Curtis Suttle

The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.

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Arthropods are the most speciose animal on the planet, they are widely distributed, and play vital roles in global ecosystems. Arthropods have intimate ecological relationships with a broad range of organisms. Accordingly, they may serve as natural reservoirs for different viruses and drive the evolution of viruses by exchanging them with other organisms. Yet, for the vast diversity of arthropods, their associated viruses remain unexplored.This thesis started by investigating RNA viruses associated with marine copepods, including parasitic species that have significant impacts on aquaculture, and planktonic species that are essential to marine food webs and global biogeochemical cycles. Then, a systematic investigation was conducted to fully explore the RNA virus diversity in arthropods, and to study their roles in the global evolution of RNA viruses. Finally, virus-derived small RNAs (viRNAs) were analyzed, aiming to characterize the RNA interference (RNAi) antiviral immunity in different arthropods, and to identify novel viruses infecting them. The thesis reports over 1400 previously unknown RNA viruses in three subphyla of the Arthropoda, encompassing 822 novel evolutionary group (75% amino acid identity), and demonstrates the central role that arthropods have played in the macroevolution of RNA viruses. Moreover, many of these newly discovered viruses are associated with arthropods that have ecological, economic, and public health significance. Additionally, by analyzing viRNAs, I show that RNAi-mediated antiviral immune pathways are commonly present in arthropods, although the size and base distributions of the resulting viRNAs are highly variable among different species. Furthermore, by screening for typical signatures of viRNAs, more than 6000 potential parasitic sequences were identified in different species of arthropods. Overall, this work reports viruses infecting important arthropod species, cements the central role of arthropods in the evolution of RNA viruses, expands the current known diversity of RNA viruses, and systematically characterizes the RNAi-mediated antiviral immunity in arthropods.

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RNA viruses are ubiquitous and abundant in aquatic environments, but not well studied;of these, picorna-like viruses are dominant in coastal waters. They are genetically diverse, andprimarily infect microbial eukaryotes; thereby, influencing microbial community compositionand nutrient cycling. Few studies have elucidated the diversity of marine and freshwater RNAvirus assemblages. In this dissertation, metagenomic data were used to address the hypothesisthat aquatic RNA viruses are diverse and broadly distributed, as well as the abiotic factors andevolutionary pressures shaping these assemblages.Mapping reads from geographically separate sites to six reference genomes showed thatthese viruses were subject to purifying selection, with synonymous single-nucleotide variationsdominating the mutations. These marine RNA viruses exhibited distinct biogeographic patternswith different quasispecies detectable in different areas.Marine RNA virus assemblages from polar to tropical environments weretaxonomically complex. Viruses in the order Picornavirales were consistently in high relativeabundance, and dominated marine RNA virus assemblages. Virus families that are thought toonly occur in terrestrial systems were detected in oceanic samples, implying that these virusesinfect marine organisms and, therefore, likely originated in the ocean.Freshwater RNA virus assemblages are equally diverse throughout six sitescharacterized by different associated land use. A complex suite of abiotic factors is associatedwith seasonal changes in viral diversity across all sites over 14 months, with high variabilityin site-specific RNA virus diversity. Certain viruses were associated with specific abioticfactors and sites, suggesting that some RNA viral taxa may be useful as indicator species.Lastly, a sequence-dependent taxonomic framework was developed to incorporategenomes assembled from metagenomic data into the current taxonomic classification system.This led to a proposed expansion of the Marnaviridae from a single isolate to 20 virusesclassified into seven genera.The data presented here revealed unprecedented diversity in RNA aquatic viruses, andgreatly expanded our knowledge of the distribution and dynamics of aquatic RNA viruses withconsequent implications for understanding their role in aquatic ecosystems.

