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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Pseudoalteromonas Media Recipes Resource Report Resource Website |
Bonnie Poulos | DOI:10.17504/protocols.io.ek6bcze | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, The Ohio State University | 1 | 2016 | Bonnie Poulos 2016. Pseudoalteromonas Media Recipes. protocols.io https://dx.doi.org/10.17504/protocols.io.ek6bcze | 2021-04-15 09:14:38 | ||||
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Iron Chloride Precipitation of Viruses from Seawater Resource Report Resource Website |
Seth John, Bonnie Poulos, Christine Schirmer | DOI:10.17504/protocols.io.c2wyfd | VERVE Net, Sullivan Lab | This protocol describes a technique to recover viruses from natural waters using iron- based flocculation and large-pore-size filtration, followed by resuspension of virus- containing precipitates in a pH 6.5 buffer. This Fe-based virus flocculation, filtration and resuspension method (FFR) is efficient (> 90% recovery), reliable, inexpensive and adaptable to many aspects of marine viral ecology and genomics research. Recovered viruses are amenable to gene sequencing, and a variable proportion of phages, depending upon the phage, retain their infectivity when recovered if using oxalic acid in the resuspension buffer. Particles lose infectivity if resuspended with ascorbic acid in the buffer. | Matthew Sullivan Lab, University of Arizona, Ohio State University, Matthew Sullivan Lab, University of Arizona, Ohio State University, Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Seth John, Bonnie Poulos, Christine Schirmer 2015. Iron Chloride Precipitation of Viruses from Seawater. protocols.io https://dx.doi.org/10.17504/protocols.io.c2wyfd | 2021-04-15 09:14:39 | |||
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Buffered glutaraldehyde Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.c7gzjv | VERVE Net, Sullivan Lab | Formulation for a phosphate-buffered 20% glutaraldehyde stock solution. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Li Deng 2015. Buffered glutaraldehyde. protocols.io https://dx.doi.org/10.17504/protocols.io.c7gzjv | 2021-04-15 09:14:56 | |||
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Calculating burst size Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddm245 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Calculating burst size. protocols.io https://dx.doi.org/10.17504/protocols.io.ddm245 | 2021-04-15 09:14:42 | ||||
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Iodoacetamide Solution Resource Report Resource Website |
Kristin Corrier/Nathan VerBerkmoes | DOI:10.17504/protocols.io.dej3cm | VERVE Net, Sullivan Lab | For use in "FASP Kit Protocol-ORNL Developed for Bacteriophage" | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Kristin Corrier/Nathan VerBerkmoes 2016. Iodoacetamide Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dej3cm | 2021-04-15 09:14:43 | |||
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Prophage induction in marine Synechococcus Resource Report Resource Website |
John H. Paul and Markus Weinbauer | DOI:10.17504/protocols.io.dpc5iv | VERVE Net | This protocol gives a method for prophage induction in marine Synechococcus.Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_030.pdf | 1 | 2016 | John H. Paul and Markus Weinbauer 2016. Prophage induction in marine Synechococcus. protocols.io https://dx.doi.org/10.17504/protocols.io.dpc5iv | 2021-04-15 09:14:41 | ||
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DNA Extraction Protocol Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c32yqd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA Extraction Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.c32yqd | 2021-04-15 09:14:43 | ||||
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Bacteriophage isolation using enrichment cultures Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dpt5nm | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | A generally more efficient way of isolating lytic phages from marine environments is by the use of enrichment cultures. In this approach, the prefiltered water sample that is to be screened for phages against a given target bacterium, is enriched with a bacterial growth medium and amended with that target bacteria (Eisenstark 1967; Carlson 2005). This allows any lytic phages present in the sample to infect the target bacteria and propagate in the cultures, and subsequently, be isolated and purified. The two main advantages of the enrichment approach are 1) that it allows for screening for phages in a much larger volume of sample (typically 25–50 mL, rather than 5–10 µL), thus increasing the probability of isolating rare phages, and 2) that it allows the combination of different target hosts (e.g., different strains of a specific bacteria of interest) in the same incubation, again increasing the possibility of phage isolation. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Bacteriophage isolation using enrichment cultures. protocols.io https://dx.doi.org/10.17504/protocols.io.dpt5nm | 2021-04-15 09:14:43 | ||
