Production of volatile metabolites by grape-associated microorganisms

Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine

Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.

Microbial Diversity Associated with the Cabernet Sauvignon Carposphere (Fruit Surface) from Eight Vineyards in Henan Province, China

The microbial diversity on the carposphere (berry) surface of the grape cultivar Cabernet Sauvignon grown in eight different locations/vineyards of Henan Province was determined by high-throughput sequencing of the bacterial 16S rRNA gene and fungal 18S rRNA gene. The structure of bacterial and fungal communities varied according to the sampling sites, but with some common phyla. Proteobacteria and Ascomycota were dominant/common phyla for bacteria and fungi, respectively. A total of 27 and 20 bacterial and fungal families, respectively, and 39 and 20 bacterial and fungal genera, respectively, with statistically significant differences, were found among different sampling sites. The difference for metabolic pathways of bacteria among the sampling sites existed. In addition, various abundances of enzymes from different sites might indicate that different function patterns exist in microbiota from different sites. The results revealed that locations of grape vineyards might play a significant role in shaping the microbiome, as well as the fact that vineyards can be distinguished based on the abundance of several key bacterial and fungal taxa. Overall, these findings extend our understanding of the similarities and differences in microbial community and their metabolic function on Cabernet Sauvignon grape surfaces from different geographic locations.

Yeast communities of a North American hybrid wine grape differ between organic and conventional vineyards

AIMS

To compare the species diversity and composition of indigenous yeast communities of hybrid grapes from conventionally and organically cultivated vineyards of an emerging cool-climate wine producing region.

METHODS AND RESULTS

Illumina MiSeq sequences from L'Acadie blanc grape musts were processed and filtered to characterize indigenous yeast communities in organic and conventional vineyards of the Annapolis Valley wine region in Nova Scotia, Canada. While cultivation practice was not associated with yeast diversity or species richness, there was a strong effect on yeast community composition, with conventional vineyards characterized by higher proportions of Sporidiobolales and Filobasidium magnum, and organic vineyards supporting Filobasidium species other than F. magnum and higher proportions of Symmetrospora. There was also variation in yeast community composition among individual vineyards, and from year to year.

CONCLUSIONS

This is the first comprehensive assessment of yeasts associated with hybrid grapes grown using different cultivation practices in a North American cool climate wine region. Communities were dominated by basidiomycete yeasts and species composition of these yeasts differed significantly between vineyards employing organic and conventional cultivation practices. The role of basidiomycete yeasts in winemaking is not well understood, but some species may influence wine characteristics.

Diversity of fungal communities on Cabernet and Aglianico grapes from vineyards located in Southern Italy

Grape-associated microbial community is influenced by a combination of viticultural, climatic, pedological and anthropological factors, collectively known as terroir. Therefore, grapes of the same cultivar grown in different areas can be appreciated for their distinctive biogeographic characteristics. In our previous study, we showed that the phenotypic response of Aglianico and Cabernet grapevines from Molise and Sicily regions is significantly influenced by the prevailing pedoclimatic conditions, particularly soil physical properties. However, the scale at which microbial communities differ could be important in clarifying the concept of terroir, including whether it is linked to the grape variety present in a particular vineyard. To explore this further, in the research presented here, a comparative study on the fungal communities inhabiting the berry surfaces of Cabernet and Aglianico cultivars was conducted on different vineyards located in Southern Italy (Molise, Sicily and Campania regions, the first two of which had been involved in our previous study) by using high-throughput sequencing (HTS) and multivariate data analysis. The descriptive approach through relative abundance analysis showed the most abundant phyla (Ascomycota, Basidiomycota, and Chytridiomycota), families (Cladosporiaceae, Saccotheciaceae, Pleosporaceae, Saccharomycodaceae, Sporidiobolaceae, Didymellaceae, Filobasidiaceae, Bulleribasidiaceae, and Saccharomycetaceae) and genera (Cladosporium, Aureobasidium, Alternaria, Stemphylium and Filobasidium) detected on grape berries. The multivariate data analysis performed by using different packages (phyloseq, Vegan, mixOmics, microbiomeMarker and ggplot2) highlighted that the variable "vineyard location" significantly affect the fungal community, while the variable "grape variety" has no significant effect. Thus, some taxa are found to be part of specific vineyard ecosystems rather than specific grape varieties, giving additional information on the microbial contribution to wine quality, thanks to the presence of fermentative yeasts or, conversely, to the involvement in negative or detrimental roles, due to the presence of grape-deriving fungi implied in the spoilage of wine or in grapevine pathogenesis. In this connection, the main functions of core taxa fungi, whose role in the vineyard environment is still poorly understood, are also described.

Shared governance in the plant holobiont and implications for one health

The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.

Three new griseofulvin derivatives from Aureobasidium pullulans

Three new griseofulvin derivatives, griseofulvinoside A-C (1-3), were isolated from the ethyl acetate extract of the solid fermentation product of Aureobasidium pullulans. Their structures were elucidated based on extensive spectroscopic data analysis of MS, 1D and 2D NMR. The antifungal activities of new compounds were evaluated against four phytopathogenic fungi in vitro, and all test compounds demonstrated inhibitory effects. Among them, compound 2 exhibited the most potent activities against the four selected phytopathogenic fungi with inhibitory rates ranging from 40.2 to 75.8% at 0.2 mg/mL.

