Biology subjects

Onetto, C. A.

Publications and source records attributed to Onetto, C. A..

8 recordsLinked to original sources

bioRxiv2025

Genetic and phenotypic diversity of wine-associated Hanseniaspora species

The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and enological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated from wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving (FEL) lineages that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting specifically in the FEL lineage. Pangenome analysis within H. uvarum identified extensive copy number variation (CNV), particularly in genes related to xenobiotic tolerance, nutrient transport and metabolism. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the Hanseniaspora FEL lineage, with significant enrichment in genes within the lysine biosynthetic pathway, suggesting a key role for this amino acid in early FEL adaptation. In H. uvarum, signatures of recent positive selection were detected in genes linked to sulphur assimilation, sterol biosynthesis and glycerol production, indicating potential adaptation to the stresses imposed by grape and wine fermentation. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO2, and cold tolerance. These findings provide novel insights into the genomic evolution and functional diversity of Hanseniaspora, expanding our understanding of yeast adaptation to wine fermentation and laying the foundation for targeted gene investigations within this important genus.

microbiology↗

bioRxiv2024

A rapid growth rate underpins the dominance of Hanseniaspora uvarum in spontaneous grape juice fermentations

Hanseniaspora uvarum is consistently observed as the dominant non-Saccharomyces species in spontaneous grape juice fermentations. However, the physiological mechanisms and physicochemical variables influencing the prevalence of H. uvarum over other non-Saccharomyces species remain unclear. We tested the physicochemical parameters contributing to H. uvarum dominance by inoculating a chemically diverse set of grape juices with a mock community whose composition was defined following a comprehensive microbial survey of spontaneous fermentations. Our findings indicated that the chemical composition of grape juice had minimal impact on the microbial dynamics of fermentation, with H. uvarum emerging as the dominant non-Saccharomyces species in nearly all conditions tested. Grape juice composition primarily influenced the total yeast abundance of the mock community. Flow cytometry analysis confirmed that H. uvarum has a faster growth rate than Saccharomyces cerevisiae and several other Hanseniaspora spp.. Moreover, its growth was not affected by the presence of S. cerevisiae, explaining its rapid dominance in spontaneous fermentations. The rapid growth of H. uvarum negatively impacted the growth of S. cerevisiae, with significant implications for fermentation performance and sugar consumption. The results of this study suggest that the fast growth rate of H. uvarum enables it to quickly dominate the grape juice environment during the early stages of fermentation. This physiological advantage indicates that the initial abundance of H. uvarum may be critical to the outcome of spontaneous fermentations, as evidenced by its direct impact on the growth of S. cerevisiae and fermentation performance.

microbiology↗

bioRxiv2024

Grapevine Shiraz Disease-associated viruses lead to significant yield losses by altering transcription of genes related to defence responses and photosynthesis

Shiraz disease (SD) is a highly destructive disease of grapevines that is associated with Grapevine Virus A (GVA) infection of vineyards in Australia and South Africa. However, little is known about the transcriptional modifications in grapevine phloem tissues induced by SD. In this study, we explored the viral diversity and transcriptional changes linked to SD. Vines symptomatic for SD exhibited higher viral abundance and were also shown to be co-infected with both GVA and grapevine leafroll-associated virus (GLRaV-4) strain 9. Differential gene (DE) expression analysis revealed physiological responses of Vitis vinifera to the infection. Similar to other plant pathogen infections, SD upregulated genes associated with the systemic acquired resistance (SAR) mechanism and downregulated genes related to vine immunity. Additionally, upregulated genes suggests that callose deposition and the blocking of phloem sieve elements are likely employed by V. vinifera as a defence strategy to limit the internal spread of SD viruses. Grapevine Shiraz disease, Grapevine Virus A, Grapevine Leafroll Associated virus, Systemic Acquired Resistance, Transcriptomics

plant biology↗

bioRxiv2024

Adaptation during the transition from Ophiocordyceps entomopathogen to insect associate is accompanied by gene loss and intensified selection.