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Script P11: Functional Analysis Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ehubb6w | VERVE Net, Club Grice | This protocol provides method for KEGG Analysis, Gene Ontology Analysis, and Operational Protein Family Analysis. Based on the methods from the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P11: Functional Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ehubb6w | 2021-04-15 09:15:02 | |
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DNase I Treatment Resource Report Resource Website |
James E. Thornton | DOI:10.17504/protocols.io.c3myk5 | VERVE Net, Sullivan Lab, Culley Lab_ULaval | This protocol describes the preparation of and treatment with DNase I to degrade DNA in solutions containing iron chloride, EDTA–Mg ascorbate buffer, and cesium chloride. DNase I treatment, CsCl purification, and sucrose purification methods were compared using replicated viral metagenomics in Hurwitz et al. 2012. We use this protocol primarily to remove free host and other contaminating DNA from phage preparations prior to extracting nucleic acid from the phage particles. | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2015 | James E. Thornton 2015. DNase I Treatment. protocols.io https://dx.doi.org/10.17504/protocols.io.c3myk5 | 2021-04-15 09:14:41 | |||
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Building up chemostats for experimental eco-evolutionary studies Resource Report Resource Website |
Ana Del Arco, Noemi Woltermann, Lutz Becks | DOI:10.17504/protocols.io.tkxekxn | VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G) | Chemostats and other flow through culture systems are a powerful tool for the study of microbial and plankton communities in experimental ecology and evolutionary studies. Commercially available chemostat systems allow the control of a large number of parameters (e.g., ph, pressure, CO2 concentration) but are often expensive and offer a high level of control that is often not needed for many experimental studies. Non-commercial chemostats are more cost efficient, easily set up and flexible in volumes used. Different from semi-continuous culture systems, the flow through conditions of chemostats allow a constant inflow of resources from a reservoir (medium bottle) and outflow of unused nutrients, waste products and organisms, which are all collected in a waste bottle. Nutrient levels in the reservoir and the flow rate of the chemostat system (often referred to as dilution rate and presented as the fraction of the volume of the chemostat that is replaced per day) determines population growth rates and dynamics (for the theory behind chemostats see Smith & Waltman, 1995 and Weitz, 2015). Chemostats have been used in a number of studies and with different organisms and combinations of organisms. For example, Boer et al. (2010) studied how growth-limiting intracellular metabolites control yeast growth under diverse nutrient availability (Saccharomyces cerevisiae growing under five different nutrient supply of nitrogen: carbon: phosphorus). Becks et al. (2005) used chemostat systems to show how changes in the flow rate of a chemostat system influences the population dynamics of a three species microbial system. Frickel et al. (2016) used chemostats to investigate eco- evolutionary dynamics in a coevolving host-virus system (algae Chlorella variabilis and Chlorovirus strain PBCV-1) for 90 days.We present here an instruction for a cost efficient and flexible chemostat systems. These chemostats are composed of four main parts: a syringe unit, a glass bottle (i.e. the chemostat), a medium bottle and a waste bottle, all connected by tubing. A peristaltic pump and a low overpressure in the system allow the flow of medium from the reservoir to the chemostat bottle and of unused nutrients, waste products and organisms to the waste bottle. Chemostats are put on stirring plates to create a homogenosus environment within.Becks, L., Hilker, F.M., Malchow, H., Jürgens, K., Arndt, H., 2005. Experimental demonstration of chaos in a microbial food web. Nature 435, 1226–1229. https://doi.org/10.1038/nature03627Boer, V.M., Crutchfield, C.A., Bradley, P.H., Botstein, D., Rabinowitz, J.D., 2010. Growth-limiting Intracellular Metabolites in Yeast Growing under Diverse Nutrient Limitations 21, 198–211. https://doi.org/10.1091/mbc.E09Frickel, J., Sieber, M., Becks, L., 2016. Eco-evolutionary dynamics in a coevolving host – virus system. Ecol. Lett. 19, 450–459. https://doi.org/10.1111/ele.12580Smith, H., Waltman, P., 1995.The Theory of the Chemostat: Dynamics of Microbial Competition (Cambridge Studies in Mathematical Biology). Cambridge: Cambridge University Press. doi:10.1017/CBO9780511530043Weitz, J.S. 2015. Quantitative Viral Ecology. Dynamics of viruses and their microbial host. Princeton University Press. ISBN: 9780691161549 .justify:after { content: ""; display:inline-block; width: 100%; } | Limnological Institute University Konstanz, Aquatic Ecology and Evolution, Konstanz/Egg Germany. , Max Planck for Evolutionary Biology, Plön, Germany , Limnological Institute University Konstanz, Aquatic Ecology and Evolution, Konstanz/Egg Germany. | 2 | 2020 | Ana Del Arco, Noemi Woltermann, Lutz Becks 2020. Building up chemostats for experimental eco-evolutionary studies. protocols.io https://dx.doi.org/10.17504/protocols.io.tkxekxn | 2021-04-15 09:14:41 | |||
