Volatile communication in Actinobacteria: a language for secondary metabolism regulation

Abstract

Background: Volatile compounds are key elements in the interaction and communication between organisms at both interspecific and intraspecific levels. In complex bacterial communities, the emission of these fast-acting chemical messengers allows an exchange of information even at a certain distance that can cause different types of responses in the receiving organisms. The changes in secondary metabolism as a consequence of this interaction arouse great interest in the field of searching for bioactive compounds since they can be used as a tool to activate silenced metabolic pathways. Regarding the great metabolic potential that the Actinobacteria group presents in the production of compounds with attractive properties, we evaluated the reply the emitted volatile compounds can generate in other individuals of the same group.

Results: We recently reported that volatile compounds released by different streptomycete species trigger the modulation of biosynthetic gene clusters in Streptomyces spp. which finally leads to the activation/repression of the production of secondary metabolites in the recipient strains. Here we present the application of this rationale in a broader bacterial community to evaluate volatiles as signaling effectors that drive the activation of biosynthesis of bioactive compounds in other members of the Actinobacteria group. Using cocultures of different actinobacteria (where only the volatile compounds reach the recipient strain) we were able to modify the bacterial secondary metabolism that drives overproduction (e.g., granaticins, actiphenol, chromomycins) and/or de novo production (e.g., collismycins, skyllamycins, cosmomycins) of compounds belonging to different chemical species that present important biological activities.

Conclusions: This work shows how the secondary metabolism of different Actinobacteria species can vary significantly when exposed in co-culture to the volatile compounds of other phylum-shared bacteria, these effects being variable depending on strains and culture media. This approach can be applied to the field of new drug discovery to increase the battery of bioactive compounds produced by bacteria that can potentially be used in treatments for humans and animals.

Keywords: Streptomyces sp.; Actinobacteria; Antibiotic; Biosynthetic potential; Metabolites; Secondary metabolism; Volatile compounds.

Fig. 1

VOC chamber. A Schematic representation of a VOC chamber. B Overview of each part of the VOC chamber device. The hole in the middle allows the exchange of VOCs between cultures (modified from [39])

Fig. 2

Co-culture Streptomyces sp. CS014 against Verrucosispora ML1 in YMA medium. A Comparative UPLC profile of CS014 cultured on YMA against Verrucosispora ML1 and extracted with ethyl acetate. P1-4 show the overproduction of granaticins A and C and the activation of the synthesis of collismycins A and D. P1 = collismycins A-B, P2 = granaticin A, P3 = granaticin C, P4 = collismycin D. B Streptomyces sp. CS014 plates after co-culture against Verrucosispora ML1 (left) and in monoculture (right). Due to the blue color of granaticins, the production of this metabolite can be appreciated visually. C Structure of granaticin A and collismycin A

Fig. 3

Plate of Streptomyces sp. CS057 in co-culture against Verrucosispora ML1 (left) and in monoculture (right) in YMA medium. It is shown that, when Streptomyces sp. CS057 is co-cultured with Verrucosispora ML1, its sporulation capacity is lost

Fig. 4

Co-culture Streptomyces sp. CS065a against R. erythropolis in SFM medium. A Comparative UPLC profile of CS065a against R. erythropolis and extracted with ethyl acetate containing 1% formic acid, pointing to the overproduction of chromomycins (P1) and the activation of alteramides production (P2). B Bioassay from the SFM agar plug of the monoculture Streptomyces sp. CS065a (65 +) and the co-culture against R. erythropolis (65-R) against M. luteus (left, 65 +  = 15 ± 2 mm inhibition zone; 65-R = 26 ± 2.52 mm inhibition zone) and E. coli (luteus (right, 65 +  = 0 ± 0 mm inhibition zone; 65-R = 16 ± 0.57 mm inhibition zone). C Bioassay from the YMA agar plug of the monoculture Streptomyces sp. CS065a (65 +) and the co-culture against R. erythropolis (65-R) against M. luteus (left, 65 +  = 23 ± 1.52 mm inhibition zone; 65-R = 26 ± 0.57 mm inhibition zone) and E. coli (right, 65 +  = 16 ± 1.15 mm inhibition zone; 65-R = 19 ± 2.30 mm inhibition zone)

