Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Abstract

The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo-and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryoteselected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

Characterization and Phylogenetic Analysis of a Novel GH43 β-Xylosidase From Neocallimastix californiae

“…GH43 enzymes have been detected in anaerobic fungi previously (Youssef et al, 2013;Couger et al, 2015;Henske et al, 2017;Hagen et al, 2020) but none has been kinetically and thermodynamically characterized to the best of our knowledge. Xyl43Nc showed a very low temperature optimum at 32 • C when compared to the growth optimum of 39 • C for anaerobic fungi (Theodorou et al, 2005).…”

“…For example, despite several having been identified just one enzyme with xylosidase activity has been fully characterized (Morrison et al, 2016a ). These potential xylosidases include members of the GH family 43 (Youssef et al, 2013 ; Couger et al, 2015 ; Henske et al, 2017 ; Hagen et al, 2020 ). GH43 is one of the most prominent families containing xylosidases showing some of the highest reported xylosidase activities so far (Jordan et al, 2013 , 2016 ; Falck et al, 2016 ).…”

Innovations in CAZyme gene diversity and its modification for biorefinery applications

“…GH48 was found to be the most abundant and the other representatives of this family detected also included the dockerin domains. The dockerin domains were associated with cellulosomes of these fungi [ 62 ]. Similarly another muti-omic study which included a meta-proteomic and metagenomic analysis of various microorganisms carrying out anaerobic digestion of plant biomass have been done.…”