The oceans are microbial-dominated ecosystems, where protists (single-celled eukaryotes) play fundamental roles performing multiple functions as primary producers, consumers, decomposers as well as trophic linkers in aquatic food webs. Due to their ecological relevance, it is important to characterize protist communities along temporal and spatial gradients to understand their biogeography and dynamics. This will allow us to infer the processes that drive the assembly of protist communities. In this dissertation, we focused in the study of natural protists communities aiming to understand their distributions and responses within different dimensions. We first focused in the temporal dimension, analyzing the dynamics of pico- and nanoeukaryotic communities, aiming to characterize the diverse strategies of their members and to determine seasonality. We identified an annual seasonal pattern in the protist community as well as in several composing taxa. Then, we addressed the spatial dimension, analyzing the changes in community composition along the water column in 13 stations distributed in the global ocean, exploring also the vertical variation in the relative metabolic activity of different taxa. Our results showed a clear vertical stratification of the community and indicated that the mesopelagic layer is the region with the highest metabolic activity. Another aim of this thesis was to explore the response of natural protists to chemical gradients. The ocean is a complex ecosystem with nutrients heterogeneously distributed along several patches, so there may be a lot of chemical gradients promoting diverse responses on marine microbes. For that purpose, we performed chemotactic experiments to identify individual responses towards different attractants within a natural protist community. The experimental results showed a preferential response towards some of the tested chemical cues, mainly bacterial exudates. Finally, since studies on microbial diversity generally use the relative abundances of phylotypes in a given sample, we explored the relationship between the latter relative abundances to cell abundances in several chosen taxa. In sum, this dissertation determines temporal and spatial patterns in protists communities as well as chemotactic preferences in different taxa, contributing to broaden our understanding of the structuring processes operating across temporal, spatial and behavioral dimensions in the protist world.

In the modeling of near-shore fisheries, it is important to realistically simulate larval dispersal, accounting for many oceanographic processes. This is especially vital for species with relatively sessile adults because the only long-distance migration occurs during the pelagic larval stage. I used stochastic dispersal of larvae that was correlated over the source and settlement locations, which was derived from oceanographic modeling of passive larvae transported by turbulent eddies. I studied the temporal and spatial patterns that were generated in the fish population by this form of stochastic dispersal. I also looked at how these patterns and variability in the population changed with different intensities of harvest. Then, I focused on the impact of this type of dispersal on two similar species of fish that compete for resources at the settlement locations. Decorrelation in the settlement of the two species, which is generated by the stochastic dispersal, allows them to coexist when theory would otherwise predict they would not. Nonlinear averaging of the variable settlement gives the weaker species higher-than-average recruitment, so it can invade when rare. This turbulence-driven method of dispersal is a new mechanism for species coexistence.

Biogeography, the study of species distributions over space and time, provides valuable information on the factors controlling biodiversity. Microorganisms are now widely recognized as exhibiting biogeographic patterns similar to larger organisms. However, the biogeography of viruses has been slower to develop despite their important role in ecosystems. After first proposing a theoretical framework with which to study microbial biogeographic patterns, the goal of this dissertation was to demonstrate whether an ecologically important subset of viruses - cyanophages, or viruses that infect the marine cyanobacterium, Synechococcus - also exhibit such patterns. I isolated cyanophages every month for three years in Southern California, and at one point in time at two additional locations in the coastal U.S.I then taxonomically characterized nearly 4,000 isolates by amplifying and sequencing a cyanophage-specific marker gene in each isolate. To more accurately detect possible spatial patterns, I also characterized a subset of isolates for their host range phenotypes, which provided additional biological variability than could be assessed by the marker gene alone. I found that coastal marine cyanophage communities are both temporally dynamic as well as spatially structured. Within the regional scale of Southern California, these communities were strikingly seasonal - that is, their composition changed in tune with the seasons in an annually recurring manner. I found that this seasonal pattern over three years was primarily related to forecasted UV irradiance, with UV explaining nearly 33% of the temporal variation in cyanophage composition. Moreover, I found that at larger spatial scales, cyanophage community composition was also highly structured in space, both taxonomically and phenotypically. These results provide strong evidence that phages exhibit spatial and temporal biogeographic patterns. Because phages are susceptible to degradation by light, the results further suggest that their distributional patterns may be partially driven by selective environmental factors, namely UV radiation, acting directly on phages; rather than solely being influenced by the presence of susceptible hosts. The library of isolates collected here offers a unique opportunity to test this hypothesis. Overall, this work adds to the growing evidence that all microbes, including phages, exhibit biogeographic patterns that are in large part driven by environmental selection.

This book aims at providing students and researchers an advanced integrative overview on zooplankton ecology, covering marine and freshwater organisms, from microscopic phagotrophic protists, to macro-jellyfishes and active fish larvae. The first book section addresses zooplanktonic organisms and processes, the second section is devoted to zooplankton spatial and temporal distribution patterns and trophic dynamics, and the final section is dedicated to emergent methodological approaches (e.g., omics). Book chapters include comprehensive synthesis, observational and manipulative studies, and sediment-based analysis, a vibrant imprint of benthic-pelagic coupling and ecosystem connectivity. Most chapters also address the impacts of anticipated environmental changes (e.g., warming, acidification).

Conservation and biodiversity of protists The conservation of biodiversity is not just an issue of plants and vertebrates. It is the scarcely visible invertebrates and myriads of other microscopic organisms that are crucial to the maintenance of ecological processes on which all larger organisms and the composition of the atmosphere ultimately depend. Biodiversity and Conservation endeavours to take an holistic view of biodiversity, and when the opportunity arises to issue collections of papers dealing with too-often neglected groups of organisms. The protists, essentially eukaryotes that cannot be classi?ed in the kingdoms of animals, fungi, or plants, include some of the lea- known groups of organisms on earth. They are generally treated as a separate kingdom, commonly named Protista (or Protoctista) in textbooks, but in reality they are a mixture of organisms with disparate a?nities. Some authors have hypothesized that the numbers of protists are not especially large, and that many have extraordinarily wide distributions. However, the p- ture that unfolds from the latest studies discussed in this issue is di?erent. There are many species with wide ranges, and proportionately more cosmopolitan species than in macroorganism groups, as a result of their long evolutionary histories, but there are also de?nite patterns and geographical restrictions to be found. Further, some protists are linked to host organisms as mutualists or parasites and necessarily con?ned to the distributions of their hosts.

This comprehensive book provides a unique overview of advances in the biology and ecology of marine protists. Nowadays marine protistology is a hot spot in science to disclose life phenomena using the latest techniques. Although many protistological textbooks deal with the cytology, genetics, ecology, and pathology of specific organisms, none keeps up with the quick pace of new discoveries on the diversity and dynamics of marine protists in general. The bookMarine Protists: Diversity and Dynamics gives an overview of current research on the phylogeny, cytology, genomics, biology, ecology, fisheries, applied sciences, geology and pathology of marine free-living and symbiotic protists. Poorly known but ecologically important protists such as labyrinthulids and apostome ciliates are also presented in detail. Special attention is paid to complex interactions between marine protists and other organisms including human beings. An understanding of the ecological roles of marine protists is essential for conservation of nature and human welfare. This book will be of great interest not only to scientists and students but also to a larger audience, to give a better understanding of protists’ diverse roles in marine ecosystems.