Monitoring the viable grapevine microbiome to enhance the quality of wild wines
Brady L. Welsh A * , Raphael Eisenhofer A B , Susan E. P. Bastian C and Stephen P. Kidd A D EA School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia.
B Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, DK-1353 Copenhagen, Denmark.
C School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Waite Campus, PMB 1, Glen Osmond, SA 5064, Australia.
D Research Centre of Infectious Disease, The University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia.
E Australian Centre for Antimicrobial Resistance Ecology (ACARE), The University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia.
Brady Welsh is a student at The University of Adelaide undertaking a Doctor of Philosophy (PhD) in the field of grapevine microbiology investigating the interactions between the living grapevine microbiome and common vineyard fungicides. |
Dr Raphael Eisenhofer is a postdoctoral researcher at the Globe Institute, University of Copenhagen, Denmark, and an adjunct assistant lecturer at the University of Adelaide. His research focus is studying the microbiomes of native Australian mammals, though he applies his metagenomic expertise to diverse study systems. |
Assoc. Prof. Susan Bastian is a qualified winemaker and has been a wine educator and researcher at the University of Adelaide for more than two decades. Broadly, her research group examines the whole wine value chain, specifically grape and wine quality; viticultural and winemaking production impacts, including the influence of wine yeasts, on wine sensory and chemical composition; and wine consumer preference. |
Dr Stephen Kidd is a research group leader at the University of Adelaide. His group studies the bacterial response to environmental stress, specifically the adaptation over long periods of time and the impact on the functionality of the microorganisms. This has extended to the responses of microbial communities, such as the grapevine microbiome. |
Microbiology Australia 44(1) 13-17 https://doi.org/10.1071/MA23004
Submitted: 17 January 2023 Accepted: 26 February 2023 Published: 9 March 2023
© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing on behalf of the ASM. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)
Abstract
Grapevines that are used for winemaking host a diverse range of microorganisms that make up their microbiome. The microbes that inhabit the grapevine have been used by winemakers to produce wine for centuries, although modern wine producers often rely on inoculated microorganisms such as Saccharomyces cerevisiae. In the Australian wine industry, there is a movement towards returning to the utilisation of the microbiome for wine fermentation. With the recent increase in the understanding of the role of the grapevine microbiome in grapevine health, fermentation and subsequent wine sensory traits, the microbial world offers a new level of complexity that can be harnessed for winemaking. In order to develop and maintain a desired vineyard micro-biodiversity, extensive microbial monitoring is required. Here we discuss the utilisation of a viability selection dye in order to distinguish between microorganisms that are live and associated with the host, and relic signals generated from non-living sources.
Keywords: fermentation, metagenomics, micro-biodiversity, microbiome, microbiota, wild, wine.
References
[1] Styger, G et al. (2011) Wine flavor and aroma. J Ind Microbiol Biotechnol 38, 1145–1159.| Wine flavor and aroma.Crossref | GoogleScholarGoogle Scholar |
[2] Piao, H et al. (2015) Insights into the bacterial community and its temporal succession during the fermentation of wine grapes. Front Microbiol 6, 809.
| Insights into the bacterial community and its temporal succession during the fermentation of wine grapes.Crossref | GoogleScholarGoogle Scholar |
[3] Gutiérrez, AR et al. (1999) Ecology of spontaneous fermentation in one winery during 5 consecutive years. Lett Appl Microbiol 29, 411–415.
| Ecology of spontaneous fermentation in one winery during 5 consecutive years.Crossref | GoogleScholarGoogle Scholar |
[4] Beneduce, L et al. (2004) Molecular characterization of lactic acid populations associated with wine spoilage. J Basic Microbiol 44, 10–16.
| Molecular characterization of lactic acid populations associated with wine spoilage.Crossref | GoogleScholarGoogle Scholar |
[5] Clemente-Jimenez, JM et al. (2004) Molecular characterization and oenological properties of wine yeasts isolated during spontaneous fermentation of six varieties of grape must. Food Microbiol 21, 149–155.
| Molecular characterization and oenological properties of wine yeasts isolated during spontaneous fermentation of six varieties of grape must.Crossref | GoogleScholarGoogle Scholar |
[6] Combina, M et al. (2005) Dynamics of indigenous yeast populations during spontaneous fermentation of wines from Mendoza, Argentina. Int J Food Microbiol 99, 237–243.
| Dynamics of indigenous yeast populations during spontaneous fermentation of wines from Mendoza, Argentina.Crossref | GoogleScholarGoogle Scholar |
[7] Hiltner, L (1904) Uber nevere Erfahrungen und Probleme auf dem Gebiet der Boden Bakteriologie und unter besonderer Beurchsichtigung der Grundungung und Broche. Arbeit Deut Landw Ges Berlin 98, 59–78.
