Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables

Dynamic Succession of Natural Microbes during the Ecolly Grape Growth under Extremely Simplified Eco-Cultivation

The composition and continuous succession of natural microbial communities during grape growth play important roles in grape health and flavor quality as well as in characterizing the regional wine terroir. This study explored the diversity and dynamics of fruit epidermal microbes at each growth and developmental stage of Ecolly grapes under an extremely simplified eco-cultivation model, analyzed microbial interactions and associations of weather parameters to specific communities, and emphasized metabolic functional characteristics of microecology. The results indicated that the natural microbial community changed significantly during the grape growth phase. The dominant fungal genera mainly included Gibberella, Alternaria, Filobasidium, Naganishia, Ascochyta, Apiotrichum, Comoclathris, and Aureobasidium, and the dominant bacterial genera mainly contained Sediminibacterium, Ralstonia, Pantoea, Bradyrhizobium, Brevundimonas, Mesorhizobium, Planococcus, and Planomicrobium. In summary, filamentous fungi gradually shifted to basidiomycetous yeasts along with fruit ripening, with a decline in the number of Gram-negative bacteria and a relative increase in Gram-positive bacteria. The community assembly process reflects the fact that microbial ecology may be influenced by a variety of factors, but the fungal community was more stable, and the bacterial community fluctuated more from year to year, which may reflect their response to weather conditions over the years. Overall, our study helps to comprehensively profile the ecological characteristics of the grape microbial system, highlights the natural ecological viticulture concept, and promotes the sustainable development of the grape and wine industry.

Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons

Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.

Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts

An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.

Bacterial community changes in strawberry fruits (Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination

Background

Strawberry (Fragaria × ananassa) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality.

Methodology

An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed.

Results

Strawberries carries a high microorganisms diversity, with Pseudomonaceae, Yearsiniaceae, and Hafniaceae being the most abundant families across the samples. Among the groups, Pseudomonaceae and Clostridiaceae were the most abundant families at breaking (phase two) and ripe (phase four), whereas Yearsiniaceae, Hafniaceae, Aeromonadaceae, and Streptococcaceae were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. Serratia spp. were prevalent (above 60%) in samples collected from the market group, and Pseudomonas (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, Escherichia coli and Salmonella enterica were detected in the ready-to-eat samples from both the field and the market, while Enterococcus gallinarum was detected in the samples that originated from the market. Interestingly, Shewanella putrefaciens and Shewanella profunda, two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences (P < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin.

Conclusion

This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.

Bioprotective yeasts: Potential to limit postharvest spoilage and to extend shelf life or improve microbial safety of processed foods

Yeasts are a widespread group of microorganisms that are receiving increasing attention from scientists and industry. Their diverse biological activities and broad-spectrum antifungal activity make them promising candidates for application, especially in postharvest biocontrol of fruits and vegetables and food biopreservation. The present review focuses on recent knowledge of the mechanisms by which yeasts inhibit pathogenic fungi and/or spoilage fungi and bacteria. The main mechanisms of action of bioprotective yeasts include competition for nutrients and space, synthesis and secretion of antibacterial compounds, mycoparasitism and the secretion of lytic enzymes, biofilm formation, quorum sensing, induced systemic resistance of fruit host, as well as the production of reactive oxygen species. Preadaptation of yeasts to abiotic stresses such as cold acclimatization and sublethal oxidative stress can improve the effectiveness of antagonistic yeasts and thus more effectively play biocontrol roles under a wider range of environmental conditions, thereby reducing economic losses. Combined application with other antimicrobial substances can effectively improve the efficacy of yeasts as biocontrol agents. Yeasts show great potential as substitute for chemical additives in various food fields, but their commercialization is still limited. Hence, additional investigation is required to explore the prospective advancements of yeasts in the field of biopreservation for food.

