Structural and functional analysis of the active cow rumen's microbial community provides a catalogue of genes and microbes participating in the deconstruction of cardoon biomass

• Published in: Biotechnology for biofuels 2024-04, Vol.17 (1), p.53-53, Article 53
• Main Authors: Firrincieli, Andrea, Minuti, Andrea, Cappelletti, Martina, Ferilli, Marco, Ajmone-Marsan, Paolo, Bani, Paolo, Petruccioli, Maurizio, Harfouche, Antoine L
• Format: Article
• Language: English
• Subjects: Alternative energy sources; Analysis; Biodiesel fuels; Biofuels; Biomass; Bioreactors; Biorefineries; Biotechnology; Carbohydrate active enzymes; Carbohydrates; Carbon dioxide; Cell walls; Cellulolytic enzymes; Cellulose; Cow rumen microbiome; Cynara cardunculus; Dairy cattle; Depolymerization; Energy crops; Enzymes; Esterases; Functional analysis; Gene expression; Genetic aspects; Glycosidases; Glycoside hydrolase; Glycosides; Lignin; Lignocellulose; Metatranscriptomics; Methanogenesis; Microbial activity; Microbiomes; Microbiota; Microbiota (Symbiotic organisms); Microorganisms; Neocallimastigaceae; Physiological aspects; Polysaccharides; Properties; Renewable energy; Ribonucleic acid; RNA; rRNA 16S; Rumen; Ruminococcus; Saccharides; Structure-function relationships; Taxonomy; Treponema
• ISSN: 2731-3654; 2731-3654; 1754-6834
• DOI: 10.1186/s13068-024-02495-4

Ruminal microbial communities enriched on lignocellulosic biomass have shown considerable promise for the discovery of microorganisms and enzymes involved in digesting cell wall compounds, a key bottleneck in the development of second-generation biofuels and bioproducts, enabling a circular bioeconomy. Cardoon (Cynara cardunculus) is a promising inedible energy crop for current and future cellulosic biorefineries and the emerging bioenergy and bioproducts industries. The rumen microbiome can be considered an anaerobic "bioreactor", where the resident microbiota carry out the depolymerization and hydrolysis of plant cell wall polysaccharides (PCWPs) through the catalytic action of fibrolytic enzymes. In this context, the rumen microbiota represents a potential source of microbes and fibrolytic enzymes suitable for biofuel production from feedstocks. In this study, metatranscriptomic and 16S rRNA sequencing were used to profile the microbiome and to investigate the genetic features within the microbial community adherent to the fiber fractions of the rumen content and to the residue of cardoon biomass incubated in the rumen of cannulated cows. The metatranscriptome of the cardoon and rumen fibre-adherent microbial communities were dissected in their functional and taxonomic components. From a functional point of view, transcripts involved in the methanogenesis from CO and H , and from methanol were over-represented in the cardoon-adherent microbial community and were affiliated with the Methanobrevibacter and Methanosphaera of the Euryarchaeota phylum. Transcripts encoding glycoside hydrolases (GHs), carbohydrate-binding modules (CBMs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), and glycoside transferases (GTs) accounted for 1.5% (6,957) of the total RNA coding transcripts and were taxonomically affiliated to major rumen fibrolytic microbes, such as Oscillospiraceae, Fibrobacteraceae, Neocallimastigaceae, Prevotellaceae, Lachnospiraceae, and Treponemataceae. The comparison of the expression profile between cardoon and rumen fiber-adherent microbial communities highlighted that specific fibrolytic enzymes were potentially responsible for the breakdown of cardoon PCWPs, which was driven by specific taxa, mainly Ruminococcus, Treponema, and Neocallimastigaceae. Analysis of 16S rRNA and metatranscriptomic sequencing data revealed that the cow rumen microbiome harbors a repertoire of new enzymes capable of degrading PCWPs. Our results demonstrate