Diversity of 'Cabernet Sauvignon' Grape Epidermis and Environmental Bacteria in Wineries from Different Sub-Regions of the Eastern Foothills of Helan Mountain, Ningxia

Understanding the composition of the bacterial community on the epidermis of wine grapes and in winery environments, as well as the response of grape epidermal bacteria to climatic factors, plays a significant role in ensuring grape health and promoting grape conversion into wine. This study utilized high-throughput sequencing to explore the composition of the bacterial community on the wine grape epidermis and representative wineries of three sub-regions of the Eastern Foothills of Helan Mountain, Ningxia. The results showed that the bacterial diversity and richness in the Yongning (YN) sub-region were the highest, with Qingtongxia (QTX) having the lowest levels of grape epidermal bacteria. The bacterial diversity and richness were the highest in Yinchuan (YC) and the lowest in YN in the winery environment (p < 0.05). The composition of dominant bacteria on the grape epidermis and in winery environments of the three sub-regions was not different at the phylum and genus level, but the levels of these dominant bacteria were different among the sub-regions. There was a correlation between grape epidermal bacteria and climatic factors. Approximately 93% of the bacterial genera on the grape epidermal genera in the three sub-regions are present in the winery environment and contain all the dominant bacterial genera on the epidermis.

Role of Microbial Volatile Organic Compounds in Promoting Plant Growth and Disease Resistance in Horticultural Production

Microbial volatile organic compounds (MVOCs) are a diverse group of volatile organic compounds that microorganisms may produce and release into the environment. These compounds have both positive and negative effects on plants, as they have been shown to be effective at mitigating stresses and functioning as immune stimulants. Furthermore, MVOCs modulate plant growth and systemic plant resistance, while also serving as attractants or repellents for insects and other stressors that pose threats to plants. Considering the economic value of strawberries as one of the most popular and consumed fruits worldwide, harnessing the benefits of MVOCs becomes particularly significant. MVOCs offer cost-effective and efficient solutions for disease control and pest management in horticultural production, as they can be utilized at low concentrations. This paper provides a comprehensive review of the current knowledge on microorganisms that contribute to the production of beneficial volatile organic compounds for enhancing disease resistance in fruit products, with a specific emphasis on broad horticultural production. The review also identifies research gaps and highlights the functions of MVOCs in horticulture, along with the different types of MVOCs that impact plant disease resistance in strawberry production. By offering a novel perspective on the application and utilization of volatile organic compounds in sustainable horticulture, this review presents an innovative approach to maximizing the efficiency of horticultural production through the use of natural products.

Fungal dynamic during apricot wine spontaneous fermentation and aromatic characteristics of Pichia kudriavzevii for potential as starter

Microbial activity during spontaneous fermentation in alcoholic beverages have driven in developing the chemical and aromatic characteristic of products but not clear in apricot wines. We have characterised the composition of fungal communities and volatile metabolites in apricot wine spontaneous fermentation among two Shaanxi regions. Results showed that Aureobasidium, Alternaria, Pichia and Saccharomyces, were the dominant fungi in apricot wine fermentation. A total of 80 volatiles including esters, alcohols, acids and terpenes were detected from two apricot wines. Their correlations suggested that apricot wine aroma was mainly affected by Pichia kudriavzevii, rather than Saccharomyces cerevisiae we commonly considered. Furthermore, reinforced inoculation of P. kudriavzevii LQD20 has exhibited the commendable potential in enhancing sensory qualities. The results of this study provide fundamental information of the indigenous microbiota in microbial dynamic during apricot wine fermentation, which would be helpful in exploiting the strains with potential for industrial use as starter cultures.

The Combined Effect of Lactic Acid Bacteria and Galactomyces geotrichum Fermentation on the Aroma Composition of Sour Whey

The increase in demand for food flavorings due to the shortening and simplification of food production technology also entails an increase in the demand for new technologies for their production. The biotechnological production of aromas is a solution characterized by a high efficiency, an independence from environmental factors and a relatively low cost. In this study, the influence of the implementation of lactic acid bacteria pre-fermentation into the production of aroma compounds by Galactomyces geotrichum on a sour whey medium on the intensity of the obtained aroma composition was analyzed. The monitoring of the culture in terms of biomass buildup, the concentration of selected compounds, and the pH resulted in the confirmation of interactions between the analyzed microorganisms. The post-fermentation product underwent a comprehensive sensomic analysis for the identification and quantification of the aroma-active compounds. The use of gas chromatography-olfactometry (GC-O) analysis and the calculation of odor activity values (OAVs) allowed 12 key odorants to be identified in the post-fermentation product. The highest OAV was found for phenylacetaldehyde with a honey odor (1815). The following compounds with the highest OAVs were 2,3-butanedione with a buttery aroma (233), phenylacetic acid with a honey aroma (197), 2,3-butanediol with a buttery aroma (103), 2-phenylethanol with a rosy aroma (39), ethyl octanoate with a fruity aroma (15), and ethyl hexanoate with a fruity aroma (14).

Emission of odor pollutants and variation in microbial community during the initial decomposition stage of municipal biowaste

Odor pollution often occurs in the initial decomposition stage of municipal biowaste, including throwing/collection and transportation. However, this aspect of odor impact from municipal biowaste has not been well studied. In this study, a practical dustbin (120 L) equipped with flux chamber and filled with three types of municipal biowaste was used to simulate garbage storage conditions. The result indicated that the emission rate of odor pollutants for uncooked food waste (UFW) represented a nearly linear growth trend, reaching the maximum (3963 ± 149 μg kg^-1 DM h^-1) at 72 h. Cooked food waste (CFW) increased rapidly from 8 h to 24 h, and then remain fluctuated, reached the maximum (2026 ± 77 μg kg^-1 DM h^-1) at 72 h. Comparatively, household kitchen waste (HKW) reached the maximum emission rate (10,396 ± 363 μg kg^-1 DM h^-1) at 16 h. Sulfide and aldehydes ketones were identified as dominant odor contributor to UFW and CFW, respectively. While aldehydes ketones and sulfides were both dominant odor contributor to HKW. Moreover, the microbial diversity analysis suggests that Acinetobacter was the dominant genus in UFW, and Lactobacillus was the dominant genus in CFW and HKW. In addition, it was evident that each odorous pollutant was significantly associated with two or more bacterial genera, and most bacterial genera such as Acinetobacter, were also significantly associated with multiple odorous pollutants. The variation of odorants composition kept consistent with microbial composition. The present study could provide essential evidence for a comprehensive understanding of odorant generation in the initial decomposition stage of municipal biowaste. It could contribute to setting out strategies for odor control and abatement in municipal biowaste management systems.