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Microbial parasitoids that exploit other microbes are abundant but remain a poorlyexplored frontier in microbiology. To study such pathogens, a high throughput screen wasdeveloped using ultrafiltration and flow cytometry, resulting in the isolation of five giantviruses and one bacterial pathogen infecting heterotrophic flagellates, as well as a bacterialpredator of prokaryotes. Bodo saltans virus (BsV) is the first characterized representative ofthe most abundant group of giant viruses in oceans, so far only known from metagenomic data.Its 1.39 Mb genome encodes 1227 predicted ORFs; yet, much of its translational apparatus hasbeen lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encodingself-splicing introns that may defend against competing viruses. Ankyrin-repeat proteins thatare putative anti-host factors show extensive gene duplication via a genomic accordion,indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomicplasticity leading to genome gigantism in giant viruses. Chromulinavorax destructans is anisolate from the TM6/Dependentiae phylum that infects and lyses the abundant heterotrophicflagellate Spumella elongata. Chromulinavorax destructans is characterized by a high degreeof reduction and specialization. Its 1.2 Mb genome shows no metabolic potential, relying onan extensive transporter system to import nutrients and energy in the form of ATP from thehost. It replicates by extensively reorganizing and expanding the host mitochondrion. Almosthalf of the inferred proteins contain signal sequences for secretion, which include manyproteins of unknown function as well as 98 copies of ankyrin-repeat proteins, suggesting thepresence of an extensive host-manipulation apparatus. Bdellovibrio salishius was found toexploit a beta-proteobacterium in an epibiotic manner. Despite this, B. salishius encodes acomplex genomic complement more similar to periplasmic species as well as severalbiosynthesis pathways not previously found in epibiotic species. Bdellovibrio salishius is arepresentative of a widely distributed basal cluster within the genus Bdellovibrio, suggestingthat epibiotic feeding might be a common predation type in nature and ancestral feature in thegenus. The microorganisms described here broaden our understanding of microbial diversityand the unusual genomic functions associated with a parasitoid lifestyle amongst microbes.

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Marine viruses are the most abundant and genetically diverse biological entity in the oceans. Viruses infecting phytoplankton have a role in maintaining phytoplankton diversity, but also affect the cycling of carbon and nutrients through the microbial loop, which has substantial implications for the marine food chain and the planet’s climate system. It has also become evident that viral replication is affected by environmental conditions. In turn, viruses appear to possess a repertoire of metabolic genes to compensate for environmental adversities. However, it is not well understood how environmental variables affect viral replication in the environment or what the role of their genetic repertoire is in the selection to replicate. This thesis investigates the abundance and genetic diversity of viruses, the composition of viral communities and how the dynamics of viral replication is affected by in situ environmental conditions in four projects which are presented in Chapters 2, 3, 4 and 5. Chapter 2 describes the influence of environmental variables on the variation in viral and host abundance, and how this dynamic changes among different environments. Chapter 3 shows that phycodnaviruses infecting prasinophytes have a highly variable genetic repertoire with several metabolic genes of diverse origins. This genetic variability is reflected in their distribution in the environment, indicating selection on viruses. Chapter 4 establishes an approach to study cyanomyovirus communities and their associated genetic repertoires in the environment. It shows that the distribution of cyanomyovirus ecotypes on temporal and spatial scales is a function of environmental variables. Chapter 5 unveils a considerable mismatch between free cyanomyovirus communities, representing the seed bank, and replicating cyanomyoviruses in the cellular fraction. The emergence of replicating viruses out of the viral seed bank is highly variable and affected by environmental factors. In conclusion, total viral abundance as well as the community composition of specific virus types show a relationship to environmental variables. The genetic repertoire of viruses appears to be an adaptation to selection pressure and specific viruses can occupy environmental niches that are not only defined by the presence of susceptible hosts but also by a virus's ability to compensate for adversities.

