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Applied and Environmental Microbiology, June 2006, p. 4440-4445, Vol. 72, No. 6
0099-2240/06/$08.00+0 doi:10.1128/AEM.00021-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Depth-Related Gradients of Viral Activity in Lake Pavin
J. Colombet,1
T. Sime-Ngando,1*
H. M. Cauchie,2
G. Fonty,1
L. Hoffmann,2 and
G. Demeure1
Laboratoire de Biologie des Protistes, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177 Aubière Cedex, France,1
CRP-Gabriel Lippmann, Cellule de Recherche en Environnement et Biotechnologies, 162a Avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg2
Received 4 January 2006/
Accepted 14 March 2006

ABSTRACT
High-resolution vertical sampling and determination of viral
and prokaryotic parameters in a deep volcanic lake shows that
in the absence of thermal stratification but within light, oxygen,
and chlorophyll gradients, host availability empirically is
prevalent over the physical and chemical environments and favors
lytic over lysogenic "viral life cycles."

INTRODUCTION
Viral activity is crucial to microbial mortality, diversity,
potential gene transfer, and lysogenic conversion in aquatic
systems (see references
18 and
19 for recent reviews). Viruses
can affect ecological processes and nutrient cycles (
23), but
this ultimately depends on whether the virus is lytic or temperate.
Studies examining large data sets have revealed that prokaryotes
form the major host reservoir for viruses in pelagic systems
(
2). Protistan grazing and viral lysis are major sources of
bacterial mortality in these systems. In general, bacterivory
dominates, but losses of bacteria from viral lysis at times
are comparable to those from protistan bacterivory (
13). In
conditions such as anoxia, bacteriolysis generally is much higher
than bacterivory based on evidence from theoretical (
12) and
empirical (
2) field investigations. In contrast to bacterivory
and lytic viral infection, which have been examined in a variety
of marine systems, only two studies have investigated the two
viral "life cycles" simultaneously, but not together with bacterivory
(
11,
21). For freshwater, one study has examined temperate phages
in the surface layer of Lake Superior (
17).
Pelagic viral ecology thus lacks studies in which potential prophage induction, lytic viral infection, and bacterivory are investigated simultaneously. In addition, most of the studies on these processes have ignored the well-known contribution of depth-related gradients as a major forcing factor in aquatic systems. Inclusion of such a contribution is needed to fully assess the potential roles of viruses for microbial food web processes and to address hypotheses that (i) in suboxic and anoxic waters the importance of lytic viral infection increases relative to bacterivory (2, 13, 20) and (ii) lysogeny increases as lytic viruses decrease with their host densities and production (21). Here we address these questions by examining the vertical distribution of the frequencies of lytically and lysogenically infected cells together with the potential bacterivory from heterotrophic nanoflagellates in a deep meromictic lake. Samples were collected in early spring, when the isothermal water column showed gradients of light, oxygen, and chlorophyll, in order to avoid false interpretations of correlations that often result from the covariation of two variables with respect to a third factor, usually temperature.
Lake Pavin is a deep (Zmax = 92 m) meromictic mountain lake located in the French Massif Central (2°56'E, 45°29'N). Samples were taken in triplicate on 20 April 2004 at the reference station (located in the middle and the deepest part of the lake), using an 8-liter Van Dorn bottle. A total of 15 depths were sampled in three distinct layers, comprising 7 depths in the mixolimnion (0.5, 5, 15, 20, 30, 40, and 50 m), 5 depths in the oxycline, (56, 57, 57.5, 58, and 59 m), and 3 depths in the anoxic monimolimnion (60, 70, and 80 m). Water temperature and dissolved oxygen were measured in situ with an Oxycal-SL 197 multiparameter probe (WWT, Limonest, France). Secchi depth (Zs) measurements were used to estimate the euphotic depth (Zeu) according to the relationship Zeu = 2.42Zs (22). Chlorophyll a concentrations were determined spectrophotometrically following extraction in 90% acetone (16). For determination of viral and bacterial abundances, subsamples were fixed with 0.02-µm-filtered buffered alkaline formalin (final concentration, 2% [vol/vol]) immediately after sampling and filtered (<15-kPa vacuum) through 0.02-µm-pore-size Anodisc filters (Whatman, Maidstone, United Kingdom). Counts were done under a Leica DC 300F epifluorescence microscope (Episcope) following staining with SYBR green I fluorochrome (Molecular Probes Europe, Leiden, The Netherlands) as described by Noble and Fuhrman (10). When not analyzed immediately, slides were stored at 20°C until counting was performed.
Bacterial production was determined by the incorporation of [3H]leucine (final concentration, 40 nM; specific activity, 71 Ci mmol1) (Amersham Biosciences, United Kingdom) into bacterial biomass by using the microcentrifuge method (9). The incubation time (30 min in situ in the dark) was fixed from preliminary experiments conducted on 25 March 2004, and protein precipitation in controls (i.e., organisms killed with 5% trichloroacetic acid) and fixed assays was aided by treatment with NaCl (final concentration, 3.5% [vol/vol]) at 18°C for 30 min. After centrifuge washings, microbial pellets were dissolved in 0.2 ml 1.2 N NaOH at 80°C for 20 min, and scintillation cocktail (1 ml) (Ready Safe; Beckman Coulter) was added for radioactivity counting with a Beckman LS 6500 liquid scintillation counter. For suboxic and anoxic samples, incubations were done in 5-ml sterile serum bottles sealed with rubber and aluminum crimp caps and flushed with N2. Leucine incorporation was converted into the number of cells produced by using conversion factors (0.27 x 1018 cells mol1 for oxic waters and 0.25 x 1018 cells mol1 for suboxic and anoxic waters) determined during preliminary experiments conducted on 25 March 2004.
For viral lytic infection, the frequency of infected cells (FIC) and the virus-induced bacterial mortality were calculated from the frequency of visibly infected cells obtained from observations under a JEOL 1200EX transmission electron microscope, following ultracentrifugation and uranyl acetate staining. The procedure is detailed elsewhere (2, 13). For each sample, mean burst size was estimated from the number of viruses in those infected cells which were filled with phages. In addition, free viruses were examined for the relative abundances of three arbitrary divided size classes based on the capsid diameter: <60, 60 to 100, and >100 nm. Viral lytic production was estimated by multiplying bacterial cell production by FIC/100 and the burst size. The frequency of lysogenically infected cells (FLC) was determined from the induction of prophages by using mitomycin C (8). Mitomycin C was added to samples (final concentration, 1 µg ml1) in 20-ml sterile serum bottles, and untreated samples served as controls. For the suboxic and anoxic samples, serum bottles were sealed with rubber and aluminum crimp caps and flushed with N2. The incubation time (24 h in situ) was fixed from a 76-hour time series preliminary experiment conducted on 25 March 2004. Subsamples were removed with syringes at 0 and 24 h and fixed with glutaraldehyde for viral and bacterial counts. FLC was estimated from viral abundances in mitomycin C-treated (VAm) and control (VAc) incubations and bacterial abundance (BAt0) and burst size (BSt0) in original samples, as follows: FLC = 100[(VAm VAc)/(BSt0 x BAt0)] (21).
Samples for enumeration of heterotrophic nanoflagellates (HNF) were fixed with glutaraldehyde (final concentration, 1%) immediately after sampling. Primulin-stained HNF collected on 0.8-µm polycarbonate black filters were counted under UV excitation using the LEICA Episcope (2, 13). Potential grazing rates of heterotrophic nanoflagellates were estimated as the product of bacterial concentration, flagellate concentration, and assumed mean clearance rate of 6.1 nl flagellate1 h1 (range, 0.7 to 11.5 nl flagellate1 h1) reported by Carrias et al. (5) for a seasonal study on Lake Pavin. These values fell within the range of values published for freshwater systems (15).
Differences between mixolimnion, oxycline, and monimolimnion were compared with standard analysis of variance. Potential relationships among variables were tested by Pearson correlation analysis. All data were analyzed after logarithmic transformations.