Comparative microbiome analysis reveals the variation in microbial communities between 'Kyoho' grape and its bud mutant variety

Microbes are an important part of the vineyard ecosystem, which significantly influence the quality of grapes. Previously, we identified a bud mutant variety (named 'Fengzao') from 'Kyoho' grapes. The variation of microbial communities in grape and its bud mutant variety has not been studied yet. So, in this study, with the samples of both 'Fengzao' and 'Kyoho', we conducted high-throughput microbiome sequencing and investigated their microbial communities in different tissues. Obvious differences were observed in the microbial communities between 'Fengzao' and 'Kyoho'. The fruit and the stem are the tissues with relatively higher abundance of microbes, while the leaves contained less microbes. The fruit and the stem of 'Kyoho' and the stem of 'Fengzao' had relatively higher species diversity based on the alpha diversity analysis. Proteobacteria, Enterobacteriaceae and Rhodobacteraceae had significantly high abundance in 'Fengzao'. Firmicutes and Pseudomonas were highly abundant in the stems of 'Kyoho', and family of Spirochaetaceae, Anaplasmataceae, Chlorobiaceae, and Sphingomonadaceae, and genera of Spirochaeta, Sphingomonas, Chlorobaculum and Wolbachia were abundant in the fruits of 'Kyoho'. These identified microbes are main components of the microbial communities, and could be important regulators of grapevine growth and development. This study revealed the differences in the microbial compositions between 'Kyoho' and its bud mutant, and these identified microbes will be significant resources for the future researches on the quality regulation and disease control of grapevines.

Microbial antagonists to biologically control postharvest decay and preserve fruit quality

Postharvest waste due to decay of fruits and vegetables negatively affects food security, while at the same time control of decay and therefore waste can be limited because of consumer concerns about use of synthetic chemicals. Use of antagonistic microorganisms is an eco-friendly technique that represents a promising alternative approach to the use of chemical methods. Understanding the interactions between antagonists and the fruit microbiome will enable the discovery of new methods to reduce postharvest waste. This article reviews different microbial agents, fungi, bacteria and yeasts that could control decay. Recent developments in the use of microorganisms for preserving postharvest fruit quality, formulation of effective antagonists, and the commercialization steps are also discussed. Antagonists control decay through either direct or indirect mechanisms while preserving the appearance, flavor, texture and nutritional value of horticultural products. Microorganisms do not fully control pathogens, and therefore they are usually used with other treatments or have their biocontrol ability modified through genetic manipulations. Despite of these limitations, commercialization of biocontrol products based on antagonists with required stability and biocontrol potential is occurring. Biocontrol of postharvest decay and waste agent is promising technology for fruit and vegetable industries. Further study is necessary to better understand mechanisms and increasing efficiency of this method.

Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli

BACKGROUND

Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.

RESULTS

Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.

CONCLUSIONS

Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.

Relationships between fungal diversity and fruit quality of Yuluxiang pear during low temperature storage

Postharvest decay is an urgent problem that affects the storage of pears. Low temperature storage is one of the most important methods to reduce the prevalence of fruit diseases during storage. In this study, the microbial diversity of postharvest Yuluxiang pear (Pyrus × michauxii "Yu Lu Xiang") fruits stored at low temperature for different lengths of times was analyzed. Illumina MiSeq high-throughput sequencing was used to analyze the composition and diversity of fungal communities. The results showed that the fungi within fruit were classified into 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera based on the 97% sequence similarity level. They belonged to 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera. The highest richness of fungi was obtained after 30 d of treatment. The β-diversity index showed that the fungal community composition of these fruit was significantly different at the beginning of storage compared with the different timepoints of samples at low temperature during storage. The comparison of fungal composition at the phylum level indicated that Ascomycota was dominant in the different timepoints of samples at low temperature, while Alternaria was the primary fungus at the genus level. A correlation analysis was used to further explore the correlation between fungi and fruit firmness, titratable acid, and solid soluble contents at low temperatures during storage. Aureobasidium and Didymella positively correlated with the soluble solids and hardness. Phoma positively correlated with the titratable acid, and Aspergillus positively correlated with titratable acid and hardness. This study can guide the industrial production of Yulu pear and also provide a theoretical basis to prevent and control diseases during the storage period of Yulu pear.