Fungal and bacterial symbiosis is an important adaptation that has occurred within many insect species, which usually results in the relaxation of selection across the symbiont genome. However, the evolutionary pressures and genomic consequences associated with this transition are not well understood. Pathogenic fungi of the genus Ophiocordyceps have undergone multiple, independent transitions from pathogen to associate, infecting soft-scale insects trans-generationally without killing them. To gain an understanding of the genomic adaptations underlying this transition, long-read sequencing was utilized to assemble the genomes of both Parthenolecanium corni and its Ophiocordyceps associate from a single insect. A highly contiguous haploid assembly was obtained for Part. corni, representing the first assembly from a single Coccoidea insect, in which 97% of its 227.8 Mb genome was contained within 24 contigs. Metagenomic-based binning produced a chromosome-level genome for Part. cornis Ophiocordyceps associate. The associate genome contained 524 gene loss events compared to free-living pathogenic Ophiocordyceps relatives, with predicted roles in hyphal growth, cell wall integrity, metabolism, gene regulation and toxin production. Contrasting patterns of selection were observed between the nuclear and mitochondrial genomes specific to the associate lineage. Intensified selection was most frequently observed across nuclear orthologs, while selection on mitochondrial genes was found to be relaxed. Furthermore, scans for diversifying selection identified associate specific selection within three adjacent enzymes catalyzing acetoacetates metabolism to acetyl-COA. This work provides insight into the adaptive landscape during the transition to an associate life history, along with a base for future research into the genomic mechanisms underpinning the evolution of Ophiocordyceps.

genomics↗

bioRxiv2024

Temporal and spatial dynamics within the fungal microbiome of grape fermentation

Wine fermentation is a highly complex and competitive environment, imposing harsh selective pressures on fungal community ecology and diversity. The composition of fungal communities inhabiting the surface of grapes will directly impact fermentation progression, wine quality, and contribute to the distinctiveness between wines from different geographical regions. Despite this, the extent of microbial community diversity between geographies, termed microbial terroir, remains highly debated. We amassed a large survey of grape spontaneous ferments over six years, encompassing 3105 fungal microbiomes across 14 geographically separated grape-growing regions, and nine grape cultivars. Investigation into the biodiversity of these ferments identified that few high abundance genera form the core of the initial grape microbiome. In line with previous studies, various consistent taxa were linked to specific geographical locations and grape varieties. However, these taxa accounted for a small portion of the overall diversity in the dataset. Through unsupervised clustering, we identified three distinct community types in the grape fungal microbiome, each exhibiting variations in the abundance of key genera. Analysing ferments across temporal and spatial scales revealed significant differences in species richness and compositional heterogeneity between wineries and grape growing regions. However, microbial communities were transient between years in the same winery, regularly transitioning between the three broad community types. We then investigated microbial community composition throughout the fermentative process and observed that initial microbial community composition is predictive of the diversity during the early stages of fermentation, with Hanseniaspora uvarum detected as the main non-Saccharomyces species within this large cohort of samples. Our results help to formulate a clear understanding of the spatial and temporal characteristics of the grape juice fungal microbiome and suggest that these communities are mainly defined by the grape niche and in a minor way shaped by local environmental conditions.

microbiology↗

bioRxiv2023

Metagenomic ecosystem monitoring of soft scale and mealybug infestations in Australian vineyards

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 sampled, 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.

ecology↗

bioRxiv2023

The genomic landscape of wild Saccharomyces cerevisiae is shaped by complex patterns of admixture, aneuploidy and recombination.

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 diversity. 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 diversity and demonstrates the presence of non-domesticated, non-European derived lineages of S. cerevisiae in Australian ecological niches that are actively admixing.

genomics↗

bioRxiv2022

The phased diploid genome assembly of Vitis vinifera cv. Shiraz.

Shiraz (Syrah) is a dark-skinned cultivar of the wine grape Vitis vinifera that forms the basis of some of the worlds 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 diversity 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.

genomics↗