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

Abstract

Background Mitigating the effects of global warming has become the main challenge for humanity in recent decades. Livestock farming contributes to greenhouse gas emissions, with an important output of methane from enteric fermentation processes, mostly in ruminants. Because 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 analysed whole rumen metagenome using long reads and considering its compositional nature in order to disentangle the role of rumen microbes in methane emissions. Results The β-diversity analyses suggested a subtle association between methane production and overall microbiota composition (0.01 < R2 < 0.02). Differential abundance analysis identified 36 genera and 279 KEGGs as significantly associated with methane production (Padj < 0.05). Those genera associated with high methane production were Eukaryota from Alveolata and Fungi clades, while Bacteria were associated with low methane emissions. The genus-level association network showed 2 clusters grouping Eukaryota and Bacteria, respectively. Regarding microbial gene functions, 41 KEGGs were found 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 with high methane emissions. The KEGG network showed 3 clusters grouping KEGGs associated with high emissions, low emissions, and not differentially abundant in either. A deeper analysis of the differentially abundant KEGGs revealed that genes related with anaerobic respiration through nitrate degradation were more abundant in low-emission animals. Conclusions Methane emissions are largely associated with the relative abundance of ciliates and fungi. The role of nitrate electron acceptors can be particularly important because this respiration mechanism directly competes with methanogenesis. Whole metagenome sequencing is necessary to jointly consider the 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.

Methane prediction equations including genera of rumen bacteria as predictor variables improve prediction accuracy

“…Regarding the genus Oribacterium , it had a negative coefficient in both the final ANIM-B and the DMI-B models. This aligns with Oribacterium being a potential H 2 sink in the rumen of sheep 33 and its negative association with CH 4 emissions documented in dairy cows 34 . Future research is warranted to explore and verify if Oribacterium has a quantitative relationship with rumen CH 4 production and can be used as a predictor variable or biomarker of CH 4 emissions.…”

The effects of Selenohomolanthionine supplementation on the rumen eukaryotic diversity of Shaanbei white cashmere wether goats

“…However, this assumption needs further more investigation. Previous research confirmed that protozoa associated prokaryotes displayed a variety of functions, such as the adaptability of host cells 34 , 46 , nitrogen fixation 47 , methanogenesis 48 , acetogenesis 33 , provide a defense against predators 49 , and provide nutrients to host cells 35 , 46 . Therefore, other scientific methods such as metagenomics and metatranscriptomics analysis are required to further characterization of the prokaryotic communities associated with the eukaryotic population and their composition and roles in the rumen receiving Se supplemented in the diet.…”

Effect of Chitosan on Ruminal Fermentation and Microbial Communities, Methane Emissions, and Productive Performance of Dairy Cattle

“…Ciliate protozoa and rumen fungus have been found to be the main rumen microbes associated with methane emissions in dairy cattle [ 79 , 80 ]. Relationships between ruminal archaea and methane emissions are more contradictory, with some authors finding a positive relationship [ 81 ] and others not [ 79 ].…”