Research Article: Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor

Date Published: October 5, 2018

Publisher: Public Library of Science

Author(s): Stephen J. Callister, Lee Ann McCue, Amy A. Boaro, Brian LaMarche, Richard A. White, Joseph M. Brown, Birgitte K. Ahring, John M. Senko.


Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community. After stable operation was established in the bioreactor, the mixing intensity was increased in order to investigate the effect of a physical disruption of the microbial community structure. Finally, the original conditions were re-established to understand the stability of the microbial community after a perturbation. All factors measured were found to be inter-correlated during these three distinct phases of operation (establishment, perturbation and re-establishment). In particular, the return of community structure and function to pre-perturbed conditions suggests that propionate fermentation and acetate utilization were the explanatory factors for community establishment and re-establishment.

Partial Text

The successful operation of a bioreactor employing a microbial community for industrial and biotechnological applications is often based upon the optimization of operational parameters and environmental factors that have been empirically investigated and modeled to provide process performance and stability. The established microbial community driving the biological processes within the bioreactor is typically a consortium acquired from an external environment, such as a bioreactor already in operation, or from a natural environment. The introduction of the inoculum microbiome to the bioreactor represents an important step in the start-up of the bioreactor, and it is generally accepted that the development of community networks within a new environment represents a critical factor for achieving the desired process performance through preservation of diversity and functional redundancy [1–3]. In many instances, the established community only partially resembles the initial consortium as the final populations thriving in the bioreactor must acclimate to controlled conditions within the bioreactor.

Each NMDS cluster pertains to different stages of community dynamics and community function during bioreactor operation, namely: 1) Early acclimation of populations (Fig 5; C1) to operational parameters and environmental conditions within the bioreactor leading to, 2) the establishment of a community (Fig 5; C2) which, 3) is temporarily modified through perturbation (Fig 5; C3), resulting in process performance decline verging upon failure. A return to community structure and function similar to the pre-perturbed state occurred following removal of the perturbation. These different stages of community dynamics and community function are generalizable to engineered bioreactors. However, because of the low retention time (4-days) the operation of a replicate bioreactor was not obtainable making the omics findings described below specific for this cellulose-degrading engineered bioreactor.




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