The vertical environment.
During the study, the isothermal water column temperature was
at about the point of maximum density (4.3°C). The water
transparency (Secchi depth = 6 m) represented half of the annual
maximum (
5), and the euphotic zone extended over one-third of
the mixolimnion (
22). Oxygen concentrations in the water column
reflected the annual range, i.e., from anoxia to 12 mg liter
1 (
2,
5). Based on these concentrations, the three layers of the
water column were characterized as oxic (O
2 concentration of
>8 mg liter
1), suboxic (O
2 concentration of between
0.5 and 8 mg liter
1), and anoxic (O
2 concentration of
between 0 and 0.5 mg liter
1), corresponding to mixolimnion
(depth of 0 to 50 m), oxycline (50 to 59 m), and monimolimnion
(60 to 92 m), respectively (Table
1; Fig.
1). Pigment concentrations
(2 to 13 µg liter
1) also reflected the typical
annual range and were related to the development of the large
diatoms
Aulacoseira italica and
Asterionella formosa, which,
during the sampling period, typically accounted for 50 to 98%
of the total phytoplankton biomass in Lake Pavin. Deep chlorophyll
a peaks in Lake Pavin, observed at depths of 40 and 57.5 m during
this study, typically are known to be the result of the sedimentation
of these diatoms (
1).

