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

Microbiome

David Swarbreck¹  Mark Alston¹  Wanchang Lin²  Pauline Rees Stevens²  Alison H. Kingston-Smith²  Justin Pachebat²  Joan E. Edwards³  Mi-Young Won⁴  Francesco Rubino⁴  Sharon A. Huws⁵  Linda B. Oyama⁵  Christopher J. Creevey⁵  Shabhonam Caim⁶ 

[1] Earlham Institute, NR4 7UH, Norwich, UK;Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3FG, Aberystwyth, UK;Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3FG, Aberystwyth, UK;Laboratory of Microbiology, Wageningen University & Research, 6708, Wageningen, WE, Netherlands;Current work address: Palital Feed Additives, Velddriel, Netherlands;Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL, Belfast, Northern Ireland, UK;Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, 19 Chlorine Gardens, BT9 5DL, Belfast, Northern Ireland, UK;Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3FG, Aberystwyth, UK;Quadram Institute, NR4 7UA, Norwich, UK;

关键词: Rumen;    Bacteria;    Archaea;    Biofilm;    Microbiome;    Temporal;    Colonisation;    Metatranscriptome;    Ecology;    Niche;   

DOI  :  10.1186/s40168-021-01087-w

来源: Springer

【 摘 要 】

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 ‘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.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.CnT8ee8Emnfj-Y7oyo5rXtVideo Abstract

【 授权许可】

CC BY