Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

Abstract

Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. However, we lack a holistic view of the microbial food web responsible for carbon processing in this ecosystem. Here, we sampled rumen-fistulated moose, allowing access to rumen microbial communities actively degrading woody plant biomass in real time. We resolved 1,193 viral contigs and 77 unique, near-complete microbial metagenome-assembled genomes, many of which lacked previous metabolic insights. Plant-derived metabolites were measured with NMR and carbohydrate microarrays to quantify the carbon nutrient landscape. Network analyses directly linked measured metabolites to expressed proteins from these unique metagenome-assembled genomes, revealing a genome-resolved three-tiered carbohydrate-fuelled trophic system. This provided a glimpse into microbial specialization into functional guilds defined by specific metabolites. To validate our proteomic inferences, the catalytic activity of a polysaccharide utilization locus from a highly connected metabolic hub genome was confirmed using heterologous gene expression. Viral detected proteins and linkages to microbial hosts demonstrated that phage are active controllers of rumen ecosystem function. Our findings elucidate the microbial and viral members, as well as their metabolic interdependencies, that support in situ carbon degradation in the rumen ecosystem.

Evidence for a multi-level trophic organization of the human gut microbiome

“…The concept of trophic levels has been widely used in macro-ecosystems to make sense of flow 269 of nutrients and energy in large food webs [24,25,26], but it has only received limited attention 270 in microbial ecosystems, one example being ref. [27]. There is no absolute consensus definition 271 of a trophic level with several interpretations discussed in Refs.…”

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

“…In accordance with recent research efforts to elucidate the role of the rumen virome, a significant portion of the RUS-refDB proteins (switchgrass: 56; rumen fluid: 62) were assigned to the 913 viral scaffolds we recovered from our switchgrass-associated rumen metagenome 31,56 . Recent studies have demonstrated that some viruses contribute to polysaccharide degradation directly, as they encode glycoside hydrolases 57 , or indirectly through infection of carbohydrate-degrading microorganisms 5 . Accordingly, when mining the genomic content of the viral scaffolds, we identified CAZyme domains within 444 proteincoding genes (Supplementary Figure S3).…”

“…Over the last decade, targeted efforts to isolation and cultivate novel rumen microorganisms have resulted in a more detailed understanding of the physiology of anaerobic rumen archaea and bacteria and their contribution to the overall function of the rumen ecosystem 6 . Recent studies have also shed light on the viral rumen population and although work in this area is still nascent, it suggests that the rumen virome modulates carbon cycling within the rumen ecosystem through cell lysis or re-programming of the metabolism of the host microbiome 5,7,8 . Anaerobic rumen ciliate protozoa and fungi have largely remained recalcitrant to both cultivation and molecular exploration efforts 9 , and although recent cultivation efforts have provided important insight into the lifestyle and enzymatic capacity 4,10 , their quantitative metabolic contributions to the greater rumen ecosystem are still unclear.…”

“…This group of enzymes is categorized further into different classes and families, which include carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), glycosyltransferases (GTs), and polysaccharide lyases (PLs) 3 . Previous studies have mostly been dedicated to CAZymes from rumen bacteria, although it is becoming increasingly clear that fungi and viruses also possess key roles in the carbon turnover within the rumen 4,5 . Over the last decade, targeted efforts to isolation and cultivate novel rumen microorganisms have resulted in a more detailed understanding of the physiology of anaerobic rumen archaea and bacteria and their contribution to the overall function of the rumen ecosystem 6 .…”

To dereplicate or not to dereplicate?

“…Instead, the correct conclusion would be that one more abundant population exists across all samples ( Figure 1). This issue has been acknowledged in multiple studies, and authors have chosen varying cutoffs to avoid this issue (e.g., >95% average nucleotide identity (Almeida, 2019); >98% average nucleotide identity (3,17), >95 % amino acid identity (18), >99.5% amino acid identity (4)).…”