To access this work you must either be on the Smith College campus OR have valid Smith login credentials.

On Campus users: To access this work if you are on campus please Select the Download button.

Off Campus users: To access this work from off campus, please select the Off-Campus button and enter your Smith username and password when prompted.

Non-Smith users: You may request this item through Interlibrary Loan at your own library.

Alternative Title

Diversity and community dynamics of Epizoic foraminifera

Publication Date


First Advisor

Laura A. Katz

Document Type

Honors Project

Degree Name

Bachelor of Arts


Biological Sciences


Protists, Foraminifera, Symbiosis, Epizoic, Metabarcoding, Phylogeny, SSU rDNA


Epibionts, organisms that live on other organisms, are widespread across the eukaryotic tree of life. Some familiar examples of epibionts include barnacles and algae which live on marine animals such as whales and turtles. The relationship between host and epibiont is critical to understanding interactions among organisms at various ecological scales as epibionts contribute to environmental nutrient cycling and food webs. Here, I focus on foraminifera, which are single-celled amoeba able to colonize and live on the shells of clams, snails, crabs, and other marine invertebrates. However, to date few studies have investigated the diversity of animal-associated foraminifera, and these have solely relied on morphological approaches. In this study, we used molecular techniques to assess the diversity of epizoic foraminifera on the shells of clams, snails, and crabs from three environments (two built fish tank environments and one salt marsh). We characterized both DNA (total) and RNA (active) of these communities using foraminifera-specific PCR primers. After quality filtering, we first assigned operational taxonomic units (OTUs) using a clustering method SWARM and we also estimated amplicon sequence variants (ASVs) using DADA2. We then compared these estimates of diversity to reference sequences from GenBank to infer their taxonomic identity. For our analysis, we focussed on 438 OTUs clustered with SWARM3 to evaluate ecological partitioning of the epizoic foraminifera. This subset was selected by analyzing a foraminifera-specific SSU rDNA gene tree, alpha diversity measures, and phylogenetically-informed beta diversity measures. In this preliminary analysis, I found that epizoic foraminifera communities differ mainly by habitat type and change over time. This study brings us one step closer to understanding the ecological roles and diversity of these key marine microbial communities.


©2021 Adena Beth Collens




62 pages : color illustrations Includes bibliographical references (pages 58-62)