Fig. 5

Activation of chromomycin production in Streptomyces sp. CS065a. Plate of Streptomyces sp. CS065a in co-culture against Verrucosispora ML1 (left) and in monoculture (right) in YMA medium. Due to the brown color of chromomycins, the production of this metabolite can be appreciated by the change of color

Fig. 6

Cosmomycin production in Streptomyces sp. CS081a. A Comparative UPLC profile extracted with ethyl acetate of Streptomyces sp. CS081a against R. erythropolis. P1 indicates the overproduction of dihydrotetrodecamycin. B Comparative UPLC profile extracted with ethyl acetate of Streptomyces sp. CS081a against S. erythraea. P2 indicates the activation of the production of cosmomycin-related compounds

Fig. 7

Alteramide activation in Streptomyces sp. CS090a. A Comparative UPLC profile of Streptomyces sp. CS090a cultured on SFM against S. erythraea and extracted with ethyl acetate 1% formic acid. P1 and P2 show the activation of the synthesis of maltophilins and alteramides, respectively. B Bioassay plate against E. coli (left) and M. luteus (right) with samples obtained from Streptomyces sp. CS090a cultured in SFM against R. erythropolis. The inhibition zone against E. coli is 0 ± 0 for control (CS90 +) and 15 ± 1.73 mm for CS090a co-cultured (CS90-R). The diameter inhibition against M. luteus is 9 ± 0.57 mm for control (CS90 +) and 13 ± 1.15 mm for Streptomyces sp. CS090a co-cultured (CS90-R). C Chemical structure of alteramides

Fig. 8

Comparative UPLC profile of Streptomyces sp. CS113 against Verrucosispora ML1 and extracted with ethyl acetate. P1 indicates the overproduction of germicidin and P2 the overproduction of cervimycin

Fig. 9

Results of the co-culture Streptomyces sp. CS131—S. erythraea sp. A Comparative UPLC profile of Streptomyces sp. CS131 cultured on YMA against S. erythraea and extracted with ethyl acetate. P1 indicates the overproduction of actinomycin G4, P2 the activation of actinomycin I synthesis and P3 the overproduction of actinomycin D. B Bioassay plate against M. luteus when microorganisms are cultured in SFM. CS131 +corresponds with the control monoculture while CS131-R stands for the agar plug from the co-culture against R. erythropolis. An inhibition zone of 30 ± 1.15 mm of diameter is produced by CS131-R sample while there is no antibacterial activity exerted by the metabolites from the control agar plug

Fig. 10

Comparative UPLC profile of Streptomyces sp. CS147 cultured on SFM against Verrucosispora ML1. P1 indicates the overproduction of cyclo (pro-leu) and P2 the overproduction of coproporphyrin

Fig. 11

Comparative UPLC profile of Streptomyces sp. CS149 cultured on YMA against M. melanospora. P1 and P2 indicate the activation of rumycin 1 and rumycin 2 biosynthesis, respectively

Fig. 12

Comparative UPLC profile of Streptomyces sp. CS159 cultured on YMA against R. erythropolis. P1 indicates the overproduction of inthomycins

Fig. 13

Comparative UPLC profile of Streptomyces sp. CS207 cultured on YMA against R. erythropolis. P1 indicates the overproduction of 3-cyanomethyl-6-prenylindole

Fig. 14

Results of the co-culture of Verrucosispora ML1.—R. erythropolis DSM43006 (A) Comparative UPLC profile of Verrucosispora ML1. Cultured on YMA against R. erythropolis DSM43006 and extracted with ethyl acetate containing 1% formic acid. It can be appreciated the inhibition of the production of several metabolites. B Plate of Verrucosispora ML1 in co-culture against R. erythropolis DSM43006 (left) and in monoculture (right) in YMA medium. Due to the inhibition of the production of several metabolites, differences can be appreciated visually