Spatial and Seasonal Structure of Bacterial Communities Within Alpine Vineyards: Trentino as a Case Study

Bacteria have a fundamental role in determining the fitness of grapevine, the composition of grapes and the features of wines but at present, little information is available. In this work, the bacteria colonizing the different portions of grapevine (bark, leaves and grapes) were explored in the vineyards of the Alpine region of Trentino, considering the impact of different environmental and agronomical variables. The vineyards included in the work were selected based on their different geographical positions (altitude) and grapevine training systems in order to explore the whole variability of the grapevine ecosystem. Moreover, the surface amount of copper was measured on grapes and leaves during the vegetative growth. Bacterial analysis, performed using plate counts and Illumina MiSeq, revealed an increase in the concentration of grape bacteria proportional to the progress of the ripening stage. Conversely, the peak of bacterial concentration onto leaf and bark samples occurred in August, probably due to the more favourable environmental conditions. In bark samples, the bacterial microbiota reached the 7 log CFU/cm², while 6 log UFC/g were measured in grape samples. A remarkable biodiversity was observed, with 13 phyla, 35 classes, 55 orders, 78 families and 95 genera of bacteria present. The presence of some taxa (Alphaproteobacteria, Desulfovibrionaceae, Clostriadiales, Oscillospira, Lachnospiraceae and Bacteroidales) was ubiquitous in all vineyards, but differences in terms of relative abundance were observed according to the vegetative stage, altitude of the vineyard and training system. Bacteria having oenological implication (Lactobacillus, Pediococcus and Oenococcus) were detected in grape samples collected in August, in low abundance. The data revealed a complex bacterial ecosystem inside the vineyard that, while maintaining common traits, evolves according to environmental and agronomical inputs. This study contributes to define the role of bacteria in the complex balance established in each vineyard between human actions and agricultural environment, known as terroir.

The mature phyllosphere microbiome of grapevine is associated with resistance against Plasmopara viticola

Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.

Volatile biomarkers for non-invasive detection of American foulbrood, a threat to honey bee pollination services

Honey bees provide essential environmental services, pollinating both agricultural and natural ecosystems that are crucial for human health. However, these pollination services are under threat by outbreaks of the bacterial honey bee disease American foulbrood (AFB). Caused by the bacterium, Paenibacillus larvae, AFB kills honey bee larvae, converting the biomass to a foul smelling, spore-laden mass. Due to the bacterium's tough endospores, which are easily spread and extremely persistent, AFB management requires the destruction of infected colonies in many countries. AFB detection remains a significant problem for beekeepers: diagnosis is often slow, relying on beekeepers visually identifying symptoms in the colony and molecular confirmation. Delayed detection can result in large outbreaks during high-density beekeeping pollination events, jeopardising livelihoods and food security. In an effort to improve diagnostics, we investigated volatile compounds associated with AFB-diseased brood in vitro and in beehive air. Using Solid Phase Microextraction and Gas Chromatography Mass-Spectrometry, we identified 40 compounds as volatile biomarkers for AFB infections, including 16 compounds previously unreported in honey bee studies. In the field, we detected half of the biomarkers in situ (in beehive air) and demonstrated their sensitivity and accuracy for diagnosing AFB. The most sensitive volatile biomarker, 2,5-dimethylpyrazine, was exclusively detected in AFB-disease larvae and hives, and was detectable in beehives with <10 AFB-symptomatic larvae. These, to our knowledge, previously undescribed biomarkers are prime candidates to be targeted by a portable sensor device for rapid and non-invasive diagnosis of AFB in beehives.

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

BACKGROUND

Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.

RESULTS

Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10⁷-10¹⁰ marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa.

CONCLUSION

Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.

Co-cultures of Propionibacterium freudenreichii and Bacillus amyloliquefaciens cooperatively upgrade sunflower seed milk to high levels of vitamin B12 and multiple co-benefits

BACKGROUND

Sunflower seeds (Helianthus annuus) display an attractive source for the rapidly increasing market of plant-based human nutrition. Of particular interest are press cakes of the seeds, cheap residuals from sunflower oil manufacturing that offer attractive sustainability and economic benefits. Admittedly, sunflower seed milk, derived therefrom, suffers from limited nutritional value, undesired flavor, and the presence of indigestible sugars. Of specific relevance is the absence of vitamin B12. This vitamin is required for development and function of the central nervous system, healthy red blood cell formation, and DNA synthesis, and displays the most important micronutrient for vegans to be aware of. Here we evaluated the power of microbes to enrich sunflower seed milk nutritionally as well as in flavor.

RESULTS

Propionibacterium freudenreichii NCC 1177 showed highest vitamin B12 production in sunflower seed milk out of a range of food-grade propionibacteria. Its growth and B12 production capacity, however, were limited by a lack of accessible carbon sources and stimulants of B12 biosynthesis in the plant milk. This was overcome by co-cultivation with Bacillus amyloliquefaciens NCC 156, which supplied lactate, amino acids, and vitamin B7 for growth of NCC 1177 plus vitamins B2 and B3, potentially supporting vitamin B12 production by the Propionibacterium. After several rounds of optimization, co-fermentation of ultra-high-temperature pre-treated sunflower seed milk by the two microbes, enabled the production of 17 µg (100 g)-1 vitamin B12 within four days without any further supplementation. The fermented milk further revealed significantly enriched levels of L-lysine, the most limiting essential amino acid, vitamin B3, vitamin B6, improved protein quality and flavor, and largely eliminated indigestible sugars.

