Growth and metabolite production of a grape sour rot yeast-bacterium consortium on different carbon sources

Knowledge gaps on grape sour rot inferred from a systematic literature review

Sour rot (SR) is one of the major diseases affecting grapevine berries, causing severe yield losses and deterioration of wine quality. SR is caused by an etiologic complex of microorganisms, including yeasts, bacteria, and filamentous fungi. This systematic review focuses on the etiology, epidemiology, and control of SR. A total of 74 papers published between 1986 and 2023 were assessed in this review. Description of disease symptoms was quite consistent across the papers, including oxidation of the grape skin, disaggregation of the internal tissues, and detachment of the rotten berries from the pedicel. The affected bunches are characterized by the smell of acetic acid and ethyl acetate that attracts fruit flies (Drosophila spp.). However, several knowledge gaps and/or inconsistencies were identified with respect to SR etiology, epidemiology, and control. Overall, 146 microorganisms were isolated from the affected berries (44.5% yeasts, 34.3% bacteria, and 21.2% filamentous fungi); however, the selected papers could not definitively clarify which species are primarily involved in the etiology of the disease. A general inconsistency was also observed in the methods used to assess the incidence and severity of SR in vineyards, making inter-study comparisons extremely challenging. Inconsistencies were also found in the methods used for pathogenicity assessment in artificial inoculation studies. Furthermore, gaps were detected in terms of SR epidemiology, with a focus on environmental conditions affecting the disease development. The SR management options are limited, and efficacy trials often result in poor, variable, and inconsistent levels of control, which might be attributed to the lack of knowledge on disease epidemiology. These knowledge gaps and inconsistencies were analyzed in this review to inform future research activities.

Antibacterial Activity of Oregano (Origanum vulgare L.) Essential Oil Vapors against Microbial Contaminants of Food-Contact Surfaces

The antimicrobial effect of eight essential oils' vapors against pathogens and spoilage bacteria was assayed. Oreganum vulgare L. essential oil (OVO) showed a broad antibacterial effect, with Minimum Inhibitory Concentration (MIC) values ranging from 94 to 754 µg cm-3 air, depending on the bacterial species. Then, gaseous OVO was used for the treatment of stainless steel, polypropylene, and glass surfaces contaminated with four bacterial pathogens at 6-7 log cfu coupon-1. No viable cells were found after OVO treatment on all food-contact surfaces contaminated with all pathogens, with the exception of Sta. aureus DSM 799 on the glass surface. The antimicrobial activity of OVO after the addition of beef extract as a soiling agent reduced the Sta. aureus DSM 799 viable cell count by more than 5 log cfu coupon-1 on polypropylene and glass, while no viable cells were found in the case of stainless steel. HS-GC-MS analysis of the headspace of the boxes used for the antibacterial assay revealed 14 different volatile compounds with α-Pinene (62-63%), and p-Cymene (21%) as the main terpenes. In conclusion, gaseous OVO could be used for the microbial decontamination of food-contact surfaces, although its efficacy needs to be evaluated since it depends on several parameters such as target microorganisms, food-contact material, temperature, time of contact, and relative humidity.

The Effect of Dekkera bruxellensis Concentration and Inoculation Time on Biochemical Changes and Cellulose Biosynthesis by Komagataeibacter intermedius

Bacterial Cellulose (BC) is a biopolymer with numerous applications. The growth of BC-producing bacteria, Komagataeibacter intermedius, could be stimulated by Dekkera bruxellensis, however, the effect on BC yield needs further investigation. This study investigates BC production and biochemical changes in the K. intermedius-D. bruxellensis co-culture system. D. bruxellensis was introduced at various concentrations (103 and 106 CFU/mL) and inoculation times (days 0 and 3). BC yield was ~24% lower when D. bruxellensis was added at 103 CFU/mL compared to K. intermedius alone (0.63 ± 0.11 g/L). The lowest BC yield was observed when 103 CFU/mL yeast was added on day 0, which could be compromised by higher gluconic acid production (10.08 g/L). In contrast, BC yields increased by ~88% when 106 CFU/mL D. bruxellensis was added, regardless of inoculation time. High BC yield might correlate with faster sugar consumption or increased ethanol production when 106 CFU/mL D. bruxellensis was added on day 0. These results suggest that cell concentration and inoculation time have crucial impacts on species interactions in the co-culture system and product yield.

