Measurements of DNA damage and photoreactivation imply that most viruses in marine surface waters are infective

Wilhelm, Steven W.; Weinbauer, Markus G.; Suttle, Curtis A.; Pledger, Ralph J.; Mitchell, David L.

doi:10.3354/ame014215

Cited by 68 publications

(62 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The two that are newly described for viruses include genes encoding an endonuclease (uvdE) and a phosphate transport protein (phoU). Photorepair of ultravioletdamaged viral DNA has been well documented (for example, Wilhelm et al, 1998) and uvdE may provide a genetic mechanism for how some viruses achieve such repair. Although phoU has not been observed in viruses, phosphate stress and acquisition genes (for example, pstS, phoA, phoH) are common in T4-like cyanophages isolated from low-phosphate waters (Sullivan et al, 2010).…”

Section: Co-localized With Viral Genes On Contigs (Includes Genes Idementioning

confidence: 99%

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

2014

View full text Add to dashboard Cite

Microbes drive myriad ecosystem processes, and their viruses modulate microbial-driven processes through mortality, horizontal gene transfer, and metabolic reprogramming by viral-encoded auxiliary metabolic genes (AMGs). However, our knowledge of viral roles in the oceans is primarily limited to surface waters. Here we assess the depth distribution of protein clusters (PCs) in the first large-scale quantitative viral metagenomic data set that spans much of the pelagic depth continuum (the Pacific Ocean Virome; POV). This established ‘core’ (180 PCs; one-third new to science) and ‘flexible’ (423K PCs) community gene sets, including niche-defining genes in the latter (385 and 170 PCs are exclusive and core to the photic and aphotic zones, respectively). Taxonomic annotation suggested that tailed phages are ubiquitous, but not abundant (<5% of PCs) and revealed depth-related taxonomic patterns. Functional annotation, coupled with extensive analyses to document non-viral DNA contamination, uncovered 32 new AMGs (9 core, 20 photic and 3 aphotic) that introduce ways in which viruses manipulate infected host metabolism, and parallel depth-stratified host adaptations (for example, photic zone genes for iron–sulphur cluster modulation for phage production, and aphotic zone genes for high-pressure deep-sea survival). Finally, significant vertical flux of photic zone viruses to the deep sea was detected, which is critical for interpreting depth-related patterns in nature. Beyond the ecological advances outlined here, this catalog of viral core, flexible and niche-defining genes provides a resource for future investigation into the organization, function and evolution of microbial molecular networks to mechanistically understand and model viral roles in the biosphere.

show abstract

Section: Co-localized With Viral Genes On Contigs (Includes Genes Idementioning

confidence: 99%

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

2014

View full text Add to dashboard Cite

show abstract

“…Nevertheless, we could not detect a significant decrease in CPD levels, suggesting that photorepair is not the prevailing pathway for CPD removal in these organisms, although we cannot completely rule (1997) reported recovery of protein synthesis in marine bacterioplankton under exposure to UVAR and PAR. In marine viruses host-mediated photorepair is potentially essential for the maintenance of high concentrations of viruses in surface waters (Weinbauer et al 1997, Wilhelm et al 1998. It is unclear whether DNA damage is uniformly distributed over all cells or whether most of the damage is accumulated in a few heavily damaged cells, as suggested by Buma et al (1995).…”

mentioning

confidence: 97%

Accumulation and removal of UVBR-induced DNA damage in marine tropical plankton subjected to mixed and simulated non-mixed conditions

Boelen¹,

Veldhuis²,

Buma³

2001

Aquat. Microb. Ecol.