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Marine viruses are ubiquitous, abundant, and genetically diverse in natural waters. They play key roles in nutrient and carbon cycles. The composition of marine viral communities changes seasonally and repeats annually, and such patterns can be driven by their hosts in response to environmental changes. Moreover, environmental parameters can also directly affect the viral community through the decay of viruses, and differences in viral infectivity under different conditions. Marine viral communities show changes over time and space, but the mechanisms that drive compositional changes and maintain high diversity are largely unexplored. Determining factors affecting viral community composition and structure is essential to explain how viral diversity is maintained. This dissertation will assess the diversity of marine viral communities, and the role of the environment and putative viral hosts in driving this diversity.The relationship between environmental parameters and the diversity of viruses and their putative hosts was explored in coastal seawater samples along a transect and over a 13-month time series at a nearshore location. I used PCR amplification to target ecologically-important double-stranded DNA (T4-like myoviruses) and single-stranded RNA (picorna-like) viruses, as well as their putative bacterial (16S rRNA gene) and eukaryotic (18S rRNA gene) hosts were examined. These were interpreted in the context of nutrients, salinity, and temperature.I observed patchiness in the distribution and diversity of viral communities across space and time (Chapter 2). Chapter 2 greatly increased the known genetic diversity of marine picorna-like viruses with 145 operational taxonomic units (OTUs) occurring within previously seen phylogenetic clades. In Chapter 3 there were temporal shifts in dominance of phylogenetically-related viruses and most viral OTUs were ephemeral. In Chapter 4, I demonstrated that nutrients, salinity, and temperature drive the co-occurrence of viruses and their putative hosts. Finally, in Chapter 5, I revealed that specific viral and protistan taxa were associated with controlling species composition and the demise of a phytoplankton bloom.Altogether, this dissertation advances the understanding of the phylogenetic structure of viral communities over time, the drivers of host-virus relationships, and the dynamics of viral and microbial communities during blooms by assessing multiple groups of viruses and microbes.

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There is wide recognition that cyanobacteria are major primary producers in polar freshwater regions. Filamentous cyanobacteria are commonly found in benthic mats and biofilms at the bottom of lakes, ponds and streams, while picocyanobacteria dominate the planktonic communities of many polar lakes. However, no representative viruses infecting this group of organisms have been characterized. This dissertation, which is a culmination of experiments and genomic and metagenomic analyses, presents the first characterization of viruses infecting freshwater polar cyanobacteria and the discovery of previously unknown groups of viruses. First, I isolated and genetically characterized a polar freshwater cyanophage (S-EIV1) that represents a new evolutionary lineage of bacteriophages that are globally widespread and abundant. Second, I described a new group of viruses (Cyanophage A-1 and Cyanophage N-1) infecting freshwater filamentous cyanobacteria that contain a distinct DNA polymerase. Third, during genomic analysis of Cyanophage N-1, I identified a DNA repeat region similar to a Clustered Regularly Interspaced Short Palindromic (CRISPR) array. The CRISPR array had direct repeats with high similarity to those commonly found in filamentous cyanobacteria. I showed that the viral-encoded CRISPR was transcribed and have the potential be viral-mediated transferred to its host. Finally, DNA-stable isotope probing (DNA-SIP) was used to recover and sequence viruses infecting primary producers in a polar cyanobacterial mat. Arctic freshwater systems are some of the most threatened environments because of rapid climate change, and viruses encompass the greatest genetic and biological diversity on Earth. This work presents previously unknown groups of viruses and a newly discovered virus-host system that provide new tools for investigating host-virus interactions and examining arctic viral diversity.

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Current studies indicate that viruses of marine bacteria are biological carbon sinks, transforming bacterial carbon into dissolved organic matter, the majority of which is respired rather than incorporated back into biomass. In contrast, this dissertation focusses on viruses, not as a carbon sink but as a catalyst of nitrogen cycling, benefiting phytoplankton by liberating nitrogen from bacterial lysates that would otherwise be tied up in bacterial biomass. The results in this dissertation show that organic nitrogen released by viral lysis of heterotrophic marine bacteria is remineralised by uninfected bacteria, and the resulting ammonium taken up by phytoplankton.In an initial laboratory experiment, only a portion of the amino acids derived from heterotrophic bacterial lysates could be taken up by other heterotrophic bacteria within the duration of the experiment. Both D- and L-amino acids were taken up in proportion to their initial concentrations, demonstrating a lack of preference for the generally more labile L-amino acids. In a subsequent field experiment, reduction of the viral fraction in a marine microbial community resulted in reduced ammonium remineralisation and phytoplankton abundance, suggesting that remineralised nitrogen from bacterial metabolism of viral lysates contributes to phytoplankton growth. Another experiment added a marine bacterium labeled with 15N and infected with a lytic virus to microbial communities. This experiment directly demonstrated that remineralised nitrogen from bacterial lysates released through the action of viruses was a significant source of nitrogen for phytoplankton. In a final series of experiments, viruses were reduced from seawater from 22 field stations using bacterial concentration techniques to explore correlations between environmental factors and ammonium remineralisation from viral lysis. Viral mediated ammonium remineralisation changed with different chlorophyll a concentrations and salinities, suggesting potential predictive associations. These results show that liberated nitrogen from viral lysis of bacteria is readily degraded by heterotrophic marine bacteria and remineralised into ammonium for uptake by autotrophic organisms. The results in this dissertation demonstrate that viruses are key players in the cycling of nitrogen in marine systems and stress the need to incorporate viral mediated nutrient release into models of global biogeochemical cycling.