Towards the Development of Microbial Ecotoxicology Testing Using Chlorpyrifos Contaminated Sediments and Marine Yeast Isolates as a Model

Chlorpyrifos (CP), a widely used pesticide, and its metabolite 3,5,6-trichloro-2-pyridinol (3,5,6-TCP), are xenobiotic compounds detected in many biomes, notably in marine sediments, all over the world. These compounds are posing a serious environmental and health problem given their toxicity to wildlife and possible exposure effects to human neurodevelopment. Microorganisms at CP-impacted environments could harbor metabolic capabilities that can be used as indicators of the biological effects of the contaminant and could encode selected functions reactive against contaminants. Those features could be used for microbial ecotoxicology applications by collectively using analytical, enzymatic, microbiological and toxicological techniques in order to assess the biological effects of pollutants and other environmental/climatic stressors in ecosystems. The objective of this study was to assess the variability in the metabolic responses of yeast isolates from CP-contaminated marine sediments as potential biological indicators for microbial ecotoxicology testing. Sediment samples from a South Caribbean tropical shore (Cartagena Bay, Colombia) were collected, and deoxyribonucleic acid (DNA) was recovered from lyophilized aliquots. The DGGE (Denaturing Gradient Gel Electrophoresis) technique targeting fungal Internal Transcribed Spacer (ITS) showed the great diversity of fungal types. Simultaneously, yeast strains were isolated from the freshly collected sediment samples. Physiological characterization including API 20C and antibiosis tests, growth patterns at salt concentrations (2/4/10/25%), temperatures (4/25/37/45 °C), esterase activity assay and resistance tests to CP/TCP toxicity resulted in 10 isolated yeast strains, identified as Candida spp. (6), Cryptococcus spp. (3). and Rhodotorula spp. (1), showing promising characteristics to be used as a test for yeast-based ecotoxicity indicators. The patterns of carbohydrate assimilation, low antibiosis, presence of esterases/lipases, growth in a wide range of temperatures and salt concentrations, and tolerance to minimal inhibitory concentrations of CP and TCP are factors useful for testing environmental samples.

Microbial and Chemical Dynamics during Marula Wine Fermentation

Marula wine is traditionally produced through a spontaneous fermentation process and has a huge economic potential in Africa. The current study investigated the contributing microbiota and the metabolites produced during the wine fermentation process. Microbial communities were analyzed by selective cultivation and identified by biotyping and rDNA sequencing. Sugars and volatile compounds were determined with the high performance liquid chromatography and gas chromatography, respectively. Different Lactobacillus spp. were present throughout the fermentation process but dominated the earlier stages of fermentation, together with non-Saccharomyces yeasts, whereas Saccharomyces cerevisiae and acetic acid bacteria dominated the latter stages. Sucrose, glucose and fructose were detected during the early stages, while ethanol and butanol were present during the latter stages of fermentation. Interestingly, acetic acid and formic acid were detected in relatively high amounts at the latter stages of fermentation. Lactobacillus spp. and S. cerevisiae were identified as the primary contributing microbiota, and Acetobacter aceti and Acetobacter pasteuriannus were associated with the off taste and spoilage of the marula wine.

Trials of Commercial- and Wild-Type Saccharomyces cerevisiae Strains under Aerobic and Microaerophilic/Anaerobic Conditions: Ethanol Production and Must Fermentation from Grapes of Santorini (Greece) Native Varieties

