Benthic and Pelagic Viral Decay Experiments: a Model-Based Analysis and Its Applicability

ABSTRACT The viral decay in sediments, that is, the decrease in benthic viral concentration over time, was recorded after inhibiting the production of new viruses. Assuming that the viral abundance in an aquatic system remains constant and that viruses from lysed bacterial cells replace viruses lost by decay, the decay of viral particles can be used as a measure of viral production. Decay experiments showed that this approach is a useful tool to assess benthic viral production. However, the time course pattern of the decay experiments makes their interpretation difficult, regardless of whether viral decay is determined in the water column or in sediments. Different curve-fitting approaches (logarithmic function, power function, and linear regression) to describe the time course of decay experiments found in the literature are used in the present study and compared to a proposed “exponential decay” model based on the assumption that at any moment the decay is proportional to the amount of viruses present. Thus, an equation of the form dVA/dt = −k Ã¯Â¿Â½ VA leading to the time-integrated form VA t = VA0 Ã¯Â¿Â½ e−k Ã¯Â¿Â½ t was used, where k represents the viral decay rate (h−1), VA t is the viral abundance (viral particles ml−1) at time t (h), and VA0 is the initial viral abundance (viral particles ml−1). This approach represents the best solution for an accurate curve fitting based on a mathematical model for a realistic description of viral decay occurring in aquatic systems. Decay rates ranged from 0.0282 to 0.0696 h−1 (mean, 0.0464 h−1). Additionally, a mathematical model is presented that enables the quantification of the viral control of bacterial production. The viral impact on bacteria based on decay rates calculated from the different mathematical approaches varied widely within one and the same decay experiment. A comparison of the viral control of bacterial production in different aquatic environments is, therefore, improper when different mathematical formulas are used to interpret viral decay experiments.

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Viral Production, Decay Rates, and Life Strategies along a Trophic Gradient in the North Adriatic Sea

Applied and Environmental Microbiology ◽

10.1128/aem.71.11.6644-6650.2005 ◽

2005 ◽

Vol 71 (11) ◽

pp. 6644-6650 ◽

Cited By ~ 65

Author(s):

Lucia Bongiorni ◽

Mirko Magagnini ◽

Monica Armeni ◽

Rachel Noble ◽

Roberto Danovaro

Keyword(s):

Water Column ◽

Decay Rates ◽

Life Strategies ◽

Trophic Gradient ◽

Viral Production ◽

Trophic Conditions ◽

The North ◽

Viral Particles ◽

Causative Agents ◽

North Adriatic Sea

ABSTRACT Although the relationships between trophic conditions and viral dynamics have been widely explored in different pelagic environments, there have been few attempts at independent estimates of both viral production and decay. In this study, we investigated factors controlling the balance between viral production and decay along a trophic gradient in the north Adriatic basin, providing independent estimates of these variables and determining the relative importance of nanoflagellate grazing and viral life strategies. Increasing trophic conditions induced an increase of bacterioplankton growth rates and of the burst sizes. As a result, eutrophic waters displayed highest rates of viral production, which considerably exceeded observed rates of viral decay (up to 2.9 × 109 VLP liter−1 h−1). Viral decay was also higher in eutrophic waters, where it accounted for ca. 40% of viral production, and dropped significantly to 1.3 to 10.7% in oligotrophic waters. These results suggest that viral production and decay rates may not necessarily be balanced in the short term, resulting in a net increase of viruses in the system. In eutrophic waters nanoflagellate grazing, dissolved-colloidal substances, and lysogenic infection were responsible together for the removal of ca. 66% of viral production versus 17% in oligotrophic waters. Our results suggest that different causative agents are primarily responsible for the removal of viruses from the water column in different trophic conditions. Factors other than those considered in the past might shed light on processes responsible for the removal and/or decay of viral particles from the water column.

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Viral Abundance, Decay, and Diversity in the Meso- and Bathypelagic Waters of the North Atlantic

Applied and Environmental Microbiology ◽

10.1128/aem.00029-07 ◽

2007 ◽

Vol 73 (14) ◽

pp. 4429-4438 ◽

Cited By ~ 69

Author(s):

Verónica Parada ◽

Eva Sintes ◽

Hendrik M. van Aken ◽

Markus G. Weinbauer ◽

Gerhard J. Herndl

Keyword(s):

