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Curtis A. Suttle - One of the best experts on this subject based on the ideXlab platform.
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author correction re examination of the relationship between Marine Virus and microbial cell abundances
Nature microbiology, 2017Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Derek L Sonderegger, Charles A StockAbstract:The original publication of this Article included analysis of Virus and microbial cell abundances and Virus-to-microbial cell ratios. Data in the Article came from 25 studies intended to be exclusively from Marine sites. However, 3 of the studies included in the original unified dataset were erroneously classified as Marine sites during compilation. The records with mis-recorded longitude and latitude values were, in fact, taken from inland, freshwater sources. The three inland, freshwater datasets are ELA, TROUT and SWAT. The data from these three studies represent 163 of the 5,671 records in the original publication. In the updated version of the Article, all analyses have been recalculated using the same statistical analysis pipeline released via GitHub as part of the original publication. Removal of the three studies reduces the unified dataset to 5,508 records. Analyses involving all grouped datasets have been updated with changes noted in each figure. All key results remain qualitatively unchanged. All data and scripts used in this correction have been made available as a new, updated GitHub release to reflect the updated dataset and figures.
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Re-examination of the relationship between Marine Virus and microbial cell abundances
Nature Microbiology, 2016Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Derek Sonderegger, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Charles StockAbstract:Marine Viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10^8 per ml. Over many years, a consensus has emerged that Virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,508 microbial cell and Virus abundance estimates from 22 distinct Marine surveys and find substantial variation in the Virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, Virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the Virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales. Analysis of microbial cell and Virus abundance estimates from 25 distinct Marine surveys reveals that Virus-to-microbial cell ratio decreases with microbial cell density, questioning the idea that viral abundance is always 10-fold higher.
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re examining the relationship between Virus and microbial cell abundances in the global oceans
bioRxiv, 2015Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Derek L Sonderegger, Charles A StockAbstract:Marine Viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotem- porally in the global oceans, with upper estimates exceeding 10 8 per ml. Over many years, a con- sensus has emerged that Virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between Virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and Virus abundance estimates from 25 distinct Marine surveys to characterize the relationship between Virus and prokaryote abundances. We find that the median Virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near- and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, Virus abundances are better described as nonlinear, power-law functions of prokaryote abundances - par- ticularly when considering relationships within distinct Marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of Marine Virus- microbe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using “representative” abundances or abundance- ratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.
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giant Virus with a remarkable complement of genes infects Marine zooplankton
Proceedings of the National Academy of Sciences of the United States of America, 2010Co-Authors: Matthias G. Fischer, Michael J Allen, William H Wilson, Curtis A. SuttleAbstract:As major consumers of heterotrophic bacteria and phytoplankton, microzooplankton are a critical link in aquatic foodwebs. Here, we show that a major Marine microflagellate grazer is infected by a giant Virus, Cafeteria roenbergensis Virus (CroV), which has the largest genome of any described Marine Virus (≈730 kb of double-stranded DNA). The central 618-kb coding part of this AT-rich genome contains 544 predicted protein-coding genes; putative early and late promoter motifs have been detected and assigned to 191 and 72 of them, respectively, and at least 274 genes were expressed during infection. The diverse coding potential of CroV includes predicted translation factors, DNA repair enzymes such as DNA mismatch repair protein MutS and two photolyases, multiple ubiquitin pathway components, four intein elements, and 22 tRNAs. Many genes including isoleucyl-tRNA synthetase, eIF-2γ, and an Elp3-like histone acetyltransferase are usually not found in Viruses. We also discovered a 38-kb genomic region of putative bacterial origin, which encodes several predicted carbohydrate metabolizing enzymes, including an entire pathway for the biosynthesis of 3-deoxy-d-manno-octulosonate, a key component of the outer membrane in Gram-negative bacteria. Phylogenetic analysis indicates that CroV is a nucleocytoplasmic large DNA Virus, with Acanthamoeba polyphaga mimiVirus as its closest relative, although less than one-third of the genes of CroV have homologs in MimiVirus. CroV is a highly complex Marine Virus and the only Virus studied in genetic detail that infects one of the major groups of predators in the oceans.
