Alexander Ian Culley

Alexander Ian Culley
University of Hawaiʻi at Mānoa | UH Manoa · Pacific Biosciences Research Center

Ph.D.

About

79
Publications
34,530
Reads
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2,575
Citations
Citations since 2017
52 Research Items
1699 Citations
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Introduction
A critical aspect to predicting the breadth and magnitude of the impact of climate change in the Arctic is elucidating how the organisms endemic to this region are being affected. As in the majority of ecosystems on Earth, the most abundant and diverse groups of biological entities in the Arctic are the microbes. The overarching objective of my research program is to characterize the diversity and dynamics of viruses that infect microbes and elucidate their role in Arctic microbial ecology.
Additional affiliations
April 2009 - August 2013
University of Hawaiʻi at Mānoa
Position
  • Research Associate
January 2007 - March 2009
University of Hawaiʻi at Mānoa
Position
  • PostDoc Position
January 2000 - May 2006
University of British Columbia - Vancouver
Position
  • PhD Student
Education
October 2000 - May 2007
University of British Columbia - Vancouver
Field of study
  • Marine Viral Ecology
January 1997 - August 2000
Moss Landing Marine Labs
Field of study
  • Biological Oceanography
September 1989 - June 1993
University of Oregon
Field of study
  • Biology

Publications

Publications (79)
Article
Full-text available
Viruses are abundant in the ocean and a major driving force in plankton ecology and evolution. It has been assumed that most of the viruses in seawater contain DNA and infect bacteria, but RNA-containing viruses in the ocean, which almost exclusively infect eukaryotes, have never been quantified. We compared the total mass of RNA and DNA in the vir...
Article
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Shallow lakes are common across the Arctic landscape and their ecosystem productivity is often dominated by benthic, cyanobacterial biofilms. Many of these water bodies freeze to the bottom and are biologically inactive during winter, but full freeze-up is becoming less common with Arctic warming. Here we analyzed the microbiome structure of newly...
Article
Full-text available
Aquatic ecosystems in the High Arctic are facing unprecedented changes as a result of global warming effects on the cryosphere. Snow pack is a central feature of northern landscapes, but the snow microbiome and its microbial connectivity to adjacent and downstream habitats have been little explored. To evaluate these aspects, we sampled along a hyd...
Article
We describe limnological datasets from Thores Lake, a large ice-contact proglacial lake in northern Ellesmere Island, Nunavut (82.65°N). The lake is formed due to damming by Thores Glacier at its northwest margin, has multi-year ice cover and a cold (< 1.54°C), freshwater column with a layer of < 0°C, high-conductivity water in the deepest basin. T...
Article
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Relatively little is known about the glaciers of northern Ellesmere Island, Canada. Here we describe the first field and remote sensing observations of Thores Glacier, located 50 km inland from the Arctic Ocean. The glacier is slow-moving, with maximum velocities of 26 m a −1 and a maximum observed thickness of 360 ± 4.3 m. There has been little ch...
Article
Full-text available
Milne Fiord, located on the coastal margin of the Last Ice Area (LIA) in the High Arctic (82°N, Canada), harbors an epishelf lake, a rare type of ice-dependent ecosystem in which a layer of freshwater overlies marine water connected to the open ocean. This microbe-dominated ecosystem faces catastrophic change due to the deterioration of its ice env...
Article
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Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly und...
Article
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their eco...
Article
Viruses are suspected to be lynchpins in ecosystem function, but so far we can only guess at their significance. DNA viruses are increasingly being recognized as significant components of biogeochemical cycling in the oceans. Dominguez-Huerta et al. explored global patterns of marine RNA virus occurrence by extracting virus sequences from Tara Ocea...
Article
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their eco...
Article
DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and “species”-level diversity and contextualize their eco...
Article
Full-text available
Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was...
Article
Full-text available
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine bi...
Article
Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine bi...
Article
Full-text available
Arctic lakes are experiencing increasingly shorter periods of ice cover due to accelerated warming at northern high latitudes. Given the control of ice cover thickness and duration over many limnological processes, these changes will have pervasive effects. However, due to their remote and extreme locations even first-order data on lake ecology is...
Article
The family Marnaviridae comprises small non-enveloped viruses with positive-sense RNA genomes of 8.6-9.6 kb. Isolates infect marine single-celled eukaryotes (protists) that come from diverse lineages. Some members are known from metagenomic studies of ocean virioplankton, with additional unclassified viruses described from metagenomic datasets deri...
Presentation
