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. 2017 Feb 14;12(2):e0171369.
doi: 10.1371/journal.pone.0171369. eCollection 2017.

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

Allison R Perrotta  1 , Rajkumari Kumaraswamy  2 , Juan R Bastidas-Oyanedel  2 , Eric J Alm  1   3   4 , Jorge Rodríguez  2
Affiliations

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

Allison R Perrotta et al. PLoS One. .

Abstract

The sustainable recovery of resources from wastewater streams can provide many social and environmental benefits. A common strategy to recover valuable resources from wastewater is to harness the products of fermentation by complex microbial communities. In these fermentation bioreactors high microbial community diversity within the inoculum source is commonly assumed as sufficient for the selection of a functional microbial community. However, variability of the product profile obtained from these bioreactors is a persistent challenge in this field. In an attempt to address this variability, the impact of inoculum on the microbial community structure and function within the bioreactor was evaluated using controlled laboratory experiments. In the course of this work, sequential batch reactors were inoculated with three complex microbial inocula and the chemical and microbial compositions were monitored by HPLC and 16S rRNA amplicon analysis, respectively. Microbial community dynamics and chemical profiles were found to be distinct to initial inoculate and highly reproducible. Additionally we found that the generation of a complex volatile fatty acid profile was not specific to the diversity of the initial microbial inoculum. Our results suggest that the composition of the original inoculum predictably contributes to bioreactor community structure and function.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Sequential Batch Reactor (SBR) cycling was performed.
SBR cycles involved centrifuging microcosms, for 20 minutes at 4,000 g, removal of the supernatant, and addition of fresh media. A total of 7 SBR cycles were performed per reactor.
Fig 2
Fig 2. Microbial communities are reproducible and distinct to the initial microbial inoculum.
Relative abundances of OTUs are represented as log relative abundances. Only OTUs that were present at equal or greater than 1% across all time points have been included. OTUs are organized vertically by phylogenetic relationship and horizontally by time point within a replicate, cycle 0 to cycle 7.
Fig 3
Fig 3. Divergence between reactors decreases overtime but remains low between replicates of the same inoculum.
A) Average pairwise Jensen-Shannon divergence (family level) between Mangrove and Camel (dark blue), Mangrove and Sludge (light blue), and Sludge and Camel (orange) bioreactors. B) Average pairwise Jensen-Shannon divergence (family level) between Camel (blue), Mangrove (red), and Sludge (green) replicate bioreactors.
Fig 4
Fig 4. Dynamics of enriched OTUs and reactor chemical profiles are distinct to initial microbial inoculum.
We illustrate changes in average relative abundances of enriched OTUs over time (A) and the changes in average product yields in terms of electron equivalents over glucose consumed from provided feed (B) for the three inocula sources Camel, Mangrove, and Sludge reactors, respectively.
Fig 5
Fig 5. Initial inoculum alpha diversity is not correlated with reactor diversity.
The microbial inocula used vary in diversity. The diversity of the microbial communities present in the reactors decreases over the course of the experiment. Diversity is presented as the effective number of species over time for Camel (dark blue), Mangrove (purple), and Sludge (red) bioreactors.
Fig 6
Fig 6. Dynamics of abundant Clostridia species are distinct to starting inoculum.
We illustrate changes in average relative abundances of Clostridia OTUs over time in Camel (A), Mangrove (B), and Sludge (C) bioreactors. Abundance is represented as average percent relative abundance. OTUs were filtered for equal or greater than 0.1% relative abundance across all time points, and are labeled with the lowest taxonomic classification identified, genus level unless otherwise noted (f, family; o, order; c, class).
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