In modern wine-making technology, there is an increasing concern in relation to the preservation of the biodiversity, and the employment of “new”, “novel” and wild-type Saccharomyces cerevisiae strains as cell factories amenable for the production of wines that are not “homogenous”, expressing their terroir and presenting interesting and “local” sensory characteristics. Under this approach, in the current study, several wild-type Saccharomyces cerevisiae yeast strains (LMBF Y-10, Y-25, Y-35 and Y-54), priorly isolated from wine and grape origin, selected from the private culture collection of the Agricultural University of Athens, were tested regarding their biochemical behavior on glucose-based (initial concentrations ca 100 and 200 g/L) shake-flask experiments. The wild yeast strains were compared with commercial yeast strains (viz. Symphony, Cross X and Passion Fruit) in the same conditions. All selected strains rapidly assimilated glucose from the medium converting it into ethanol in good rates, despite the imposed aerobic conditions. Concerning the wild strains, the best results were achieved for the strain LMBF Y-54 in which maximum ethanol production (EtOHmax) up to 68 g/L, with simultaneous ethanol yield on sugar consumed = 0.38 g/g were recorded. Other wild strains tested (LMBF Y-10, Y-25 and Y-35) achieved lower ethanol production (up to ≈47 g/L). Regarding the commercial strains, the highest ethanol concentration was achieved by S. cerevisiae Passion Fruit (EtOHmax = 91.1 g/L, yield = 0.45 g/g). Subsequently, the “novel” strain that presented the best technological characteristics regards its sugar consumption and alcohol production properties (viz. LMBF Y-54) and the commercial strain that equally presented the best previously mentioned technological characteristics (viz. Passion Fruit) were further selected for the wine-making process. The selected must originated from red and white grapes (Assyrtiko and Mavrotragano, Santorini Island; Greece) and fermentation was performed under wine-making conditions showing high yields for both strains (EtOHmax = 98–106 g/L, ethanol yield = 0.47–0.50 g/g), demonstrating the production efficiency under microaerophilic/anaerobic conditions. Molecular identification by rep-PCR carried out throughout fermentations verified that each inoculated yeast was the one that dominated during the whole bioprocess. The aromatic compounds of the produced wines were qualitatively analyzed at the end of the processes. The results highlight the optimum technological characteristics of the selected “new” wild strain (S. cerevisiae LMBF Y-54), verifying its suitability for wine production while posing great potential for future industrial applications.

Liquor Flavour Is Associated With the Physicochemical Property and Microbial Diversity of Fermented Grains in Waxy and Non-waxy Sorghum (Sorghum bicolor) During Fermentation

The fermentation process of Chinese Xifeng liquor involves numerous microbes. However, the sources of microbes in fermented grain and the link between liquor flavour and physicochemical properties and microbial diversity during fermentation still remain unknown. Herein, two waxy (JiNiang 2 [JN-2] and JinNuo 3 [JN-3]) and four non-waxy (JiZa 127 [JZ-127], JinZa 34 [JZ-34], LiaoZa 19 [LZ-19], and JiaXian [JX]) sorghum varieties were selected for the comprehensive analysis of the relationship between liquor flavour and the physicochemical properties and microbial diversity of fermented grains. Results showed that ethyl acetate was the main flavour component of JZ-127, JZ-34, and JX, whereas ethyl lactate was mainly detected in JN-2, JN-3, and LZ-19. Ethyl lactate accounted for half of the ethyl acetate content, and JX exhibited a higher liquor yield than the other sorghum varieties. The fermented grains of waxy sorghum presented higher temperature and reducing sugar contents but lower moisture and starch contents than their non-waxy counterparts during fermentation. We selected JN-3 and JX sorghum varieties to further investigate the microbial changes in the fermented grains. The bacterial diversity gradually reduced, whereas the fungal diversity showed nearly no change in either JN-3 or JX. Lactobacillus was the most abundant bacterial genus, and its level rapidly increased during fermentation. The abundance of Lactobacillus accounted for the total proportion of bacteria in JX, and it was higher than that in JN-3. Saccharomyces was the most abundant fungal genus in JX, but its abundance accounted for a small proportion of fungi in JN-3. Four esters and five alcohols were significantly positively related to Proteobacteria, Bacteroidetes, and Actinobacteria; Alphaproteobacteria, Actinobacteria, and Bacteroidia; Bacillales, Bacteroidales, and Rhodospirillales; and Acetobacter, Pediococcus, and Prevotella_7. This positive relation is in contrast with that observed for Firmicutes, Bacilli, Lactobacillales, and Lactobacillus. Meanwhile, Aspergillus was the only fungal microorganism that showed a significantly negative relation with such compounds (except for butanol and isopentanol). These findings will help in understanding the fermentation mechanism and flavour formation of fermented Xifeng liquor.