North Atlantic ◽

Deep Water ◽

Pulsed Field Gel Electrophoresis ◽

Decay Rates ◽

Leucine Incorporation ◽

Taxon Richness ◽

Viral Production ◽

Viral Abundance ◽

The North ◽

Order Of Magnitude

ABSTRACT To elucidate the potential importance of deep-water viruses in controlling the meso- and bathypelagic picoplankton community, the abundance, decay rate, and diversity of the virioplankton community were determined in the meso- and bathypelagic water masses of the eastern part of the subtropical North Atlantic. Viral abundance averaged 1.4 × 106 ml−1 at around 100 m of depth and decreased only by a factor of 2 at 3,000 to 4,000 m of depth. In contrast, picoplankton abundance decreased by 1 order of magnitude to the Lower Deep Water (LDW; 3,500- to 5,000-m depth). The virus-to-picoplankton ratio increased from 9 at about 100 m of depth to 110 in the LDW. Mean viral decay rates were 3.5 × 10−3 h−1 between 900 m and 2,750 m and 1.1 × 10−3 h−1 at 4,000 m of depth, corresponding to viral turnover times of 11 and 39 days, respectively. Pulsed-field gel electrophoresis fingerprints obtained from the viral community between 2,400 m and 4,000 m of depth revealed a maximum of only four bands from 4,000 m of depth. Based on the high viral abundance and the low picoplankton production determined via leucine incorporation, we conclude that the viral production calculated from the viral decay is insufficient to maintain the high viral abundance in the deep North Atlantic. Rather, we propose that substantial allochthonous viral input or lysogenic or pseudolysogenic production is required to maintain the high viral abundance detected in the meso- and bathypelagic North Atlantic. Consequently, deep-water prokaryotes are apparently far less controlled in their abundance and taxon richness by lytic prokaryotic phages than the high viral abundance and the virus-to-picoplankton ratio would suggest.

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Viral Lysis and Bacterivory during a Phytoplankton Bloom in a Coastal Water Microcosm

Applied and Environmental Microbiology ◽

10.1128/aem.65.5.1949-1958.1999 ◽

1999 ◽

Vol 65 (5) ◽

pp. 1949-1958 ◽

Cited By ~ 44

Author(s):

Núria Guixa-Boixereu ◽

Kristine Lysnes ◽

Carlos Pedrós-Alió

Keyword(s):

Steady State ◽

Bacterial Production ◽

Phytoplankton Bloom ◽

Decay Rates ◽

Heterotrophic Nanoflagellates ◽

Viral Production ◽

Viral Lysis ◽

Bacterial Growth Rate ◽

Bacterial Assemblage ◽

Bacterial Mortality

ABSTRACT The relative importance of viral lysis and bacterivory as causes of bacterial mortality were estimated. A laboratory experiment was carried out to check the kind of control that viruses could exert over the bacterial assemblage in a non-steady-state situation. Virus-like particles (VLP) were determined by using three methods of counting (DAPI [4′,6-diamidino-2-phenylindole] staining, YOPRO staining, and transmission electron microscopy). Virus counts increased from the beginning until the end of the experiment. However, different methods produced significantly different results. DAPI-stained VLP yielded the lowest numbers, while YOPRO-stained VLP yielded the highest numbers. Bacteria reached the maximal abundance at 122 h (3 × 107 bacteria ml−1), after the peak of chlorophyll a (80 μg liter−1). Phototrophic nanoflagellates followed the same pattern as for chlorophylla. Heterotrophic nanoflagellates showed oscillations in abundance throughout the experiment. The specific bacterial growth rate increased until 168 h (2.6 day−1). The bacterivory rate reached the maximal value at 96 hours (0.9 day−1). Bacterial mortality due to viral infection was measured by using two approaches: measuring the percentage of visibly infected bacteria (%VIB) and measuring the viral decay rates (VDR), which were estimated with cyanide. The %VIB was always lower than 1% during the experiment. VDR were used to estimate viral production. Viral production increased 1 order of magnitude during the experiment (from 106 to 107 VLP ml−1h−1). The percentage of heterotrophic bacterial production consumed by bacterivores was higher than 60% during the first 4 days of the experiment; afterwards, this percentage was lower than 10%. The percentage of heterotrophic bacterial production lysed by viruses as assessed by the VDR reached the highest values at the beginning (100%) and at the end (50%) of the experiment. Comparing both sources of mortality at each stage of the bloom, bacterivory was found to be higher than viral lysis at days 2 and 4, and viral lysis was higher than bacterivory at days 7 and 9. A balance between bacterial losses and bacterial production was calculated for each sampling interval. At intervals of 0 to 2 and 2 to 4 days, viral lysis and bacterivory accounted for all the bacterial losses. At intervals of 4 to 7 and 7 to 9 days, bacterial losses were not balanced by the sources of mortality measured. At these time points, bacterial abundance was about 20 times higher than the expected value if viral lysis and bacterivory had been the only factors causing bacterial mortality. In conclusion, mortality caused by viruses can be more important than bacterivory under non-steady-state conditions.

