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Applied and Environmental Microbiology, October 1999, p. 4451-4457, Vol. 65, No. 10
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Pelagic-Benthic Coupling of Nucleic Acids in an
Abyssal Location of the Northeastern Atlantic Ocean
A.
Dell'Anno,1
M.
Fabiano,2
M. L.
Mei,1 and
R.
Danovaro1,3,*
Institute of Marine Science, University of
Ancona, 60131 Ancona,1 Department for
the Study of the Territory and Its Resources, University of Genoa,
16132 Genoa,2 and Department of
Zoology, University of Bari, 70125 Bari,3
Italy
Received 13 May 1999/Accepted 6 August 1999
 |
ABSTRACT |
Spatial and temporal changes in sedimentary nucleic acid
concentrations in an abyssal locality of the northeastern Atlantic Ocean were investigated in relation to fluxes of nucleic acids produced
in the photic layer. Sediment trap material, collected between 1996 and
1998 at depths of 1,000, 3,000, and 4,700 m, and sediment samples were
analyzed for DNA and RNA content. Nucleic acid concentrations in the
sediments were very high and displayed significant temporal changes,
whereas mesoscale variability was low. DNA and RNA concentrations
generally displayed opposite temporal patterns, which are likely to be
dependent on the nature and characteristics of DNA and RNA molecules.
Nucleic acid fluxes were high and displayed clear seasonal changes
apparently coupled with seasonal pulses of primary production. However,
while median values of DNA fluxes were relatively similar in all
sediment traps, median values of RNA fluxes almost doubled from the
1,000- to the 4,700-m depth, suggesting differences in the metabolic
activity of microbes associated with sinking particles. Significant
relationships between DNA concentrations in the sediments and DNA
fluxes and between RNA concentrations and RNA fluxes, indicating the
presence of a clear pelagic-benthic coupling of particulate nucleic
acids, were observed. The benthic system investigated was not steady
state since we estimated that, from September 1996 to October 1998, nucleic acid concentration in the sediments decreased by about 165 mg
of DNA m
2. Vertical profiles revealed a significant
decrease in DNA concentration with depth in the sediments, reaching an
asymptotic value of about 5 µg g1. This DNA fraction
constitutes a pool of potentially refractory DNA (accounting for 16 to
40% of the total DNA pool) that might be buried in the sediments.
| |
INTRODUCTION |
Phytodetritus sinking to the sea
floor contains large amounts of living (e.g., microbial
[28]) and detrital (15, 27) DNA, and the
latter fraction accounts for the large majority of DNA pools in marine
sediments (6). In all marine environments, nucleic acids are
present in low concentrations in comparison to other organic
macromolecules, but nonetheless, detrital nucleic acids represent an
important N and P trophic source (21). This might apply, to
an even larger extent, to the deep-sea environments, where organic N,
P, and/or nucleotides may limit secondary production (5, 6).
The available information on sedimentary nucleic acid concentrations
demonstrated the presence of large amounts of DNA (about 0.5 g of
DNA m2 cm1) also in deep-sea environments
such as in the highly oligotrophic eastern Mediterranean Sea
(5). Such DNA pools (converted to carbon equivalents) were
1.3 times higher than the total benthic biomass (5). Nucleic
acid accumulation in the eastern Mediterranean Sea could be a basin
scale anomaly due to an uncoupling between input and consumption
(4) or a worldwide phenomenon in deep-sea sediments.
In general terms, the quantitative relevance of the nucleic acid
concentrations in the sediments is the result of a complex budget,
including (i) fluxes from the photic layer, (ii) inputs from
resuspension and/or lateral advection, (iii) biomass accumulation and
turnover, (iv) production of detrital DNA, (v) rate of DNA uptake by
heterotrophs, (vi) burial of the detrital DNA, and (vii) export due to
resuspension. On the other hand, information on these processes is
still too limited to fully understand pathways, dynamics, and
ecological significance of nucleic acids in marine sediments.
In the present study, we investigated DNA and RNA dynamics in abyssal
sediments of the northeastern Atlantic Ocean in order to (i) gather
information on pelagic-benthic coupling of nucleic acids and (ii)
provide quantitative estimates of DNA distribution and accumulation in
deep-sea sediments.
(This research was conducted by A. Dell'Anno in partial fulfillment of
the requirements for a Ph.D. from the University of Messina, Messina,
Italy, 1996 to 1999.)
| |
MATERIALS AND METHODS |
Study area and sampling.
Sediment sampling and trap
deployments were carried out in the Porcupine Abyssal Plain (PAP;
northeastern Atlantic Ocean, at a 4,800-m depth at 48°50.2'N,
16°29.9'W). This area is characterized by high sedimentation rates
(18) and a strong seasonality (23).
