Isolation and characterisation of novel viruses infecting marine phytoplankton

Viruses are the most abundant biological agents in the global marine environment. Through cellular lysis viruses influence many biogeochemical and ecological processes, including energy and nutrient cycling, host distribution and abundance, algal bloom control and genetic transfer. Nano- and picophytoplankton are ubiquitous in the world’s oceans and are responsible for a high proportion of the annual global carbon fixation. However, relatively few viruses have been isolated and described that infect these key primary producers and little is known of their diversity, dynamics or propagation strategies. The aims of this study were to detect, isolate and characterise novel marine viruses that infect these important members of the phytoplankton assemblage. Screening of seawater samples for viruses that infect a broad representation of nano and picophytoplankton species was undertaken here. To enable this, a large culture collection of 106 phytoplankton species was established and used to screen seawater samples for viruses on a weekly basis over a two year period. A total of 12 novel viruses infecting the prasinophyte species’ Ostreococcus tauri and Micromonas pusilla were isolated from seawater sampled in coastal waters of the Western English Channel. Viruses were purified by plaque purification or liquid serial dilution techniques. Characterisation of novel virus isolates included growth kinetics, visualisation using transmission electron microscopy, host range analysis and estimates of viral genome sizes using pulsed field gel electrophoresis. Phylogenetic analysis of these viruses was conducted based on the sequence of the conserved DNA polymerase gene. Genome sequencing of two of the viruses infecting O. tauri was completed and revealed many exciting features, including a suite of genes hitherto unreported, or with rare occurrence, in viruses. Evidence is presented for horizontal gene transfer between viruses isolated in this study and their hosts, as well as between other eukaryotic and bacterial sources. Functional characterisation of the viral genomes sequenced and described in this study will provide clearer insights into viral dynamics and evolutionary history

Extremophiles in an Antarctic Marine Ecosystem

Recent attempts to explore marine microbial diversity and the global marine microbiome have indicated a large proportion of previously unknown diversity. However, sequencing alone does not tell the whole story, as it relies heavily upon information that is already contained within sequence databases. In addition, microorganisms have been shown to present small-to-large scale biogeographical patterns worldwide, potentially making regional combinations of selection pressures unique. Here, we focus on the extremophile community in the boundary region located between the Polar Front and the Southern Antarctic Circumpolar Current in the Southern Ocean, to explore the potential of metagenomic approaches as a tool for bioprospecting in the search for novel functional activity based on targeted sampling efforts. We assessed the microbial composition and diversity from a region north of the current limit for winter sea ice, north of the Southern Antarctic Circumpolar Front (SACCF) but south of the Polar Front. Although, most of the more frequently encountered sequences were derived from common marine microorganisms, within these dominant groups, we found a proportion of genes related to secondary metabolism of potential interest in bioprospecting. Extremophiles were rare by comparison but belonged to a range of genera. Hence, they represented interesting targets from which to identify rare or novel functions. Ultimately, future shifts in environmental conditions favoring more cosmopolitan groups could have an unpredictable effect on microbial diversity and function in the Southern Ocean, perhaps excluding the rarer extremophiles