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Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering

Bioinformatics ◽

10.1093/bioinformatics/btl016 ◽

2006 ◽

Vol 22 (7) ◽

pp. 843-848 ◽

Cited By ~ 15

Author(s):

K. Hakamada ◽

M. Okamoto ◽

T. Hanai

Keyword(s):

Mathematical Model ◽

Dna Microarray ◽

Time Course ◽

High Dimensional ◽

Model Based Clustering ◽

Novel Technique ◽

Model Based ◽

Time Course Data

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Analysis of Approaches to Constructing a Plant Mathematical Model Based on Inaccurate Experimental Data

Vestnik MEI ◽

10.24160/1993-6982-2019-3-108-115 ◽

2019 ◽

Vol 3 (3) ◽

pp. 108-115

Author(s):

Nikita V. Skribitsky ◽

Keyword(s):

Experimental Data ◽

Mathematical Model ◽

Model Based

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Optimal control strategy for cancer remission using combinatorial therapy: A mathematical model-based approach

Chaos Solitons & Fractals ◽

10.1016/j.chaos.2021.110789 ◽

2021 ◽

Vol 145 ◽

pp. 110789

Author(s):

Parthasakha Das ◽

Samhita Das ◽

Pritha Das ◽

Fathalla A. Rihan ◽

Muhammet Uzuntarla ◽

...

Keyword(s):

Mathematical Model ◽

Optimal Control ◽

Control Strategy ◽

Optimal Control Strategy ◽

Combinatorial Therapy ◽

Model Based ◽

Cancer Remission

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A note on design-based versus model-based variance estimation in stereology

Advances in Applied Probability ◽

10.1017/s000186780001171x ◽

2002 ◽

Vol 34 (03) ◽

pp. 484-490 ◽

Cited By ~ 1

Author(s):

Asger Hobolth ◽

Eva B. Vedel Jensen

Keyword(s):

Mathematical Model ◽

Original Problem ◽

Variance Estimation ◽

Point Of View ◽

Systematic Sampling ◽

Variance Estimator ◽

Shape Model ◽

Model Based ◽

Versus Model ◽

Special Case

Recently, systematic sampling on the circle and the sphere has been studied by Gual-Arnau and Cruz-Orive (2000) from a design-based point of view. In this note, it is shown that their mathematical model for the covariogram is, in a model-based statistical setting, a special case of the p-order shape model suggested by Hobolth, Pedersen and Jensen (2000) and Hobolth, Kent and Dryden (2002) for planar objects without landmarks. Benefits of this observation include an alternative variance estimator, applicable in the original problem of systematic sampling. In a wider perspective, the paper contributes to the discussion concerning design-based versus model-based stereology.

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Light-dependent hydration of the space surrounding photoreceptors in the cat retina

Visual Neuroscience ◽

10.1017/s0952523800003047 ◽

1994 ◽

Vol 11 (4) ◽

pp. 743-752 ◽

Cited By ~ 38

Author(s):

Jian-Dong Li ◽

Victor I. Govardovskii ◽

Roy H. Steinberg

Keyword(s):

Mathematical Model ◽

Time Course ◽

Distal Portion ◽

Subretinal Space ◽

Volume Increase ◽

Physiological Event ◽

Cat Retina ◽

Interphotoreceptor Matrix ◽

Space Marker

AbstractWe have studied the effect of retinal illumination on the concentration of the extracellular space marker tetramethylammonium (TMA+) in the dark-adapted cat retina using double-barreled ion-selective microelectrodes. The retina was loaded with TMA+ by a single intravitreal injection. Retinal illumination produced a slow decrease in , which was maximal in amplitude in the most distal portion of the space surrounding photoreceptors, the subretinal space. The light-evoked decrease in was considerably slower and of a different overall time course than the light-evoked decrease in , also recorded in the subretinal space. decreased to a peak at 38 s after the onset of illumination, then slowly recovered towards the baseline, and transiently increased following the offset of illumination. It resembled the light-evoked decreases previously recorded in the in vitro preparations of frog (Huang & Karwoski, 1990, 1992) and chick (Li et al., 1992, 1994) but was considerably larger in amplitude, 22% compared with 7%. As in frog, where it was first recorded, the light-evoked decrease is considered to originate from a light-evoked increase in the volume of the subretinal space (or subretinal hydration). A mathematical model accounting for diffusion predicted that the volume increase underlying the response was 63% on average and could be as large as 95% and last for minutes. The estimated volume increase was then used to examine its effect on K+ concentration in the subretinal space. We conclude that a light-dependent hydration of the subretinal space represents a significant physiological event in the intact cat eye, which should affect the organization of the interphotoreceptor matrix, and the concentrations of all ions and metabolites located in the subretinal space.

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