CONCLUSION

The fermented sunflower seed milk, obtained by using two food-grade microbes without further supplementation, displays an attractive, clean-label product with a high level of vitamin B12 and multiple co-benefits. The secret of the successfully upgraded plant milk lies in the multifunctional cooperation of the two microbes, which were combined, based on their genetic potential and metabolic signatures found in mono-culture fermentations. This design by knowledge approach appears valuable for future development of plant-based milk products.

The microbiome and resistome of apple fruits alter in the post-harvest period

BACKGROUND

A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing.

RESULTS

All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing.

CONCLUSION

Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.

Grapevine rootstock and soil microbiome interactions: Keys for a resilient viticulture

Soil microbiota has increasingly been shown to play an integral role in viticulture resilience. The emergence of new metagenomic and culturomic technologies has led to significant advances in the study of microbial biodiversity. In the agricultural sector, soil and plant microbiomes have been found to significantly improve resistance to environmental stressors and diseases, as well as influencing crop yields and fruit quality thus improving sustainability under shifting environments. Grapevines are usually cultivated as a scion grafted on rootstocks, which are selected according to pedoclimatic conditions and cultural practices, known as terroir. The rootstock connects the surrounding soil to the vine's aerial part and impacts scion growth and berry quality. Understanding rootstock and soil microbiome dynamics is a relevant and important field of study, which may be critical to improve viticulture sustainability and resilience. This review aims to highlight the relationship between grapevine roots and telluric microbiota diversity and activity. In addition, this review explores the concept of core microbiome regarding potential applications of soil microbiome engineering with the goal of enhancing grapevine adaptation to biotic and abiotic stress.

Antibiotic Effects of Volatiles Produced by Bacillus tequilensis XK29 against the Black Spot Disease Caused by Ceratocystis fimbriata in Postharvest Sweet Potato

Black spot disease caused by Ceratocystis fimbriata is destructive to the production, transportation, and storage of sweet potato. The antifungal effects of Bacillus tequilensis XK29 against C. fimbriata through volatile organic compounds (VOCs) were evaluated in this study. The activated carbon assay proved that XK29 could exert antibiotic effects through volatiles. By optimizing the wheat seed weight, inoculation method, concentration, volume, and time, the antifungal activity of XK29 was significantly improved. XK29 fumigation inhibited spore formation and germination and changed the cell morphology of C. fimbriata. During the storage of sweet potato tuber roots, XK29 effectively controlled black spot disease and reduced the weight loss and malondialdehyde content. Metabolomic analysis revealed that 21 volatile compounds were released from XK29. Isovaleric acid, isobutyric acid, and 2-methylbutanoic acid effectively inhibited the growth of C. fimbriata. These results indicate that B. tequilensis XK29 has a good potential to be developed as a microbial fumigation agent.

Analysis of the Ability to Produce Pleasant Aromas on Sour Whey and Buttermilk By-Products by Mold Galactomyces geotrichum: Identification of Key Odorants

Currently, there is a growing demand for flavorings, especially of natural origin. It is worth paying attention to the biotechnological processes of flavor production, characterized by simplicity, high efficiency and relatively low cost. In this study, we analyzed the ability of the Galac tomyces geotrichum mold to transform by-products of the dairy industry: sour whey and buttermilk to complex flavour mixtures with pleasant, honey-rose aroma. Furthermore, the aroma complexity of the fermentation product has been carefully identified applying a sensomic approach involving the use of gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS) and stable isotope dilution assay (SIDA) to identify and quantify aroma compounds. Based on the calculation of odor activity value (OAV), 13 key aroma compounds were present in both tested variants. The highest OAVs were found for phenylacetaldehyde (honey-like) in the buttermilk variant (912) and 2-phenylethanol (rose-like) in the sour whey variant (524). High values of this indicator were also recorded for phenylacetaldehyde (319) and 3-methyl-1-butanol with a fruity aroma (149) in the sour whey culture. The other compounds identified are 3-methylbutanal (malty), 2,3-butanedione (cheesy), isovaleric acid (cheesy), 3-(methylthio)-propanal (boiled potato), butanoic acid (vinegar), (E)-2-nonenal (fatty), ethyl furaneol (burnt sugar), dimethyl trisulfide (cabbage), and acetic acid (vinegar).

Bacterial volatile compound-based tools for crop management and quality

Bacteria produce a huge diversity of metabolites, many of which mediate ecological relations. Among these, volatile compounds cause broad-range effects at low doses and, therefore, may be exploited for plant defence strategies and agricultural production, but such applications are still in their early development. Here, we review the latest technologies involving the use of bacterial volatile compounds for phytosanitary inspection, biological control, plant growth promotion, and crop quality. We highlight a variety of effects with a potential applicative interest, based on either live biocontrol and/or biostimulant agents, or the isolated metabolites responsible for the interaction with hosts or competitors. Future agricultural technologies may benefit from the development of new analytical tools to understand bacterial interactions with the environment.

Genome-based selection and application of food-grade microbes for chickpea milk fermentation towards increased L-lysine content, elimination of indigestible sugars, and improved flavour

Background

Plant-based milk alternatives are more popular than ever, and chickpea-based milks are among the most commercially relevant products. Unfortunately, limited nutritional value because of low levels of the essential amino acid l-lysine, low digestibility and unpleasant taste are challenges that must be addressed to improve product quality and meet consumer expectations.

Results

Using in-silico screening and food safety classifications, 31 strains were selected as potential l-lysine producers from approximately 2,500 potential candidates. Beneficially, 30% of the isolates significantly accumulated amino acids (up to 1.4 mM) during chickpea milk fermentation, increasing the natural level by up to 43%. The best-performing strains, B. amyloliquefaciens NCC 156 and L. paracasei subsp. paracasei NCC 2511, were tested further. De novo lysine biosynthesis was demonstrated in both strains by ¹³C metabolic pathway analysis. Spiking small amounts of citrate into the fermentation significantly activated l-lysine biosynthesis in NCC 156 and stimulated growth. Both microbes revealed additional benefits in eliminating indigestible sugars such as stachyose and raffinose and converting off-flavour aldehydes into the corresponding alcohols and acids with fruity and sweet notes.