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Iron Chloride Solution Resource Report Resource Website |
B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John | DOI:10.17504/protocols.io.c8wzxd | VERVE Net, Sullivan Lab | For use in Wet-Mount Method for Enumeration of Aquatic Viruses | Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University, Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Iron Chloride Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.c8wzxd | 2021-04-15 09:15:00 | |||
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One-step growth experiments (bacteriophages) Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dpw5pd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | The life cycle of phages can be characterized by one-step growth experiments, which are designed in a way that allows only a single infection cycle to take place (i.e., no re-infections occurring by phages produced during the experiment). | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. One-step growth experiments (bacteriophages). protocols.io https://dx.doi.org/10.17504/protocols.io.dpw5pd | 2021-04-15 09:14:46 | ||
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MetaVir- Analysis of viromes Resource Report Resource Website |
Simon Roux | DOI:10.17504/protocols.io.d5i84d | VERVE Net, Hurwitz Lab | METAVIR is a web server designed to annotate viral metagenomic sequences (raw reads or assembled contigs). A set of published viromes, identified as "public projects", is already available, and your own data sets can be processed in a private environment. | Université Blaise Pascal | http://metavir-meb.univ-bpclermont.fr/ | 1 | 2016 | Simon Roux 2016. MetaVir- Analysis of viromes. protocols.io https://dx.doi.org/10.17504/protocols.io.d5i84d | 2021-04-15 09:15:08 | ||
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CsCl purified phage lysate, Proteinase K, SDS Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c68zhv | VERVE Net, Sullivan Lab | This mixture is used for the DNA Extraction Protocol. | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. CsCl purified phage lysate, Proteinase K, SDS. protocols.io https://dx.doi.org/10.17504/protocols.io.c68zhv | 2021-04-15 09:14:45 | |||
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Quantification of aquatic viruses by flow cytometry Resource Report Resource Website |
Corina P. D. Brussaard, Jérôme P. Payet, Christian Winter, and Markus G. Weinbauer | DOI:10.17504/protocols.io.dpj5km | VERVE Net | This is a protocol from: Brussaard, C. P. D., J. P. Payet, C. Winter, and M. G. Weinbauer. 2010. Chapter 11: Quantification of aquatic viruses by flow cytometry. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_102.pdf | 1 | 2016 | Corina P. D. Brussaard, Jérôme P. Payet, Christian Winter, and Markus G. Weinbauer 2016. Quantification of aquatic viruses by flow cytometry. protocols.io https://dx.doi.org/10.17504/protocols.io.dpj5km | 2021-04-15 09:14:45 | ||
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Transformation of Bacterial Cultures Using The Calcium Chloride Procedure Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.erbbd2n | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Transformation of Bacterial Cultures Using The Calcium Chloride Procedure. protocols.io https://dx.doi.org/10.17504/protocols.io.erbbd2n | 2021-04-15 09:15:15 | ||||
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Script P4: Assigning Viral Taxonomy Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.efqbbmw | VERVE Net, Club Grice | This protocol provides a method for identifying bacteriophage/virus taxonomy without a virome dataset using UniProt reference database. Based on the methods found in the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | Grice Lab, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, Grice Lab, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, Grice Lab, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P4: Assigning Viral Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.efqbbmw | 2021-04-15 09:15:17 | |
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DNA/RNA Extractions from Sterivex Filters Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.c4bysm | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. DNA/RNA Extractions from Sterivex Filters. protocols.io https://dx.doi.org/10.17504/protocols.io.c4bysm | 2021-04-15 09:14:49 | ||||
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Script R12: Functional Analysis Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.ejibcke | VERVE Net, Club Grice | This protocol outlines the analysis used to plot KEGG functional annotation. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R12: Functional Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.ejibcke | 2021-04-15 09:15:16 |
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