For 3000 years, the Milne Ice Shelf had harboured unique ecosystems, including the last epishelf lake of the Northern Hemisphere, a stratified environment where fresh and marine waters meet behind the ice. Microbial life often dominates polar aquatic ecosystems where viruses regulate host biomass, drive microbial community evolution, and affect the...
Article
Nostoc (Nostocales, Cyanobacteria) has a global distribution in the Polar Regions. However, the genomic diversity of Nostoc is little known and there are no genomes available for polar Nostoc. Here we carried out the first genomic analysis of the N. commune morphotype with a recent sample from the High Arctic and a herbarium specimen collected duri...
Article
Full-text available
Background: The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways invol...
Article
Full-text available
Background The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules and plays a fundamental role in cellular and ecosystem-level processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways involv...
Article
Full-text available
Ice cover persists throughout summer over many lakes at extreme polar latitudes but is likely to become increasingly rare with ongoing climate change. Here we addressed the question of how summer ice-cover affects the underlying water column of Ward Hunt Lake, a freshwater lake in the Canadian High Arctic, with attention to its vertical gradients i...
Presentation
Full-text available
Polar aquatic ecosystems are dominated by microbial communities, and viruses are a major component. Viruses affect the aquatic microbiome by regulating the size of host populations, driving community evolution and shunting the circulation of energy through trophic webs, which ultimately impacts biogeochemical processes. Because of rapid mutation ra...
Article
Full-text available
Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aero...
Article
Full-text available
In ice-covered polar lakes, a narrow ice-free moat opens up in spring or early summer, and then persists at the edge of the lake until complete ice loss or refreezing. In this study, we analyzed the horizontal gradients in Ward Hunt Lake, located in the High Arctic, and addressed the hypothesis that the transition from its nearshore open-water moat...
Article
Full-text available
Mean annual air temperatures in the High Arctic are rising rapidly, with extreme warming events becoming increasingly common. Little is known, however, about the consequences of such events on the ice-capped lakes that occur abundantly across this region. Here, we compared 2 years of high-frequency monitoring data in Ward Hunt Lake in the Canadian...
Preprint
Full-text available
Background The sulfur cycle encompasses a series of complex aerobic and anaerobic transformations of S-containing molecules, and plays a fundamental role in cellular and ecosystems level-processes, influencing biological carbon transfers and other biogeochemical cycles. Despite their importance, the microbial communities and metabolic pathways invo...
Article
Full-text available
High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of ma...
Article
Full-text available
We isolated two closely related strains that belong to the Myoviridae family and infect cyanobacteria in a shallow subarctic rock basin lake. Their host was identified as a member of the Synechococcus-Cyanobium complex. Sequenced genomes of the two phages were 244,930 bp and 243,633 bp. We describe their annotation and highlight some noteworthy fea...
Article
Full-text available
The candidate phyla radiation (CPR) is a diverse group of uncultured bacterial lineages with poorly understood metabolic functions. CPR bacteria can represent a large proportion of the total planktonic microbial community in subarctic thermokarst lakes, but their functional roles remain unexplored. We applied sequential water filtration and metagen...
Article
Full-text available
Protists are key stone components of aquatic ecosystems, sustaining primary productivity and aquatic food webs. However, their diversity, ecology and structuring factors shaping their temporal distribution remain strongly misunderstood in freshwaters. Using high-throughput sequencing on water samples collected over 16 different months (including tw...
Poster
Full-text available
Global warming conditions are causing significant changes in subarctic landscapes, including thawing of ice-rich permafrost and the expansion of thermokarst lakes and ponds. These aquatic ecosystems are rich in organic matter and shallow, yet during the summer, their water columns are highly stratified with a warm, well-oxygenated layer at the surf...
Article
Full-text available
Permafrost thawing results in the formation of thermokarst lakes, which are biogeochemical hotspots in northern landscapes and strong emitters of greenhouse gasses to the atmosphere. Most studies of thermokarst lakes have been in summer, despite the predominance of winter and ice-cover over much of the year, and the microbial ecology of these water...
Article
Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow and metabolic outputs. However, ecosystem-level impacts of viral community diversity remains difficult to assess due to classification issues and few reference genomes. Here we establish a ~12-fold expanded global ocean DNA virome dataset of 195,728 vi...
Article
Full-text available
Bacteria are key players in biogeochemical cycles and control water quality in freshwater ecosystems. Nevertheless, little is known about the identity and ecology of riverine bacteria, especially during ice‐covered periods that are often mistakenly perceived as periods with negligible biological activities. Here, we analyzed in detail the effects o...