Conclusions

B. amyloliquefaciens NCC 156 and L. paracasei subsp. paracasei NCC 2511 emerged as multi-benefit microbes for chickpea milk fermentation with strong potential for industrial processing of the plant material. Given the high number of l-lysine-producing isolates identified in silico, this concept appears promising to support strain selection for food fermentation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01595-2.

Analysis of microbial community diversity of muscadine grape skins

Microorganisms in grape skins play vital roles in grapevine health, productivity, wine quality and organoleptic properties. To investigate microbial diversity of muscadine grape skins, 16S and ITS sequences of 30 samples from six muscadine (Muscadinia rotundifolia Michx.) cultivars grown in Guangxi, China, were sequenced using Illumina Novaseq platform. A total of 7,317 bacterial operational taxonomic units (OTUs) and 1,611 fungal OTUs were obtained, and clustered into 38 bacterial and 7 known fungal phyla. The dominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, Verrucomicrobia, Acidobacteria, and Patescibacteria, and the dominant genera were Lelliottia, Prevotella_9, Escherichia-Shigella, Lactobacillus, Pseudomonas, Akkermansia, Faecalibacterium, Rahnella, and Acinetobacter. For fungi, the dominant phyla were Ascomycota, Basidiomycota, and Mortierellomycota, and the dominant genera were Acaromyces, Uwebraunia, Penicillium, Zygosporium, Ilyonectria, Aspergillus, Neodevriesia, Strelitziana, Mortierella, and Fusarium. Alpha diversity analysis and Kruskal-Wallis H test demonstrated that microbial diversity and composition were affected by the cultivar. The Pearson correlation analysis of species revealed complex interactions among microbes. PICRUSt2 predicted that the metabolism of carbohydrates, cofactors, vitamins, amino acids, terpenoids, polyketides, lipids and biosynthesis of other secondary metabolites were abundant. These results contribute to understanding the uniqueness of muscadine grapes and the links among microorganisms in grape skins.

Native yeast and non-yeast fungal communities of Cabernet Sauvignon berries from two Washington State vineyards, and persistence in spontaneous fermentation

To address a knowledge gap about the grape berry mycobiome from Washington State vineyards, next-generation sequencing of the internal transcribed spacer region (ITS1) was used to identify native yeast and fungal species on berries of cultivar 'Cabernet Sauvignon' from two vineyards at veraison and harvest in 2015 and 2016. Four hundred fifty-six different yeast amplicon sequence variants (ASV), representing 184 distinct taxa, and 2467 non-yeast fungal ASV (791 distinct taxa) were identified in this study. A set of 50 recurrent yeast taxa, including Phaeococcomyces, Vishniacozyma and Metschnikowia, were found at both locations and sampling years. These yeast species were monitored from the vineyard into laboratory-scale spontaneous fermentations. Taxa assignable to Metschnikowia and Saccharomyces persisted during fermentation, whereas Curvibasidium, which also has possible impact on biocontrol and wine quality, did not. Sulfite generally reduced yeast diversity and richness, but its effect on the abundance of specific yeasts during fermentation was negligible. Among the 106 recurring non-yeast fungal taxa, Alternaria, Cladosporium and Ulocladium were especially abundant in the vineyard. Vineyard location was the primary factor that accounted for the variation among both communities, followed by year and berry developmental stage. The Washington mycobiomes were compared to those from other parts of the world. Sixteen recurrent yeast species appeared to be unique to Washington State vineyards. This subset also contained a higher proportion of species associated with cold and extreme environments, relative to other localities. Certain yeast and non-yeast fungal species known to suppress diseases or modify wine sensory properties were present in Washington vineyards, and likely have consequences to vineyard health and wine quality.

Yeast-nectar interactions: metacommunities and effects on pollinators

About 90% of all flowering plant species are pollinated by animals. Animals are attracted to flowers because they often provide food in the form of nectar and pollen. While floral nectar is assumed to be initially sterile, it commonly becomes colonized by yeasts after animals have visited the flowers. Although yeast communities in floral nectar appear simple, community assembly depends on a complex interaction between multiple factors. Yeast colonization has a significant effect on the scent of floral nectar, foraging behavior of insects and nectar consumption. Consumption of nectar colonized by yeasts has been shown to improve bee fitness, but effects largely depended on yeast species. Altogether, these results indicate that dispersal, colonization history and nectar chemistry strongly interact and have pronounced effects on yeast metacommunities and, as a result, on bee foraging behavior and fitness. Future research directions to better understand the dynamics of plant-microbe-pollinator interactions are discussed.

Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves

Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine’s resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.