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sequence analysis of Marine Virus communities reveals that groups of related algal Viruses are widely distributed in nature
Applied and Environmental Microbiology, 2002Co-Authors: Steven M Short, Curtis A. SuttleAbstract:Algal-Virus-specific PCR primers were used to amplify DNA polymerase (pol) gene fragments from geographically isolated natural Virus communities. Natural algal Virus communities were obtained from coastal sites in the Pacific Ocean in British Columbia, Canada, and the Southern Ocean near the Antarctic peninsula. Genetic fingerprints of algal Virus communities were generated using denaturing gradient gel electrophoresis (DGGE). Sequencing efforts recovered 33 sequences from the gradient gel. Of the 33 sequences examined, 25 encoded a conserved amino acid motif indicating that the sequences were pol gene fragments. Furthermore, the 25 pol sequences were related to pol gene fragments from known algal Viruses. In addition, similar Virus sequences (>98% sequence identity) were recovered from British Columbia and Antarctica. Results from this study demonstrate that DGGE with degenerate primers can be used to qualitatively fingerprint and assess genetic diversity in specific subsets of natural Virus communities and that closely related Viruses occur in distant geographic locations. DGGE is a powerful tool for genetically fingerprinting natural Virus communities and may be used to examine how specific components of Virus communities respond to experimental manipulations.
Steven M Short - One of the best experts on this subject based on the ideXlab platform.
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sequence analysis of Marine Virus communities reveals that groups of related algal Viruses are widely distributed in nature
Applied and Environmental Microbiology, 2002Co-Authors: Steven M Short, Curtis A. SuttleAbstract:Algal-Virus-specific PCR primers were used to amplify DNA polymerase (pol) gene fragments from geographically isolated natural Virus communities. Natural algal Virus communities were obtained from coastal sites in the Pacific Ocean in British Columbia, Canada, and the Southern Ocean near the Antarctic peninsula. Genetic fingerprints of algal Virus communities were generated using denaturing gradient gel electrophoresis (DGGE). Sequencing efforts recovered 33 sequences from the gradient gel. Of the 33 sequences examined, 25 encoded a conserved amino acid motif indicating that the sequences were pol gene fragments. Furthermore, the 25 pol sequences were related to pol gene fragments from known algal Viruses. In addition, similar Virus sequences (>98% sequence identity) were recovered from British Columbia and Antarctica. Results from this study demonstrate that DGGE with degenerate primers can be used to qualitatively fingerprint and assess genetic diversity in specific subsets of natural Virus communities and that closely related Viruses occur in distant geographic locations. DGGE is a powerful tool for genetically fingerprinting natural Virus communities and may be used to examine how specific components of Virus communities respond to experimental manipulations.
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Genetic Diversity in Marine Algal Virus Communities as Revealed by Sequence Analysis of DNA Polymerase Genes
Applied and Environmental Microbiology, 1996Co-Authors: Feng Chen, Curtis A. Suttle, Steven M ShortAbstract:Algal-Virus-specific PCR primers were used to amplify DNA polymerase gene (pol) fragments (683 to 689 bp) from the Virus-sized fraction (0.02 to 0.2 microns) concentrated from inshore and offshore water samples collected from the Gulf of Mexico. Algal-Virus-like DNA pol genes were detected in five samples collected from the surface and deep chlorophyll maximum. PCR products from an offshore station were cloned, and the genetic diversity of 33 fragments was examined by restriction fragment length polymorphism and sequence analysis. The five different genotypes or operational taxonomic units (OTUs) that were identified on the basis of restriction fragment length polymorphism banding patterns were present in different relative abundances (9 to 34%). One clone from each OTU was sequenced, and phylogenetic analysis showed that all of the OTUs fell within the family Phycodnaviridae. Four of the OTUs fell within a group of Viruses (MpV) which infect the photosynthetic picoplankter Micromonas pusilla. The genetic diversity among these genotypes was as large as that previously found for MpV isolates from different oceans. The remaining genotype formed its own clade between Viruses which infect M. pusilla and Chrysochromulina brevifilum. These results imply that Marine Virus communities contain a diverse assemblage of MpV-like Viruses, as well as other unknown members of the Phycodnaviridae.
Corina P. D. Brussaard - One of the best experts on this subject based on the ideXlab platform.
