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The post-Paleozoic history of the silica cycle involves just two groups of marine plankton, radiolarians and diatoms. I apply paleobiological methods to better understand the Cenozoic evolution of both groups. The Cenozoic rise in diatom diversity has long been related to a concurrent decline in radiolarian test silicification. I address evolutionary questions on both sides of this coevolutionary coin: Was the taxonomic diversification of diatoms accompanied by morphological diversification? Is our view of morphological diatom diversification affected by sampling biases? What evolutionary mechanisms underlie the macroevolutionary decline in radiolarian silicification? Conventionally, diatom diversification describes a steep, monotonic rise, a view recently questioned due to sampling bias. For a different perspective, I constructed a diatom morphospace based on discrete characters, populated through time using an occurrence-level database. Distances between taxa in morphospace and on a molecular phylogeny are not strongly correlated, suggesting that morphospace was explored early in their evolutionary history, followed by relative stasis. I quantified morphospace occupancy through time using several disparity metrics. Metrics describing average separation of taxa show stasis, while metrics describing occupied volume show an increase with time. Disparity metrics are also subject to sampling biases. Under subsampling, I find that disparity metrics show varied responses: metrics describing separation of taxa into morphospace are unaffected, while those describing occupied volume lose their clear increases. Disparity can have geographic components, analogous to \(\alpha\) and \(\beta\) taxonomic diversity; I find more evidence of stasis in an analysis of \(\bar{\alpha}\) disparity. Overall, these results suggest stasis in Cenozoic diatom disparity. The radiolarian decline in silicification could result from either macroevolutionary processes operating above the species level (punctuated queilibria) or anagenetic changes within lineages. I measured silicification in three phyletic lineages, Stichocorys, Didymocyrtis, and Centrobotrys, from four tropical Pacific DSDP sites. Likelihood-based model fitting finds no strong support for directional evolution, pointing toward selection among species, rather than within species. Each lineage shows a different trajectory, perhaps due to differences in the ecological role played by the test. Because Stichocorys shows close correspondence to the assemblage-level trend, abundance may be an important factor through which within-lineage changes can influence the macroevolutionary pattern. / Earth and Planetary Sciences

abstract: Some cyanobacteria, referred to as boring or euendolithic, are capable of excavating tunnels into calcareous substrates, both mineral and biogenic. The erosive activity of these cyanobacteria results in the destruction of coastal limestones and dead corals, the reworking of carbonate sands, and the cementation of microbialites. They thus link the biological and mineral parts of the global carbon cycle directly. They are also relevant for marine aquaculture as pests of mollusk populations. In spite of their importance, the mechanism by which these cyanobacteria bore remains unknown. In fact, boring by phototrophs is geochemically paradoxical, in that they should promote precipitation of carbonates, not dissolution. To approach this paradox experimentally, I developed an empirical model based on a newly isolated euendolith, which I characterized physiologically, ultrastructurally and phylogenetically (Mastigocoleus testarum BC008); it bores on pure calcite in the laboratory under controlled conditions. Mechanistic hypotheses suggesting the aid of accompanying heterotrophic bacteria, or the spatial/temporal separation of photosynthesis and boring could be readily rejected. Real-time Ca2+ mapping by laser scanning confocal microscopy of boring BC008 cells showed that boring resulted in undersaturation at the boring front and supersaturation in and around boreholes. This is consistent with a process of uptake of Ca2+ from the boring front, trans-cellular mobilization, and extrusion at the distal end of the filaments (borehole entrance). Ca2+ disequilibrium could be inhibited by ceasing illumination, preventing ATP generation, and, more specifically, by blocking P-type Ca2+ ATPase transporters. This demonstrates that BC008 bores by promoting calcite dissolution locally at the boring front through Ca2+ uptake, an unprecedented capacity among living organisms. Parallel studies using mixed microbial assemblages of euendoliths boring into Caribbean, Mediterranean, North and South Pacific marine carbonates, demonstrate that the mechanism operating in BC008 is widespread, but perhaps not universal. / Dissertation/Thesis / Ph.D. Microbiology 2010

abstract: Cyanobacteria and algae living inside carbonate rocks (endoliths) have long been considered major contributors to bioerosion. Some bore into carbonates actively (euendoliths); others simply inhabit pre-existing pore spaces (cryptoendoliths). While naturalistic descriptions based on morphological identification have traditionally driven the field, modern microbial ecology has shown that this approach is insufficient to assess microbial diversity or make functional inferences. I examined endolithic microbiomes using 16S rRNA genes and lipid-soluble photosynthetic pigments as biomarkers, with the goal of reassessing endolith diversity by contrasting traditional and molecular approaches. This led to the unexpected finding that in all 41 littoral carbonate microbiomes investigated around Isla de Mona (Puerto Rico) and Menorca (Spain) populations of anoxygenic phototrophic bacteria (APBs) in the phyla Chloroflexi and Proteobacteria, were abundant, even sometimes dominant over cyanobacteria. This was not only novel, but it suggested that APBs may have been previously misidentified as morphologically similar cyanobacteria, and opened questions about their potential role as euendoliths. To test the euendolithic role of photosynthetic microbes, I set a time-course experiment exposing virgin non-porous carbonate substrate in situ, under the hypothesis that only euendoliths would be able to initially colonize it. This revealed that endolithic microbiomes, similar in biomass to those of mature natural communities, developed within nine months of exposure. And yet, APB populations were still marginal after this period, suggesting that they are secondary colonizers and not euendolithic. However, elucidating colonization dynamics to a sufficiently accurate level of molecular identification among cyanobacteria required the development of a curated cyanobacterial 16S rRNA gene reference database and web tool, Cydrasil. I could then detect that the pioneer euendoliths were in a novel cyanobacterial clade (named UBC), immediately followed by cyanobacteria assignable to known euendoliths. However, as bioerosion proceeded, a diverse set of likely cryptoendolithic cyanobacteria colonized the resulting pore spaces, displacing euendoliths. Endolithic colonization dynamics are thus swift but complex, and involve functionally diverse agents, only some of which are euendoliths. My work contributes a phylogenetically sound, functionally more defined understanding of the carbonate endolithic microbiome, and more specifically, Cydrasil provides a user-friendly framework to routinely move beyond morphology-based cyanobacterial systematics. / Dissertation/Thesis / APPENDIX A / APPENDIX B / APPENDIX C / Doctoral Dissertation Microbiology 2020

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