Anaerobic microbiomes are among the most diverse microbial communities on earth, yet the mechanisms that control community structure and stability are poorly understood. For example, the rumen microbiome within large herbivores consists of four interdependent microbial populations (bacteria, protozoans, fungi, and methanogens) that work together to drive crude biomass into sugars and fermentation waste products. However, the interdependency of these microbes and their impact on microbial metabolism has been difficult to characterize since the vast majority of these microbes cannot be cultured. We have recently overcome these challenges by isolating co-cultures of anaerobic fungi with dependent methanogens from herbivore fecal materials. This co-culture platform creates a simplified system to model the cooperative action of anaerobic microbes, and our prokaryotic/eukaryotic systems are stable in culture &gt; 40 weeks. We have modeled the regulatory patterns for fungal genes from the <i>Piromyces, Neocallimastix, and Anaeromyces </i>genera during hydrolysis of reed canary grass and discovered several conserved regulons of genes that govern function, which are catabolite repressed. Addition of methanogens (e.g. <i>Methanocorpusculum</i>) during biomass breakdown shows that fungal-methanogen syntrophy drastically accelerates cellulose breakdown by the fungi. As biomass deconstruction by the fungi is disproportionate to growth, we hypothesize that syntrophic interactions also reprogram fungal metabolism. We will further discuss transcriptional and physiological impacts of co-culture, as well as strategies to link non-native anaerobes to the consortia.

Reconstructing anaerobic microbiomes from the "bottom-up": New techniques to decipher interwoven metabolism

249th National Meeting (2015)

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