Isolation and characterisation of novel viruses infecting marine phytoplankton

Viruses are the most abundant biological agents in the global marine environment. Through cellular lysis viruses influence many biogeochemical and ecological processes, including energy and nutrient cycling, host distribution and abundance, algal bloom control and genetic transfer. Nano- and picophytoplankton are ubiquitous in the world’s oceans and are responsible for a high proportion of the annual global carbon fixation. However, relatively few viruses have been isolated and described that infect these key primary producers and little is known of their diversity, dynamics or propagation strategies. The aims of this study were to detect, isolate and characterise novel marine viruses that infect these important members of the phytoplankton assemblage. Screening of seawater samples for viruses that infect a broad representation of nano and picophytoplankton species was undertaken here. To enable this, a large culture collection of 106 phytoplankton species was established and used to screen seawater samples for viruses on a weekly basis over a two year period. A total of 12 novel viruses infecting the prasinophyte species’ Ostreococcus tauri and Micromonas pusilla were isolated from seawater sampled in coastal waters of the Western English Channel. Viruses were purified by plaque purification or liquid serial dilution techniques. Characterisation of novel virus isolates included growth kinetics, visualisation using transmission electron microscopy, host range analysis and estimates of viral genome sizes using pulsed field gel electrophoresis. Phylogenetic analysis of these viruses was conducted based on the sequence of the conserved DNA polymerase gene. Genome sequencing of two of the viruses infecting O. tauri was completed and revealed many exciting features, including a suite of genes hitherto unreported, or with rare occurrence, in viruses. Evidence is presented for horizontal gene transfer between viruses isolated in this study and their hosts, as well as between other eukaryotic and bacterial sources. Functional characterisation of the viral genomes sequenced and described in this study will provide clearer insights into viral dynamics and evolutionary history.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Generalized Rate-Distortion Functions of Videos

Customers are consuming enormous digital videos every day via various kinds of video services through terrestrial, cable, and satellite communication systems or over-the-top Internet connections. To offer the best possible services using the limited capacity of video distribution systems, these video services desire precise understanding of the relationship between the perceptual quality of a video and its media attributes, for which we term it the GRD function. In this thesis, we focus on accurately estimating the generalized rate-distortion (GRD) function with a minimal number of measurement queries. We first explore the GRD behavior of compressed digital videos in a two-dimensional space of bitrate and resolution. Our analysis on real-world GRD data reveals that all GRD functions share similar regularities, but meanwhile exhibit considerable variations across different combinations of content and encoder types. Based on the analysis, we define the theoretical space of the GRD function, which not only constructs the groundwork of the form a GRD model should take, but also determines the constraints these functions must satisfy. We propose two computational GRD models. In the first model, we assume that the quality scores are precise, and develop a robust axial-monotonic Clough-Tocher (RAMCT) interpolation method to approximate the GRD function from a moderate number of measurements. In the second model, we show that the GRD function space is a convex set residing in a Hilbert space, and that a GRD function can be estimated by solving a projection problem onto the convex set. By analyzing GRD functions that arise in practice, we approximate the infinite-dimensional theoretical space by a low-dimensional one, based on which an empirical GRD model of few parameters is proposed. To further reduce the number of queries, we present a novel sampling scheme based on a probabilistic model and an information measure. The proposed sampling method generates a sequence of queries by minimizing the overall informativeness of the remaining samples. To evaluate the performance of the GRD estimation methods, we collect a large-scale database consisting of more than $4,000$ real-world GRD functions, namely the Waterloo generalized rate-distortion (Waterloo GRD) database. Extensive comparison experiments are carried out on the database. Superiority of the two proposed GRD models over state-of-the-art approaches are attested both quantitatively and visually. Meanwhile, it is also validated that the proposed sampling algorithm consistently reduces the number of queries needed by various GRD estimation algorithms. Finally, we show the broad application scope of the proposed GRD models by exemplifying three applications: rate-distortion curve prediction, per-title encoding profile generation, and video encoder comparison

MOLECULAR AND ECOLOGICAL ASPECTS OF THE INTERACTIONS BETWEEN \u3ci\u3eAUREOCOCCUS ANOPHAGEFFERENS\u3c/i\u3e AND ITS GIANT VIRUS

