Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay

Drake, Lisa A.; Choi, Kyung Hwan; Haskell, A. G. Edward; Dobbs, Fred C.

doi:10.3354/ame016017

Cited by 74 publications

(79 citation statements)

References 21 publications

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“…In most aquatic environments, viral abundance is closely correlated to bacterial biomass (Boehme et al 1993, Cochlan et al 1993, Drake et al 1998, Middelboe et al 2003) and activity (Heldal & Bratbak 1991, Middelboe et al 2003. In this study, VLP distributions were significantly correlated to bacteria in all microscale profiles (mean r = 0.81, p < 0.05), but to bacterial activity (percentage of HDNA bacteria) in only 1 out of 4 samples.…”

Section: Microscale Distributionsmentioning

confidence: 76%

Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system

Seymour¹,

Patten²,

Bourne³

et al. 2005

Mar. Ecol. Prog. Ser.

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Variations in the abundance and community characteristics of virus-like particles (VLP) and heterotrophic bacteria within a shallow, near-shore coral reef were determined using flow cytometric analysis. Mean concentrations of 6.5 × 10 5 and 1.3 × 10 5 ml -1 were observed for VLP and bacterioplankton, respectively, although concentrations of both populations varied significantly (p < 0.05) between 4 distinct reef water types. Significant (p < 0.05) variability in the percentage of high DNA (HDNA) bacteria, applied here as an estimate of the proportion of active bacterial cells, and the virus:bacteria ratio (VBR) was also observed between different reef water types. Microscale profiles were taken in the 12 cm layer of water directly above the surface of coral colonies to determine the small-scale spatial relationships between coral colonies and planktonic microbial communities. Across these profiles, mean changes of 2-and 3.5-fold were observed for bacterioplankton and VLP communities, respectively, with VLP abundance positively correlated to bacteria in 75% of profiles. Bacterial and VLP abundance, percentage of HDNA bacteria, and VBR all generally exhibited increasing trends with proximity to the coral surface. VLP abundance was significantly higher (p < 0.05) in the 4 cm closest to the coral surface, and the VBR was higher at the coral surface than in any other zone. The patterns observed here indicate that VLP represent an abundant and dynamic community within coral reefs, are apparently coupled to the spatial dynamics of the bacterioplankton community, and may consequently significantly influence nutrient cycling rates and food-web structure within coral reef ecosystems. KEY WORDS: Coral reefs · Virus-like particles · BacterioplanktonResale or republication not permitted without written consent of the publisher

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Section: Microscale Distributionsmentioning

confidence: 76%

Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system

Seymour¹,

Patten²,

Bourne³

et al. 2005

Mar. Ecol. Prog. Ser.

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“…Maranger & Bird 1996, Steward et al 1996, Drake et al 1998, Hewson et al 2001, Lawrence et al 2002, Fischer et al 2003. Studies using EFM to estimate viruses in sediments applied a variety of protocols, without testing whether the procedures carried out before enumeration (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, sediment samples have usually been centrifuged prior to virus estimation by EFM (e.g. Drake et al 1998, Danovaro et al 2001, Hewson et al 2001, Lawrence et al 2002, Middelboe et al 2003, under the assumption that this process does not remove viruses, and hence does not falsify viral counts. However, none of these studies tested whether this assumption is valid.…”

mentioning

confidence: 99%

“…After fixation with glutaraldehyde, sonication and further dilution, the viruses in samples containing DNase and in untreated samples were counted. To confirm the DNase-digested DNA in water from the Kühwörther Wasser, its activity was assayed following the protocol of Drake et al (1998): 250 Kunitz units of DNase were added to 40 µg ml -1 DNA (Type I, 'highly polymerized' from calf thymus, Sigma) in water samples. The temporal change in absorbance at 260 nm within 10 min, monitored using a Hitachi U-2000 spectrophotometer (Hitachi), was 0.002 min -1 (data not shown).…”

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confidence: 99%

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Optimization of extraction and estimation of viruses in silty freshwater sediments

Fischer¹,

Kirschner²,

Velimirov

2005

Aquat. Microb. Ecol.

