Back to basics: simplifying microbial communities to decrypt complex interactions

Informations

Funding country

Norway

Acronym

-

URL

-

Start date

1/1/2016

End date

12/31/2020

Budget

951,036 EUR

Fundings

Abstract

All life on earth depends on the actions of microorganisms. For example, the digestion system of humans depends on a vital relationship with a community of microorganisms that control the breakdown of ingested food whilst forming a protective barrier against disease and infection. Microorganisms also play a central role in the turnover of biomass, be it in natural ecosystems or in the production of bioenergy. With the help of microbial communities, we can convert a wide range of plant biomass and agricultural waste into renewable fuels and bioproducts. The microbial degradation of organic matter is usually not carried out by one bacterium, but rather a complex network of microbial populations where microbes work together by performing different tasks that complement each other. Researchers who wish to study these important microorganisms and their relation to each other, encounter many technical challenges. One key bottleneck is that the vast majority of microorganisms that exist in nature cannot be grown and studied in the laboratory, which means a complete understanding of how they operate and collaborate is restricted. This project utilized recent advancements in molecular and computational technologies to create new knowledge into how microorganisms, which cannot be grown in the lab, can work together to perform important tasks in mammalian digestion as well as bio-industries. We developed methods that pieced together the DNA and proteins that are used by different microorganisms who work together in a community to convert organic material. Important fragments of DNA (called genes) and proteins were examined in detail and their suitability to industrial applications was also assessed. The "Back to Basics" project revealed exciting results that illustrated the cooperation between uncultured microbes, which play significant roles in dictating microbial conversion of biomass. We produced and analyzed several minimalistic model communities that contained the key microbial populations required to convert complex carbohydrates to useful metabolites. Using both culture-dependent and -independent approaches we revealed that key protein-degrading species that are known to numerically dominate industrial biogas plants, are in fact configured in complex populations of closely related strains that have genetically evolved via horizontal gene transfer to a plant biomass-degrading lifestyle. From the human gut, we uncovered a novel community of microbes, which work together to degrade xanthan, a commonly used dietary supplement that has hitherto believed to be resistant to microbial attack. We also uncovered that anaerobic fungi are major players in the rumen and produce many enzymes to degrade plant fiber. We further utilized novel computational approaches to demonstrate co-expression patterns between multiple strains and other specialist species, suggesting inter-population cooperation to perform critical functions (i.e. degrade complex carbohydrates) that are central to mammalian digestion as well as industrial processes such as biogas production and waste-water treatment.