Curtis Suttle

Professor

Research Classification

Marine Environment

Research Interests

Microbial Diversity
Marine Microbiology
Environmental Virology
Biological Oceanography
Viral Discovery
Viruses
Phage

Relevant Degree Programs

 

Research Methodology

Metagenomics
Flow cytometry (viruses)
Nucleic-acid technologies

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Master's students
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Any time / year round

Generally students will need to be funded through external scholarships, or be funded through a University Graduate Fellowship, or other UBC Fellowship.

I support public scholarship, e.g. through the Public Scholars Initiative, and am available to supervise students and Postdocs interested in collaborating with external partners as part of their research.
I am open to hosting Visiting International Research Students (non-degree, up to 12 months).

Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - May 2019)
Distribution and diversity of aquatic RNA virus assemblages in an environmental context (2018)

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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Microbial parasitoids: giant viruses and tiny bacteria (2018)

No abstract available.

Environmental and genomic insights into marine virus populations and communities (2017)

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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Drivers of Viral Density and Community Compositional Change Over Spatial and Temporal Scales in Coastal British Columbia (2016)

No abstract available.

Genomic characterization of viruses infecting freshwater polar cyanobacteria (2014)

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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Influence of bacterial viruses on nitrogen cycling in the ocean (2014)

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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Metagenomic and genomic analyses of modern freshwater microbialites : unmasking a community of complex metabolic potential (2014)

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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Diversity and evolution of ssDNA viruses in marine environments (2013)

No abstract available.

Ecology and diversity of marine viruses on the Canadian Arctic Shelf, Arctic Ocean (2012)

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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Genetic and ultrastructural characterization of Cafeteria roenbergensis virus and its virophage Mavirus (2011)

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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News Releases

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