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The present study focused on the optimization of procedures for the extraction of viruses from silty freshwater sediments for subsequent enumeration. Viral abundance in 2 different shallow backwater systems of the River Danube (Austria) ranged from 1.45 × 10 9 to 9.58 × 10 9 particles ml -1 wet sediment. The highest virus yields from the bulk of the sediments were obtained by 1 min sonication (3 × 20 s intervals, with 10 s interruptions). An increase in sonication time of up to 5 min decreased viral counts by an average of 15%. Since dissolved DNA within sediment samples could bind to the nucleic acid stain and thereby inflate viral estimates, sediment samples are often treated with DNase before the staining procedure. Moreover, they are usually centrifuged and diluted to a high extent in order to avoid interference of particulate material with virus counting. Centrifugation led to a reduction of viral numbers by 2 to 36% compared to untreated samples and did not reduce the background fluorescence; thus counting of viruses was not facilitated. Diluting 2000 × with Milli-Q water always provided an average of 19% lower viral numbers than diluting 4000 ×. Treatment with DNase had no significant effect on virus counting, with viral numbers in untreated samples being on average 96% of those in DNase-containing samples. Additionally, 2 different nucleic acid stains were compared -viruses stained with SYBR Gold fluoresced brighter than those stained with SYBR Green I and fluorescence lasted longer, while background fluorescence was reduced sufficiently, thus facilitating virus counting. Viral numbers using SYBR Gold were on average twice of those obtained with SYBR Green I. The mean efficiency of virus extraction was 88.8% using the protocol outlined in this paper, and was thus slightly higher than that obtained in previous sediment investigations. KEY WORDS: Virus extraction · Virus counting · Epifluorescence microscopy · Silty freshwater sedimentResale or republication not permitted without written consent of the publisher Aquat Microb Ecol 40: 207-216, 2005 Moreover, EFM yields higher and more precise viral counts than TEM (Hennes & Suttle 1995, Weinbauer & Suttle 1997, Noble & Fuhrman 1998. Enumeration of viruses by EFM is based on using highly fluorescent nucleic acid dyes such as DAPI (Hara et al. 1991, Weinbauer & Suttle 1997, Yo-Pro I (Hennes & Suttle 1995, Xenopoulos & Bird 1997, SYBR Green I (Noble & Fuhrman 1998) or SYBR Gold (Chen et al. 2001). Viral abundance in sediment systems is 10-to 1000-fold higher than in the overlying water column (e.g. Maranger & Bird 1996, Steward et al. 1996, Drake et al. 1998, Hewson et al. 2001, Lawrence et al. 2002, Fischer et al. 2003. Studies using EFM to estimate viruses in sediments applied a variety of protocols, without testing whether the procedures carried out before enumeration (e.g. virus dislodgement from particles, centrifugation, dilution) affect viral counts (Danovaro & Serresi 2000, RicciardiRigault et al. 2000, Danovaro et al. 2001, Fischer et a...

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“…There is an increasing interest for the quantification of virus abundance (Maranger and Bird 1996;Bird et al 2001) and infectivity in benthic systems (Fischer et al 2003). However, the limited information gathered so far on benthic viruses has not allowed a clarification of the effect of viral infection in aquatic sediments (Paul et al 1993;Steward et al 1996;Drake et al 1998;Danovaro and Serresi 2000;Hewson et al 2001a), and data on factors regulating top-down bacterial production and mortality in marine sediments have been so far limited to the analysis of the nanoflagellate grazing (Wieltschnig et al 1999). …”

mentioning

confidence: 99%

Virus production and life strategies in aquatic sediments

Danovaro

2004

Limnology & Oceanography

114

146

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Aquatic sediments host much of the bacterial biomass and biodiversity and play a key role in biogeochemical cycles. However, the potential effect of viral infection remains unknown. We present estimates of virus production in a variety of benthic habitats of the Mediterranean Sea, characterized by different contamination levels and trophic states. Viriobenthos abundance in aquatic sediments ranged 10 8 -10 9 ml Ϫ1 of sediment and was ϳ20 times higher than virioplankton abundance. Vertical profiles in sediment cores revealed large virus numbers at 1-m depth below the sediment surface. Virus production in both marine and freshwater sediments was 1-2 orders of magnitude higher than typical values reported for virioplankton (0.13-1.60 ϫ 10 8 virus-like particles ml Ϫ1 sediment h Ϫ1 ), which indicates that virus turnover and infection rates can be higher in aquatic sediments than in the water column. Eutrophic and contaminated sediments displayed the highest virus production rates. Virus production was significantly correlated with the abundance of active bacteria and with bacterial cell production. We estimated an average burst size (BS) of 15-18 in marine and freshwater sediments. Virus-mediated bacterial mortality was high (on average, Ͼ40% of bacterial production) and increased from surface to deeper sediment levels, down to 100-cm depth. The fraction of bacteria with lysogenic infection (range, 0.0-1.8%) increased in deeper sediment layers (3.3% at 100-cm depth). Our results suggest that high benthic virus production rates can have a significant effect on benthic bacterial dynamics and indicate that virus production should be included in biogeochemical models of aquatic sediments.

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Vertical profiles of virus-like particles and bacteria in the water column and sediments of Chesapeake Bay

Cited by 74 publications

References 21 publications

Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system

Spatial dynamics of virus-like particles and heterotrophic bacteria within a shallow coral reef system

Optimization of extraction and estimation of viruses in silty freshwater sediments

Virus production and life strategies in aquatic sediments

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