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Marine Virus predation by non-host organisms
Scientific Reports, 2020Co-Authors: Jennifer E. Welsh, Peter Steenhuis, Karlos Ribeiro Moraes, Jaap Meer, David W. Thieltges, Corina P. D. BrussaardAbstract:Viruses are the most abundant biological entities in Marine environments, however, despite its potential ecological implications, little is known about Virus removal by ambient non-host organisms. Here, we examined the effects of a variety of non-host organisms on the removal of Viruses. The Marine algal Virus PgV-07T (infective to Phaeocystis globosa ) can be discriminated from bacteriophages using flow cytometry, facilitating its use as a representative model system. Of all the non-host organisms tested, anemones, polychaete larvae, sea squirts, crabs, cockles, oysters and sponges significantly reduced viral abundance. The latter four species reduced viral abundance the most, by 90, 43, 12 and 98% over 24 h, respectively. Breadcrumb sponges instantly removed Viruses at high rates (176 mL h^−1 g tissue dry wt^−1) which continued over an extended period of time. The variety of non-host organisms capable of reducing viral abundance highlights that viral loss by ambient organisms is an overlooked avenue of viral ecology. Moreover, our finding that temperate sponges have the huge potential for constant and effective removal of Viruses from the water column demonstrates that natural viral loss has, thus far, been underestimated.
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author correction re examination of the relationship between Marine Virus and microbial cell abundances
Nature microbiology, 2017Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Derek L Sonderegger, Charles A StockAbstract:The original publication of this Article included analysis of Virus and microbial cell abundances and Virus-to-microbial cell ratios. Data in the Article came from 25 studies intended to be exclusively from Marine sites. However, 3 of the studies included in the original unified dataset were erroneously classified as Marine sites during compilation. The records with mis-recorded longitude and latitude values were, in fact, taken from inland, freshwater sources. The three inland, freshwater datasets are ELA, TROUT and SWAT. The data from these three studies represent 163 of the 5,671 records in the original publication. In the updated version of the Article, all analyses have been recalculated using the same statistical analysis pipeline released via GitHub as part of the original publication. Removal of the three studies reduces the unified dataset to 5,508 records. Analyses involving all grouped datasets have been updated with changes noted in each figure. All key results remain qualitatively unchanged. All data and scripts used in this correction have been made available as a new, updated GitHub release to reflect the updated dataset and figures.
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Re-examination of the relationship between Marine Virus and microbial cell abundances
Nature Microbiology, 2016Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Derek Sonderegger, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Charles StockAbstract:Marine Viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10^8 per ml. Over many years, a consensus has emerged that Virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,508 microbial cell and Virus abundance estimates from 22 distinct Marine surveys and find substantial variation in the Virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, Virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the Virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from ‘representative’ abundances require substantial refinement to be extrapolated to regional or global scales. Analysis of microbial cell and Virus abundance estimates from 25 distinct Marine surveys reveals that Virus-to-microbial cell ratio decreases with microbial cell density, questioning the idea that viral abundance is always 10-fold higher.
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re examining the relationship between Virus and microbial cell abundances in the global oceans
bioRxiv, 2015Co-Authors: Charles H. Wigington, Curtis A. Suttle, Mathias Middelboe, Corina P. D. Brussaard, Alison Buchan, Jan F. Finke, Jed A. Fuhrman, Jay T. Lennon, Derek L Sonderegger, Charles A StockAbstract:Marine Viruses are critical drivers of ocean biogeochemistry and their abundances vary spatiotem- porally in the global oceans, with upper estimates exceeding 10 8 per ml. Over many years, a con- sensus has emerged that Virus abundances are typically 10-fold higher than prokaryote abundances. The use of a fixed-ratio suggests that the relationship between Virus and prokaryote abundances is both predictable and linear. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5671 prokaryote and Virus abundance estimates from 25 distinct Marine surveys to characterize the relationship between Virus and prokaryote abundances. We find that the median Virus-to-prokaryote ratio (VPR) is 10:1 and 16:1 in the near- and sub-surface oceans, respectively. Nonetheless, we observe substantial variation in the VPR and find either no or limited explanatory power using fixed-ratio models. Instead, Virus abundances are better described as nonlinear, power-law functions of prokaryote abundances - par- ticularly when considering relationships within distinct Marine surveys. Estimated power-laws have scaling exponents that are typically less than 1, signifying that the VPR decreases with prokaryote density, rather than remaining fixed. The emergence of power-law scaling presents a challenge for mechanistic models seeking to understand the ecological causes and consequences of Marine Virus- microbe interactions. Such power-law scaling also implies that efforts to average viral effects on microbial mortality and biogeochemical cycles using “representative” abundances or abundance- ratios need to be refined if they are to be utilized to make quantitative predictions at regional or global ocean scales.
