Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
- Jennifer R. Brum &
- Matthew B. Sullivan
Competing interests statement
The authors declare no competing interests.
Jennifer R. Brum
Jennifer R. Brum is a postdoctoral research associate at the University of Arizona, Tucson, USA. She received her Master's degree in 2003 and her Ph.D. in 2009 in oceanography from the University of Hawaii, Honolulu, USA. Her research focuses on viral influences on biogeochemistry and microbial community dynamics in aquatic systems.
Matthew B. Sullivan
Matthew B. Sullivan is an associate professor at the University of Arizona, Tucson, USA. He received his M.Phil. degree in 1998 in biology from the Queens University of Belfast, Northern Ireland, and his Ph.D. in 2004 in biological oceanography from the Woods Hole Oceanographic Institution, Massachusetts, USA, and the Massachusetts Institute of Technology, USA. His research focuses on ocean viral ecology and evolution.
- Phytoplankton blooms
Temporally limited increases in phytoplankton abundances, which are often dominated by one phytoplankton species.
- Microbial loop
The flow of materials (for example, organic matter and nutrients) and energy within a microbial community, including the recycling of materials by heterotrophic microorganisms.
- Viral shunt
Refers to the role of viral lysis in the conversion of living microbial biomass into dissolved organic matter, which can be consumed by heterotrophic microorganisms.
- Kill the Winner hypothesis
(KtW hypothesis). This refers to the ability of predators to exert top-down control on the abundance of their hosts. In the context of this Review, the hypothesis refers to the ability of viruses to prevent their microbial hosts from becoming dominant through increased viral-induced mortality of the most proliferative hosts (the 'winners').
- Genome fingerprinting
An electrophoresis-based method to quantify the distribution of viruses with varying genome sizes in a sample.
The metagenomes of all viruses present in a specific sample.
- Iron chloride flocculation
A method to concentrate viruses from aquatic samples by binding viruses to iron flocs that can then be captured by filtration and dissolved to release the viruses.
- Tangential flow filtration
A method to concentrate viruses from aquatic samples, in which the sample is passed at pressure across a filter membrane of defined size to retain viruses and remove smaller materials.
- Linker amplification
A method to amplify DNA using ligated primers to obtain sufficient quantities of genomic material for downstream applications, such as metagenomic sequencing.
- Multiple displacement amplification
A method to amplify DNA using the phi29 polymerase in order to obtain sufficient quantities of genomic material for downstream applications, such as metagenomic sequencing.
- Rarefaction curves
Assessment of a community richness metric (for example, the total number of species, populations or protein clusters) versus the number of samples examined.
- Contig spectra
The number of contigs (overlapping sequences) per size of contig (the number of sequences in each contig) after assembly of metagenomic sequences.
- Aphotic zone
The region of the ocean that is not illuminated by sunlight.
- Particle biology
The study of the composition and activity of microbial communities on particulate matter in the ocean.
A fragment of a genomic sequence with a specific length 'k' (number of base pairs).
- Social network analysis
Quantitative measurement of the relationships between defined groups or samples using network theory.
- Oxygen minimum zone
(OMZ). Region of the ocean in which little or no dissolved oxygen is present.
- Gene transfer agents
(GTAs). Phage-like entities that package cellular DNA at random and facilitate horizontal gene transfer.
- Membrane vesicles
Fluid-filled, membrane-bound sacs containing proteins and other molecules, which are formed by 'pinching off' from the outer membrane of a cell.
Cloning vectors derived from the bacterial F plasmid in which large genomic segments (~40 kb) are stably maintained. These are used to identify genes or genomes of interest by end-sequencing or hybridization.
- Single amplified genomes
(SAGs). Amplified genomic sequences obtained from a single cell that has been separated from other cells by flow cytometry. These sequences can be mined to identify the presence of viral DNA.
- Microfluidic digital PCR
PCR-based amplification of individual genes from organisms that are trapped in microfluidic chambers.
An epifluorescence microscopy-based method to determine the colocalization of viral and host gene markers by fluorescence in situ hybridization (FISH), which enables the visualization of specific types of intracellular and extracellular viruses.
- Viral tagging
A flow cytometry method in which fluorescently labelled viruses are used as probes to detect and obtain wild viruses associated with cultivated cells.
- Quantitative host range analysis
(qHR analysis). A method for evaluating the magnitude of viral proliferation when individual cultivated virus types encounter individual cultivated microbial hosts in a laboratory setting.
- King of the Mountain hypothesis
(KoM hypothesis). This hypothesis describes the influence of increased recombination rates that enable particular microorganisms to dominate a community.
- NPZ-type ecosystem models
Numerical models that describe oceanic plankton dynamics using the three state variables of nutrient concentration (often nitrogen), phytoplankton abundance and zooplankton abundance.