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Microbialites represent the oldest known persistent ecosystems and potentially the earliest evidence of life on the planet, having existed for ~85% of the geologic history of Earth (Dupraz et al., 2009). Despite over one hundred years of active research, little is known about modern freshwater microbialite ecosystems with regards to metabolic potential and microbialite-specific community structure. We performed metagenomic analysis of freshwater thrombolithic clotted microbialites from Pavilion Lake (British Columbia, Canada) and Clinton Creek (Yukon, Canada). In addition, metagenomes were obtained from the surrounding water and sediments to sort out which members of the microbial community were microbialite-specific. Pavilion Lake microbialites are distinct from the surrounding environments in microbial community structure and metabolic potential. The microbialites are dominated by heterotrophic processes with high abundances of heavy metal, antibiotic resistance, and alcohol fermentation pathways from the numerically dominant Proteobacteria. Clinton Creek houses the northern-most and fastest growing microbialites, which have a high proportion of photosynthetic genes, supporting isotopic data that photosynthesis drives microbialite formation. Clinton Creek has distinct communities, with microbialites dominated by Alphaproteobacteria (photoheterotrophs) and sediments dominated by Gammaproteobacteria (mainly heterotrophic nitrogen-fixers). To complement the metagenomic study of Pavilion Lake, a culturing based study was performed that yielded over one hundred new bacterial isolates. The new bacterial isolates were further screened for pigment containing strains that were non-photosynthetic. Amongst these pigment containing bacteria two new isolates were found and designated as an Exiguobacterium and an Agrococcus. Polyphasic analysis revealed that both are new species, which were named Agrococcus pavilionensis strain RW1 and Exiguobacterium pavilionensis strain RW2. Genome sequencing of both strain RW1 andiiiRW2 was completed and a comparative genomic and phylogenetic study was performed to evaluate their evolutionary placement and metabolic potential. Both isolates have low abundance in the Pavilion Lake microbialites, although they contribute heavy metal resistance genes that are found amongst the microbialite metagenomes. Hypothetical carotenoid biosynthesis pathways are also described which may be responsible for the coloration in Agrococcus and Exiguobacterium and may be related to photo-protection.

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Viruses are the most abundant and genetically diverse life forms in the biosphere. Byinfecting specific subsets of microbial communities, they influence community composition,thereby affecting nutrient and energy cycling.Single-stranded (ss) DNA viruses are major pathogens of plants and animals that have beenwell studied for years due to their economic and human-health effects. Recent advances inmetagenomics show that marine ssDNA viruses are widespread in marine and freshwaterenvironments, but their diversity and evolutionary relationships remain relatively unexplored.This dissertation focuses on characterizing the diversity and evolutionary relationshipsamong marine ssDNA viruses. First, metagenomic data were gathered and analyzed toassess the genetic diversity of ssDNA viruses, leading to the identification 129 geneticallydistinct groups of ssDNA viruses that had no recognizable similarity to each other or to othersequenced viruses. Each group was represented by at least one complete genome, withmost falling into 11 well-defined groups. Comparison and phylogenetic analysis ofsequences from marine and terrestrial viruses indicate that ssDNA viruses share a commonorigin and that terrestrial viruses likely co-evolved with their hosts when they transitionedfrom the ocean to the land.The second part focused on one particular subfamily of viruses, the Gokushovirinae (familyMicroviridae) to understand their relationship with the environment. Five complete genomeswere assembled and primers were designed to amplify a fragment of the major capsidprotein to look at the distribution of gokushoviruses in various marine environments.Phylogenetic analysis revealed that most sequences were distantly related to those fromcultured representatives, falling into many new distinct evolutionary groups. Finally, aprotocol for fluorescence in situ hybridization was developed to observe cells infected bygokushoviruses.The results presented in this dissertation greatly expand the known sequence space forssDNA, nearly doubling the number of complete available genomes, and revealing muchgreater genetic richness than previously though. The vast diversity of ssDNA viruses in thesea and their similarity with viruses infecting eukaryotes is consistent with their role assignificant pathogens of marine phytoplankton and microzooplankton.

