User:Ferrellb/sandbox

Marine bacteriophages or marine phages are viruses that live as obligate parasitic agents in marine bacteria such as cyanobacteria. Their existence was discovered through electron microscopy and epifluorescence microscopy of ecological water samples, and later through metagenomic sampling of uncultured viral samples. Marine phages, although microscopic and essentially unnoticed by scientists until recently, appear to be the most abundant and diverse form of DNA replicating agent on the planet. There are approximately 4x1030 phage in oceans or 5x107 per millilitre. Quantification of marine viruses was originally performed using transmission electron microscopy but has been replaced by epifluorescence or flow cytometry.

In the marine water column
The viral shunt is a critical step in nutrient cycling, releasing organic matter through host lysis back into the dissolved organic matter pool and supporting ocean productivity. Marine bacteriophages appear to influence biogeochemical cycles globally, provide and regulate microbial biodiversity, cycle carbon through marine food webs, and are essential in preventing bacterial population explosions. Scientists are exploring the potential of marine cyanophages to be used to prevent or reverse eutrophication.

Marine bacteriophage are presumed to outnumber bacteria by at least 10-fold but the virus to bacteria ratio (VBR) is often substantially higher. VBR estimations are more accurate on a site-specific basis, supporting observed heterogeneity in the water column and contributing to difficulties in estimating viral abundance based on bacterial abundance alone. VBR, as an indicator of the possible contact rate between viruses and hosts, impact our ability to predict viruses’ effects on marine microbial turnover and nutrient cycling. Decreasing VBR with increasing host abundance may indicate the prevalence of temperate phages which either integrate into the host genome or are maintained as an extrachromosomal element, replicating with the bacterial host.

Viral morphology, determined by transmission electron microscopy (TEM), provides insights into viral populations across spatiotemporal and other environmental gradients. Non-tailed viruses appear to be dominant in multiple depths and oceanic regions, followed by the Caudovirales myoviruses, podoviruses, and siphoviruses. However, viruses belonging to families Corticoviridae, Inoviridae and Microviridae are also known to infect diverse marine bacteria. Metagenomic evidence suggests that microviruses (icosahedral ssDNA phages) are particularly prevalent in marine habitats.

Metagenomic approaches to assess viral diversity are often limited by a lack of reference sequences, leaving many sequences unannotated. However, viral contigs are generated through direct sequencing of a viral fraction, typically generated after 0.02-um filtration of a marine water sample, or through bioinformatics approaches to identify viral contigs or viral genomes from a microbial metagenome. Novel tools to identify putative viral contigs, such as VirSorter and VirFinder, allow for the assessment of patterns of viral abundance, host range, and functional content of marine bacteriophage.

In sediments
Marine bacteriophage form an important part of deep sea ecosystems. There are between 5x1012 and 1x1013 phage per square metre in deep sea sediments and their abundance closely correlates with the number of prokaryotes found in the sediments. They are responsible for the death of 80% of the prokaryotes found in the sediments, and almost all of these deaths are caused by cell lysis (bursting). They therefore play an important part in shifting nutrients from living forms into dissolved organic matter and detritus. This explains the high rate of nutrient turnover in deep sea sediments. The release of nutrients from infected bacteria stimulates the growth of uninfected bacteria and then these also become infected. Because of the importance of deep sea sediments in biogeochemical cycles, marine bacteriophage must influence the carbon, nitrogen and phosphorus cycles, but the exact influences are currently not understood.

Nutrient cycles
Marine viruses may play an important role in nutrient cycles by increasing the efficiency of the biological pump. The argument is that lysis releases unstable compounds, such as amino acids and nucleic acids, which tend to be recycled near the surface, whereas more indigestible carbon-rich material, such as that found in cell walls, is probably exported to deeper waters. Thus, the material that is exported to deeper waters by the 'viral shunt' is probably more carbon rich than the material from which it was derived. This would increase the efficiency of the biological pump.

Marine bacteriophages often contain auxiliary metabolic genes, host-derived genes thought to sustain viral replication by supplementing host metabolism during viral infection. These genes can impact multiple biogeochemical cycles, including carbon, phosphorus, sulfur, and nitrogen.