Essential Oils Reduce Grey Mould Rot of Apples and Modify the Fruit Microbiome during Postharvest Storage

Botrytis cinerea is the causal agent of grey mould rot of apples. The efficacy of biofumigation with thyme (Thymus vulgaris), savoury (Satureja montana), and basil (Ocimum basilicum) essential oils (EOs) at 1%, 0.5%, and 0.1% concentrations were tested against B. cinerea. In vitro, the results showed 100% growth inhibition at 1% concentration for all oils. Subsequent biofumigation experiments on apples of cultivar 'Opal' with 1% EOs showed that, after 60 d storage, thyme and savoury EOs significantly reduced grey mould rot incidence (average incidence 2% for both treatments) compared to the control (7%). Analyses of quality indicated slightly higher fruit firmness for 1% thyme at 30 d and slightly higher titratable acidity for 1% thyme and savoury at 60 d. Sampling of the atmosphere inside the cabinets was performed to characterize and quantify the volatile components of EOs released through biofumigation. Though thymol and p-cymene were the main components of thyme EO, the antimicrobial activity was mainly due to the presence of thymol and, to a lower extent, of carvacrol. In savoury EO, carvacrol and p-cymene were the main components, whereas in basil EO, linalool and estragole were mainly present. Metabarcoding analyses showed that the epiphytic microbiome had higher richness and evenness compared to their endophytic counterpart. By the end of shelf-life, treatments with thyme EO reduced B. cinerea abundance compared to the inoculated control for both endophytes (from 36.5% to 1.5%) and epiphytes (from 7.0% to 0.7%), while favouring a significant increase in Penicillium species both in endophytes (from 0.2% to 21.5%) and epiphytes (from 0.5% to 18.6%). Results indicate that thyme EO (1%) and savoury EO (1%) are equally effective in hampering grey mould rot development in vivo.

Impact of Cultivation and Origin on the Fruit Microbiome of Apples and Blueberries and Implications for the Exposome

Vegetables and fruits are a crucial part of the planetary health diet, directly affecting human health and the gut microbiome. The objective of our study was to understand the variability of the fruit (apple and blueberry) microbiome in the frame of the exposome concept. The study covered two fruit-bearing woody species, apple and blueberry, two countries of origin (Austria and Finland), and two fruit production methods (naturally grown and horticultural). Microbial abundance, diversity, and community structures were significantly different for apples and blueberries and strongly influenced by the growing system (naturally grown or horticultural) and country of origin (Austria or Finland). Our results indicated that bacterial communities are more responsive towards these factors than fungal communities. We found that fruits grown in the wild and within home gardens generally carry a higher microbial diversity, while commercial horticulture homogenized the microbiome independent of the country of origin. This can be explained by horticultural management, including pesticide use and post-harvest treatments. Specific taxonomic indicators were identified for each group, i.e., for horticultural apples: Pseudomonas, Ralstonia, and Stenotrophomonas. Interestingly, Ralstonia was also found to be enriched in horticultural blueberries in comparison to such that were home and wildly grown. Our study showed that the origin of fruits can strongly influence the diversity and composition of their microbiome, which means that we are exposed to different microorganisms by eating fruits from different origins. Thus, the fruit microbiome needs to be considered an important but relatively unexplored external exposomic factor.

Biotechnology approaches to reduce antimicrobial resistant postharvest pathogens, mycotoxin contamination, and resulting product losses

Postharvest fungal pathogens of stored fruits, nuts, and vegetables cause food spoilage and some produce mycotoxins that harm human health. These fungi can develop resistance to the chemicals used for their control despite judicious use, rotating different chemistries, and routine resistance monitoring. Once antimicrobial resistance develops, these fungi are difficult to control and persist in the field, packing, and storage environments. Therefore, new tools and approaches for control with reduced emphasis on chemicals and movement toward durable, innovative approaches (e.g. double-stranded RNA, translational metagenomics, and host-induced gene silencing) are warranted. The focus of this review is on formative breakthroughs to combat postharvest pathogens and the mycotoxins they produce via translation of fundamental science using biotechnology tools.

Microbiome-based biotechnology for reducing food loss post harvest

Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety.

