@article{2d60eef158b3408aa03b895fcdc6fb60,
title = "Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches",
abstract = "BackgroundGut 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.ResultsNetwork 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 {\textquoteleft}cheating{\textquoteright} 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.ConclusionsIn 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.",
keywords = "Archaea, Bacteria, Biofilm, Colonisation, Ecology, Metatranscriptome, Microbiome, Niche, Rumen, Temporal",
author = "Huws, {Sharon A.} and Edwards, {Joan E.} and Wanchang Lin and Francesco Rubino and Mark Alston and David Swarbreck and Shabhonam Caim and Stevens, {Pauline Rees} and Justin Pachebat and Won, {Mi Young} and Oyama, {Linda B.} and Creevey, {Christopher J.} and Kingston-Smith, {Alison H.}",
note = "Funding Information: This work was supported by the Biotechnology and Biological Sciences Research Council Institute Strategic Programme Grant, Rumen Systems Biology (grant number BBS/E/W/10964), Core Strategic Programme in Resilient Crops (BBS/E/W/0012843D) and The Genome Analysis Centre (now the Earlham Institute) Capacity and Capability Challenge Programme. Publisher Copyright: {\textcopyright} 2021, The Author(s).",
year = "2021",
month = dec,
day = "1",
doi = "10.1186/s40168-021-01087-w",
language = "English",
volume = "9",
journal = "Microbiome",
issn = "2049-2618",
publisher = "Springer Nature",
number = "1",
}