Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizing Bacillus species as bionematicides

Abstract

Root‐knot nematodes are destructive phytopathogens that damage agricultural crops globally, and there is growing interest in the use of biocontrol based on rhizobacteria such as Bacillus to combat Meloidogyne species. It is hypothesized that nematicidal activity of Bacillus can be attributed to the production of secondary metabolites and hydrolytic enzymes. Yet, few studies have characterized these metabolites and their identities remain unknown. Others are speculative or fail to elaborate on how secondary metabolites were detected or distinguished from primary metabolites. Metabolites can be classified based on their origin as either intracellular or extracellular and based on their function, as either primary or secondary. Although this classification is in general use, the boundaries are not always well defined. An understanding of the secondary metabolite and hydrolytic enzyme classification of Bacillus species will facilitate investigations aimed at bionematicide development. This review summarizes the significance of Bacillus hydrolytic enzymes and secondary metabolites in bionematicide research and provides an overview of known classifications. The importance of appropriate cultivation conditions for optimum metabolite and enzyme production is also discussed. Finally, the use of metabolomics for the detection and identification of nematicidal compounds is considered.

Mass spectrometry based metabolomics approach on the elucidation of volatile metabolites formation in fermented foods: A mini review

“…Multiple microbial metabolic are linked to each metabolite, but certain volatile metabolites can be generated only from specific ones. (Horak et al, 2019). For example, some intermediate metabolites such as pyruvate and acetyl-CoA are linked to several metabolic processes.…”

Optimizing and purifying extracellular amylase from soil bacteria to inhibit clinical biofilm-forming bacteria

“…It is worth noting that the isolated bacteria filtrate showed great antibiofilm activity compared to the purified amylase enzyme from the selected isolates. This may be due to the accumulation of some extracellular and intracellular metabolites in the medium, which is further explained by the metabolic overflow theory (Pinu, Villas-Boas & Aggio, 2017;Pinu et al, 2018;Horak et al, 2019). Bacillus also showed great efficacy in the production of carbohydrate-active enzymes and bioactive compounds, as well as the secretion of a variety of extracellular metabolites and lytic enzymes (Abdel-Aziz, 2013).…”

The Role of Purified α-amylase from Soil Bacteria Versus Crude Cell Supernatant from Medium against Clinical Biofilm-forming Bacteria

“…The results showed greatest inhibition obtained by B. circulans against K. pneumoniae biofilm with percentage of 93.6% and the lowest inhibition recorded by B. cereus against P. aeruginosa biofilm with percentage of 21.7%. This may be due to presence of some extracellular and intracellular metabolites in the medium where intracellular can release into extracellular medium when accumulated in the cell and this has been explained by the metabolic overflow theory [47][48][49].…”