Propionate as the preferred carbon source to produce 3-indoleacetic acid in B. subtilis: comparative flux analysis using five carbon sources

Response of a new rumen-derived Bacillus licheniformis to different carbon sources

Introduction

Bacillus licheniformis (B. licheniformis) is a microorganism with a wide range of probiotic properties and applications. Isolation and identification of novel strains is a major aspect of microbial research. Besides, different carbon sources have varying effects on B. licheniformis in regulating the microenvironment, and these mechanisms need to be investigated further.

Methods

In this study, we isolated and identified a new strain of B. licheniformis from bovine rumen fluid and named it B. licheniformis NXU98. The strain was treated with two distinct carbon sources-microcrystalline cellulose (MC) and cellobiose (CB). A combination of transcriptome and proteome analyses was used to investigate different carbon source effects.

Results

The results showed that B. licheniformis NXU98 ABC transporter proteins, antibiotic synthesis, flagellar assembly, cellulase-related pathways, and proteins were significantly upregulated in the MC treatment compared to the CB treatment, and lactate metabolism was inhibited. In addition, we used MC as a distinct carbon source to enhance the antibacterial ability of B. licheniformis NXU98, to improve its disease resistance, and to regulate the rumen microenvironment.

Discussion

Our research provides a potential new probiotic for feed research and a theoretical basis for investigating the mechanisms by which bacteria respond to different carbon sources.

Global landscape of lysine acylomes in Bacillus subtilis

Lysine acetylation is a common posttranslational modification that regulates numerous biochemical functions in both eukaryotic and prokaryotic species. In addition, several new non-acetyl acylations are structurally different from lysine acetylation and participate in diverse physiological functions. Here, a comprehensive analysis of several lysine acylomes was performed by combining the high-affinity antibody enrichment with high-resolution LC-MS/MS. In total, we identified 2536 lysine acetylated sites, 4723 propionylated sites, 2150 succinylated sites and 3001 malonylated sites in Bacillus subtilis, respectively. These acylated proteins account for 35.8% of total protein in this bacterium. The four lysine acylomes showed a motif preference for glutamate surrounding the modified lysine residues, and a functional preference for several metabolic pathways, such as carbon metabolism, fatty acid metabolism, and ribosome. In addition, more protein-protein interaction clusters were identified in the propionylated substrates than other three lysine acylomes. In summary, our study presents a global landscape of acylation in the Gram-positive model organism Bacillus and their potential functions in metabolism and physiology.

Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production

The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA.

Bacillus as a source of phytohormones for use in agriculture

Microbial plant biostimulants (MPBs) are capable of improving the productivity and quality of crops by activating plant physiological and molecular processes, representing an efficient tool in sustainable agriculture. Through phytohormone production, MPBs are capable of regulating plant physiological processes, increasing the productivity and quality of crops, in addition to being an efficient alternative in the industrial production of phytohormones. Bacillus is a bacterial genus with various species on the market being used as biopesticides, due to their ability to produce antimicrobial, nematicidal and insecticidal compounds. The capability of Bacillus species to protect plants against pests and/or pathogens also entails the triggering or increase of plant defense responses. Furthermore, a relevant number of species from the genus Bacillus provoke plant growth promotion by different mechanisms such as increasing the tolerance of their host plants under abiotic stress conditions or improving plant nutrition. In several cases, the plant response is mediated by the bacterial production of phytohormones. In the present work, all studies from recent decades where the production of phytohormones by Bacillus species are reported, highlighting their role in host plants and the mechanisms by which they are capable of increasing plant growth, promoting their development, and improving their response to different stresses. KEY POINTS: • Different Bacillus-species are known as agricultural biopesticides. • Bacillus role as biostimulants is being increasingly addressed. • Bacillus represents a good source of phytohormones of agricultural interest.