Diversity of bacterial community in Jerusalem artichoke (Helianthus tuberosus L.) during storage is associated with the genotype and carbohydrates

Jerusalem artichoke (JA) is a fructan-accumulating crop that has gained popularity in recent years. The objective of the present study was to determine the dynamics of the JA-microbiome during storage. The microbial population on the surface of the JA tuber was determined by next-generation sequencing of 16S rRNA amplicons. Subsequently, the changes in carbohydrate and degree of polymerization of fructan in tubers during storage were measured. Among different genotypes of JA varieties, intergeneric differences were observed in the diversity and abundance of bacterial communities distributed on the surface of tubers. Additionally, bacterial diversity was significantly higher in storage-tolerant varieties relative to the storage-intolerant varieties. Redundancy analysis (RDA) and the correlation matrix indicated a relationship between changes in the carbohydrates and microbial community succession during tuber storage. The tuber decay rate correlated positively with the degree of polymerization of fructan. Moreover, Dysgonomonas and Acinetobacter in perishable varieties correlated significantly with the decay rate. Therefore, the bacteria associated with the decay rate may be involved in the degradation of the degree of polymerization of fructan. Furthermore, Serratia showed a significant positive correlation with inulin during storage but a negative correlation with the decay rate, suggesting its antagonistic role against pathogenic bacteria on the surface of JA tubers. However, the above correlation was not observed in the storage-tolerant varieties. Functional annotation analysis revealed that storage-tolerant JA varieties maintain tuber quality through enrichment of biocontrol bacteria, including Flavobacterium, Sphingobacterium, and Staphylococcus to resist pathogens. These results suggested that crop genotype and the structural composition of carbohydrates may result in differential selective enrichment effects of microbial communities on the surface of JA varieties. In this study, the relationship between microbial community succession and changes in tuber carbohydrates during JA storage was revealed for the first time through the combination of high-throughput sequencing, high-performance liquid chromatography (HPLC), and high-performance ion-exchange chromatography (HPIC). Overall, the findings of this study are expected to provide new insights into the dynamics of microbial-crop interactions during storage.

Assembly and dynamics of the apple carposphere microbiome during fruit development and storage

Microbial communities associated with fruit can contribute to quality and pathogen resistance, but little is known about their assembly and dynamics during fruit development and storage. Three apple cultivars growing under the same environmental conditions were utilized to examine the apple carposphere microbiome composition and structure at different developmental stages and storage. There was a significant effect (Adonis, p ≤ 0.001) of fruit genotype and its developmental stages and storage times on the fruit surface microbial assemblage and a strong temporal microbial community succession was detected (Mantel test: R ≤ 0.5, p = 0.001) in both bacterial and fungal communities. A set of 15 bacterial and 35 fungal core successional taxa and members exhibiting differential abundances at different fruit stages were identified. For the first time, we show the existence of underlying universal dynamics in the assembly of fruit-associated microbiomes. We also provide evidence of strong microbial cross-domain associations and uncover potential microbe-microbe correlations in the apple carposphere. Together our findings shed light on how the fruit carposphere assemble and change over time, and provide new insights into fruit microbial ecology.

Selenium Combined with Methyl Jasmonate to Control Tomato Gray Mold by Optimizing Microbial Community Structure in Plants

Tomato cultivation is seriously affected by infection from Botrytis cinerea. The safe and effective control of tomato gray mold remains elusive. Plant-related microbial communities regulate not only plant metabolism but also plant immune systems. In this study, we observed that Selenium application in soil combined with foliar spraying of methyl jasmonate could reduce Botrytis cinerea infection in tomato fruits and leaves and improve tomato fruit quality. The infection rate of leaves decreased from 42.19% to 25.00%, and the vitamin C content increased by 22.14%. The bacterial community structure of the tomato was studied by using amplicon sequencing technology. The leaf bacterial alpha diversity of tomatoes treated with Se plus methyl jasmonate was significantly higher than that of the control. Then we isolated five strains antagonistic to Botrytis cinerea in vitro from tomato leaves in the treatment of Se plus methyl jasmonate. The antagonistic strains were identified as Bacillus subtilis and Bacillus velezensis. Spraying mixed antagonistic strain suspension significantly inhibited the diameter of Botrytis cinerea with an inhibition rate of 40.99%. This study revealed the key role of plant-beneficial bacteria recruited by Se combined with methyl jasmonate in improving tomato plant disease resistance. These findings may benefit our understanding of the new regulation of microorganisms on Botrytis cinerea.

Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity

The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.

