Metabolic Profiling of Rhizobacteria Serratia plymuthica and Bacillus subtilis Revealed Intra- and Interspecific Differences and Elicitation of Plipastatins and Short Peptides Due to Co-cultivation

Abstract

Rhizobacteria live in diverse and dynamic communities having a high impact on plant growth and development. Due to the complexity of the microbial communities and the difficult accessibility of the rhizosphere, investigations of interactive processes within this bacterial network are challenging. In order to better understand causal relationships between individual members of the microbial community of plants, we started to investigate the inter- and intraspecific interaction potential of three rhizobacteria, the S. plymuthica isolates 4Rx13 and AS9 and B. subtilis B2g, using high resolution mass spectrometry based metabolic profiling of structured, low-diversity model communities. We found that by metabolic profiling we are able to detect metabolite changes during cultivation of all three isolates. The metabolic profile of S. plymuthica 4Rx13 differs interspecifically to B. subtilis B2g and surprisingly intraspecifically to S. plymuthica AS9. Thereby, the release of different secondary metabolites represents one contributing factor of inter- and intraspecific variations in metabolite profiles. Interspecific co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g showed consistently distinct metabolic profiles compared to mono-cultivated species. Thereby, putative known and new variants of the plipastatin family are increased in the co-cultivation of S. plymuthica 4Rx13 and B. subtilis B2g. Interestingly, intraspecific co-cultivation of S. plymuthica 4Rx13 and S. plymuthica AS9 revealed a distinct interaction zone and showed distinct metabolic profiles compared to mono-cultures. Thereby, several putative short proline-containing peptides are increased in co-cultivation of S. plymuthica 4Rx13 with S. plymuthica AS9 compared to mono-cultivated strains. Our results demonstrate that the release of metabolites by rhizobacteria alters due to growth and induced by social interactions between single members of the microbial community. These results form a basis to elucidate the functional role of such interaction-triggered compounds in establishment and maintenance of microbial communities and can be applied under natural and more realistic conditions, since rhizobacteria also interact with the plant itself and many other members of plant and soil microbiota.

Underexplored bacteria as reservoirs of novel antimicrobial lipopeptides

“…This lipopeptide has a peptide moiety of two amino acid residues (i.e., Ser-Ser) linked to two C 10 fatty acid chains ( Figure 1A ) ( Matsuyama et al, 1985 ). Numerous analogues of this compound have been identified, which are produced by pigmented and non-pigmented S. marcescens, S. ureilytica, and S. plymuthica strains (as well as a Serratia liquefaciens strain that was reclassified as a S. marcescens strain), that vary based on the length and saturation/unsaturation of the fatty acid moiety and can be cyclic or open-ring structures ( Eberl et al, 1999 ; Labbate et al, 2007 ; Dwivedi et al, 2008 ; Kuo et al, 2012 ; Clements et al, 2021 ; Menezes et al, 2021 ). Serratamolides exhibit promising activity against Gram-positive bacteria, such as Enterococcus faecalis , Mycobacterium spp.…”

“…Recently, several bacterial genera such as Serratia , Brevibacillus and Burkholderia , have emerged as underexplored sources of novel antimicrobial lipopeptides ( Etzbach et al, 2014 ; Burgard et al, 2017 ; Ganley et al, 2018 ; Li et al, 2018 ; Sang et al, 2019 ; Ning et al, 2021 ). For example, four species within the Serratia genus, including Serratia marcescens ( S. marcescens ) , Serratia plymuthica ( S. plymuthica ) , Serratia ureilytica ( S. ureilytica ), and Serratia surfactantfaciens ( S. surfactantfaciens ), have been reported as lipopeptide producers, with serrawettin W1 (also referred to as serratamolide), serrawettin W2 or stephensiolides families, produced by various strains ( Kuo et al, 2012 ; Menezes et al, 2021 ; Clements-Decker et al, 2022 ). Strains of Brevibacillus laterosporus ( B. laterosporus ) and Brevibacillus brevis ( Br.…”

Screening of Antimicrobial Activities and Lipopeptide Production of Endophytic Bacteria Isolated from Vetiver Roots

“…As a result, some of the compounds involved in the antagonistic activities observed in dual cultures may not have been produced or produced only weakly. Indeed, it has been shown that resource competition and inter-and intraspecific microbial interactions are often implicated in the induction of the biosynthesis of antimicrobial compounds [35][36][37].…”

Metabolome and transcriptome related dataset for pheromone biosynthesis in an aggressive forest pest Ips typographus

“…Data filtering was implemented by detecting and removing non-informative variables characterized by near-constant values throughout the experimental conditions by comparing their robust estimate interquartile ranges (IQR). Data was auto-scaled out of the 3020 mass features originally detected, using the Principal Least Square Discriminant Analysis PLS-DA [4] .…”