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Viruses are the most abundant, ubiquitous and diverse biological entities in the world’s oceans. Through infection and lysis, viruses play critical roles in shaping marine microbial assemblages, with consequences for ecosystem functioning and biogeochemical processes. Despite their global-scale importance in oceanic processes, relatively little is currently known about the distribution, ecological roles and diversity of marine viruses. Furthermore, this existing knowledge is largely limited to temperate and lower latitude ecosystems, leaving the role of viruses in polar waters relatively unexplored. The Canadian Arctic Shelf (CAS) is a heterogeneous and productive marine ecosystem within the Arctic Ocean that plays a key role in carbon cycling. Emerging data suggest that the microbial assemblages on the CAS are active and diverse and can respond rapidly to changes in environmental conditions. This dissertation addresses a knowledge gap regarding marine viruses in polar waters by examining ecology and diversity of marine viruses on the CAS. Toward this end, multiple approaches such as flow cytometry and epifluorescence microscopy, experimental incubations and filtration, molecular techniques (polymerase chain reaction, denaturing gradient gel electrophoresis fingerprint analysis, cloning and sequencing) and statistical analyses were used to investigate 1) spatio-temporal variations in viral distribution and abundance, 2) significance of lysogenic and lytic viral infections and their impacts on host mortality and carbon cycling, 3) patterns in the genetic structure of T4-like viruses (Myoviridae) and phycodnaviruses (Phycodnaviridae), two virus families infecting bacteria and eukaryotic phytoplankton, respectively and 4) phylogenetic diversity and richness of T4-like viruses and phycodnaviruses. Together, the results of these studies have demonstrated that viruses are abundant, active and diverse components of the CAS microbial assemblages, and are strongly coupled with environmental conditions and microbial abundance, productivity and composition. In addition, these studies indicate that viruses are significant agents of microbial mortality on the CAS, and can influence energy fluxes and carbon cycling. Overall, this dissertation has increased our understanding of the marine viruses in arctic environments. Moreover, the results stress the need to include viruses in models when studying the influence of climate changes on biogeochemical cycles in the Arctic Ocean.

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Giant viruses infecting unicellular eukaryotes have genomes that overlap in size and coding content with the smallest cellular life forms, thereby blurring the boundary between what is considered living and non-living. Due to their recent discovery, little is known about the biology and host range of giant viruses. In this dissertation, I characterize Cafeteria roenbergensis virus (CroV), the largest marine virus known to date. CroV infects the phagotrophic nanoflagellate C. roenbergensis, a widespread and ecologically important marine zooplankton species. CroV has a 730 kilobase pair DNA genome which is predicted to encode 544 proteins and 22 transfer RNAs. Four genes contained an intein insertion and several genes have not been found before in viruses, including an isoleucyl-tRNA synthetase and a histone acetyltransferase. A 38 kilobase pair region of putative bacterial origin encoded predicted enzymes for the biosynthesis of 3-deoxy-D-manno-octulosonate, a key component of the bacterial lipopolysaccharide layer. Microarray analysis revealed that at least 274 CroV genes were transcribed during infection and that different genes were expressed at early and late stages of viral replication. Promoter sequences specific for each stage were identified. Proteomic analyses showed that the virion is composed of at least 129 CroV-encoded proteins, including a large set of transcription enzymes and several DNA repair proteins. Phylogenetically, CroV was found to belong to the group of nucleocytoplasmic large DNA viruses and was most closely related to Acanthamoeba polyphaga mimivirus, although only a third of the CroV genes had homologues in Mimivirus. I also discovered a smaller virus, the Mavirus virophage, whose replication was dependent on co-infection by CroV and led to decreased CroV production and increased host-cell survival. Mavirus particles co-localized within the CroV virion factory, as shown by transmission electron microscopy of infected cells. Remarkably, the 19 kilobase pair DNA genome of Mavirus was most similar to the Maverick/Polinton eukaryotic DNA transposons, which led to the hypothesis that these transposons have originated from the endogenization of ancient virophages into eukaryotic genomes. This work describes the first giant virus infecting a zooplankton species and demonstrates a clear link between Mavirus and Maverick transposons.

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