Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations

Abstract

French PDO Nyons black table olives are produced according to a traditional slow spontaneous fermentation in brine. The manufacture and unique sensorial properties of these olives thus only rely on the autochthonous complex microbiota. This study aimed at unraveling the microbial communities and dynamics of Nyons olives during a 1.5-year-long spontaneous fermentation to determine the main microbial drivers and link microbial species to key metabolites. Fermentations were monitored at a local producer plant at regular time intervals for two harvests and two olive types (organically and conventionally grown) using culture-dependent and metabarcoding (ITS2 for fungi, V3-V4 region for bacteria) approaches. Olives and brines were also sampled for volatiles, organic acids and phenolic compounds. No major differences in microbiota composition were observed according to olive type or harvest period. Throughout the fermentation, yeasts were clearly the most dominant. ITS2 sequencing data revealed complex fungal diversity dominated by Citeromyces nyonsensis , Wickerhamomyces anomalus , Zygotorulaspora mrakii , Candida boidinii and Pichia membranifaciens species. Bacterial communities were dominated by the Celerinatantimonas genus, while lactic acid bacteria remained scarce. Clear shifts in microbial communities and biochemical profiles were observed during fermentation and, by correlating metabolites and microbiota changes, four different phases were distinguished. During the first 7 days, phase I, a fast decrease of filamentous fungal and bacterial populations was observed. Between days 21 and 120, phase II, W. anomalus and C. nyonsensis for fungi and Celerinatantimonas diazotrophica for bacteria dominated the fermentation and were linked to the pH decrease and citric acid production. Phase III, between 120 and 183 days, was characterized by an increase in acids and esters and correlated to increased abundances of Z. mrakii , P. membranifaciens and C. boidinii. During the last months of fermentation, phase IV, microbial communities were dominated by P. membranifaciens and C. boidinii . Both species were strongly correlated to an increase in fruity esters and alcohol abundances. Overall, this study provides an in-depth understanding about microbial species succession and how the microbiota shapes the final distinct olive characteristics. It also constitutes a first step to identify key drivers of this fermentation.

Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays

“…Species succession is a very common attribute of the lactic acid microbiota of spontaneously fermented products. Indeed, it has been reported in a variety of fermented vegetable, fruit, meat and dairy products [13,[37][38][39]. In general, this succession is commonly attributed to the level of adaptation to a specific niche, in terms of ability to utilize available nutrient resources and tolerate metabolite accumulation.…”

Microbial Ecology of French Dry Fermented Sausages and Mycotoxin Risk Evaluation During Storage

“…already described in diverse salty to highly salty fermented foods (i.e., cheese, table olives, soy sauce, fish sauce, soybean paste, etc.). These bacterial genera participate to the fermentation process and can contribute to the sensory characteristics of the fermented foods (Sitdhipol et al, 2013;Amadoro et al, 2015;Yunita and Dodd, 2018;Penland et al, 2020;Sawada et al, 2021). For fungi, only slight quantitative variations in fungal populations were observed between samples during conservation (up to a 2.6 log 10 TFU/cm 2 ).…”

Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future

“…According to the literature, there have been several studies already applied on table olive fermentation, in terms of metabarcoding by using several HTS technologies such as Illumina and Roche ( Cocolin et al, 2013a ; De Angelis et al, 2015 ; Arroyo-López et al, 2016 ; Randazzo et al, 2017 ; Zinno et al, 2017 ; de Castro et al, 2018 ; Medina et al, 2018 ; Benítez-Cabello et al, 2019b , 2020a ; Anagnostopoulos et al, 2020b ; Kazou et al, 2020 ; Penland et al, 2020 ; Demirci et al, 2021 ; López-García et al, 2021 ; Michailidou et al, 2021 ). Table 2 summarizes the main microbial groups detected by studies so far through metataxonomic approach, in different olive varieties and processes.…”

“…In the same study, the presence of yeasts was also studied, indicating the dominance of Citeromyces followed by Candida and Penicillium . Furthermore, Citeromyces and Pichia were reported to play a key role during fermentation of Nyons Black Olive ( Penland et al, 2020 ). Finally, de Castro et al (2018) studied the bacterial and metabolite profile of spoiled green olives, indicating the high abundance of Cardiobacteriaceae and Ruminococcus .…”