc, L.G.; Merritt, T.J.S. Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques. J. Microbiol. Methods 2013, 93, 108–115. [Google Scholar] [CrossRef] [PubMed]
- Romão, D.; Staley, C.; Ferreira, F.; Rodrigues, R.; Sabino, R.; Veríssimo, C.; Wang, P.; Sadowsky, M.; Brandão, J. Next-generation sequencing and culture-based techniques offer complementary insights into fungi and prokaryotes in beach sands. Mar. Pollut. Bull. 2017, 119, 351–358. [Google Scholar] [CrossRef]
- Stefani, F.O.P.; Bell, T.H.; Marchand, C.; De La Providencia, I.E.; El Yassimi, A.; St-Arnaud, M.; Hijri, M. Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PLoS ONE 2015, 10. [Google Scholar] [CrossRef] [Green Version]
- Crépin, L.; Sanchez, I.; Nidelet, T.; Dequin, S.; Camarasa, C. Efficient ammonium uptake and mobilization of vacuolar arginine by Saccharomyces cerevisiae wine strains during wine fermentation. Microb. Cell Fact. 2014, 13, 109. [Google Scholar] [CrossRef] [Green Version]
- Gutiérrez, A.; Sancho, M.; Beltran, G.; Guillamon, J.M.; Warringer, J. Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth. Appl. Microbiol. Biotechnol. 2016, 100, 3255–3265. [Google Scholar] [CrossRef]
- Jolly, N.P.; Varela, C.; Pretorius, I.S. Not your ordinary yeast: non- Saccharomyces yeasts in wine production uncovered. FEMS Yeast Res. 2014, 14, 215–237. [Google Scholar] [CrossRef] [Green Version]
- Lencioni, L.; Romani, C.; Gobbi, M.; Comitini, F.; Ciani, M.; Domizio, P. Controlled mixed fermentation at winery scale using Zygotorulaspora florentina and Saccharomyces cerevisiae. Int. J. Food Microbiol. 2016, 234, 36–44. [Google Scholar] [CrossRef]
- Lencioni, L.; Taccari, M.; Ciani, M.; Domizio, P. Zygotorulaspora florentina and Starmerella bacillaris in multistarter fermentation with Saccharomyces cerevisiae to reduce volatile acidity of high sugar musts. Aust. J. Grape Wine Res. 2018, 24, 368–372. [Google Scholar] [CrossRef]
- Hranilovic, A.; Gambetta, J.M.; Jeffery, D.W.; Grbin, P.R.; Jiranek, V. Lower-alcohol wines produced by Metschnikowia pulcherrima and Saccharomyces cerevisiae co-fermentations: The effect of sequential inoculation timing. Int. J. Food Microbiol. 2020, 329, 108651. [Google Scholar] [CrossRef] [PubMed]
© 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Mandakovic, D.; Pulgar, R.; Maldonado, J.; Mardones, W.; González, M.; Cubillos, F.A.; Cambiazo, V. Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms 2020, 8, 956. https://doi.org/10.3390/microorganisms8060956
Mandakovic D, Pulgar R, Maldonado J, Mardones W, González M, Cubillos FA, Cambiazo V. Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures. Microorganisms. 2020; 8(6):956. https://doi.org/10.3390/microorganisms8060956
Chicago/Turabian StyleMandakovic, Dinka, Rodrigo Pulgar, Jonathan Maldonado, Wladimir Mardones, Mauricio González, Francisco A. Cubillos, and Verónica Cambiazo. 2020. "Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures" Microorganisms 8, no. 6: 956. https://doi.org/10.3390/microorganisms8060956