Date of Award

December 2018

Document Type


Degree Name

Doctor of Philosophy (PhD)


Biological Sciences

Committee Member

Barbara J Campbell

Committee Member

Antonio J Baeza

Committee Member

Annette S Engel

Committee Member

Vincent P Richards


Extant bivalve members from the family Lucinidae harbor chemosynthetic gammaproteobacterial gill endosymbionts capable of thioautotrophy. These endosymbionts are environmentally acquired and belong to a paraphyletic group distantly related to other marine chemosymbionts. In coastal habitats, lucinid chemosymbionts participate in facilitative interactions with their hosts and surrounding seagrass habitat that results in symbiotic sulfide detoxification, oxygen release from seagrass roots, carbon fixation, and/or symbiotic nitrogen fixation. Currently, the structural and functional complexity of whole lucinid gill microbiomes, as well as their interactions with lucinid bivalves and their surrounding environment, have not been comprehensively characterized. This dissertation focuses on the taxonomic, genetic, and functional diversity in the gill microbiomes of three Floridian coastal lucinid bivalve species, Phacoides pectinatus, Ctena orbiculata, and Stewartia floridana, in the context of environmental data where appropriate.

Analyses of these lucinid gill microbiomes showed taxonomic diversity that was unaffected by spatial distribution patterns. Phacoides pectinatus gill microbiomes sampled from a coastal mangrove habitat contained, in order of relative abundances, a chemosynthetic symbiont species that was taxonomically and functionally distinct from seagrass-associated chemosynthetic lucinid symbionts, a heterotrophic Kistimonas-like species, and a heterotrophic Spirochaeta-like species. In comparison, gill microbiomes of a seagrass-dwelling C. orbiculata population comprised four strains of chemosymbionts that belonged to two separate species and low abundances of an uncharacterized Endozoicomonas-like operational taxonomy unit (OTU). Gill microbiomes of a separate seagrass-dwelling S. floridana population consisted of another chemosynthetic symbiont species and low abundances of a heterotrophic Spirochaeta-like species that was distantly related to the Spirochaeta-like species in P. pectinatus.

Functional characterization of host- and microbiome-related genes/transcripts in these bivalve species revealed previously unreported C1-compound oxidation functions in some chemosymbionts and other functions relevant to microbe-microbe competition, symbiont selection, metabolism support, and symbiont-to-host nutrient transfer. Preliminary differential expression analyses on host- and microbiome genes across micro-habitats with different vegetation coverages showed potential upregulation of C. orbiculata functions involved in aerobic respiration, aerobic stress, electron transport, and mitochondrial sulfide detoxification, as well as downregulation of a sulfurtransferase gene encoded by its chemosynthetic symbionts, in a seagrass-covered quadrat compared to an algae-covered quadrat. In comparison, very few genes mappable to S. floridana and its chemosymbiont were differentially expressed between predominantly sand-covered and seagrass-covered quadrats, but the Spirochaeta-like species over-expressed carbon, nitrogen, phosphate, transport, synthesis, transcriptional regulation, and protein degradation functions in predominantly sand-covered quadrats.

These findings reaffirm the overlooked notion of heterogeneous lucinid gill microbiomes that can vary within and between host species and populations. At the same time, this project advances understanding of the functional diversity across chemosynthetic lucinid symbionts and offers insights on lucinid-microbiome-environment interactions.



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