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

Sharon A. Huws, Joan E. Edwards, Wanchang Lin, Francesco Rubino, Mark Alston, David Swarbreck, Shabhonam Caim, Pauline Rees Stevens, Justin Pachebat, Mi Young Won, Linda B. Oyama, Christopher J. Creevey, Alison H. Kingston-Smith

Research output: Contribution to journalArticlepeer-review

8 Citations (SciVal)
204 Downloads (Pure)


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.

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.

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.
Original languageEnglish
Article number143
Number of pages17
Issue number1
Early online date21 Jun 2021
Publication statusPublished - 01 Dec 2021


  • Archaea
  • Bacteria
  • Biofilm
  • Colonisation
  • Ecology
  • Metatranscriptome
  • Microbiome
  • Niche
  • Rumen
  • Temporal


Dive into the research topics of 'Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches'. Together they form a unique fingerprint.

Cite this