Undisturbed sediment samples were collected with a multicorer
(Maxicorer; inside diameter, 9.0 cm; depth penetration, >20 cm) in
September 1996; March, July, and October 1997; and March and October
1998. During each cruise, 4 to 10 cores were taken from four to seven
different deployments. Upon recovery, all cores were vertically divided
into nine layers of 0 to 5, 5 to 10, 10 to 20, 20 to 30, 30 to 40, 40 to 50, 50 to 60, 60 to 100, and 100 to 150 mm, and frozen at 
20°C
until analysis. For bacterial analyses, three to five replicate
subsamples (0.63 cm3) were collected in September 96 with
sterile cutoff syringes from the same cores utilized for the nucleic
acid analyses. The subsamples were fixed with filtered (0.2-µm pore
size) and sterilized seawater containing 2% buffered formalin and
stored at 4°C until later analysis (within 20 days).
Trap material was collected by using three sediment traps (PARFLUX;
surface, 0.5 m2) mounted on the same mooring line and
placed at 1,000, 3,000 and about 4,700-m depths (the deepest trap was
about 100 m above the bottom) and armed with 13 collecting
funnels. Sediment traps were deployed during four sampling periods
covering September 1996 to September 1998. Each 6-month deployment was
programmed for open and closed periods of 7 and 28 days, respectively
(generally longer in winter and shorter in spring-summer). Sediment
trap samples were fixed in situ with buffered and prefiltered formalin in order to minimize bacterial activity (9). Trap samples
were processed by the method of Heussner et al. (10). The
sediment trap material was split into eight fractions and stored in the dark until analysis.
Nucleic acid analysis in the sediments.
Before analysis,
large macroscopic organisms (macrofauna; i.e., organisms larger than
0.5 mm) were removed from the sediment. Nucleic acid extraction and
determination from sediment samples were carried out by the
spectrophotometric method described by Dell'Anno et al.
(6). Briefly, 1 g of wet sediment (three replicates) was treated with 3.0 ml of 0.5 N perchloric acid, stirred for 3 min,
and sonicated three times for 1 min (with intervals of 30 s).
Nucleic acids were hydrolyzed at 75°C for 30 min with continuous stirring. After centrifugation (3,000 × g, 10 min),
the absorbance of the total nucleic acid content (TNA) in the
supernatant was measured at 260 nm. DNA absorbance was determined with
a diphenylamine (2% in acetic acid) light-activated reaction (40 W,
12 h) at 598 nm and converted into concentration by using standard
solutions of DNA type I from calf thymus. DNA concentration was then
expressed as equivalents of absorbance at 260 nm in order to calculate
(by difference) the absorbance (ABS) due to RNA:
ABSRNA = ABSTNA ABSDNA. RNA absorbance (260 nm) was then converted into
concentration by using standard solutions of RNA type III from baker's
yeast. The interference in TNA determination due to organic and
inorganic compounds was tested on sediment subsamples, previously
treated at 100°C (2 h) and in a muffle furnace (550°C, 4 h),
respectively. Data were normalized to sediment dry weight after
desiccation (60°C, constant weight).
Nucleic acid analysis in sediment trap material.
Subsamples
(5 to 10 ml) of sediment trap material were filtered, in duplicate,
under vacuum (<100 mm Hg) onto GS-type membrane filters (0.22-µm
pore size). Particulate nucleic acid extraction was carried out by the
procedure described by Bailiff and Karl (1). The filters
were extracted in 100% acetone for 1 h at 20°C and
centrifuged, and the supernatants were discarded. The pellets were
newly resuspended in cold acetone (100%, 20°C) and extracted for
30 min at 20°C until the filters were completely dissolved (usually
two or three separate rinses were required). The samples were then
washed once with 90% acetone (4°C), once with 10% trichloroacetic
acid (TCA (4°C) and twice with 95% ethanol (4°C), and the
resulting pellet was resuspended in NH4OH. In order to
determine DNA and RNA from the same subsample, we combined spectrofluorometric DNA determination (using diaminobenzoic acid [1]) and spectrophotometric analyses for TNA (by
absorbance at 260 nm [7]). Particulate DNA
concentrations in trap samples were calculated by using a calibration
curve of calf thymus DNA and then expressed as equivalents of
absorbance at 260 nm in order to calculate (by difference) the
absorbance due to RNA as explained above.
Bacterial analyses.
For bacterial analyses, subsamples were
sonicated three times (Sonifier Branson 2200; 60 W for 1 min)
(3), diluted 100 times, stained with acridine orange
(0.01%, final concentration), and filtered on black Nuclepore
0.2-µm-pore-size filters. The filters were analyzed under
epifluorescence microscopy (3). Bacterial DNA and bacterial
RNA contribution to the total DNA and RNA pool were calculated by
assuming a conversion factor of 3.3 fg of DNA cell1
(26) and 4.2 fg of RNA cell1 (8).
These conversion factors were selected as estimated for cells of the
same average size encountered in this study. Data were normalized to
sediment dry weight after desiccation (60°C, constant weight).
| |
RESULTS |
Nucleic acid concentrations in the sediments.
