ORCID Profile
0000-0003-0875-3093
Current Organisations
Universidade Nova de Lisboa
,
Australian Wine Research Institute
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Publisher: American Society for Microbiology
Date: 26-04-2018
Abstract: Here, we report the first sequenced genome of an indigenous Australian wine isolate of Torulaspora delbrueckii using the Oxford Nanopore MinION and Illumina HiSeq sequencing platforms. The genome size is 9.4 Mb and contains 4,831 genes.
Publisher: Frontiers Media SA
Date: 23-05-2018
Publisher: MDPI AG
Date: 24-08-2021
DOI: 10.3390/FERMENTATION7030165
Abstract: The use of non-Saccharomyces yeast species generally involves sequential or co-inoculation of a Saccharomyces cerevisiae strain to complete fermentation. While most studies have focused on characterising the impact that S. cerevisiae has on the growth and metabolic activity of these non-Saccharomyces species, microbial interactions work reciprocally. Antagonism or competition of non-Saccharomyces species against S. cerevisiae has been shown to impact subsequent fermentation performance. To date, it remains unclear whether these negative interactions are strain specific. Hence, characterisation of strain-specific responses to co-inoculation would enable the identification of specific S. cerevisiae strain/non-Saccharomyces combinations that minimise the negative impacts of sequential fermentation on fermentation performance. The competitive fitness response of 93 S. cerevisiae strains to several non-Saccharomyces species was simultaneously investigated using a barcoded library to address this knowledge gap. Strain-specific fitness differences were observed across non-Saccharomyces treatments. Results obtained from experiments using selected S. cerevisiae strains sequentially inoculated after Metschnikowia pulcherrima and Torulaspora delbrueckii were consistent with the competitive barcoded library observations. The results presented in this study indicate that strain selection will influence fermentation performance when using non-Saccharomyces species, therefore, appropriate strain/yeast combinations are required to optimise fermentation.
Publisher: Elsevier BV
Date: 12-2017
Publisher: Elsevier BV
Date: 09-2020
Publisher: Public Library of Science (PLoS)
Date: 28-03-2023
DOI: 10.1371/JOURNAL.PGEN.1010692
Abstract: Copper tolerance and SO 2 tolerance are two well-studied phenotypic traits of Saccharomyces cerevisiae . The genetic bases of these traits are the allelic expansion at the CUP1 locus and reciprocal translocation at the SSU1 locus, respectively. Previous work identified a negative association between SO 2 and copper tolerance in S . cerevisiae wine yeasts. Here we probe the relationship between SO 2 and copper tolerance and show that an increase in CUP1 copy number does not always impart copper tolerance in S . cerevisiae wine yeast. Bulk-segregant QTL analysis was used to identify variance at SSU1 as a causative factor in copper sensitivity, which was verified by reciprocal hemizygosity analysis in a strain carrying 20 copies of CUP1 . Transcriptional and proteomic analysis demonstrated that SSU1 over-expression did not suppress CUP1 transcription or constrain protein production and provided evidence that SSU1 over-expression induced sulfur limitation during exposure to copper. Finally, an SSU1 over-expressing strain exhibited increased sensitivity to moderately elevated copper concentrations in sulfur-limited medium, demonstrating that SSU1 over-expression burdens the sulfate assimilation pathway. Over-expression of MET 3/14/16 , genes upstream of H 2 S production in the sulfate assimilation pathway increased the production of SO 2 and H 2 S but did not improve copper sensitivity in an SSU1 over-expressing background. We conclude that copper and SO 2 tolerance are conditional traits in S . cerevisiae and provide evidence of the metabolic basis for their mutual exclusivity. These findings suggest an evolutionary driver for the extreme lification of CUP1 observed in some yeasts.
