Distribution of 2,4-Diacetylphloroglucinol Biosynthetic Genes among the Pseudomonas spp. Reveals Unexpected Polyphyletism

Abstract

Fluorescent pseudomonads protecting plant roots from phytopathogens by producing 2,4-diacetylphloroglucinol (DAPG) are considered to form a monophyletic lineage comprised of DAPG+ Pseudomonas strains in the “P. corrugata” and “P. protegens” subgroups of the “Pseudomonas fluorescens” group. However, DAPG production ability has not been investigated for many species of these two subgroups, and whether or not the DAPG+ Pseudomonas are truly monophyletic remained to be verified. Thus, the distribution of the DAPG biosynthetic operon (phlACBD genes) in the Pseudomonas spp. was investigated in sequenced genomes and type strains. Results showed that the DAPG+ Pseudomonas include species of the “P. fluorescens” group, i.e., P. protegens, P. brassicacearum, P. kilonensis, and P. thivervalensis, as expected, as well as P. gingeri in which it had not been documented. Surprisingly, they also include bacteria outside the “P. fluorescens” group, as exemplified by Pseudomonas sp. OT69, and even two Betaproteobacteria genera. The phl operon-based phylogenetic tree was substantially congruent with the one inferred from concatenated housekeeping genes rpoB, gyrB, and rrs. Contrariwise to current supposition, ancestral character reconstructions favored multiple independent acquisitions rather that one ancestral event followed by vertical inheritance. Indeed, based on synteny analyses, these acquisitions appeared to vary according to the Pseudomonas subgroup and even the phylogenetic groups within the subgroups. In conclusion, our study shows that the phl+ Pseudomonas populations form a polyphyletic group and suggests that DAPG biosynthesis might not be restricted to this genus. This is important to consider when assessing the ecological significance of phl+ bacterial populations in rhizosphere ecosystems.

Genomic insights into a plant growth‐promoting Pseudomonas koreensis strain with cyclic lipopeptide‐mediated antifungal activity

“…Some Pseudomonas species, such as P. fluorescens, P. protegens, P. kilonensis, P. chlororaphis, and P. simiae, have been used widely in agriculture to control plant disease and to improve production (Raaijmakers, Weller, & Thomashow, 1997;Ramamoorthy, Raguchander, & Samiyappan, 2002). Among them, P. kilonensis F113, P. protegens strains CHA0 and Pf-5, and some other typical PGPR strains produced polyketides, such as 2,4-diacetylphloroglucinol (DAPG), phenazines, pyoluteorin, and pyrrolnitrin, that defended against a broad range of plant pathogens (Almario et al, 2017;Iavicoli, Boutet, Buchala, & Métraux, 2003;Keel et al, 1992;Nowak-Thompson, Gould, & Loper, 1997;Ramette et al, 2011). In addition to polyketides, many PGPR strains synthesized cyclic lipopeptides (CLPs) by non-ribosomal peptide synthetases (NRPSs) as potent secondary metabolites that can destroy microbial membranes (Geudens & Martins, 2018).…”

Root‐associated microbes in sustainable agriculture: models, metabolites and mechanisms

“…The polyketide antibiotic DAPG, which targets key physiological processes involving membrane function, reactive oxygen regulation, and cellular homeostasis, is active against a wide variety of organisms including viruses, bacteria, fungi, oomycetes, parasitic worms, and even plants including different cultivars of wheat . DAPG producers have been recovered from plant rhizospheres worldwide, with the biosynthesis genes broadly conserved and embedded within the genomes of members of at least five species ( P. protegens, P. brassicacearum, P. kilonensis, P. thivervalensis, and P. gingeri ) within the P. corrugata and P. protegens subgroups of P. fluorescens , as well as a few β‐proteobacteria ( Chromobacterium vaccinii , C. piscinae , and Pseudogulbenkiania ferrooxidans ) . The antibiotic is a strong inducer of systemic resistance (ISR) in Arabidopsis , a form of plant immunity defined as the ‘enhanced defensive capacity of the entire plant against a broad spectrum of pathogens; acquired upon local induction, for example, at roots, by beneficial microbes” .…”

“…17 DAPG producers have been recovered from plant rhizospheres worldwide, with the biosynthesis genes broadly conserved and embedded within the genomes of members of at least five species (P. protegens, P. brassicacearum, P. kilonensis, P. thivervalensis, and P. gingeri) within the P. corrugata and P. protegens subgroups of P. fluorescens, as well as a few -proteobacteria (Chromobacterium vaccinii, C. piscinae, and Pseudogulbenkiania ferrooxidans). 18 The antibiotic is a strong inducer of systemic resistance (ISR) in Arabidopsis, a form of plant immunity defined as the 'enhanced defensive capacity of the entire plant against a broad spectrum of pathogens; acquired upon local induction, for example, at roots, by beneficial microbes". 19 It is important to note that not all members of the microbiome are capable of inducing ISR, that other bacterial inducers may function in different plant hosts, and that the phenomenon ultimately depends on production of chemical signals that mediate communication between the inducing organism and the host plant, a hallmark of the level of interaction within the holobiont.…”

Thioesters as Acyl Donors in Biocatalytic Friedel‐Crafts‐type Acylation Catalyzed by Acyltransferase from Pseudomonas Protegens

“…[8] The acylations are mostly performed in organic solvents (e. g., nitrobenzene or nitromethane) or at elevated temperatures of up to 300°C. [10] Subsequently, it was shown that a homologue acyltransferase from Pseudomonas protegens (PpATaseCH) exhibits promiscuous activity, accepting also non-natural, activated esters, like isopropenyl acetate, phenyl acetate and N-acetyl imidazole for the biocatalytic Friedel-Crafts acylation of resorcinol derivatives leading to C4-acylated products. As an alternative, a biocatalytic approach running the reaction in aqueous media was recently published: originally an acyltransferase from Pseudomonas fluorescens was found to be involved in CÀ C bond formation in the biosynthesis of 2,4-diacetylphloroglucinol (DAPG).…”