Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation

Abstract

Consortia-based approaches are a promising avenue towards efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability. The rumen of large herbivores harbors a network of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work together to degrade lignocellulose, yet the microbial interactions responsible for consortia stability and activity remain uncharacterized. In this work, we demonstrate a novel enrichment-based isolation method selecting for a minimal biomass-degrading community containing anaerobic fungi, methanogenic archaea, and bacteria. The enriched culture displayed an increase of up to 2.1 times the growth rate and 1.9 times the fermentation gas produced by the isolated fungus from the enriched culture alone. Metagenomic sequencing revealed functional compartmentalization of the community spread across anaerobic fungi (Piromyces), bacteria (Sphaerochaeta), and methanogens (Methanosphaera and Methanocorpusculum). The minimal consortium enabled more complete degradation of biomass, including 2 hemicelluloses like xylan and pectin and a wider range of sugar utilization like xylose and galacturonate. Complementing the "top-down" enrichment analysis, a synthetic rumen system was formed from the "bottom-up" with isolated fungi (Piromyces finnis or Neocallimastix californiae) and methanogens (Methanobacterium bryantii) where only the hydrogenotrophic connection was preserved between members. These synthetic consortia also showed improved growth rate and degradation compared to fungi alone, yet lack the temporal stability seen in native consortia, remaining in culture together for fewer than 10 transfers on average. Taken together, these two complementary approaches both resulted in productive microbial consortia with faster growth rates and wider substrate uptake than mono-cultured fungi.

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

“…By taking a topdown approach as we do here, we allowed the community to self-select members and enrich for critical interactions needed for growth. This top-down approach has previously been shown to be superior to a bottom-up approach when developing representative environmental communities (Gilmore et al, 2019). In addition, the larger size of this community (35 detected OTUs with ∼13 dominant species, compared to 2-3) means that a greater amount of the soil functional potential and species interactions was captured and examined.…”

Anaerobic Fungi: Past, Present, and Future

“…To date, AF have been most extensively studied in ruminants, where they are recognized as an important microbe for good rumen function. This is primarily due to their role as highly efficient degraders of recalcitrant plant material (Li et al, 2017;Gilmore et al, 2019). Rumen AF are also syntrophic partners of the methanogenic archaea (Li et al, 2017;Gilmore et al, 2019).…”

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

“…maintained equal degradative capacities compared to KMCG6. Top-down enrichment-based methodology is considered as an effective way to get microbial consortia for biomass degradation (Gilmore et al, 2019). We further explored the optimization procedure to obtain SMC.…”