Date of Award

Fall 2020

Project Type


Program or Major

Molecular and Evolutionary Systems Biology

Degree Name

Doctor of Philosophy

First Advisor

Michael P Lesser

Second Advisor

Marc Slattery

Third Advisor

Stephen Jones


Emergent sponges are crucial to the functional ecology of coral reef ecosystems, playing key roles in benthic-pelagic coupling, biogeochemical cycling of key nutrients, and provision of food and habitat to a variety of coral reef fauna. In mesophotic coral reef ecosystems (MCEs), sponges show a repeatable pattern of increasing abundance and diversity with increasing depth. Mesophotic coral reef ecosystems are typically found between 30 – 150 m and are characterized by depth-dependent gradients in photosynthetically active radiation (PAR), and trophic resources such as increases in particulate organic matter (POM) and decreases in dissolved organic matter (DOM). Increased concentrations of POM appear to support increases in open reef sponge abundance, growth rates and diversity in MCEs, however the role of bottom-up control compared to top-down control of sponge distributions is contested in the literature. Given the importance of sponges on MCEs, increasing our understanding of what regulates their distribution and abundances is crucial in understanding MCEs function as a whole. To address this knowledge gap, we conducted a series of studies to assess the role of bottom-up forcing on the trophic ecology of sponges. We hypothesized that sponges on MCEs would be more abundant and have higher growth rates relative to their shallow conspecifics due to increased POM consumption. First, we used both bulk stable isotope analysis (SIA) and compound-specific isotope analysis of amino acids (CSIA-AA) of d13C and d15N to disentangle the host and microbiome signal, in order to better understand dietary changes between shallow and mesophotic depths, the trophic position of sponges and the potential translocation of resynthesized amino acids by the sponges microbiomes (Chapter 1). We then conducted a reciprocal transplant experiment and natural growth experiment with Agelas tubulata between shallow (22 m) and mesophotic (61 m) depths in order to quantify growth rates, feeding on POM and DOM and nutrient cycling between depths (Chapter 2). As it our data appears to show that a sponge’s growth is controlled by gradients in POM and DOM concentrations, we then conducted a “natural” experiment along a shallow to mesophotic depth gradient. We collected tissue samples of four sponges to assess their microbiome community structure and function, SIA and proximate biochemical composition (Chapter 3). While these open reef sponges show increases in abundance and growth rate in MCEs due to increased POM consumption, low light adapted sponges such as the sclerosponge, Ceratoporella nicholsoni, are also abundant in mesophotic habitats. We quantified percent cover between a shallow and mesophotic depths and took tissue samples for 16s rRNA metabarcoding and stable isotope analyses (Chapter 4). The collective findings in these studies show that bottom-up forcing is the principle factor influencing the distribution, abundances and growth rates of emergent sponges due to the increased concentrations of more bioavailable POM on MCEs. While there is species-specific translocation of resynthesized amino acids by sponges, the total contributions by heterotrophic microbes through DOM consumption to sponge energetic budgets is still unknown. Species-specific changes in microbial community composition and function were observed in these studies, indicating that gradients in PAR or trophic resources can influence the microbiome of sponges between depths. This has important implications for both sponge trophic strategy and biogeochemical cycling of carbon and nitrogen between shallow and mesophotic depths We also found that cryptic and low light sponges in MCE may not be influenced by the increases in POM and warrant further study given the abundances of these sponges on Caribbean MCEs.