Publisher: Elsevier BV
Date: 09-2020
Publisher: Cold Spring Harbor Laboratory
Date: 09-06-2023
DOI: 10.1101/2023.06.07.544145
Abstract: Cultural exchange of fermentation techniques has driven the spread of Saccharomyces cerevisiae across the globe, establishing wild populations in many countries. Despite this, most modern commercial fermentations are inoculated using monocultures, rather than relying on natural populations, potentially impacting wild population ersity. Here we investigate the genomic landscape of 411 wild S. cerevisiae isolated from spontaneous grape fermentations in Australia across multiple locations, years, and grape cultivars. Spontaneous fermentations contained highly recombined mosaic strains that commonly exhibited aneuploidy of chromosomes 1, 3, 6 and 9. Assigning wild genomic windows to putative ancestral origin revealed that few closely related commercial lineages have come to dominate the genetic landscape, contributing most of the genetic variation. Fine-scale phylogenetic analysis of loci not observed in strains of commercial wine origin identified widespread admixture with the Beer2 clade along with three independent admixture events from potentially endemic Oceanic lineages that last shared an ancestor with modern East Asian S. cerevisiae populations. Our results illustrate how commercial use of microbes can affect local microorganism genetic ersity and demonstrates the presence of non-domesticated, non-European derived lineages of S. cerevisiae in Australian ecological niches that are actively admixing.
Publisher: Cold Spring Harbor Laboratory
Date: 30-07-2023
DOI: 10.1101/2023.07.30.551191
Abstract: Soft scale insects and mealybugs are phloem feeding Hemipterans that are considered majors pests in agricultural and horticultural settings throughout the world. Viticulturally, scale are a major issue due to their ability to secrete honeydew, which facilitates the development of sooty mould and for their propensity as transmission vectors for several viral diseases of grapevine. To facilitate the rapid identification and quantification of vineyard-associated insects a metagenomic-based bioinformatic pipeline was developed for generalised ecosystem monitoring that automated the assembly and classification of insect mitochondrial genomes from shotgun sequencing data using the Barcode of Life Database API. Parthenolecanium corni (European fruit scale), which was thought to be absent from Australian grapevines, was identified as the dominant coccid species infesting all vines s led, along with secondary infestation by Pseudococcus viburni (obscure mealybug) and Pseudo. longispinus (long-tailed mealybug). In addition, parisitoidism by Coccophagus scutellaris (Aphelinidae) wasps was also detected. The discovery of Parth. corni as a significant member of scale infestations in Australia has significant implications for the development of effective control strategies for this important group of pests.
Publisher: American Chemical Society (ACS)
Date: 21-10-2020
Abstract: Glycosides are sugar conjugates of aroma compounds that are found in many fruits and vegetables, and while glycosides are non-volatile, they can release flavor during eating, through enzyme hydrolysis from oral microbiota. Recently, a range of sensory phenotypes for glucoside perception have been observed, reflecting interin idual variation in response to precursors of floral and smoky flavors, geranyl glucoside and guaiacyl glucoside. To understand this variation and investigate the role of oral microbiota on
Publisher: Public Library of Science (PLoS)
Date: 04-2022
DOI: 10.1371/JOURNAL.PGEN.1010153
Abstract: Eutypa dieback of grapevine is an important disease caused by the generalist Ascomycete fungus Eutypa lata . Despite the relevance of this species to the global wine industry, its genomic ersity remains unknown, with only a single publicly available genome assembly. Whole-genome sequencing and comparative genomics was performed on forty Australian E . lata isolates to understand the genome evolution, adaptation, population size and structure of these isolates. Phylogenetic and linkage disequilibrium decay analyses provided evidence of extensive gene flow through sexual recombination between isolates obtained from different geographic locations and hosts. Investigation of the genetic ersity of these isolates suggested rapid population expansion, likely as a consequence of the recent growth of the Australian wine industry. Genomic regions affected by selective sweeps were shown to be enriched for genes associated with secondary metabolite clusters and included genes encoding proteins with a role in nutrient acquisition, degradation of host cell wall and metal and drug resistance, suggesting recent adaptation to both abiotic factors and potentially host genotypes. Genome synteny analysis using long-read genome assemblies showed significant intraspecific genomic plasticity with extensive chromosomal rearrangements impacting the secondary metabolite production potential of this species. Finally, k-mer based GWAS analysis identified a potential locus associated with mycelia recovery in canes of Vitis vinifera that will require further investigations.
