Purdue University Graduate School
Zach Biddle Thesis Final.pdf (2.84 MB)

Effects of commercially available amino acid Products on the growth and structure of a synthetic microbial community

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posted on 2024-04-19, 13:30 authored by Zachary Lee BiddleZachary Lee Biddle

Synthetic microbial communities (SynComs) are an important focus in modern microbiology. SynComs are used for studying the dynamics of naturally occurring microbial communities ranging from soil to the human gut. Synthetic refers to the assemblage of some or all the members of these communities in a laboratory setting. SynComs allow for communities difficult to study in situ to be studied in a controlled environment, or they may be used to create beneficial products like biofertilizers. When SynComs are used as products, the focus shifts to optimizing a desired outcome of a culture. For biofertilizers, a high diversity is key to producing a functionally redundant product for stimulating plant growth. Media manipulation is a common approach for inducing community changes in a SynCom. Amino acids (AA) are a media supplement that soil microbes (often the components of biofertilizers) are particularly fond of to support their metabolic activities. This study took a scale-up approach to assess the changes in growth dynamics of a SynCom (Environoc© 401) when supplemented with different concentrations of commercially available AA products from plant and animal sources. Expanding from microplates, to shake flasks, then into a 4L bioreactor, Environoc© 401 cultures were compared for their maximum growth rate, time in lag phase, and final growth (optical density or viable cell density) when supplemented with these AA products at various concentrations. Furthermore, Illumina sequencing of the 16S rRNA gene was used to evaluate community-level changes from these treatments based on taxonomic, alpha (Chao 1 and Shannon indices), and beta diversity (Generalized UniFrac) of shake flask and bioreactor samples. Quantitative PCR was also used to assess the relative change of three select species of the SynCom in each AA treatment. Shake flask data revealed significant changes in the growth dynamics of the SynComs within AA treatment groups. Whether the AA was animal or plant derived, generally as the concentration of AA increased, the maximum growth rate decreased, lag time increased, and final growth readings increased. The best AA supplement and rate according to the growth metrics and Curveball analysis was Stimtide at a 33% supplementation rate. This was compared with the control at the bioreactor scale where it showed higher overall final growth and a higher taxonomic and alpha diversity. The scale-up approach to this study was successful at selecting the best amino acid supplement type and rate despite having less sophisticated control and monitoring compared to larger scales (i.e. the bioreactor). Use of the Curveball modeling program was useful for treatment group selection but did not always predict the outcomes seen in the live cultures. The use of AA as a media supplement can increase growth and diversity of a SynCom, though not all AA supplements or rates affect growth and community dynamics in the same way.


Degree Type

  • Master of Science


  • Biological Sciences

Campus location

  • Fort Wayne

Advisor/Supervisor/Committee Chair

Tanya Soule

Advisor/Supervisor/Committee co-chair

Jose Thekkiniath

Additional Committee Member 2

Dong Chen