Characterization of Microbial Dynamics and Volatile Metabolome Changes During Fermentation of Chambourcin Hybrid Grapes From Two Pennsylvania Regions

Microbial diversity present on grapes in wineries, and throughout fermentation has been associated with important metabolites for final wine quality. Although microbiome-metabolome associations have been well characterized and could be used as indicators of wine quality, the impact of regionality on the microbiome and metabolome is not well known. Additionally, studies between microbiome and metabolome have been conducted on single species grape such as Vitis vinifera instead of other species and interspecific hybrids. Although the Pennsylvania wine industry is relatively young compared to California, the industry has been experiencing rapid growth over the past decade and is expected to continue to grow in the future. Pennsylvania's climate of cold winters and high levels of rainfall throughout the growing season favors cultivation of interspecific hybrid grapes such as Vitis ssp. Chambourcin, one of the most commonly grown hybrid varieties in the state. Chambourcin is a prime candidate for studying the impact of regionality on microbiome-metabolome interactions as interspecific hybrid varieties could shape the future of winemaking. Here, we identify for the first time the regional distribution of microbial communities and their interactions with volatile metabolome during fermentation (0-20 days) by integrating high throughput Illumina sequencing (16S and ITS) and headspace-solid phase microextraction-gas chromatography-mass spectrometry. Analyzing 88 samples from nine wineries in the Central and East Pennsylvania regions, we observed high microbial diversity during early stages of fermentation (1-4 days) where non-Saccharomyces yeasts such as Starmerella and Aureobasidium and non-Oenococcus bacteria, Sphingomonas, likely contribute to microbial terroir to the resulting wines. Furthermore, key differentiators between two regions in Pennsylvania, as identified by LEfSe analysis, include the fungal genera Cladosporium and Kazachstania and the bacterial genera Lactococcus and Microbacterium. Moreover, 29 volatile fermentation metabolites were discriminated significantly (variable importance in projection > 1) between the two regions as shown by Partial Least Squares-Discriminant Analysis. Finally, Spearman's correlation identified regional differences of microbial-metabolite associations throughout fermentation that could be used for targeted microbiome manipulation to improve wine quality and preserve regionality. In summary, these results demonstrate the microbial signatures during fermentation and differential microorganisms and metabolites further support impact of regionality on Chambourcin wines in Pennsylvania.

The Important Contribution of Non-Saccharomyces Yeasts to the Aroma Complexity of Wine: A Review

Non-Saccharomyces yeast plays an important role in the initial stages of a wild ferment, as they are found in higher abundance in the vineyard than Saccharomyces cerevisiae. As such, there has been a focus in recent years to isolate these yeast species and characterize their effect on wine fermentation and subsequent aroma. This effect on wine aroma is often species and strain dependent, as the enzymatic profile of each yeast will determine which aroma compounds are formed as secondary metabolites. Semi-fermentative yeast, such as Hanseniaspora spp., Candida spp. and Metschnikowia pulcherrima, are commonly in high abundance in fresh grape must and have diverse enzymatic profiles, however they show a weak tolerance to ethanol, limiting their impact to the initial stages of fermentation. Fully fermentative non-Saccharomyces yeast, characterized by high ethanol tolerance, are often found at low abundance in fresh grape must, similar to Saccharomyces cerevisiae. Their ability to influence the aroma profile of wine remains high, however, due to their presence into the final stages of fermentation. Some fermentative yeasts also have unique oenological properties, such as Lanchancea thermotolerans and Schizosaccharomyces pombe, highlighting the potential of these yeast as inoculants for specific wine styles.

Identification of bacteria and fungi inhabiting fruiting bodies of Burgundy truffle (Tuber aestivum Vittad.)

Tuber species may be regarded as complex microhabitats hosting diverse microorganisms inside their fruiting bodies. Here, we investigated the structure of microbial communities inhabiting the gleba of wild growing (in stands) T. aestivum, using Illumina sequencing and culture-based methods. The two methods used in combination allowed to extract more information on complex microbiota of Tuber aestivum gleba. Analysis of the V3-V4 region of 16S rDNA identified nine phyla of bacteria present in the gleba of T. aestivum ascomata, mostly Proteobacteria from the family Bradyrhizobiaceae. Our results ideally match the earlier data for other Tuber species where the family Bradyrhizobiaceae was the most represented. The ITS1 region of fungal rDNA represented six alien fungal species belonging to three phyla. To complement the metagenomic analysis, cultivable fungi and bacteria were obtained from the gleba of the same T. aestivum fruiting bodies. The identified fungi mostly belong to the phylum Basidiomycota and same to Ascomycota. Analysis of cultivable bacteria revealed that all the specimens were colonized by different strains of Bacillus. Fungal community inhabiting T. aestivum fruiting bodies was never shown before.

Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine

Microbial ecology is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial activity influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus forming wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, and Saccharomyces cerevisiae populations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, and S. cerevisiae between geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance of S. cerevisiae during fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest that S. cerevisiae plays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeast S. cerevisiae can be distinct in a local setting. These findings provide further evidence for microbial contributions to wine terroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.

The Use of Sour and Sweet Whey in Producing Compositions with Pleasant Aromas Using the Mold Galactomyces geotrichum: Identification of Key Odorants

Fermented products with a pleasant aroma and with strong honey, rose, and fruit odor notes were developed through the biotransformation of a medium containing sour or sweet whey with the addition of l-phenylalanine by the Galactomyces geotrichum mold. In order to obtain the strong honey-rose aroma, G. geotrichum strains were screened and fermentation conditions were optimized to achieve a preferable ratio (>1) of phenylacetaldehyde to 2-phenylethanol by the Ehrlich pathway. This allowed post-fermentation products with the ratio of concentrations of phenylacetaldehyde to 2-phenylethanol being 1.7:1. Additionally, the use of gas chromatography-olfactometry (GC-O) analysis and the calculation of odor activity values (OAVs) allowed 10 key odorants to be identified in post-fermentation products. The highest OAVs were found for phenylacetaldehyde with a honey odor in both sour and sweet whey cultures (3010 and 1776, respectively). In the variant with sour whey, the following compounds with the highest OAVs were 3-methyl-1-butanol (131), 3-(methylthio)-propanal (119), 3-methylbutanal (90), dimethyl trisulfide (71), 2,3-butanedione (37), and 2-phenylethanol (29). In the post-fermentation product with sweet whey, the following compounds with the highest OAVs were 3-(methylthio)-propanal (112), dimethyl trisulfide (69), and 2,3-butanedione (41).