Publisher: Cold Spring Harbor Laboratory
Date: 14-12-2022
DOI: 10.1101/2022.12.12.520163
Abstract: Shiraz (Syrah) is a dark-skinned cultivar of the wine grape Vitis vinifera that forms the basis of some of the world’s most iconic wines. Worldwide, Shiraz is the fourth most planted grapevine cultivar, however it represents the most planted cultivar in Australia. Given the importance of Shiraz to worldwide wine production, a long-read based reference genome assembly for this cultivar was produced and used to investigate the unique genetic ersity and ancestral origins of this iconic variety. Phylogenetic reconstruction using high-quality genome assemblies for wine grape cultivars provided further support of a kinship between Shiraz and Pinot Noir. Harnessing long-read data, transposable element insertions potentially affecting gene function were characterized in Shiraz and assessed relative to other cultivars. This revealed a heterogenous landscape of transposon insertion points across cultivars and uncovered a specific combination of allelic variants at the TPS24 terpene synthase locus, which when combined with appropriate environmental triggers, may allow Shiraz to produce high levels of rotundone, the aroma compound responsible for the distinctive peppery characteristics of this cultivar.
Publisher: Hindawi Limited
Date: 11-05-2023
DOI: 10.1155/2023/6686706
Abstract: Background and Aims. Shiraz (Syrah) is a dark-skinned cultivar of the wine grape Vitis vinifera that forms the basis of some of the world’s most iconic wines. Worldwide, Shiraz is the fourth most planted grapevine cultivar however, it represents the most planted cultivar in Australia. Given the importance of Shiraz to worldwide wine production, this study aimed to produce a reference genome for this cultivar while investigating the unique genetic variants and ancestral origins of this iconic variety. Methods and Results. Long-read ONT data were selected to produce a highly contiguous genome assembly for Shiraz. Phylogenetic reconstruction using high-quality genome assemblies for wine grape cultivars provided further support of a kinship between Shiraz and Pinot Noir. Harnessing long-read data, transposable element insertions potentially affecting gene function were characterized in Shiraz and assessed relative to other cultivars. This revealed a heterogenous landscape of transposon insertion points across cultivars and uncovered a specific combination of allelic variants at the VviTPS24 terpene synthase locus. Conclusions. This establishment of a Shiraz genome provides a detailed view of the genetics that underpin this cultivar, including the discovery of a specific combination of VviTPS24 variants, which when combined with appropriate environmental triggers may allow Shiraz to produce high levels of rotundone, the aroma compound responsible for the distinctive peppery characteristics of this cultivar. Significance of the Study. The availability of a reference genome for Shiraz expands the pool of genomes available for wine grapes while providing a foundation resource for whole-genome studies involving this iconic cultivar, including intracultivar variant identification and transcriptomic studies using a matching reference genome.
Publisher: Springer Science and Business Media LLC
Date: 24-06-2022
DOI: 10.1038/S41467-022-31305-4
Abstract: The Synthetic Yeast Genome Project ( Sc 2.0) represents the first foray into eukaryotic genome engineering and a framework for designing and building the next generation of industrial microbes. However, the laboratory strain S288c used lacks many of the genes that provide phenotypic ersity to industrial and environmental isolates. To address this shortcoming, we have designed and constructed a neo-chromosome that contains many of these erse pan-genomic elements and which is compatible with the Sc 2.0 design and test framework. The presence of this neo-chromosome provides phenotypic plasticity to the Sc 2.0 parent strain, including expanding the range of utilizable carbon sources. We also demonstrate that the induction of programmable structural variation (SCRaMbLE) provides genetic ersity on which further adaptive gains could be selected. The presence of this neo-chromosome within the Sc 2.0 backbone may therefore provide the means to adapt synthetic strains to a wider variety of environments, a process which will be vital to transitioning Sc 2.0 from the laboratory into industrial applications.
