Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms

• Published in: Frontiers in microbiology Vol. 12; p. 757856
• Main Authors: Kosina, Suzanne M, Rademacher, Peter, Wetmore, Kelly M, de Raad, Markus, Zemla, Marcin, Zane, Grant M, Zulovich, Jennifer J, Chakraborty, Romy, Bowen, Benjamin P, Wall, Judy D, Auer, Manfred, Arkin, Adam P, Deutschbauer, Adam M, Northen, Trent R
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Research Foundation 09-12-2021; Frontiers Media S.A
• Subjects: BASIC BIOLOGICAL SCIENCES; biofilm; consortia; exometabolomics; mass spectrometry; metabolomics; microbial interaction; Microbiology; morphology; mutant fitness profiling; microbial interaction; exometabolomics; morphology; metabolomics; biofilm; mass spectrometry; consortia; mutant fitness profiling
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2021.757856

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing
have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of
biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between
strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.