Metabolic Profiling of Interspecies Interactions During Sessile Bacterial Cultivation Reveals Growth and Sporulation Induction in Paenibacillus amylolyticus in Response to Xanthomonas retroflexus

Abstract

The toolbox available for microbiologists to study interspecies interactions is rapidly growing, and with continuously more advanced instruments, we are able to expand our knowledge on establishment and function of microbial communities. However, unravelling molecular interspecies interactions in complex biological systems remains a challenge, and interactions are therefore often studied in simplified communities. Here we perform an in-depth characterization of an observed interspecies interaction between two co-isolated bacteria, Xanthomonas retroflexus and Paenibacillus amylolyticus. Using microsensor measurements for mapping the chemical environment, we show how X. retroflexus promoted an alkalization of its local environment through degradation of amino acids and release of ammonia. When the two species were grown in proximity, the modified local environment induced a morphological change and growth of P. amylolyticus followed by sporulation. 2D spatial metabolomics enabled visualization and mapping of the degradation of oligopeptide structures by X. retroflexus and morphological changes of P. amylolyticus through e.g. the release of membrane-associated metabolites. Proteome analysis and microscopy were used to validate the shift from vegetative growth towards sporulation. In summary, we demonstrate how environmental profiling by combined application of microsensor, microscopy, metabolomics and proteomics approaches can reveal growth and sporulation promoting effects resulting from interspecies interactions.

Bradyrhizobiumand the soybean rhizosphere: Species level bacterial population dynamics in established soybean fields, rhizosphere and nodules

“…To better understand competition among bacteria in the rhizosphere, it is imperative to characterize rhizosphere communities at the species level. While reductionist interaction experiments have been performed using two strains (Herschend et al 2022) (Galet et al 2015) (Du et al 2024),(Lyng et al 2024) species level data of rhizosphere in field conditions is lacking. Moreover, species level characterization would improve understanding of how Bradyrhizobium inoculants perform in the rhizosphere community and how this impacts nodulating capacity.…”