Induction of antibiotic specialized metabolism by co‐culturing in a collection of phyllosphere bacteria

Abstract

A diverse set of bacteria live on the above-ground parts of plants, composing the phyllosphere, and play important roles for plant health. Phyllosphere microbial communities assemble in a predictable manner and diverge from communities colonizing other plant organs or the soil. However, how these communities differ functionally remains obscure. We assembled a collection of 258 bacterial isolates representative of the most abundant taxa of the phyllosphere of Arabidopsis and a shared soil inoculum. We screened the collection for the production of metabolites that inhibit the growth of Gram-positive and Gram-negative bacteria either in isolation or in co-culture. We found that isolates capable of constitutive antibiotic production in monoculture were significantly enriched in the soil fraction. In contrast, the proportion of binary cultures resulting in the production of growth inhibitory compounds differed only marginally between the phyllosphere and soil fractions. This shows that the phyllosphere may be a rich resource for potentially novel molecules with antibiotic activity, but that production or activity is dependent upon induction by external signals or cues. Finally, we describe the isolation of antimicrobial acyloin metabolites from a binary culture of Arabidopsis phyllosphere isolates, which inhibit the growth of clinically relevant Acinetobacter baumannii.

Genomic Aromatic Compound Degradation Potential of Novel Paraburkholderia Species: Paraburkholderia domus sp. nov., Paraburkholderia haematera sp. nov. and Paraburkholderia nemoris sp. nov.

“…In the frame of several efforts to maximally isolate the cultivable bacterial community of a topsoil sample of the Aelmoeseneie forest, more than 5000 isolates have been examined thus far ( [36] and data from the present study). These isolates have all been dereplicated by MALDI-TOF MS using the SPeDE algorithm [45] to remove redundant isolates.…”

“…Sixty seven forest soil isolates were selected after matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS) dereplication analyses performed in the present and previous studies [36] (Table 1). Of these isolates, 23 were picked from 1/100 diluted nutrient broth solidified with Gelzan CM (DNG), 24 from B. cepacia complex enrichment medium (BCEM), 17 from 1/10 diluted Pseudomonas cepacia azaleic acid tryptamine medium (PCAT) and 3 from modified Pikovskaya medium.…”

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

“…For instance, in a recent study, Qi et al . analysed about 3400 forest soil isolates which were dereplicated into 258 MALDI-TOF mass spectrometry-defined independent strains [10]. While subsequent publications reported three novel Pedobacter and six novel Paenibacillus species [11, 12], near full length 16S rRNA sequence analyses revealed dozens of additional novel species and genera in this collection [10].…”

“…analysed about 3400 forest soil isolates which were dereplicated into 258 MALDI-TOF mass spectrometry-defined independent strains [10]. While subsequent publications reported three novel Pedobacter and six novel Paenibacillus species [11, 12], near full length 16S rRNA sequence analyses revealed dozens of additional novel species and genera in this collection [10]. A major reason why only nine novel species from this collection have been formally named so far is the frequently encountered insistence of journal editors that authors provide ‘polyphasic’ taxonomic descriptions that are as comprehensive as possible and that include multiple types of chemotaxonomic data, reflecting recommendations from a decade ago [13].…”

Salicylic Acid-Mediated Disturbance Increases Bacterial Diversity in the Phyllosphere but Is Overcome by a Dominant Core Community

“…However, multiple significant differences in the predicted functions of the core and SA-selected communities suggests that SA signaling results in many gained functions, whether beneficial or detrimental to the host plant. Previous research has demonstrated that the bacterial phyllosphere microbiome has the capacity to both produce and metabolize antibiotics, but that the magnitude is dependent on extrinsic cues, including biotic stress responses ( Chen et al, 2018 ; Qi et al, 2021 ; Yan et al, 2021 ). The research presented here predicts that SA signaling selects for bacteria associated with the biosynthesis of antibiotics.…”