Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

Microbiome

David Swarbreck¹  Mark Alston¹  Alison H. Kingston-Smith²  Pauline Rees Stevens²  Wanchang Lin²  Justin Pachebat²  Joan E. Edwards²  Francesco Rubino³  Mi-Young Won³  Sharon A. Huws³  Christopher J. Creevey³  Linda B. Oyama³  Shabhonam Caim⁴ 

[1] Earlham Institute;Institute of Biological, Environmental and Rural Sciences, Aberystwyth University;Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast;Quadram Institute;

关键词: Rumen;    Bacteria;    Archaea;    Biofilm;    Microbiome;    Temporal;   

DOI  :  10.1186/s40168-021-01087-w

来源: DOAJ

【 摘 要 】

Abstract Background Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling. Results Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be ‘cheating’ in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry. Conclusions In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract

【 授权许可】

Unknown