Growth of ɣ-Proteobacteria in Low Salt Cucumber Fermentation Is Prevented by Lactobacilli and the Cover Brine Ingredients

This study investigated the ability of ɣ-proteobacteria, indigenous to fresh cucumber, to grow in the expressed fruit juice (CJM) and fermentation. It was hypothesized that fresh cucumbers can support prolific growth of ɣ-proteobacteria but that the cover brine composition and acid production by the competing lactobacilli in the fermentation of the fruit act as inhibitory agents. The ɣ-proteobacteria proliferated in CJM with an average maximum growth rate (μmax) of 0.3895 ± 0.0929 and doubling time (Td) of 1.885 ± 0.465/h. A significant difference was found between the ɣ-proteobacteria μmax and Td relative to Lactiplantibacillus pentosus LA0445 (0.2319 ± 0.019; 2.89/h) and Levilactobacillus brevis 7.2.43 (0.221 ± 0.015; 3.35/h) but not Lactiplantibacillus plantarum 3.2.8 (0.412 ± 0.119; 1.87/h). While inoculation level insignificantly altered the μmax and Td of the bacteria tested; it impacted the length of lag and stationary phases for the lactobacilli. Unlike the lactobacilli, the ɣ-proteobacteria were inhibited in CJM supplemented with a low salt fermentation cover brine containing calcium chloride, acetic acid and potassium sorbate. The ɣ-proteobacteria, P. agglomerans, was unable to proliferate in cucumber fermentations brined with calcium chloride at a pH of 6.0 ± 0.1 and the population of Enterobacteriaceae was outcompeted by the lactobacilli within 36 h. Together these observations demonstrate that the prolific growth of ɣ-proteobacteria in CJM is not replicated in cucumber fermentation. While the ɣ-proteobacteria growth rate is faster that most lactobacilli in CJM, their growth in cucumber fermentation is prevented by the cover brine and the acid produced by the indigenous lactobacilli. Thus, the lactobacilli indigenous to cucumber and cover brine composition influence the safety and quality of fermented cucumbers. IMPORTANCE While the abundance of specific ɣ-proteobacteria species varies among vegetable type, several harbor Enterobacteriaceae and Pseudomonadaceae that benefit the plant system. It is documented that such bacterial populations decrease in density early in vegetable fermentations. Consequently, it is assumed that they do not contribute to the quality of finished products. This study explored the viability of ɣ-proteobacteria in CJM, used as a model system, CJM supplemented with fermentation cover brine and cucumber fermentation, which are characterized by an extremely acidic endpoint pH (3.23 ± 0.17; n = 391). The data presented demonstrates that fresh cucumbers provide the nutrients needed by ɣ-proteobacteria to proliferate and reduce pH to 4.47 ± 0.12. However, ɣ-proteobacteria are unable to proliferate in cucumber fermentation. Control of ɣ-proteobacteria in fermentations depends on the cover brine constituents and the indigenous competing lactobacilli. This knowledge is of importance when developing guidelines for the safe fermentation of vegetables, particularly with low salt.

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.

Extract from the Macroalgae Ulva rigida Induces Table Grapes Resistance to Botrytis cinerea

Fungal pathogens are a central cause of the high wastage rates of harvested fruit and vegetables. Seaweeds from the genus Ulva are fast-growing edible green macroalgae whose species can be found on the shore of every continent, and therefore present a resource that can be utilized on a global scale. In this study, we found that the application of ulvan extract, a sulfated polysaccharide extracted from Ulva rigida (1000 mg/L), elicited table grapes defense and reduced the incidence and decay area of Botrytis cinerea by 43% and 41%, respectively. In addition, compared to the control group at two days post-treatment, ulvan extract elicited a variety of defense-related biomarkers such as a 43% increase in the activity of reactive oxygen species, 4-fold increase in the activity of catalase, 2-fold increase in the activity of superoxide dismutase and 1.4-fold increase in the activity of chitinase. No increase was observed in phenylalanine ammonia-lyase activity, and the treatment did not affect fruit quality parameters such as the pH levels, sugar levels, and titratable acidity of grapes. These results illustrate the potential of ulvan extract to naturally induce the plant defense response and to reduce postharvest decay.