Genetic, Physiological, and Industrial Aspects of the Fructophilic Non-Saccharomyces Yeast Species, Starmerella bacillaris

Starmerella bacillaris (synonym Candida zemplinina) is a non-Saccharomyces yeast species, frequently found in enological ecosystems. Peculiar aspects of the genetics and metabolism of this yeast species, as well as potential industrial applications of isolated indigenous S. bacillaris strains worldwide, have recently been explored. In this review, we summarize relevant observations from studies conducted on standard laboratory and indigenous isolated S. bacillaris strains.

Microbial Composition of SCOBY Starter Cultures Used by Commercial Kombucha Brewers in North America

Kombucha fermentation is initiated by transferring a solid-phase cellulosic pellicle into sweetened tea and allowing the microbes that it contains to initiate the fermentation. This pellicle, commonly referred to as a symbiotic culture of bacteria and yeast (SCOBY), floats to the surface of the fermenting tea and represents an interphase environment, where embedded microbes gain access to oxygen as well as nutrients in the tea. To date, various yeast and bacteria have been reported to exist within the SCOBY, with little consensus as to which species are essential and which are incidental to Kombucha production. In this study, we used high-throughput sequencing approaches to evaluate spatial homogeneity within a single commercial SCOBY and taxonomic diversity across a large number (n = 103) of SCOBY used by Kombucha brewers, predominantly in North America. Our results show that the most prevalent and abundant SCOBY taxa were the yeast genus Brettanomyces and the bacterial genus Komagataeibacter, through careful sampling of upper and lower SCOBY layers. This sampling procedure is critical to avoid over-representation of lactic acid bacteria. K-means clustering was used on metabarcoding data of all 103 SCOBY, delineating four SCOBY archetypes based upon differences in their microbial community structures. Fungal genera Zygosaccharomyces, Lachancea and Starmerella were identified as the major compensatory taxa for SCOBY with lower relative abundance of Brettanomyces. Interestingly, while Lactobacillacae was the major compensatory taxa where Komagataeibacter abundance was lower, phylogenic heat-tree analysis infers a possible antagonistic relationship between Starmerella and the acetic acid bacterium. Our results provide the basis for further investigation of how SCOBY archetype affects Kombucha fermentation, and fundamental studies of microbial community assembly in an interphase environment.

Biotechnological Processes in Fruit Vinegar Production

The production of fruit vinegars as a way of making use of fruit by-products is an option widely used by the food industry, since surplus or second quality fruit can be used without compromising the quality of the final product. The acetic nature of vinegars and its subsequent impact on the organoleptic properties of the final product allows almost any type of fruit to be used for its elaboration. A growing number of scientific research studies are being carried out on this matrix, and they are revealing the importance of controlling the processes involved in vinegar elaboration. Thus, in this review, we will deal with the incidence of technological and biotechnological processes on the elaboration of fruit vinegars other than grapes. The preparation and production of the juice for the elaboration of the vinegar by means of different procedures is an essential step for the final quality of the product, among which crushing or pressing are the most employed. The different conditions and processing methods of both alcoholic and acetic fermentation also affect significantly the final characteristics of the vinegar produced. For the alcoholic fermentation, the choice between spontaneous or inoculated procedure, together with the microorganisms present in the process, have special relevance. For the acetic fermentation, the type of acetification system employed (surface or submerged) is one of the most influential factors for the final physicochemical properties of fruit vinegars. Some promising research lines regarding fruit vinegar production are the use of commercial initiators to start the acetic fermentation, the use of thermotolerant bacteria that would allow acetic fermentation to be carried out at higher temperatures, or the use of innovative technologies such as high hydrostatic pressure, ultrasound, microwaves, pulsed electric fields, and so on, to obtain high-quality fruit vinegars.

