Supporting data for "Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle"

Resumen

Mitigating the effects of global warming has become the main challenge for humanity in the last decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. As ruminal microbiota is directly involved in digestive fermentation processes and methane biosynthesis, understanding the ecological relationships between rumen microorganisms and their active metabolic pathways is essential for reducing emissions. This study analyzed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions. <br>The beta-diversity analyses suggested an association between methane production and overall microbiota composition (0.01 &lt; R2 &lt; 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (Padj&lt;0.05). Those genera associated to high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated to low methane emissions. The genus-level association network showed two clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs resulted to be differentially abundant between low and high emission animals, and were mainly involved in metabolic pathways. No KEGGs included in the methane metabolism pathway (ko00680) were detected as associated to high methane emissions. The KEGG network showed three clusters grouping KEGGs associated to high emissions, low emissions and not differentially abundant in either of them. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low emissions animals. <br>Methane emissions are largely associated to the relative abundance of ciliate and fungi. The role of nitrate electron acceptors can be particularly important as this respiration mechanism directly competes with methanogenesis. Therefore, whole metagenome sequencing is necessary to jointly consider relative abundance of Bacteria, Archaea and Eukaryota in the statistical analyses. Nutritional and genetic strategies to reduce CH4 emissions should focus on reducing the relative abundance of Alveolata and Fungi in the rumen. This experiment has generated the largest ONT ruminal metagenomic dataset currently available.