Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts.

Zhipeng Li,Xiaoxu Wang,Shengyong Mao,Zhenyu Zhong,Chengli Zheng,Antton Alberdi,Jiabo Deng,Zhigang Zhang,Jianming Wang,André-Denis G Wright,Guangyu Li,Huazhe Si,Yifeng Yang,Leluo Guan,Hanlin Zhou

doi:10.3389/fmicb.2020.01311

Abstract

Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.

Highlights

Climate change resulting from the anthropogenic emission of greenhouse gases (GHGs), such as carbon dioxide (CO2), and methane (CH4), presents one of the major challenges the planet is facing (Jose et al, 2016)
The development of effective microbial manipulation strategies that are designed to decrease CH4 production requires an understanding of the composition of methanogen and acetogen communities in different ruminant species, as well as an understanding of the relationship of rumen methanogens and acetogens with the host
Methanogen communities of 97 rumen samples from 14 ruminant species were characterized by sequencing the V1–V3 regions of PCR-amplified 16S rRNA genes

Summary

Introduction

Climate change resulting from the anthropogenic emission of greenhouse gases (GHGs), such as carbon dioxide (CO2), and methane (CH4), presents one of the major challenges the planet is facing (Jose et al, 2016). The continuous removal of H2 is crucial to maintaining the normal fermentative function of the rumen because excessive H2 accumulation inhibits carbohydrate fermentation through preventing the regeneration of NAD+ (Hungate, 1967; Wolin et al, 1997). Dietary additives such as secondary plant metabolites and chemical inhibitors have been shown to reduce rumen CH4 emissions by affecting H2 disposal and increasing the ratio of propionate and acetate (Kumar et al, 2014). Other approaches need to be considered and developed to regulate CH4 emissions

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Conclusion