Viruses are increasingly being recognized as an important biotic component of all ecosystems including agents that control the rapid ecological events that are harmful algal blooms (HABS). Aureococcus anophagefferens is a pelagophyte which causes recurrent ecosystem devastating brown tide blooms along the east coast of the USA and has recently spread to China and South Africa. It has been suggested that a large virus (AaV) is possibly an important agent for demise of brown tide blooms. This observation is consistent with the recognition of a number of other giant viruses modulating algal blooms in marine systems. In this dissertation, we investigated both the molecular underpinnings of Aureococcus-AaV interactions and the dynamics of AaV and the associated viral community in situ. We determined the genome sequence and phylogenetic history of AaV using high throughput sequencing approach and revealed it’s intertwined evolutionary history with the host and other organisms. Building upon the available genome of AaV and its host, we took an RNA-seq approach to provide insights on the physiological state of the AaV-infected Aureococcus ‘virocell’ that is geared towards virus production. In situ activity of AaV was detected by targeted amplicon and high throughput community RNA sequencing (metatranscriptomics) from Quantuck Bay, NY, a site with recurrent brown tide blooms. AaV and associated giant algal viruses in the Mimiviridae clade were found to respond to environmental changes, indicating that this newly recognized phylogenetic group is an important contributor to the eukaryotic phytoplankton dynamics. Analyzing time series metatranscriptomics from two distinct coastal sites recovered diverse viruses infecting microeukaryotes (including AaV) as part of interacting networks of viruses and microeukaryotes. Results from these studies testify AaV as an important factor for brown tide bloom demise, reveals the molecular underpinnings of AaV-host interactions and establishes the ecological relevance of Mimivirus-like algal viruses. We also provide foundation for using metatranscriptomics as an important tool in marine virus ecology – capable of recovering associations among coexisting marine microeukaryotes and viruses

Marine Viruses 2016

The research effort, publication rate and scientific community within the field of marine viruses have been growing rapidly over the past decade and viruses are now known to play key roles in microbial population dynamics, diversity and evolution as well as biogeochemical cycling. The compilation of papers included in the current Special Issue highlights the exploration of eukaryotic and prokaryotic viruses, from discovery to complex interplays between virus and host and virus–host interactions with ecologically relevant environmental variables. The discovery of novel viruses and new mechanisms underlying virus distribution and diversity exemplify the fascinating world of marine viruses. The oceans greatly shape Earth’s climate, hold 1.37 billion km3 of seawater, produce half of the oxygen in the atmosphere, and are integral to all known life. In a time where life in the oceans is under increasing threat (global warming, pollution, economic use) it is pressing to understand how viruses affect host population dynamics, biodiversity, biogeochemical cycling and ecosystem efficiency

Biosystematics and the evolution of gall formation in hackberry psyllids Pachypsylla (Insecta: Homoptera: Psylloidea: Psyllidae)

This dissertation is a study of the phylogeny and evolutionary biology of gall formation in psyllids of the subfamily Spondyliaspidinae, with particular focus on North American hackberry gallers in the genus Pachypsylla. Species in this genus produce a variety of gall types on the leaves, petioles, buds and twigs of their hosts, four species of Celtis subgen. Euceltis (Ulmaceae). The homogeneity of adult morphology in Pachypsylla, contrasted to the great variation in gall morphology and phenology, has led to much difficulty in delimiting species. Chapter I investigates species limits as related to gall type and host specificity in Pachypsylla. Strong differences in allozymes, morphology and life history confirm that leaf, petiole, bud and twig gallers belong to different species or species groups. Different leaf gall morphs probably also represent different species, as evidenced by significant allozyme frequency differences among sympatric pairs of gall morphs, consistent frequency difference between co-occurring morphs across localities, and discrete differences in gall type between progenies of individual females. Differences in allozymes, female phenology, adult and nymphal coloration, as well as laboratory rearings and field manipulations, show that side cell individuals within two nipple gall types represent an inquiline sibling species (Chapter II). Chapter III is an analysis of phylogenetic relationships within Pachypsylla, based on allozyme, morphological, life history and chromosome characters. Galler populations attacking the same plant tissue form monophyletic groups. The leaf galler morphs are little diverged, and phylogenetic relationships among them are unclear. Populations of inquilines from two different gall types appear closely related; the inquiline appears to be derived from a gall-forming ancestor. Phylogenetic relationships among gallers on different plant parts are consistent with an evolutionary sequence of gall position from leaf to petiole to bud to twig. Chapter IV is a morphological study of phylogenetic relationships within Spondyliaspidinae. The tribe Pachypsyllini, including Pachypsylla and two related Celtis feeders, is monophyletic. The tree favors the hypothesis of Burckhardt over that of White and Hodkinson. The distribution of lerp and gall formation is shown to be non-random within Spondyliaspidinae