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.
Highlights
Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation
To broadly sample plant-associated and planktonic microorganisms, we obtained 53.8 Gbps of Illumina HiSeq sequencing data from one size-fractionated rumen fluid sample. This included separate metagenomes for microorganisms associated with (1) plant particulate matter, those retained on a (2) 0.8-μm filter and (3) 0.2-μm filter, as well as (4) viral and small cells that pass through a 0.2-μm filter (Supplementary Fig. 1)
Because our primary goal was to profile the expressed genomic potential that contributed to the rumen carbohydrate food web, we focused on 77 unique bacterial and archaeal metagenome-assembled genomes (MAGs) that were near complete (>75%) and 810 unique viral contigs (>10,000 bp)
Summary
Because of their agricultural value, there is a great body of research dedicated to understanding the microorganisms responsible for rumen carbon degradation. Rumen fluid from winter diets, relative to spring and summer diets, had significant increases in the levels of lignin and hemicelullose, which enriched for microbial communities composed of genomically unsampled and enigmatic Bacteroidetes members[14] Many of these Bacteroidetes and other enriched taxa were described as core members conserved across 35 different species of ruminant animals[2], suggesting that they may play important roles in the degradation of recalcitrant carbon and provide benefits to host metabolism. We deeply sequenced four metagenomes from a size-fractionated rumen fluid sample representative of the winter diet[14] This approach recovered quality viral and bacterial genomes from low-abundance members, creating a genome database to annotate metaproteome data and link expression data to metabolite sources and sinks.
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