[8] Gouka, L et al. (2022) Ecology and functional potential of phyllosphere yeasts. Trends Plant Sci 27, 1109–1123.
| Ecology and functional potential of phyllosphere yeasts.Crossref | GoogleScholarGoogle Scholar |
[9] Martins, G et al. (2013) Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations. PLoS One 8, e73013.
| Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations.Crossref | GoogleScholarGoogle Scholar |
[10] Bettenfeld, P et al. (2022) The microbiota of the grapevine holobiont: a key component of plant health. J Adv Res 40, 1–15.
| The microbiota of the grapevine holobiont: a key component of plant health.Crossref | GoogleScholarGoogle Scholar |
[11] König, H and Claus, H (2018) A future place for Saccharomyces mixtures and hybrids in wine making. Fermentation 4, 67.
| A future place for Saccharomyces mixtures and hybrids in wine making.Crossref | GoogleScholarGoogle Scholar |
[12] Sustainable Winegrowing Australia (2022) Annual Operating Plan: 1 July 2022–30 June 2023. https://sustainablewinegrowing.com.au/wp-content/uploads/2022/09/SWA_AOP_2022-23_W.pdf
[13] Alperstein, L et al. (2020) Yeast bioprospecting versus synthetic biology—which is better for innovative beverage fermentation? Appl Microbiol Biotechnol 104, 1939–1953.
| Yeast bioprospecting versus synthetic biology—which is better for innovative beverage fermentation?Crossref | GoogleScholarGoogle Scholar |
[14] Hranilovic, A et al. (2021) Impact of Lachancea thermotolerans on chemical composition and sensory profiles of merlot wines. Food Chem 349, 129015.
| Impact of Lachancea thermotolerans on chemical composition and sensory profiles of merlot wines.Crossref | GoogleScholarGoogle Scholar |
[15] Hranilovic, A et al. (2022) Impact of Lachancea thermotolerans on chemical composition and sensory profiles of viognier wines. J Fungi 8, 474.
| Impact of Lachancea thermotolerans on chemical composition and sensory profiles of viognier wines.Crossref | GoogleScholarGoogle Scholar |
[16] Bashir, I et al. (2022) Phyllosphere microbiome: diversity and functions. Microbiol Res 254, 126888.
| Phyllosphere microbiome: diversity and functions.Crossref | GoogleScholarGoogle Scholar |
[17] Redford, AJ et al. (2010) The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ Microbiol 12, 2885–2893.
| The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves.Crossref | GoogleScholarGoogle Scholar |
[18] Gong, T and Xin, X-F (2021) Phyllosphere microbiota: community dynamics and its interaction with plant hosts. J Integr Plant Biol 63, 297–304.
| Phyllosphere microbiota: community dynamics and its interaction with plant hosts.Crossref | GoogleScholarGoogle Scholar |
[19] Carini, P et al. (2016) Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol 2, 16242.
| Relic DNA is abundant in soil and obscures estimates of soil microbial diversity.Crossref | GoogleScholarGoogle Scholar |
[20] Emerson, JB et al. (2017) Schrödinger’s microbes: tools for distinguishing the living from the dead in microbial ecosystems. Microbiome 5, 86.
| Schrödinger’s microbes: tools for distinguishing the living from the dead in microbial ecosystems.Crossref | GoogleScholarGoogle Scholar |
[21] Wang, Y et al. (2021) Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome 9, 17.
| Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach.Crossref | GoogleScholarGoogle Scholar |
[22] Nocker, A et al. (2006) Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs dead bacteria by selective removal of DNA from dead cells. J Microbiol Methods 67, 310–320.
| Comparison of propidium monoazide with ethidium monoazide for differentiation of live vs dead bacteria by selective removal of DNA from dead cells.Crossref | GoogleScholarGoogle Scholar |
[23] Baymiev, AK et al. (2020) Modern approaches to differentiation of live and dead bacteria using selective amplification of nucleic acids. Microbiology 89, 13–27.
| Modern approaches to differentiation of live and dead bacteria using selective amplification of nucleic acids.Crossref | GoogleScholarGoogle Scholar |