View full text Add to dashboard Cite

Accumulation and removal of UVBR (ultraviolet-B radiation: 280 to 315 nm)-induced DNA damage (cyclobutane pyrimidine dimers; CPDs) were studied in 2 size fractions (0.2 to 0.8 and 0.8 to 10 µm) of natural populations of tropical marine bacterio-and phytoplankton off Curaçao, Netherlands Antilles. Plankton was either directly sampled from the surface layer (mixed situation), or incubated in UVR-transparent bags at 2 water depths (simulated non-mixed situation). A DNA dosimeter was used to measure biologically effective UVBR doses as well as attenuation of biologically effective radiation in the surface layer. A significant difference in CPD level between the 2 plankton size fractions could not be measured. In the mixed as well as in the non-mixed situation, DNA damage was accumulated between 09:00 and 14:00 h irrespective of the variability in incident UVBR. Surface layer samplings on consecutive days showed a clear diel pattern of increase and decrease, indicating that, in the field, DNA damage is repaired or diluted during the afternoon or at night. No significant repair of DNA damage could be measured in samples that were incubated during the afternoon at 0.2 or 10 m depth. The UVBR sensitivity of surface-incubated plankton was expressed as the ratio between damage induced in the cells to damage induced in (unshielded and unrepaired) bare DNA. In both plankton size classes this ratio fluctuated around 0.32. In conclusion, the results show that plankton cells present in the clear waters off Curaçao undergo UVBR stress despite the fact that they are subjected to vertical mixing. No significant difference in CPD levels between 2 size fractions of plankton could be measured, suggesting that in this plankton population other aspects, e.g. repair capacities or cell morphology, were more important than cell size.KEY WORDS: Cyclobutane pyrimidine dimers · DNA damage · DNA repair · Caribbean Sea · Marine bacteria · Mixing · Phytoplankton · Ultraviolet-B radiation, UVBR Resale or republication not permitted without written consent of the publisherAquat Microb Ecol 24: [265][266][267][268][269][270][271][272][273][274] 2001 induced DNA damage was detected in small size classes of bacterio-and phytoplankton compared to bigger size fractions. Garcia-Pichel (1994) calculated that small plankton cells cannot efficiently use UVR-absorbing compounds as sunscreens. Taking all these aspects into consideration, it is reasonable to hypothesize that the high incident UVBR levels may have a strong impact on the biology of small plankton. Such stress can result in a decrease in primary (Behrenfeld et al. 1993) or bacterial production (Herndl et al. 1993, Visser et al. 1999 or damage to essential macromolecules, e.g. DNA , Lyons et al. 1998, Weinbauer et al. 1999, Visser et al. 1999, Boelen et al. 2000. Alternatively, it may induce the synthesis of UV-absorbing compounds (Karentz et al. 1991b). Structural changes in DNA are considered to be one of the primary consequences of the deleterious effects of UVBR on the cellular...

show abstract

“…Light intensity and wavelength are suggested to have an impact on the distribution patterns of photoautotrophs in the marine environment (Olson et al, 1990;Wilhelm et al, 1998). It seems likely that the distribution patterns of the photoautotrophs are re£ected by niche-speci¢c distribution patterns of viruses.…”

Section: Molecular Diversity Of Cyanophagesmentioning

confidence: 99%

Virus isolation studies suggest short-term variations in abundance in natural cyanophage populations of the Indian Ocean

et al. 2006

View full text Add to dashboard Cite

and a.d.millard@warwick.ac.uk Cyanophage abundance has been shown to £uctuate over long timescales and with depth, but little is known about how it varies over short timescales. Previous short-term studies have relied on counting total virus numbers and therefore the phages which infect cyanobacteria cannot be distinguished from the total count.In this study, an isolation-based approach was used to determine cyanophage abundance from water samples collected over a depth pro¢le for a 24 h period from the Indian Ocean. Samples were used to infect Synechococcus sp. WH7803 and the number of plaque forming units (pfu) at each time point and depth were counted. At 10 m phage numbers were similar for most time-points, but there was a distinct peak in abundance at 0100 hours. Phage numbers were lower at 25 m and 50 m and did not show such strong temporal variation. No phages were found below this depth. Therefore, we conclude that only the abundance of phages in surface waters showed a clear temporal pattern over a short timescale. Fifty phages from a range of depths and time points were isolated and puri¢ed. The molecular diversity of these phages was estimated using a section of the phage-encoded psbD gene and the results from a phylogenetic analysis do not suggest that phages from the deeper waters form a distinct subgroup.

show abstract

Measurements of DNA damage and photoreactivation imply that most viruses in marine surface waters are infective

Cited by 68 publications

References 10 publications

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome

Accumulation and removal of UVBR-induced DNA damage in marine tropical plankton subjected to mixed and simulated non-mixed conditions

Virus isolation studies suggest short-term variations in abundance in natural cyanophage populations of the Indian Ocean

Contact Info

Product

Resources

About