Plant-attached microbiomes temporally transition into specialised ecological niches

Gut microbiomes are essential for host health and function and the rumen is a prime example of a microbiome with a major impact on host function due to the capacity of rumen microbes to degrade ingested forage, generating energy and microbial protein for the ruminant host. The aim of this study was to investigate temporal niche specialisation during colonisation and degradation of fresh perennial ryegrass (PRG) using a ruminal in sacco approach combined with metranscriptomics. The dominant families colonising the PRG (Fibrobacteriaceae, Lachnospiraceae, Prevotellaceae, Ruminococcaceae and Selemondaceae) had less gene correlations with other families, indicating non-cooperative behaviours. Conversely, two less dominant bacterial families, Enterobacteriaceae and Flammeovirigaceae, were identified as keystone taxa families, due to having the most gene correlations. PRG-attached prokaryotic network gene correlations clearly showed distinct temporal niche specialisation, with primary (<4h) and secondary colonisation events (>4h) evident. The bacterial family Prevotellaceae were more functionally active during primary colonisation, with their core function being protein breakdown. The Lachnospiraceae were more active during secondary colonisation, with their main activities being carbohydrate and lipid breakdown. This is the first study illustrating the breadth of the interactions that occur between rumen microbes colonising fresh perennial ryegrass.