Ecological networks and ecosystem function in the rumen microbiome

To identify patterns of global community dynamics we studied forces that drive the assembly of microbiomes, with emphasis on the balance between stochastic and deterministic processes. To this end, we documented the development of the rumen microbiome throughout an animal’s life from birth to adulthood in 45 animals (15 over a 3-year period) using 16S-rRNA amplicon data. We found that the animals shared a group of core 30 successional species that invaded early on and persisted until adulthood. Along with deterministic factors, such as age and diet, early-arriving species exerted strong priority effects, whereby dynamics of late successional taxa were strongly dependent on microbiome composition at early life stages. Priority effects also manifested as dramatic changes in microbiome development dynamics between animals delivered by C-section vs. natural birth, with the former undergoing much more rapid species invasion and accelerated microbiome development. Our findings show that chance events early in life have a strong impact on development of animal microbiomes. Furthermore, we sought to understand what are the possible environmental sources for the rumen microbiome in these animals. We learned that the sources of rumen samples taken from the time of birth could be partly affiliated to maternal and environmental sources and highlight the importance of the birth canal in shaping the rumen microbiome throughout life.

In addition, we studied the extent to which history dependency can steer communities composition towards functionally different states using synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of differences in the species pool, but also because the same species have different dynamics in different community contexts. Importantly, compositional differences are proportional to differences in function, as profiles of resource use are strongly correlated with composition, despite convergence in respiration rates. Early differences in community structure can thus propagate to mature communities, conditioning their functional repertoire.