Kay D Bidle - One of the best experts on this subject based on the ideXlab platform.
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interrogating Marine Virus host interactions and elemental transfer with boncat and nanosims based methods
Environmental Microbiology, 2018Co-Authors: Alexis L Pasulka, Kimberlee Thamatrakoln, Sebastian H Kopf, Yunbin Guan, Bonnie T Poulos, Annie Moradian, Michael J Sweredoski, Sonja Hess, Mathew B Sullivan, Kay D BidleAbstract:While the collective impact of Marine Viruses has become more apparent over the last decade, a deeper understanding of Virus-host dynamics and the role of Viruses in nutrient cycling would benefit from direct observations at the single-Virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of Marine Viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1, and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of Viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of Viruses in the ocean.
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elucidating Marine Virus ecology through a unified heartbeat
Proceedings of the National Academy of Sciences of the United States of America, 2014Co-Authors: Kay D BidleAbstract:Marine environments teem with Viruses. They are not only the most abundant (109 to 1010 Virus l−1) and diverse biological entities in the oceans, but their parasitic lifestyles collectively turn over >25% of global photosynthetically fixed carbon through cell lysis, fuel upper ocean respiration by channeling dissolved organic matter to heterotrophic bacteria, and drive the tempo of microbial evolution by catalyzing the exchange of genetic material (1, 2). In these contexts, Viruses are the great engines of oceanic biogeochemistry and microbial evolution. Unfortunately, methodological limitations and the rapid “mosaic” nature of Virus evolution (3) have significantly hindered our understanding of virioplankton biology and ecology. Marine Viruses come in an astounding array of morphologies, lifestyles, genome organization, and sizes, ranging from the immense nucleocytoplasmic large double-stranded (ds)DNA-containing Viruses (NCLDVs), which contain the PandoraViruses [with up to 2.5-Mb genomes (4)], to the extremely small single-stranded (ss)DNA and RNA representatives characterized by only three to four genes and ∼0.3% the relative genome size [∼1.7–11 Kb (5⇓–7)]. Microbial autotrophs and heterotrophs alike fall prey to this parasitic pressure, with a majority of Marine Viruses targeting bacteria (bacteriophages) as high abundance targets (109 L−1). Unlike the cellular life of eukarya, bacteria, and archaea, for which universally shared small subunit ribosomal RNA genes have revolutionized our understanding of cellular diversity, ecology, and evolution (8), Viruses lack a universally conserved phylogenetic marker. PCR-based approaches have historically targeted specific genes within particular Virus subclades [e.g., DNA polymerase genes for Viruses infecting eukaryotic microalgae (9) or genes encoding the major capsid protein (g23) of T4-like myoViruses (10)]. “Omic” approaches have since provided unprecedented insight into Virus diversity and even a glimpse into inferred function (11), but infection lifestyles have remained elusive given most Virus-derived sequences have no database matches (12 … [↵][1]1Email: bidle{at}Marine.rutgers.edu. [1]: #xref-corresp-1-1
Jennifer E. Welsh - One of the best experts on this subject based on the ideXlab platform.
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Marine Virus predation by non-host organisms
Scientific Reports, 2020Co-Authors: Jennifer E. Welsh, Peter Steenhuis, Karlos Ribeiro Moraes, Jaap Meer, David W. Thieltges, Corina P. D. BrussaardAbstract:Viruses are the most abundant biological entities in Marine environments, however, despite its potential ecological implications, little is known about Virus removal by ambient non-host organisms. Here, we examined the effects of a variety of non-host organisms on the removal of Viruses. The Marine algal Virus PgV-07T (infective to Phaeocystis globosa ) can be discriminated from bacteriophages using flow cytometry, facilitating its use as a representative model system. Of all the non-host organisms tested, anemones, polychaete larvae, sea squirts, crabs, cockles, oysters and sponges significantly reduced viral abundance. The latter four species reduced viral abundance the most, by 90, 43, 12 and 98% over 24 h, respectively. Breadcrumb sponges instantly removed Viruses at high rates (176 mL h^−1 g tissue dry wt^−1) which continued over an extended period of time. The variety of non-host organisms capable of reducing viral abundance highlights that viral loss by ambient organisms is an overlooked avenue of viral ecology. Moreover, our finding that temperate sponges have the huge potential for constant and effective removal of Viruses from the water column demonstrates that natural viral loss has, thus far, been underestimated.