Date of Award

August 2021

Document Type


Degree Name

Master of Science (MS)



Committee Member

Barbara Campbell

Committee Member

Anna Seekatz

Committee Member

Kristi Whitehead


Lucinidae clams are known to harbor environmentally acquired endosymbionts within their gills. Although there has been recent work on the genomic and functional diversity of lucinid endosymbionts, there are uncertainties regarding the extent of their diversity and differences in metabolisms under various environmental conditions. In this study, the genetic and functional differences in endosymbionts was examined for six lucinid host species collected from eight total sites from Florida, USA and San Salvador, the Bahamas. There were 42 metagenome assembled genomes (MAGs) generated which clustered into three species and six subspecies. MAGs were closely related to clade A endosymbionts Candidatus Thiodiazotropha endolucinida from Codakia orbicularis or Ca. Thiodiazotropha endoloripes from Loripes orbiculatus based on phylogenetics and average nucleotide identity (ANI) and average amino acid identity (AAI) analyses. All subspecies had several genes related to the metabolic systems involved in sulfate, nitrogen, and amino acid metabolism, defense, vitamins, and structure/motility. Most of the variability between the species were found in KEGG metabolic categories involved in carbohydrate metabolism and membrane transport where the most abundant accessory genes were in energy metabolism and signaling/cellular processes. Location influenced the prophage components present more than the subspecies type. Genes were mostly horizontally transferred within the same species regardless of the location and were mostly comprised of hypothetical proteins. This research significantly expands the known diversity and representatives from three lucinid endosymbiont species and suggests key differences in genetic adaptations as assessed by phylogeny, viral infection and horizontal gene transfer.



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.