Increased Yield and High Resilience of Microbiota Representatives With Organic Soil Amendments in Smallholder Farms of Uganda

Organic matter inputs positively affect soil fertility and quality but management effects on the soil and plant microbiome are less understood. Therefore, we studied the response of microbial colonization of the East African highland banana cultivar "Mpologoma" (AAA genome) under different mulch and manure treatments on three representative smallholder farms in Uganda. In general, the gammaproteobacterial community appeared stable with no significant response to organic matter inputs after 24 months of treatment. Significant differences (p < 0.05) in the plant-associated carpo-, phyllo-, and rhizosphere microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. Gammaproteobacterial beta diversity was shaped by the microenvironment (44%) as well as the sampling site (4%). Global effects of treatments in the rhizosphere analyzed using linear discriminant analysis effect size showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. As shown in previous works, bunch size and total yield were highly increased with manure and mulch, however, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.

A Comparative Analysis of the Microbiome of Kiwifruit at Harvest Under Open-Field and Rain-Shelter Cultivation Systems

The composition of microbial communities can directly affect fruit quality, health status, and storability. The present study characterized the epiphytes and endophytes of “Hongyang” and “Cuiyu” kiwifruit at harvest under grown under open-field (OF) and rain-shelter (RS) cultivation systems. Disease incidence in kiwifruit was significantly lower (p < 0.05) under the RS system than it was under the OF system. High-throughput sequencing [16S V3-V4 ribosomal region and the fungal internal transcribed spacer (ITS2)] was conducted to compare the composition of the epiphytic and endophytic microbial community of kiwifruit under the two cultivation systems. Results indicated that the abundance of Actinobacteria, Bacteroidetes, Enterobacteriales, Acetobacterales, Sphingomonas, Pseudomonas, and Sphingobacterium was higher under the RS system, relative to the OF system, while the abundance of Capnodiales, Hypocreales, Vishniacozyma, and Plectosphaerella was also higher under the RS system. Some of these bacterial and fungal taxa have been reported to as act as biocontrol agents and reduce disease incidence. Notably, the α-diversity of the epiphytic bacterial and fungal communities on kiwifruit was higher under RS cultivation. In summary, RS cultivation reduced natural disease incidence in kiwifruit, which may be partially attributed to differences in the structure and composition of the microbial community present in and on kiwifruit.

Unravelling the fruit microbiome: The key for developing effective biological control strategies for postharvest diseases

Fruit-based diets are recognized for their benefits to human health. The safety of fruit is a global concern for scientists. Fruit microbiome represents the whole microorganisms that are associated with a fruit. These microbes are either found on the surfaces (epiphytes) or in the tissues of the fruit (endophytes). The recent knowledge gained from these microbial communities is considered relevant to the field of biological control in prevention of postharvest fruit pathology. In this study, the importance of the microbiome of certain fruits and how it holds promise for solving the problems inherent in biocontrol and postharvest crop protection are summarized. Research needs on the fruit microbiome are highlighted. Data from DNA sequencing and "meta-omics" technologies very recently applied to the study of microbial communities of fruits in the postharvest context are also discussed. Various fruit parameters, management practices, and environmental conditions are the main determinants of the microbiome. Microbial communities can be classified according to their structure and function in fruit tissues. A critical mechanism of microbial biological control agents is to reshape and interact with the microbiome of the fruit. The ability to control the microbiome of any fruit is a great potential in postharvest management of fruits. Research on the fruit microbiome offers important opportunities to develop postharvest biocontrol strategies and products, as well as the health profile of the fruit.

Microbial Biocontrol as an Alternative to Synthetic Fungicides: Boundaries between Pre- and Postharvest Applications on Vegetables and Fruits

From a ‘farm to fork’ perspective, there are several phases in the production chain of fruits and vegetables in which undesired microbial contaminations can attack foodstuff. In managing these diseases, harvest is a crucial point for shifting the intervention criteria. While in preharvest, pest management consists of tailored agricultural practices, in postharvest, the contaminations are treated using specific (bio)technological approaches (physical, chemical, biological). Some issues connect the ‘pre’ and ‘post’, aligning some problems and possible solution. The colonisation of undesired microorganisms in preharvest can affect the postharvest quality, influencing crop production, yield and storage. Postharvest practices can ‘amplify’ the contamination, favouring microbial spread and provoking injures of the product, which can sustain microbial growth. In this context, microbial biocontrol is a biological strategy receiving increasing interest as sustainable innovation. Microbial-based biotools can find application both to control plant diseases and to reduce contaminations on the product, and therefore, can be considered biocontrol solutions in preharvest or in postharvest. Numerous microbial antagonists (fungi, yeasts and bacteria) can be used in the field and during storage, as reported by laboratory and industrial-scale studies. This review aims to examine the main microbial-based tools potentially representing sustainable bioprotective biotechnologies, focusing on the biotools that overtake the boundaries between pre- and postharvest applications protecting quality against microbial decay.

