Additive-induced pH determines bacterial community composition and metabolome in traditional mustard seed fermented products

Introduction

Kahudi and Kharoli are unique naturally fermented mustard seed products prepared and consumed in the northeastern region of India. The pre-fermentation processing of mustard seeds (soaking, pan-frying, mixing with alkaline or acidic additives, airtight packaging) renders a stringent fermentation environment. The metabolic activities of fermenting bacterial populations yield a myriad of glucosinolate-derived bioactive components which have not been described earlier.

Methods

This present study employed integrated 16S rRNA amplicon sequencing and LC-MS-based metabolomics to elucidate the bacterial diversity and metabolome of the two fermented mustard seed food products.

Results and Discussion

Univariate and multivariate analyses of metabolomics data revealed differential abundances of a few therapeutically-important metabolites viz., sinapine, indole-3-carbinol, γ-linolenic acid in Kahudi, and metabolites viz., β-sitosterol acetate, 3-butylene glucosinolate, erucic acid in Kharoli. A metagenomic investigation involving the 16S rRNA (V3–V4) amplicon sequencing showed the dominance of Firmicutes (99.1 ± 0.18%) in Kahudi, and Firmicutes (79.6 ± 1.92%) and Proteobacteria (20.37 ± 1.94%) in Kharoli. The most abundant genera were Bacillus (88.7 ± 1.67% in Kahudi; 12.5 ± 1.75% in Kharoli) followed by Lysinibacillus (67.1 ± 2.37% in Kharoli; 10.4 ± 1.74% in Kahudi). Members of both these genera are well known for proteolytic and endospore-forming abilities which could have helped in colonizing and thriving in the stringent fermentation environments.

Proline confers acid stress tolerance to Bacillus megaterium G18

Proline plays a multifunctional role in several organisms including bacteria in conferring protection under stress conditions. In this paper we report the role of proline in conferring acid tolerance to Bacillus megaterium G18. An acid susceptible mutant of B. megaterium G18 which required proline for its growth under acid stress condition was generated through Tn5 mutagenesis. Further, targeted inactivation of proC involved in osmo-adaptive proline synthesis in B. megaterium G18 resulted in the loss of ability of the bacterium to grow at low pH (pH 4.5). Exogenous supply of proline (1 mM) to the growth medium restored the ability of the mutant cells to grow at pH 4.5 which was not the same in case of other osmoprotectants tested. Proline was produced and secreted to extracellular medium by B. megaterium G18 when growing in low pH condition as evidenced by the use of Escherichia coli proline auxotrophs and HPLC analysis. Further, pHT01 vector based expression of full length proC gene in the ∆proC mutant cells restored the survival capacity of the mutant cells in acidic pH, suggesting that proline production is an important strategy employed by B. megaterium G18 to survive under acid stress induced osmotic stress.

Acid tolerant bacterium Bacillus amyloliquefaciens MBNC retains biocontrol efficiency against fungal phytopathogens in low pH

Soil pH conditions have important consequences for microbial community structure, their dynamics, ecosystem processes, and interactions with plants. Low soil pH affects the growth and functional activity of bacterial biocontrol agents which may experience a paradigm shift in their ability to act antagonistically against fungal phytopathogens. In this study, the antifungal activity of an acid-tolerant soil bacterium Bacillus amyloliquefaciens MBNC was evaluated under low pH and compared to its activity in neutral pH conditions. Bacterial supernatant from 3-day-old culture (approximately 11.2 × 10⁸ cells/mL) grown in low pH conditions was found more effective against fungal pathogens. B. amyloliquefaciens MBNC harboured genes involved in the synthesis of secondary metabolites of which surfactin homologues, with varying chain length (C11-C15), were identified through High-Resolution Mass Spectroscopy. The pH of the medium influenced the production of these metabolites. Surfactin C15 was exclusive to the extract of pH 4.5; production of iturinA and surfactin C11 was detected only in pH 7.0, while surfactin C12, C13 and C14 were detected in extracts of both the pH conditions. The secretion of phytohormones viz. indole acetic acid and gibberellic acid by B. amyloliquefaciens MBNC was detected in higher amounts in neutral condition compared to acidic condition. Although, secretion of metabolites and phytohormones in B. amyloliquefaciens MBNC was influenced by the pH condition of the medium, the isolate retained its antagonistic efficiency against several fungal phyto-pathogens under acidic condition.