Viral size classes.
Phage polyhedral head sizes in our samples ranged from 10 to
130 nm, and tail sizes ranged from 10 to 180 nm. Tailed viruses
accounted for 75% of the total free viruses, indicating that
most of the viruses were bacteriophages. We considered this
to be conservative because they may have been nontailed bacteriophages
or tailed bacteriophages that lost their tails during ultracentrifugation
or had tails with low contrast or no contrast during the staining
procedure. Phages with head sizes of

60 nm clearly dominated
the viral community in oxygenated waters (Fig.
2), corroborating
reports from the world aquatic systems, where the size class
of 30 to 60 nm is normally dominant within the virioplankton
(
19,
24). However, this generalization is weakened here, because
the three viral size classes were about equally abundant in
hypoxic and anoxic deep waters, suggesting that the composition
of viral communities may differ markedly according to vertical
gradients in aquatic systems. For example, eukaryotic (algae,
metazooplankton, and fish) and allochthonous (from catchment
and atmosphere) viruses may be more prevalent in the mixolimnion
than in the monimolimnion of deep meromictic lakes such as Lake
Pavin.

Standing stocks.
Viral abundances (range 3
x 10
6 to 37
x 10
6 particles ml
1)
peaked in the anoxic monimolimnion and were lower than the seasonal
abundances (10
x 10
6 to 50
x 10
6 viruses ml
1) reported
by Bettarel et al. (
3) for the thermally stratified mixolimnion
of Lake Pavin. Our bacterial abundances (7
x 10
6 to 25
x 10
6 cells ml
1) were up to one order of magnitude higher than
those reported by Bettarel and coauthors (2
x 10
6 to 9
x 10
6 cells ml
1), due to the very high bacterial stock in the
monimolimnion. Compared to the seasonal values (mean = 7.1 ±
1.9) in the stratified mixolimnion of Lake Pavin (
3), our virus-to-bacterium
ratios (VBRs) (mean = 2.3 ± 0.4) were lower but similarly
varied little compared to abundances. In the Mediterranean and
Baltic Seas, low bacterial stocks in suboxic and anoxic deep
waters resulted in particularly high VBRs (up to 50) compared
to that in the surface layer (
21). The vertical distributions
of viral and bacterial abundances during our study were similar
and were negatively correlated with oxygen (Table
2; Fig.
2).
The numerical values and spatial fluctuations in the upper oxic
layer were low, followed by an exponential increase towards
the suboxic and anoxic layers. Together with the low variability
in VBR, this confirms previous indications that most of the
free viruses in the plankton were bacteriophages and that there
is a close coupling between viral and bacterial concentrations
(
2,
3). Similar vertical trends were reported for viruses in
a small eutrophic lake (
20) and for bacteria in a meromictic
lake (
7). Surprisingly high viral densities in mesopelagic and
deep marine waters (depth of up to 2,000 m) were also reported
(
6,
21). For Lake Pavin, the possibility that monimolimnic viruses
come from the surface layers is unlikely because of the chemocline
barrier and the indication from the size class analysis that
they were indigenous to the deep waters. It has been suggested
that high abundances of free viruses in deep marine waters may
be due to an increased survival rate of viruses in low-temperature
waters because viral infectivity decreased with decreasing temperature
(
21). Our empirical data do not seem to support this hypothesis,
at least for the meromictic Lake Pavin, which was isothermal
during our study. It is thus likely that biological processes,
including lytic activity and induction of prophages in conjunction
with host availability, were prevalent over the physical environment
in the viral proliferation in deep anoxic waters.
HNF cell numbers in this study (0 to 4
x 10
3 cells ml
1)
were at the lower end of the seasonal ranges (2
x 10
3 to 20
x 10
3 cells ml
1) in the thermally stratified mixolimnion
(
3) but were similar to those (0.8
x 10
3 to 2.2
x 10
3 cells
ml
1) reported during early spring in the same lake (
4).
The spatial pattern of HNF abundances clearly contrasted with
those of viral and bacterial abundances (Fig.
2). HNF peaked
in the surface, decreased with depth, and were almost absent
in the deep anoxic waters. This pattern was negatively correlated
with viral and bacterial abundances and positively correlated
with oxygen (Table
2), implying that deep anoxic conditions
excluded typical bacterivores.

