Bacterial ecology of fermented cucumber rising pH spoilage as determined by non-culture based methods

Authors: MEDINA-PRADAS, EDUARDO - Instituto De La Grasa; Perez Diaz, Ilenys; Breidt, Frederick; Hayes, Janet; FRANCO, WENDY - North Carolina State University; BUTZ, NATASHA - University Of North Carolina; AZCARATE-PERIL, ANDREA - University Of North Carolina

Submitted to: Journal of Food Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2015
Publication Date: 1/1/2016
Publication URL: http://handle.nal.usda.gov/10113/61817
Citation: Medina-Pradas, E., Perez Diaz, I.M., Breidt, F., Hayes, J.S., Franco, W., Butz, N., Azcarate-Peril, A. 2016. Bacterial ecology of fermented cucumber rising pH spoilage as determined by non-culture based methods. Journal of Food Science. 80(1):M121-M129. doi: 10.1111/1750-3841.13158.

Interpretive Summary: Secondary cucumber fermentation characterized by rising pH and the appearance of manure and cheese like aromas is a challenge of a significant economical impact for the pickling industry in the U.S. DNA based analysis of commercial cover brine samples collected from spoiling cucumber fermentations suggests that Acetobacter spp. play a central role in the development of secondary cucumber fermentations. The same analyses suggest that species of Gluconobacter, Prevotella, Pectinatus and Lactobacillus were present during secondary cucumber fermentation in selected samples. The presence of Acetobacter spp. in spoilage samples was confirmed by culture based methods in the laboratory. Acetobacter pasteurianus was isolated from all spoilage samples tested and their identity confirmed by the partial sequencing of the 16S rDNA. Acetobacter spp. are commonly used in the production of vinegar and are considered benign. This group of bacteria depend on the presence of oxygen for growth, a condition that is present in commercial cucumber tanks due to the use of open top tanks and air-purging. Metabolic pathways potentially involved in the conversion of lactic acid to propionic acid during secondary cucumber fermentation were also identified.

Technical Abstract: Fermented cucumber spoilage (FCS) characterized by rising pH and the appearance of manure- and cheeselike aromas is a challenge of significant economical impact for the pickling industry. Previous culture-based studies identified the yeasts Pichia manshurica and Issatchenkia occidentalis, 4 Gram-positive bacteria, Lactobacillus buchneri, Lactobacillus parrafaraginis, Clostridium sp., and Propionibacterium and 1 Gram-negative genus, Pectinatus, as relevant in various stages of FCS given their ability to metabolize lactic acid. It was the objective of this study to augment the current knowledge of FCS using culture-independent methods to microbiologically characterize commercial spoilage samples. Ion Torrent data and 16S rRNA cloning library analyses of samples collected from commercial fermentation tanks confirmed the presence of L. rapi and L. buchneri and revealed the presence of additional species involved in the development of FCS such as Lactobacillus namurensis, Lactobacillus acetotolerans, Lactobacillus panis, Acetobacter peroxydans, Acetobacter aceti, and Acetobacter pasteurianus at pH below 3.4. The culture-independent analyses also revealed the presence of species of Veillonella and Dialister in spoilage samples with pH above 4.0 and confirmed the presence of Pectinatus spp. during lactic acid degradation at the higher pH. Acetobacter spp. were successfully isolated from commercial samples collected from tanks subjected to air purging by plating on Mannitol Yeast Peptone agar. In contrast, Lactobacillus spp. were primarily identified in samples of FCS collected from tanks not subjected to air purging for more than 4 mo. Thus, it is speculated that oxygen availability may be a determining factor in the initiation of spoilage and the leading microbiota.