Article
Full-text available
The St. Lawrence hydrographic system includes freshwater, brackish, and marine habitats, and is the largest waterway in North America by volume. The food-webs in these habitats are ultimately dependent on phytoplankton. Viral lysis is believed to be responsible for a major part of phytoplankton mortality. To better understand their role, we charact...
Article
Full-text available
Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communitie...
Article
RNA viruses that infect microbes are now recognized as an active, persistent and important component of the aquatic microbial community. While some information about the diversity and dynamics of the RNA virioplankton has been derived from culture-based and single gene approaches, research based on viromic and metatransciptomic methods has generate...
Article
Full-text available
We describe an inexpensive, reliable, and easily executed improvement for the extraction of DNA from SterivexTM filter units, that involves the separation of the SterivexTM filter from its casing. Our study demonstrates that our modification of the original extraction protocol significantly increased DNA yields, with an average increase of 4.1-fold...
Article
Full-text available
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated...
Article
Full-text available
Wastewater treatment center (WTC) workers may be vulnerable to diseases caused by viruses, such as the common cold, influenza and gastro-intestinal infections. Although there is a substantial body of literature characterizing the microbial community found in wastewater, only a few studies have characterized the viral component of WTC aerosols, desp...
Article
Full-text available
The bacterium Aeromonas salmonicida subsp. salmonicida is a common pathogen in fish farms worldwide. Since the antibiotic resistance of this bacterial species is on the increase, it is important to have a broader view on this issue. In the present study, we tested the presence of known plasmids conferring multi-drug resistance as well as antibiotic...
Article
Full-text available
Early work on marine algal viruses focused exclusively on those having DNA genomes, but recent studies suggest that RNA viruses, especially those with positive-sense, single-stranded RNA (+ssRNA) genomes, are abundant in tropical and temperate coastal seawater. To test whether this was also true of polar waters, we estimated the relative abundances...
Chapter
Full-text available
Viral evolution is a complex process driven by a variety of forces including the ex-tracellular environment, the intracellular milieu, the interaction of viruses with one another, and is inextricably linked with the evolution of the host organism. There have been a number of recent interesting discussions of the potential roles of viruses in the ev...
Article
Full-text available
Unlabelled: Viruses have a profound influence on the ecology and evolution of plankton, but our understanding of the composition of the aquatic viral communities is still rudimentary. This is especially true of those viruses having RNA genomes. The limited data that have been published suggest that the RNA virioplankton is dominated by viruses wit...
Article
Full-text available
Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not b...
Chapter
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Viruses are microscopic biological entities that can only replicate inside a living cell. A viral infection can result in the death of the infected cell, but a viral genome can also forge a stable symbiotic relationship with its host cell. The genomes, morphologies, and replication mechanisms of viruses are distinct from living cells and exceptiona...
Article
Full-text available
Metagenomic analyses of marine viruses generate an overview of viral genes present in a sample, but the percentage of the resulting sequence fragments that can be reassembled is low and the phenotype of the virus from which a given sequence derives is usually unknown. In this study, we employed physical fractionation to characterize the morphologic...
Article
Full-text available
Investigating the bacteriophages of vibrios has led to significant insights into the evolution and pathogenicity of their host strains. This report presents the first complete genome sequence of a bacteriophage that infects the deadly human pathogen Vibrio vulnificus. The phage was isolated from the surface waters of the Ala Wai Canal, which is par...
Article
Full-text available
The investigation of marine viruses has advanced our understanding of ecology, evolution, microbiology, oceanography and virology. Significant findings discussed in this review include the discovery of giant viruses that have genome sizes and metabolic capabilities that distort the line between virus and cell, viruses that participate in photosynth...
Article
Full-text available
The diversity of ribonucleic acid (RNA) viruses in the ocean and the ongoing isolation and characterization of RNA viruses that infect important primary producers suggests that RNA viruses are active members of the marine microbial assemblage. At this point, little is known about the composition, dynamics, and ecology of the RNA virioplankton. In t...
Article
Full-text available
Research on the diversity and ecology of viruses in the environment has been revolutionized by the ability to detect, fingerprint, and sequence viral genes and genomes. The starting point for these molecular assays is the release and recovery of the viral nucleic acids. The complexity of this task depends in large part on the nature of the starting...