D-Fructose Assimilation and Fermentation by Yeasts Belonging to Saccharomycetes: Rediscovery of Universal Phenotypes and Elucidation of Fructophilic Behaviors in Ambrosiozyma platypodis and Cyberlindnera americana

The purpose of this study was to investigate the ability of ascomycetous yeasts to assimilate/ferment d-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the standard set of physiological properties for characterizing yeast species, despite the ubiquitous presence of fructose in the natural environment. In this study, we examined 388 strains of yeast, mainly belonging to the Saccharomycetes (Saccharomycotina, Ascomycota), to determine whether they can assimilate/ferment d-fructose. Conventional methods, using liquid medium containing yeast nitrogen base +0.5% (w/v) of d-fructose solution for assimilation and yeast extract-peptone +2% (w/v) fructose solution with an inverted Durham tube for fermentation, were used. All strains examined (n = 388, 100%) assimilated d-fructose, whereas 302 (77.8%) of them fermented d-fructose. In addition, almost all strains capable of fermenting d-glucose could also ferment d-fructose. These results strongly suggest that the ability to assimilate/ferment d-fructose is a universal phenotype among yeasts in the Saccharomycetes. Furthermore, the fructophilic behavior of Ambrosiozyma platypodis JCM 1843 and Cyberlindnera americana JCM 3592 was characterized by sugar consumption profiles during fermentation.

Native Vineyard Non-Saccharomyces Yeasts Used for Biological Control of Botrytis cinerea in Stored Table Grape

Postharvest spoilage fungi, such as Botrytis cinerea, are considered the main cause of losses of fresh fruit quality and vegetables during storage, distribution, and consumption. The current control strategy is the use of SO₂ generator pads whose application is now largely under observation. A high quantity of SO₂ can be deleterious for fresh fruits and vegetables and it is not allowed in organic agriculture. For this reason, great attention has been recently focused on identifying Biological Control Agents (BCA) to implement biological approaches devoid of chemicals. In this direction, we carried out our study in isolating five different non-Saccharomyces yeast strains from local vineyards in the South of Italy as possible BCA. We performed both in vitro and in vivo assays in semi-commercial conditions on detached grape berries stored at 0 °C, simulating the temperature normally used during cold storage, and obtained relevant results. We isolated three M. pulcherrima strains and one L. thermotolerans strain able to largely antagonize the development of the B. cinerea, at both in vitro and in vivo conditions. In particular, we detected the ability of the three isolates of M. pulcherrima strains Ale4, N20/006, and Pr7 and the L. thermotolerans strain N10 to completely inhibit (100% in reduction) the mycelial growth of B. cinerea by producing fungistatic compounds. We found, using an extracellular lytic enzymes activity assay, that such activity could be related to lipid hydrolyzation, β-1,3-glucanase and pectinase activity, and pectinase and protease activity, depending on the yeasts used. Results from our in vitro assays allowed us to hypothesize for M. pulcherrima strains Ale4 and N20/006 a possible combination of both the production of soluble metabolites and volatile organic compounds to antagonize against B. cinerea growth. Moreover, in semi-commercial conditions, the M. pulcherrima strain N20/006 and L. thermotolerans strain N10 showed relevant antagonistic effect also at low concentrations (with a significantly reduction of ‘slip skin’ incidence of 86.4% and 72.7%, respectively), thus highlighting a peculiar property to use in commercial development for organic agriculture and the handling process.

Health Promoting Properties of Cereal Vinegars

Vinegar has been used for its health promoting properties since antiquity. Nowadays, these properties are investigated, scientifically documented, and highlighted. The health benefits of vinegar have been associated with the presence of a variety of bioactive components such as acetic acid and other organic acids, phenolic compounds, amino acids, carotenoids, phytosterols, vitamins, minerals, and alkaloids, etc. These components are known to induce responses in the human body, such as antioxidant, antidiabetic, antimicrobial, antitumor, antiobesity, antihypertensive, and anti-inflammatory effects. The diversity and levels of bioactive components in vinegars depend on the raw material and the production method used. Cereal vinegars, which are more common in the Asia-Pacific region, are usually made from rice, although other cereals, such as millet, sorghum, barley, malt, wheat, corn, rye, oats, bran and chaff, are also used. A variety of bioactive components, such as organic acids, polyphenols, amino acids, vitamins, minerals, alkaloids, melanoidins, butenolides, and specific compounds such as γ-oryzanol, tetramethylpyrazine, γ-aminobutyric acid, etc., have been associated with the health properties of cereal vinegars. In this work, the bioactive components and the related health effects of cereal vinegars are reviewed, and the most recent scientific literature is presented and discussed.

