Summary Humans have been making wine for thousands of years and microorganisms play an integral part in this process as they not only drive fermentation, but also significantly influence the flavour, aroma and quality of finished wines. Since fruits are ephemeral, they cannot comprise a permanent microbial habitat; thus, an age‐old unanswered question concerns the origin of fruit and ferment associated microbes. Here we use next‐generation sequencing approaches to examine and quantify the roles of native forest, vineyard soil, bark and fruit habitats as sources of fungal diversity in ferments. We show that microbial communities in harvested juice and ferments vary significantly across regions, and that while vineyard fungi account for ∼40% of the source of this diversity, uncultivated ecosystems outside of vineyards also prove a significant source. We also show that while communities in harvested juice resemble those found on grapes, these increasingly resemble fungi present on vine bark as the ferment proceeds.

We have a limited understanding of the relative contributions of different processes that regulate microbial communities, which are crucial components of both natural and agricultural ecosystems. The contributions of selective and neutral processes in defining community composition are often confounded in field studies because as one moves through space, environments also change. Managed ecosystems provide an excellent opportunity to control for this and evaluate the relative strength of these processes by minimising differences between comparable niches separated at different geographic scales. We use next-generation sequencing to characterize the variance in fungal communities inhabiting adjacent fruit, soil and bark in comparable vineyards across 1000 kms in New Zealand. By compartmentalizing community variation, we reveal that niche explains at least four times more community variance than geographic location. We go beyond merely demonstrating that different communities are found in both different niches and locations by quantifying the forces that define these patterns. Overall, selection unsurprisingly predominantly shapes these microbial communities, but we show the balance of neutral processes also have a significant role in defining community assemblage in eukaryotic microbes.

There is increased need to identify sustainable agricultural methods which avoid environmental degradation. Previous studies have focused on the effect of specific agricultural interventions on large organisms, but we have fewer data evaluating how microbes, which are key components of ecosystems, might be affected. Additionally, previous studies have been constrained as they only examined one habitat in an ecosystem and have not gone on to evaluate the effect of agricultural approach on harvested crops. Here we take an ecosystems approach and evaluate the net effect of conventional versus biodynamic management on agricultural ecosystems by quantifying fungal communities in multiple habitats using metagenomics. We go on to measure biodiversity in the crop and key chemical quality parameters in the product consumed by humans. We find that the method of management significantly affects communities in soil, on plant structures, and on the developing crop in subtle but importantly different ways in terms of number, type, and abundance of species. However, management approach has no effect on communities in the final harvested juice, nor on product traits aligned with quality. This shows that while management approach impacts different habitats in the environment in different ways, this does not automatically flow onto the harvested crop

Aquaculture is the fastest‐growing food production sector worldwide, yet industry has been slow to implement genomic techniques as routine tools. Applying genomics to new breeding programmes can provide important information about pedigree structure and genetic diversity; key parameters for a successful long‐term breeding programme. It can also provide insights on potential gains for commercially important, yet complex, quantitative traits such as growth rate. Here we investigated a population of 1100 captive‐bred F 1 silver trevally ( Pseudocaranx georgianus ), a promising new species for New Zealand aquaculture. We used whole‐genome information, coupled with image‐based phenotypic data collected over two years, to build the pedigree of the population, assess its genetic diversity, describe growth patterns of ten growth traits and estimate their genetic parameters. Successful parentage assignment of 664 F 1 individuals showed that the pedigree consisted of a complex mixture of full‐ and half‐sib individuals, with skewed reproductive success among parents, especially in females. Growth patterns showed seasonal fluctuations (average increase across all traits of 27.3% in summer and only 7% in winter) and strong inter‐family differences. Heritability values for growth traits ranged from 0.27 to 0.76. Genetic and phenotypic correlations between traits were high and positive, ranging from 0.57 to 0.94 and 0.50 to 1.00 respectively. The implications of these findings are threefold: first, the best on‐growing conditions are in warmer months, where highest growth peaks can be achieved; second, size‐ and family‐based selection can be used as early selection criterion if pedigree structure and inbreeding risks are closely monitored; third, selection for body length results in concomitant increases in height and weight, traits of paramount importance for aquaculture. It is concluded that there is substantial potential for genetic improvement of economically important traits, suggesting that silver trevally is a promising species for selective breeding for enhanced growth.

Background and Aims: Agricultural products deriving from the same genotypic clone often have different physical and sensory properties that influence their overall quality and value. Microorganisms may play key roles throughout the production of many crops, affecting plant and fruit health and modifying plant materials to produce socially and economically important commodities. Following this idea, we investigated whether fungal diversity both prior to and during fermentation was correlated with the concentration of three volatile thiols important to Sauvignon Blanc aroma and flavour. Methods and Results: We used molecular and metagenomics approaches to quantify yeast populations and GC/MS to quantify thiols and analysed these using random forest statistical approaches. The species of Saccharomyces yeasts present at the end of fermentation are significantly correlated with the concentration of 4-mercapto-4-methylpentan-2-one, while several other fungal species present in the must, which are known to be associated with vine and fruit health, are also correlated with thiol concentration. Conclusions: These data highlight the relationship between the presence of Saccharomyces uvarum and the production of 4-mercapto-4-methylpentan-2-one, while some members of the fungal community correlate with thiol concentration generally. Thus, components of the fungal community may potentially affect the accumulation of odourless precursors in grape via pathogenic effects during fruit ripening, but further research is required to confirm such speculation. Significance of the Study: This work emphasises the need for a better understanding of the interactions between microbial populations and agricultural products, and has implications for the management of fungal diversity and disease in these systems.