Lytic viral infection versus potential bacterivory.
Inclusion of the monimolimnion layer in our study (Table
1)
resulted in higher FIC levels (7 to 79%) than the seasonal values
(5 to 40%) reported for the stratified mixolimnion of Lake Pavin
(
2). In other aquatic systems, this variable generally is <50%
(
24). Bacterial lytic mortality in the monimolimnion was about
two- and eightfold higher than those in the oxycline and mixolimnion,
respectively, and almost all the mortality in the anoxic deep
waters was through viral lysis (Fig.
3; Table
1). The same vertical
pattern was observed for the calculated viral lytic production
(Fig.
2). This implies that the high viral densities in the
monimolimnion were produced in situ. The sharp contrast observed
between the vertical patterns of viral bacteriolysis and potential
HNF bacterivory supports the idea that in environments such
as suboxic and anoxic waters, the importance of lytic viral
infection increases relative to bacterivory (
2,
13,
20). FIC
and lytic production of viruses were indeed positively correlated
with bacterial abundance and production but negatively correlated
with oxygen and HNF abundance and potential grazing (Table
2).
Increasing lytic mortality with depth has also been reported
for the anoxic deep waters of the Baltic Sea, with values up
to 71% (
21), similar to those reported here for the monimolimnion
of Lake Pavin. These values are among the highest reported for
marine and freshwater systems (
19,
24). We suggest that they
are related to the low grazing pressure and to the high host
abundance and production, perhaps of low diversity, in deep
anoxic waters.

Lysogeny versus lytic infection.
Our data suggest that a substantial proportion of bacteria in
Lake Pavin contain functional viral genomes. Mitomycin C certainly
does not induce all lysogenic bacteria and may also influence
nonlysogens, although the concentration we used is known to
induce temperate lambda phage while having only a small direct
effect on its host bacterium,
Escherichia coli (
14). It is thus
possible that our frequencies of lysogenic bacteria (range,
0.1 to 16%) are underestimates. Using the same methodological
approach, lower values (0.1 to 7.4%) were reported for the surface
layer of Lake Superior (
17). Values of up to 84% have been reported
for deep marine waters but generally are on average below 15%
in estuarine, coastal, and offshore surface waters (
21). In
contrast to other viral and bacterial variables under study,
lysogen levels were about fourfold higher in the oxic and relatively
well-illuminated mixolimnion waters than in suboxic and anoxic
waters (Table
1; Fig.
3). This indicates that the level of lysogeny,
which was significantly related to depth, apparently was not
affected by the surface light environment as expected from current
knowledge. Contrary to their original hypothesis, Tapper and
Hicks (
17) also observed higher percentages of lysogenically
infected bacteria in the surface water than in the subsurface
water of Lake Superior. In our study, the relative abundances
of lysogens were negatively correlated with bacterial abundance
and production and with FIC and viral lytic production (Table
2), supporting the hypothesis that lysogeny is a strategy for
survival of phages in environments with low host availability.
This was also recently supported by a deep profiling study in
the Mediterranean Sea, but with inversed vertical patterns compared
to our study, i.e., increasing lysogens with decreasing FIC
and the host abundance and productivity relative to depth (
21).
The relationship between the frequencies of lysogenically (
y)
and of lytically (
x) infected bacteria in this study was described
best by a power function [
y = 4.5ln(
x) + 20;
r2 = 0.65],
indicating that there are environmental characteristics, in
relation to potential host densities and availability, favoring
one of the two "viral life cycles" (
21). The contrasting vertical
patterns observed in this study and that of Weinbauer and coworkers
(
21) imply that the resource availability for phages (i.e.,
host environment) may be more important than the physical (i.e.,
temperature and light) or the chemical (i.e., O
2) environments
in favoring one of the two "viral life cycles."

ACKNOWLEDGMENTS
Jonathan Colombet was supported by a doctoral fellowship from
the Grand-Duché de Luxembourg (Ministry of Culture, High
School, and Research). The study was partly supported by the
French National Program ACI/FNS "ECCO" (VIRULAC research grant
awarded to T. Sime-Ngando).
We thank A. C. Lehours for technical and field assistance, J. Dolan for proofreading of an earlier version of the manuscript, and anonymous reviewers for helpful comments.

FOOTNOTES
* Corresponding author. Mailing address: Laboratoire de Biologie des Protistes, Université Blaise Pascal (Clermont-Ferrand II), UMR CNRS 6023, F-63177 Aubière Cedex, France. Phone: 33 4 73 40 78 36. Fax: 33 4 73 40 76 70. E-mail:
Telesphore.SIME-NGANDO{at}univ-bpclermont.fr.


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Applied and Environmental Microbiology, June 2006, p. 4440-4445, Vol. 72, No. 6
0099-2240/06/$08.00+0 doi:10.1128/AEM.00021-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.