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Dataset supporting the University of Southampton Doctoral Thesis "From communities to single cells: Exploring diversity and ecophysiology of marine microbes with a focus on coccolithophores"
No full textDataset supporting the University of Southampton Doctoral Thesis "From communities to single cells: Exploring diversity and ecophysiology of marine microbes with a focus on coccolithophores"
Datasets for this thesis have been published in external repositories.
Chapter 2: NCBI Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra - Accession Number PRJNA1044770
Chapter 3: NCBI Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra - Accession Number PRJNA952565
Chapter 4: NCBI Sequence Read Archive https://www.ncbi.nlm.nih.gov/sra - Accession Number PRJNA1068990
Chapter 6: DASSH Archive for Marine Species and Habitats Data. DOI: https://doi.org/10.17031/65afd01b4e0e2.1</span
From communities to single cells: Exploring diversity and ecophysiology of marine microbes with a focus on coccolithophores
No full textMicroeukaryotes form the basis of the marine food web and play a pivotal role in marine biogeochemical processes. However, for many clades, ecological niches and inherent patterns of diversity and abundance remain poorly understood. One of the most charismatic microbial taxa are the coccolithophores, unicellular phytoplankton characterized by the production of calcite coccoliths and important contributors to microbial standing stocks. This study set out to investigate the biogeography and ecophysiology of marine microeukaryotes, focusing on coccolithophores and their elusive life cycle. Environmental sampling, culture experiments, omics techniques, and bioinformatics were integrated to elucidate the diversity and functional attributes of microbial communities. An investigation of the distribution and physiology of marine microeukaryotes in the Pacific and Indian sector of the Great Calcite Belt in the Southern Ocean, an area of particularly high coccolithophore abundance, revealed that microbial communities are strongly influenced by environmental gradients associated with frontal and mesoscale systems. However, distinct clades exhibited significant disparities in their degree of constraint, underscoring the necessity for a more profound understanding of the underlying physiology across different taxa. The lack of coccolithophore diversity revealed by broad eukaryotic 18S metabarcoding raised concerns about the underrepresentation of this group in global genomic explorations. Re-examining the area with a combination of improved genetic markers and morphological taxonomy, revealed a much higher degree of coccolithophore diversity. This underscores the limitations of current environmental DNA methodologies, highlighting the need for supplementary techniques and advancements in gene markers and reference libraries. The morphological examination of coccolithophores further unveiled novel insights into their elusive haplo-diplontic life cycle. The finding of a new combination coccosphere, a transitionary life phase, raised important questions regarding genetic variability and cryptic speciation in coccolithophores. Further examining the underlying ecophysiology of the coccolithophore life cycle, particularly by using proteomics approaches, has highlighted life cycle-specific mechanisms and traits. This investigation expanded our understanding beyond the well-studied Gephyrocapsa (formerly Emiliania) huxleyi, elucidating the evolution of calcification-related genes and investigating the broader physiological and evolutionary significance of the findings through culture experiments and gene phylogenies. Overall, this thesis provides a comprehensive understanding of marine microeukaryotes, highlighting their intricate dynamics across biogeographic regions and offering insights into their ecological adaptations. Through a multidisciplinary approach, it advances our knowledge of microbial communities in remote oceanic realms, with implications for broader ecological and biogeochemical processes
Novel combination coccospheres from Helicosphaera spp indicate complex relationships between species
Full text linkCoccolithophores play an important role in global biogeochemical cycling, but many aspects of their ecology remain poorly understood, including their heteromorphic haplo-diplontic life cycle. The presence of combination coccospheres in environmental samples, which represent a transition between the lightly calcified haploid (HOL) and heavily calcified diploid (HET) life phases, provides crucial evidence linking the two life cycle phases of a particular species. Here, we describe combination coccospheres from the Southern Ocean that show a novel association between Helicosphaera hyalina (HET) and Helicosphaera HOL catilliferus type. The ability of Helicosphaera HET and HOL morphospecies to form multiple different combinations indicates a substantial complexity in the relationships between life cycle phases in this group. The findings suggest recent divergence within the Helicosphaera lineage may have resulted in significant inter- and intra-specific variability, with cryptic speciation in one or both life cycle phases contributing to their ability to form multiple HET/HOL associations
Gephyrocapsa huxleyi (Emiliania huxleyi) as a model system for coccolithophore biology
Full text linkCoccolithophores are the most abundant calcifying organisms in modern oceans and are important primary producers in many marine ecosystems. Their ability to generate a cellular covering of calcium carbonate plates (coccoliths) plays a major role in marine biogeochemistry and the global carbon cycle. Coccolithophores also play an important role in sulfur cycling through the production of the climate-active gas dimethyl sulfide. The primary model organism for coccolithophore research is Emiliania huxleyi, now named Gephyrocapsa huxleyi. G. huxleyi has a cosmopolitan distribution, occupying coastal and oceanic environments across the globe, and is the most abundant coccolithophore in modern oceans. Research in G. huxleyi has identified many aspects of coccolithophore biology, from cell biology to ecological interactions. In this perspective, we summarize the key advances made using G. huxleyi and examine the emerging tools for research in this model organism. We discuss the key steps that need to be taken by the research community to advance G. huxleyi as a model organism and the suitability of other species as models for specific aspects of coccolithophore biology
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Evolutionary Rates in the Haptophyta : Exploring Molecular and Phenotypic Diversity
Full text linkHaptophytes are photosynthetic protists found in both freshwater and marine environments with an origin possibly dating back to the Neoproterozoic era. The most recent molecular phylogeny reveals several haptophyte "mystery clades" that await morphological verification, but it is otherwise highly consistent with morphology-based phylogenies, including that of the coccolithophores (calcifying haptophytes). The fossil coccolith record offers unique insights into extinct lineages, including the adaptive radiations that produced extant descendant species. By combining molecular data of extant coccolithophores and phenotype-based studies of their ancestral lineages, it has become possible to probe the modes and rates of speciation in more detail, although this approach is still limited to only few taxa because of the lack of whole-genome datasets. The evolution of calcification likely involved several steps, but its origin can be traced back to an early association with organic scales typical for all haptophytes. Other key haptophyte traits, including the haplo-diplontic life cycle, are herein mapped upon the coccolithophorid phylogeny to help navigate a discussion of their ecological benefits and trade-offs in a rapidly changing ocean
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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