Publisher: FapUNIFESP (SciELO)
Date: 09-2018
Publisher: American Society for Microbiology
Date: 31-10-2021
DOI: 10.1128/SPECTRUM.01154-21
Abstract: Malolactic fermentation is an indispensable step in the elaboration of most wines and is generally performed by Oenococcus oeni , a Gram-positive heterofermentative lactic acid bacterium species. While O. oeni is tolerant to many of the wine stresses, including low pH and high ethanol concentrations, it has high sensitivity to SO 2 , an antiseptic and antioxidant compound regularly used in winemaking.
Publisher: Elsevier BV
Date: 09-2017
DOI: 10.1016/J.SYAPM.2017.06.004
Abstract: An industrial wastewater treatment plant (WWTP) in Australia has long suffered from bulking problems associated with the proliferation of Thiothrix spp. The WWTP consists of a covered anaerobic lagoon (CAL) followed by a sequencing batch reactor (SBR). The CAL functions as both an anaerobic digester and surge lagoon for the irregular flow of wastewater generated from the production of seasonal products. Chemical analysis of the raw influent showed it was composed of a mixture of organic acids, phenols and alcohols. The CAL effluent was characterised by high acetic acid and phenolic concentrations. An attempt was made to manipulate the SBR microbial community to improve settling by direct feeding small volumes of raw influent into the SBR. After raw feeding, the plant ceased bulking as the settled sludge volume reduced from 930 to 200mLL
Publisher: Oxford University Press (OUP)
Date: 09-2020
Abstract: Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice s les from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to erse environmental stresses suggest a more constrained ecological range than A. pullulans.
Publisher: Springer Science and Business Media LLC
Date: 05-10-2015
DOI: 10.1007/S10482-015-0602-4
Abstract: Red grape musts from overripe grapes are characterised by high pH and sugar concentration. Corrections with organic acids are commonly used to secure the alcoholic fermentation and improve the organoleptic characteristics of the wine. In this study we test an alternative biological acidification method using the ability of Lactobacillus plantarum to produce high concentrations of lactic acid. The time course of sugars, organic acids and pH were measured. Available sugars were consumed by L. plantarum producing up to 8.3 g L(-1) of lactic acid. Lactic acid changed the pH from 3.9 to 3.4 after 14 days post-inoculation without yielding a relevant concentration of acetic acid (0.34 g L(-1)).
Publisher: Oxford University Press (OUP)
Date: 26-11-2019
Abstract: Filamentous cluster III Defluviicoccus (DF3) are known to proliferate and cause bulking issues in industrial wastewater treatment plants. Members of the genus Defluviicoccus are also known to exhibit the glycogen accumulating organism (GAO) phenotype, which is suggested to be detrimental to enhanced biological phosphorus removal (EBPR). Despite the reported negative impact members of the DF3 have on activated sludge wastewater treatment systems, limited research has focused on understanding the physiological traits that allow them to compete in these environments. In this study, a near complete genome of an abundant filamentous DF3 named 'Candidatus Defluviicoccus seviourii' was obtained from a full-scale sequencing batch reactor (SBR) treating winery wastewater. Annotation of the 'Ca. D. seviourii' genome revealed interesting metabolic features that help to understand the abundance of this microorganism in industrial wastewater treatment plants. Their potential for the storage of polyhydroxyalkanoates (PHA) is suggested to favour these organisms with the intermittent availability of carbon in these systems. An ability to fix nitrogen and take up urea may provide them with an additional advantage with the characteristically high carbon to nitrogen content of industrial waste. The genome and preliminary findings of this study provide a foundation for further research into these biotechnologically relevant organisms.
Location: Portugal
No related grants have been discovered for Cristobal Onetto.