The enteric microbiome of a novel wood-digesting organism: diversity of lignocellulolytic and nitrogen fixing communities of the Amazonian catfish, Panaque nigrolineatus

Abstract

The Neotropical catfish Panaque nigrolineatus imbibes large quantities of wood as part of its diet. This is an unusual feeding strategy among vertebrates as it imposes many dietary challenges. The most notable of these is the lack of assimilable carbon and nitrogen compounds. To overcome these dietary limitations, wood-feeding organisms rely on the lignocellulytic and diazotrophic activities of their enteric microbiomes. Characterization of the microbiomes of P. nigrolineatus through culture-dependent and molecular methods identified bacterial and fungal communities that were taxonomically distinct from all other wood-feeding organisms. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures and DNA stable-isotope probing approaches by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Similar characterizations of the nitrogen-fixing community through enrichment culturing and community nifH sequencing revealed phylotypes that are closely related to Clostridium sp., Alpha and Gammaproteobacteria, and sequences associated with GI tracts of lower termites. In addition to the observed bacterial diversity, P. nigrolineatus also possess a resident cellulolytic fungal community comprised of Sordariomycetes and Dothideomycetes. Despite this unusual assemblage of microorganisms, the functional capacity of these communities is consistent with those observed in other wood-feeders. Manipulating enteric communities through diet revealed a high degree of taxonomic diversity but high functional resiliency. The microbiomes of both wood-fed and mixed diet-fed fish had high capacity for hemicellulose hydrolysis as the predicted metagenomes contained several classes of hemicellulases and lignin-modifying enzymes. However, communities from both diets appeared to lack the necessary cellobiohydrolases for efficient cellulose hydrolysis, suggesting that cellobiose is not the primary source of dietary carbon for the fish. Meta-analysis exploring the microbiomes of diverse wood-feeding and non-feeding animals suggest that the P. nigrolineatus gut environment selects for an enteric community based on function, rather than relying on vertically transferred symbiotic relationships. This is an unusual method of community assembly in wood feeding-organisms but may provide an advantage to organisms, like P. nigrolineatus, that switch between dietary strategies to survive in highly variable environments.