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Culminating Project Title

Anaerobic Digestion and a Core Microbiome

Date of Award


Culminating Project Type


Degree Name

Special Studies: M.S.




College of Science and Engineering

First Advisor

Ryan C Fink

Second Advisor

Matthew Davis

Third Advisor

Omar Al-Azzam

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Keywords and Subject Headings

microbiome anaerobic digestion archaea biogas methanogen


Anaerobic Digestion is a microbially mediated process turning organic matter into biogas and biofertilizer. This kind of waste decomposition is advantageous over traditional waste management for its low energy requirements, potential energy recovery, reduction of greenhouse gas released into the atmosphere, and production of environmentally friendly fertilizers. However, lack of information about the establishment and stability of the core microbial community composition needed to sustain this process and to make it economically viable has hampered its deployment. Decrease of the biogas production caused by a fatal microbial community collapse is one of the major issues encountered in a small-scaled and commercial enterprise using the technology. This study focuses on the commonalities in microbial community compositions of infeed and digestate present in four anaerobic digesters different in their designs, infeeds, sizes, and operational temperatures to determine a shared microbial community. Anaerobic digesters situated on a farm, at a wastewater treatment facility, University of Minnesota laboratories, and a bench fermentation set up at St Cloud State University were sampled: in-feed, digestate, outfeed. These digesters operate respectively on manure, wastewater and high strength waste from breweries, manure and food waste mix from the campus cafeteria, and a strictly food waste (calculated ingredients proportions). All digesters operate in mesophilic conditions; the sizes were from two liters to 1.6 million liters, and hydraulic retention times were from 9 to 58 days. Samples were collected from all points where organic matter was hypothesized to be changing composition of its microbial community. The microbial communities were characterized using bacterial and archaeal specific 16S rRNA primers and high throughput sequencing with Illumina Miseq to the genus level. Our study determined 14 genera that was high abundant and overlapping at least with two anaerobic digestion systems. Also, our analysis showed that the three out of four sites shared Methanobrevibacter as the dominating methanogenic genus; Lactobacillus and Clostridium (Ruminococcaceae family) were highly abundant (>1%) and shared between all anaerobic digesters. A repeated sampling of the same sites over time would give an even more reliable list of core microorganisms. A furthermore accurate determination of a core microbial “recipe” is a valuable instrument that allows for the establishment of a stable yet diverse community and at the same time will assist an operator in cases when a microbial community is struggling due to the changes in infeed physical or chemical composition.



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