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

Consortium-based approaches are a
promising avenue toward efficient
bioprocessing. However, many complex microbial interactions dictate
community dynamics and stability that must be replicated in synthetic
systems. The rumen and/or hindguts of large mammalian herbivores harbor
complex communities of biomass-degrading fungi and bacteria, as well
as archaea and protozoa that work collectively to degrade lignocellulose,
yet the microbial interactions responsible for stability, resilience,
and activity of the community remain largely uncharacterized. In this
work, we demonstrate a “top-down” enrichment-based methodology
for selecting a minimal but effective lignocellulose-degrading community
that produces methane-rich fermentation gas (biogas). The resulting
enrichment consortium produced 0.75–1.9-fold more fermentation
gas at 1.4–2.1 times the rate compared to a monoculture of
fungi from the enrichment. Metagenomic sequencing of the top-down
enriched consortium revealed genomes encoding for functional compartmentalization
of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic
archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several
synthetic cocultures were formed from the “bottom-up”
using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred
in synthetic co-cultures, removal of fungal metabolites by methanogens
did not increase the rate of gas production or the rate of substrate
deconstruction by the synthetic community relative to fungal monocultures.
Metabolomic characterization verified that syntrophy was established
within synthetic co-cultures, which generated methane at similar concentrations
compared to the enriched consortium but lacked the temporal stability
(resilience) seen in the native system. Taken together, deciphering
the membership and metabolic potential of an enriched gut consortium
enables the design of methanogenic synthetic co-cultures. However,
differences in the growth rate and stability of enriched versus synthetic
consortia underscore the difficulties in mimicking naturally occurring
syntrophy in synthetic systems.