Honors Theses

Date of Award


Document Type

Undergraduate Thesis



First Advisor

Colin Jackson

Relational Format



Little research has investigated particle size as a structuring factor of microbial communities in aquatic environments. One study focused on the influence of particle size on microbial community structure as observed in nature, and the study described here tested those findings in vivo. Stream water was collected and used to inoculate samples containing glass beads of various sizes, fine (106 pm), medium (500 pm), and (1000 pm), and a mixture of all particle sizes; each sample had the same total surface area. Half of the samples were left standing, and half were rotated to simulate the movement of a stream current. Samples were amended with R2A, a media commonly used for culturing aquatic microbes. After a growth period of 30 days, whole community DNA was extracted. Analysis of the 16S rRNA gene fragments, through denaturing gel gradient electrophoresis (DGGE), compared samples across the particle size gradient coarse using binary data to generate similarity scores and multi-dimensional scaling (MDS) plots. Clones produced from 16S rDNA sequenced to provide sequencing data and phylogenetic lineages for the clones of all the samples. MDS plots and cluster analysis of DGGE binary data for standing samples identified three distinct groups based on particle size: the fine particles, the medium particles, and a group consisting of the coarse particles and the mixture of all particle were sizes. Sequencing data provided more evidence that particle size can be a structunng factor for certain bacterial phyla. 75% of the observed Firmicutes clones were present on the fine and medium particles, with only 7.5% of the total number of clones being found on the coarse particles. The effect of shaking vs. standing gave the most noticeable differences in microbial communities. Notably, the Actinobacteria were present only on the shaking particle samples. Likewise, nine of ten observed Alphaproteobacteria were present on shaking particles. Previous research has investigated differences in microbial communities amongst natural particles of different size, attributing the phenomenon to subtle variations in chemical composition or particle surface texture. This study focused exclusively on the effect of particle size; by using sterile glass beads of different sizes, all of which were essentially spherical in shape and had the same chemical composition, the effect of particle size as an influence on bacterial biofilms was proven to be significant for certain bacterial phyla.

Accessibility Status

Searchable text



To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.

NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.