Virus production and life strategies in aquatic sediments

Ma, Mei; Danovaro, Roberto

doi:10.4319/lo.2004.49.2.0459

Cited by 114 publications

(170 citation statements)

References 42 publications

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“…These direct observations by TEM were never reported from marine and freshwater sediments Filippini et al, 2006;Säwströ m et al, 2009). This contrasts with viral infection rates inferred from indirect approaches where viral production is often calculated from changes in viral abundances before and after incubations (for example, dilution approach), primarily in contemporaneous marine sediments (Hewson and Fuhrman, 2003;Glud and Middelboe, 2004;Mei and Danovaro, 2004;Danovaro et al, 2008b;Corinaldesi et al, 2010).…”

Section: Discussionmentioning

confidence: 96%

“…These studies suggest (i) that the majority of sediment viruses does not originate from the upper water column (Fischer et al, 2004), and (ii) that viruses are active components of benthic environments. Indeed, the dilution or viral decay assays indicate that viruses could control a large part of microbial activities in the sediments (Mei and Danovaro, 2004;Danovaro et al, 2008b;Corinaldesi et al, 2010). However, only small numbers of visibly infected cells have been observed in both freshwater Filippini et al, 2006;Säwströ m et al, 2009) and marine benthic environments (Danovaro et al, 2008b).…”

Section: Introductionmentioning

confidence: 99%

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Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

et al. 2012

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Morphological diversity, abundance and community structure of viruses were examined in the deep and anoxic sediments of the volcanic Lake Pavin (France). The sediment core, encompassing 130 years of sedimentation, was subsampled every centimeter. High viral abundances were recorded and correlated to prokaryotic densities. Abundances of viruses and prokaryotes decreased with the depth, contrasting the pattern of virus-to-prokaryote ratio. According to fingerprint analyses, the community structure of viruses, bacteria and archaea gradually changed, and communities of the surface (0-10 cm) could be discriminated from those of the intermediate (11-27 cm) and deep (28-40 cm) sediment layers. Viral morphotypes similar to virions of ubiquitous dsDNA viruses of bacteria were observed. Exceptional morphotypes, previously never reported in freshwater systems, were also detected. Some of these resembled dsDNA viruses of hyperthermophilic and hyperhalophilic archaea. Moreover, unusual types of spherical and cubic virus-like particles (VLPs) were observed. Infected prokaryotic cells were detected in the whole sediment core, and their vertical distribution correlated with both viral and prokaryotic abundances. Pleomorphic ellipsoid VLPs were visible in filamentous cells tentatively identified as representatives of the archaeal genus Methanosaeta, a major group of methane producers on earth.

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Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

et al. 2012

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“…Bacterial cell lysis resulting from lytic infection by viruses is a major cause of bacterial mortality in pelagic systems (Fuhrman 2000) and was thought to be even more important in sediments because of higher viral and bacterial abundances (Paul et al 1993;Mei and Danovaro 2004). Recent estimates on the contribution of viral lysis in bacterial mortality show a large range of 0-40% (Fischer et al 2003;Mei and Danovaro 2004). Therefore, viral lysis may be an important cause of bacterial mortality, but large differences in reported contributions hinder generalization of the importance of this process.…”

Section: Discussionmentioning

confidence: 99%

The fate of bacterial carbon in an intertidal sediment: Modeling an in situ isotope tracer experiment

et al. 2006

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We report the results of an integrated modeling and in situ isotope tracer experiment study examining the fate of bacterial carbon in an intertidal sediment. 13 C-glucose was injected into the upper 10 cm of an intertidal sediment, which successfully tagged the bacterial community as evidenced by 13 C enrichment of bacterial specific polar-lipid-derived fatty acids. Over a period of 4.5 months, 13 C enrichment was monitored in sediment organic carbon, bacteria, meiobenthos, macrobenthos, and dissolved inorganic carbon. A mechanistic model accurately simulated label transfer among the biotic and abiotic compartments and was used to derive bacterial production and the loss processes grazing, mortality, respiration, and exchange. Bacterial production averaged 67 mmol C m 22 d 21 , of which 8% was lost from the sediment by exchange processes, 3% was grazed by meiobenthos and 24% by macrobenthos. The primary fate of bacterial production was mortality (65%) and the released bacterial carbon was recycled back to dissolved organic carbon, resulting in recycling of carbon within the dissolved organic carbon-bacteria loop. Bacterial respiration was the main loss process from this loop. Although a significant fraction of bacterial carbon production was grazed, our results show that bacterial carbon is primarily a sink of organic carbon in the food web of intertidal sediments.

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“…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 al 2003, 2004, Middelboe et al 2003, Mei & Danovaro 2004. A single study aimed at designing a protocol for determination of benthic viral numbers was done only on marine sediments (Danovaro et al 2001); freshwater systems were completely neglected.…”

Section: Abstract: Virus Extraction · Virus Counting · Epifluorescenmentioning

confidence: 99%

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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Virus production and life strategies in aquatic sediments

Cited by 114 publications

References 42 publications

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

Unexpected and novel putative viruses in the sediments of a deep-dark permanently anoxic freshwater habitat

The fate of bacterial carbon in an intertidal sediment: Modeling an in situ isotope tracer experiment

Optimization of extraction and estimation of viruses in silty freshwater sediments

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