Diversity and spoilage potential of microbial communities associated with grape sour rot in eastern coastal areas of China

As a polymicrobial disease, sour rot decreases grape berry yield and wine quality. The diversity of microbial communities in sour rot-affected grapes depends on the cultivation site, but the microbes responsible for this disease in eastern coastal China, has not been reported. To identify the microbes that cause sour grape rot in this important grape-producing region, the diversity and abundance of bacteria and fungi were assessed by metagenomic analysis and cultivation-dependent techniques. A total of 15 bacteria and 10 fungi were isolated from sour rot-affected grapes. High-throughput sequencing of PCR-amplicons generated from diseased grapes revealed 1343 OTUs of bacteria and 1038 OTUs of fungi. Proteobacteria and Firmicutes were dominant phyla among the 19 bacterial phyla identified. Ascomycota was the dominant fungal phylum and the fungi Issatchenkia terricola, Colletotrichum viniferum, Hanseniaspora vineae, Saprochaete gigas, and Candida diversa represented the vast majority ofmicrobial species associated with sour rot-affected grapes. An in vitro spoilage assay confirmed that four of the isolated bacteria strains (two Cronobacter species, Serratia marcescens and Lysinibacillus fusiformis) and five of the isolated fungi strains (three Aspergillus species, Alternaria tenuissima, and Fusarium proliferatum) spoiled grapes. These microorganisms, which appear responsible for spoiling grapes in eastern China, appear closely related to microbes that cause this plant disease around the world.

Comparison of bayberry fermented wine aroma from different cultivars by GC-MS combined with electronic nose analysis

Four bayberry cultivars (Biqi, Dongkui, Wandao, and Dingao) in eastern China were selected to produce the fermented bayberry wine. The volatile flavor compounds in different bayberry wine were compared by gas chromatography-mass spectrometry (GC-MS) and electronic nose. The results showed that 46 volatile flavor compounds were found in bayberry wine, including 19 esters, 7 alcohols, 6 acids, 2 aldehydes, 2 ketones, 3 terpenes, and 7 others compounds. The most important contribution to the aroma of bayberry wine was esters and alcohols, respectively. Differentiation of four kinds of bayberry wine was conducted analysis by E-nose. Sensory evaluation showed that Biqi bayberry wine was highly evaluated for its highest score in color, floral aroma, overall acceptability, and fruity aroma. Our results suggest that there were differences in the flavor characteristics of bayberry wine brewed from different varieties of bayberry. The results of this study will provide valuable information for bayberry wine makers to select raw materials.

Role of Glucose and 2-Oxoglutarate/Malate Translocator (OMT1) in the Production of Phenyllactic Acid and p-Hydroxyphenyllactic Acid, Two Food-Borne Pathogen Inhibitors

This work aims to uncover how glucose affected the production of phenyllactic acid (PLA) and p-hydroxyphenyllactic acid ( p-OH-PLA). The highest yields of PLA (68.53 mg/L) and p-OH-PLA (50.39 mg/L) were observed after Lactobacillus plantarum strain YM-4-3 fermentation in media containing 30 and 10 g/L glucose, respectively. Additionally, the antimicrobial activity of YM-4-3 against food-borne pathogens and the NADH/NAD⁺ ratio were positively correlated with the production of PLA and p-OH-PLA, respectively. In addition, a 2-oxoglutarate/malate translocator coding gene ( Omt1) was selected based on the qPCR results, and its knockout mutant, compared with the wild-type strain YM-4-3, showed that the PLA and p-OH-PLA production was decreased by 1.37-6.99 and 1.53-1.59 times, respectively. This result indicated that OMT1 was involved in the biosynthesis of PLA and p-OH-PLA. To conclude, this study suggests that glucose, NADH/NAD⁺ ratio and/or the Omt1 gene, PLA, and p-OH-PLA production, and antimicrobial activity contribute to a cause-and-effect relationship.