Microbial Co-Occurrence in Floral Nectar Affects Metabolites and Attractiveness to a Generalist Pollinator

Microbial metabolism can shape cues important for animal attraction in service-resource mutualisms. Resources are frequently colonized by microbial communities, but experimental assessment of animal-microbial interactions often focus on microbial monocultures. Such an approach likely fails to predict effects of microbial assemblages, as microbe-microbe interactions may affect in a non-additive manner microbial metabolism and resulting chemosensory cues. Here, we compared effects of microbial mono- and cocultures on growth of constituent microbes, volatile metabolite production, sugar catabolism, and effects on pollinator foraging across two nectar environments that differed in sugar concentration. Growth in co-culture decreased the abundance of the yeast Metschnikowia reukaufii, but not the bacterium Asaia astilbes. Volatile emissions differed significantly between microbial treatments and with nectar concentration, while sugar concentration was relatively similar among mono- and cocultures. Coculture volatile emission closely resembled an additive combination of monoculture volatiles. Despite differences in microbial growth and chemosensory cues, honey bee feeding did not differ between microbial monocultures and assemblages. Taken together, our results suggest that in some cases, chemical and ecological effects of microbial assemblages are largely predictable from those of component species, but caution that more work is necessary to predict under what circumstances non-additive effects are important.

Aureobasidium pullulans volatilome identified by a novel, quantitative approach employing SPME-GC-MS, suppressed Botrytis cinerea and Alternaria alternata in vitro

Volatile organic compounds (VOCs) produced by Aureobasidium pullulans were investigated for antagonistic actions against Alternaria alternata and Botrytis cinerea. Conidia germination and colony growth of these two phytopathogens were suppressed by A. pullulans VOCs. A novel experimental setup was devised to directly extract VOCs using solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) from antagonist-pathogen culture headspace. The proposed system is a robust method to quantify microbial VOCs using an internal standard. Multivariate curve resolution-alternating least squares deconvolution of SPME-GC-MS spectra identified fourteen A. pullulans VOCs. 3-Methyl-1-hexanol, acetone, 2-heptanone, ethyl butyrate, 3-methylbutyl acetate and 2-methylpropyl acetate were newly identified in A. pullulans headspace. Partial least squares discriminant analysis models with variable importance in projection and selectivity ratio identified four VOCs (ethanol, 2-methyl-1-propanol, 3-methyl-1-butanol and 2-phenylethanol), with high explanatory power for discrimination between A. pullulans and pathogen. The antifungal activity and synergistic interactions of the four VOCs were evaluated using a Box-Behnken design with response surface modelling. Ethanol and 2-phenylethanol are the key inhibitory A. pullulans VOCs against both B. cinerea and A. alternata. Our findings introduce a novel, robust, quantitative approach for microbial VOCs analyses and give insights into the potential use of A. pullulans VOCs to control B. cinerea and A. alternata.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew

The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using Biolog^TM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.

Real-time PCR assays for the quantification of native yeast DNA in grape berry and fermentation extracts

Native yeasts comprise part of the microbial community in grape vineyards and play roles in alcoholic fermentation and wine quality. Monitoring populations of native yeast in vineyards, during fermentation and after bottling will provide viticulturalists and oenologists with information needed to help control spoilage and to enhance desirable wine properties. This is especially crucial for low-intervention winemaking, in which fermentation is driven by native rather than starter microbes. In this study, we report real-time polymerase chain reaction (qPCR) assays for rapid quantification of seven grape yeast species or species combinations that occur in vineyards of Washington State and throughout the world. The assays targeted Candida californica, Curvibasidium pallidicorallinum, Metschnikowia spp., Meyerozyma caribbica/Me. guilliermondii, and Saccharomyces cerevisiae/S. bayanus. We also developed assays for the spoilage yeast Brettanomyces bruxellensis, and the yeast-like fungus Aureobasidium pullulans. Primers were designed for sequences in the internal transcribed spacer (ITS) and large ribosome subunit (LSU) gene. Known populations of yeast cells, added to fermentation extract, were significantly correlated to amounts of purified DNA in picograms (pg) for most of the yeasts; exceptions were A. pullulans and Cu. pallidicorallinum. The utility of the Metschnikowia, Meyerozyma and Saccharomyces assays was further validated by good correlations (R² = 0.75-0.83) between the number of target sequences and pg of DNA from qPCR for selected vineyard and fermentation samples. Overall, the assays will aid in species identification and monitoring of specific yeasts from cultures, vineyards and fermentation samples. Topics: Food Microbiology, Microbiological Method.

Novel Strategies for Soil-Borne Diseases: Exploiting the Microbiome and Volatile-Based Mechanisms Toward Controlling Meloidogyne-Based Disease Complexes

Under more intensified cropping conditions agriculture will face increasing incidences of soil-borne plant pests and pathogens, leading to increasingly higher yield losses world-wide. Soil-borne disease complexes, in particular, are especially difficult to control. In order to better understand soil-borne Meloidogyne-based disease complexes, we studied the volatile-based control mechanism of associated bacteria as well as the rhizospheric microbiome on Ugandan tomato plants presenting different levels of root-galling damage, using a multiphasic approach. The experimental design was based on representative samplings of healthy and infected tomato plants from two field locations in Uganda, to establish species collections and DNA libraries. Root galling symptoms on tomato resulted from a multispecies infection of root-knot nematodes (Meloidogyne spp.). Results revealed that 16.5% of the bacterial strain collection produced nematicidal volatile organic compounds (nVOC) active against Meloidogyne. Using SPME GC-MS, diverse VOC were identified, including sulfuric compounds, alkenes and one pyrazine. Around 28% of the bacterial strains were also antagonistic toward at least one fungal pathogen of the disease complex. However, antagonistic interactions appear highly specific. Nematicidal antagonists included Pseudomonas, Comamonas, and Variovorax and fungicidal antagonists belonged to Bacillus, which interestingly, were primarily recovered from healthy roots, while nematode antagonists were prominent in the rhizosphere and roots of diseased roots. In summary, all antagonists comprised up to 6.4% of the tomato root microbiota. In general, the microbiota of healthy and diseased root endospheres differed significantly in alpha and quantitative beta diversity indices. Bacteria-derived volatiles appear to provide a remarkable, yet wholly unexploited, potential to control Meloidogyne-based soil-borne disease complexes. The highly specific observed antagonism indicates that a combination of volatiles or VOC-producing bacteria are necessary to counter the range of pathogens involved in such complexes.