Global analysis of the apple fruit microbiome: are all apples the same?

We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.

The Good, the Bad, and the Ugly: Mycotoxin Production During Postharvest Decay and Their Influence on Tritrophic Host-Pathogen-Microbe Interactions

Mycotoxins are a prevalent problem for stored fruits, grains, and vegetables. Alternariol, aflatoxin, and patulin, produced by Alternaria spp., Aspergillus spp., and Penicillium spp., are the major mycotoxins that negatively affect human and animal health and reduce fruit and produce quality. Control strategies for these toxins are varied, but one method that is increasing in interest is through host microbiome manipulation, mirroring a biocontrol approach. While the majority of mycotoxins and other secondary metabolites (SM) produced by fungi impact host–fungal interactions, there is also an interplay between the various organisms within the host microbiome. In addition to SMs, these interactions involve compounds such as signaling molecules, plant defense and growth hormones, and metabolites produced by both the plants and microbial community. Therefore, studies to understand the impact of the various toxins impacting the beneficial and harmful microorganisms that reside within the microbiome is warranted, and could lead to identification of safe analogs for antimicrobial activity to reduce fruit decay. Additionally, exploring the composition of the microbial carposphere of host plants is likely to shed light on developing a microbial consortium to maintain quality during storage and abate mycotoxin contamination.

Biological control of postharvest fungal decays in citrus: a review

Citrus (Citrus spp.) species produce a variety of fruits that are popular worldwide. Citrus fruits, however, are susceptible to postharvest decays caused by various pathogenic fungi, including Penicillium digitatum, Penicillium italicum, Geotrichum citri-aurantii, Aspergillus niger, and Aspergillus flavus. Decays resulting from infections by these pathogens cause a significant reduction in citrus quality and marketable yield. Biological control of postharvest decay utilizing antagonistic bacteria and fungi has been explored as a promising alternative to synthetic fungicides. In the present article, the isolation of antagonists utilized to manage postharvest decays in citrus is reviewed, and the mechanism of action including recent molecular and genomic studies is discussed as well. Several recently-postulated mechanisms of action, such as biofilm formation and an oxidative burst of reactive oxygen species have been highlighted. Improvements in biocontrol efficacy of antagonists through the use of a combination of microbial antagonists and additives are also reviewed. Biological control utilizing bacterial and yeast antagonists is a critical component of an integrated management approach for the sustainable development of the citrus industry. Further research will be needed, however, to explore and utilize beneficial microbial consortia and novel approaches like CRISPR/Cas technology for management of postharvest decays.

Pre- and postharvest measures used to control decay and mycotoxigenic fungi in potato (Solanum tuberosum L.) during storage

Potato (Solanum tuberosum L.), a worldwide, staple food crop, is susceptible to postharvest rots caused by a variety of fungal pathogens, including Fusarium spp., Alternaria spp., Phytophthora infestans, Helminthosporium solani, Rhizoctonia solani, and Colletotrichum coccodes. Rots resulting from infections by these pathogens cause a significant reduction in potato quality and marketable yield. Importantly, some of these decay fungi also produce mycotoxins that represent a potential risk to human health. In the present review, an overview and discussion are provided on the epidemiology and pathogenesis of decay fungi, especially Fusarium spp., that include recent data derived from genomic and phylogenetic analyses. The biosynthesis and functional role of fungitoxic metabolites such as trichothecene mycotoxins and fusaric acid, produced in rotted potatoes are also reviewed. Advances in pre- and postharvest measures for rot management, especially eco-friendly methods including physical control, biological control, the use of natural compounds, and other agricultural management practices are also reviewed. Lastly, novel approaches to control potato dry rot such as the use of mycoviruses and CRISPR technology are highlighted.