A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community

Jakob Herschend,Zacharias B V Damholt,Andrea M Marquard,Per Hägglund,Mette Burmølle,Søren J Sørensen,Birte Svensson

doi:10.1038/s41598-017-16633-6

Jakob Herschend, Zacharias B V Damholt + Show 5 more

Open Access

https://doi.org/10.1038/s41598-017-16633-6

Copy DOI

Abstract

Microbial biofilms are omnipresent in nature and relevant to a broad spectrum of industries ranging from bioremediation and food production to biomedical applications. To date little is understood about how multi-species biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we apply a meta-proteomics approach to investigate the mechanisms influencing biofilm formation in a model consortium of four bacterial soil isolates; Stenotrophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paenibacillus amylolyticus. Protein abundances in community and single species biofilms were compared to describe occurring inter-species interactions and the resulting changes in active metabolic pathways. To obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for generating reduced reference proteomes for spectral database searches. Meta-proteomics profiling indicated that community development is dependent on cooperative interactions between community members facilitating cross-feeding on specific amino acids. Opposite regulation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, indicate that competition for limited resources also affects community development. Overall our results demonstrate the multitude of pathways involved in biofilm formation in mixed communities.

Highlights

Microbial biofilms are dynamic communities, where the architecture and community function is shaped by inter-species interactions, resulting in pH, oxygen and nutrient gradients
As the previous synergistic interactions were observed with growth in tryptic soy broth (TSB) media, TSB was utilized in the current study to elaborate on previous observations
Biofilms were scraped of the glass slides and proteins were extracted, proteolytically cleaved, fractionated and analysed by mass spectrometry (MS) based proteomics according to materials and methods

Summary

Introduction

Microbial biofilms are dynamic communities, where the architecture and community function is shaped by inter-species interactions, resulting in pH, oxygen and nutrient gradients. One of the challenges of studying complex microbial communities with current omics technologies is obtaining sufficient sampling depth and taxonomic resolution between related organisms to describe the community interactions and metabolic activity on a species and preferably strain level This becomes even more problematic when community functionality is influenced by the low abundant community members[15,23,24]. To ensure proper taxonomical resolution we developed a novel pipeline that produces trimmed reference proteomes where peptides shared between two or more species are removed, which allowed species level resolution for protein identification and quantification This approach enabled us to determine how participating members cooperate and compete for available nutrient resources, even among closely related species, in a microbial consortium

Methods

Results

Conclusion