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

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.

Population structure determined by comparative amplicon gene sequencing in biofilm and planktonic bacterial communities from pesticide-contaminated water

“…This environment for water contaminated with 30 different agrochemicals and with physicochemical conditions unfavorable to the survival of microorganisms identified in this work was considered stressful (Table 1 and S1 Table). The organization of bacteria in biofilms in tanks and containers, with their cooperative or antagonistic interactions, may lead to a specific combination of species with increased adaptability to the environment [49]. Thus, the most dominant sequences in B2, corresponding to the genera Enterobacter and Acinetobacter , are poorly represented in the other communities studied, including the biofilms in B1, G1 and G2 (Fig 2).…”

Microbial Proteomics and Their Importance in Medical Microbiology

“…Proteomics provides valuable data in the field of microbiology; proteomics characterizes the molecular model systems to investigate specific aspects of microbiological gene expression and metabolism. In medical microbiology, these data help to analyze the disease mechanism and how the pathogen interact with their hosts; these investigations are largely focused on the development of novel approaches for treatment and prevention of infectious diseases (Herschend et al, 2017;Wang et al, 2016).…”

In vitrocommunity synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

“…Work on this community has established that co-cultivation leads to enhanced biofilm formation, that all four species increase in cell counts through biofilm co-cultivation and that all four species are indispensable for the synergy to occur (31). Later studies has hinted that the synergy can be linked to a specific spatial organisation of community members during co-cultivation in biofilms (32), and meta-transcriptomics (33) and - proteomics (34) studies have identified amino acid cross-feeding as a potential driver for the synergy. However, the impact of the community on its surrounding environment, and the mutual community-environment interplay, has not been explored.…”