The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications

The plant microbiome is known to be influenced by certain biotic as well as abiotic factors. Nevertheless, the drivers for specific changes in microbial community composition and structure are largely unknown. In the present study, the effects of chemical and biological treatments for plant protection on the indigenous microbiome of Camellia sinensis (L.) Kuntze were contrasted. Assessment of bacteria-specific ribosomal RNA gene fragment amplicons from a representative set of samples showed an increased microbial diversity in treated plants when compared to untreated samples. Moreover, distinct microbial fingerprints were found for plants subjected to a conventional pesticide treatment with lime sulfur as well as for plants that were biologically treated with a Piriformospora indica spore solution. The bacterial community of pesticide-treated plants was augmented by 11 taxa assigned to Proteobacteria and Actinobacteria. In contrast, plants from biological control treatments were augmented by 10 taxa representing a more diversified community enrichment and included members of Actionobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. Complementary, molecular quantification of fungi in the samples showed a significantly lower number of internal transcribed spacer copies in plants subjected to biological control treatments, indicating the highest efficiency against fungal pathogens. The overall results show that leaves that are used for tea production show distinct microbiome shifts that are elicited by common pest and pathogen management practices. These shifts in the microbial population indicate non-target effects of the applied treatments.

The Influence of Fungicide Treatments on Mycobiota of Grapes and Its Evolution during Fermentation Evaluated by Metagenomic and Culture-Dependent Methods

The present study evaluated the impact of organic and conventional fungicide treatments compared with untreated samples (no fungicides were used) on the grape berry yeast community of the Montepulciano variety. The yeast dynamics during the spontaneous fermentation using culture-dependent and -independent methods was also evaluated. Results showed a reduction of yeast biodiversity by conventional treatments determining a negative influence on fermenting yeasts in favor of oxidative yeasts such as Aerobasidium pullulans. Starmerella bacillaris was significantly more present in organic samples (detected by next generation sequencing (NGS)), while Hanseniaspopa uvarum was significantly less present in untreated samples (detected by the culture-dependent method). The fermenting yeasts, developed during the spontaneous fermentation, were differently present depending on the fungicide treatments used. Culture-dependent and -independent methods exhibited the same most abundant yeast species during the spontaneous fermentation but a different relative abundance. Differently, the NGS method was able to detect a greater biodiversity (lower abundant species) in comparison with the culture-dependent method. In this regard, the methodologies used gave a different picture of yeast dynamics during the fermentation process. The results indicated that the fungal treatments can influence the yeast community of grapes leading must fermentation and the final composition of wine.

Diversity of epiphytic fungi on the surface of Kyoho grape berries during ripening process in summer and winter at Nanning region, Guangxi, China

The two-harvest-per-year farming system allow table grape to be harvested a year both in summer and winter in southern China. Herein, we used high-throughput sequencing to investigate the diversity of fungi on grape fruits surface during the ripening process in summer and winter at subtropical Nanning region, Guangxi, China. The results showed that 23 fungal species existed in all samples. Among them, the five most dominant species were Cladosporium ramotenellum, Pseudozyma aphidis, Gyrothrix spp., Gibberella intricans and Acremonium alternatum, with abundance from 61.62 % to 91.26 %. Analysis using the student's t-test for Shannon index indicated that components of fungal community varied significantly between the two ripening seasons. The dominant genera of core fungal community were Cladosporium, Gyrothrix, Paramycosphaerella, Acremonium, Penicillium and Tilletiopsis in the summer and Cladosporium, Pseudozyma, Gibberella, Colletotrichum, Sporobolomyces, Rhodosporidium, Alternaria and Aspergillus in the winter. Overall, fungi diversity on grape fruits surface at Nanning showed significantly differences between different ripening seasons. Our results ennrich the understanding of epiphytic communities of grape fruits in subtropics.

Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards

Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs (flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes (5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community (92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i.e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.

Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China

AIMS

Bacterial microbiome on grape berry surface may play an important role in grape quality and health. This study aims to investigate the impact of grape varieties and clones on grape berry surface bacterial microbiome from the same vineyard.

METHODS AND RESULTS

High-throughput sequencing strategy was used to investigate the bacterial diversity and abundance on the grape surfaces of 12 clones belonging to six varieties grown in the same vineyard of Zhengzhou Fruit Research Institute in Henan Province. In total, 45 bacterial phyla and 933 genera were detected from all samples. Cyanobacteria, Proteobacteria and Firmicutes were the most abundant and prevalent phyla, while Bacteroidetes, Chloroflexi, Acidobacteria and Planctomycetes were grape clone specific phyla. The nonrank genus from phylum Cyanobacteria occupied 30-81% of grape clones from Italian Riesling (GRX), Cabernet Franc (PLZ), Pinot Blanc (BBN) and Riesling (LSL). Interestingly, Bacillus, Pseudomonas and Lactococcus were the only three prevalent genera found on all the clones. Furthermore, the predicted functional activities of grape surface bacterial communities varied according to the clones.

CONCLUSIONS

The present study revealed that in addition to the grape varieties, the variations in grape clone background may also affect the bacterial microbiome on grape surfaces which may ultimately determine their functional activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

This research provides an important information for grape planting and wine fermentation that not only the grape varieties need to be paid attention but also grape clones from the specific variety need to be concerned.