Temporal changes
in DNA and RNA concentrations in the top 5 mm of the sediment and
values integrated in the whole sediment core (0 to 150 mm) are reported
in Fig. 1. In the top 5 mm of the
sediment, DNA concentrations were characterized by significant temporal
changes (analysis of variance [ANOVA], F = 9.84, P < 0.001), with the highest values in September 1996 (31.3 ± 0.6 µg g1 [mean ± standard error]) and the
lowest in March 1997 (9.5 ± 1.0 µg g1). Similar
temporal patterns were observed for DNA concentrations integrated down
to a 150-mm depth, which ranged from 2.5 ± 0.9 to 7.3 ± 2.7 µg g1 in March 1997 and September 1996, respectively.
By contrast, RNA concentrations generally showed an opposite temporal
pattern, with the highest values in July 1997 (37.9 ± 1.7 and
9.4 ± 3.9 µg g1 in the 0- to 5-mm depth and in
the integrated 0- to 150-mm depth, respectively) and the lowest in
March 1997 (9.0 ± 2.3 and 1.2 ± 0.9 µg g1
in the 0- to 5-mm depth and in the integrated 0- to 150-mm depth, respectively). DNA and RNA spatial variability on mesoscale (here defined as coefficient of variation calculated from data obtained from
sediment cores of different deployments [CV]) was low (on average,
about 10% for both parameters) (Table
1).
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FIG. 1.
Nucleic acid concentrations in the top 0 to 5 mm of
sediment and in the whole sediment core (integrated 0 to 150 mm) in the
PAP. (a) Temporal changes of DNA concentrations; (b) temporal changes
of RNA concentrations. Standard errors are shown by error bars. Data
are expressed as micrograms per gram of sediment dry weight.
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|
Vertical distributions of DNA and RNA concentrations in the sediment
core are illustrated in Fig.
2. DNA
concentrations were
characterized by a significant decrease with
increasing depth
in the sediment (ANOVA,
F = 11.8,
P < 0.001), with the highest
values in the top 0 to 5 mm of sediment
(on average for the entire
data set, 16.7 ± 3.2 µg
g
1) and the lowest values in the deepest sediment layers
(100- to
150-mm section; on average, 2.3 ± 0.7 µg
g
1). Significant differences in RNA concentrations were
observed
among sediment layers (range, 0.6 ± 0.2 to 20.2 ± 3.6 µg g
1 in the 100- to 150- and 0- to 5-mm depths of
the sediment, respectively;
ANOVA,
F = 12.1,
P < 0.001) (Fig.
2b). A detailed analysis of
the vertical patterns of
DNA during different sampling periods
revealed different shapes. Two
example cases that summarize extreme
conditions are reported in Fig
3.
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FIG. 2.
Vertical distribution of nucleic acids in the sediments.
(a) DNA distribution; (b) RNA distribution. Standard errors are shown
by error bars. Data are relative to all sampling periods and to all
depths in the sediment.
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|
Nucleic acid fluxes.
DNA and RNA concentrations determined on
trap subsamples (5 to 10 ml) were converted to nucleic acid fluxes as
follows. (i) DNA and RNA concentrations from subsamples relative to the
nucleic acid concentrations present in the total volume of the trap
cups were calculated. (ii) Total DNA and RNA concentrations were then multiplied by 2 to be reported to the surface area of 1 m2 (since the surface area of the collecting trap was 0.5 m2).
(iii) This value was divided by the number of days occurring at each
deployment (i.e., the interval between open and closed trap for each
sampling period). DNA and RNA fluxes were then expressed as micrograms
per square meter per day.
DNA flux in the PAP area was characterized by evident seasonal changes
(Fig.
4). In the trap at a depth of 1,000 m, both the
highest (172 µg m
2 day
1 in
April 1997) and the lowest (1.2 µg m
2
day
1 in December 1997) DNA fluxes were observed. On
average for the
entire sampling period, DNA fluxes were rather similar
at all
trap depths (ANOVA,
F = 3.05,
P = 0.27
[not significant]), ranging
from 30.4 ± 3.2 to 36.8 ± 5.6 µg m
2 day
1 (at 4,700- and 1,000-m depths,
respectively). Median values of
DNA fluxes for the entire sampling
period were 24.3, 25.3, and
27.3 µg m
2
day
1, respectively, at 1,000-, 3,000-, and 4,700-m
depths. RNA fluxes
showed wide seasonal changes, with the highest
values in May 1998
(194.9 µg m
2 day
1) and
the lowest in July 1998 (<0.1 µg m
2
day
1, at 1,000-m depth) (Fig.
5). On average for the entire sampling
period, RNA fluxes ranged from 35.7 ± 2.7 to 45.1 ± 3.5 µg m
2 day
1 (at 3,000- and 4,700-m depths,
respectively) and did not change
significantly between traps (ANOVA,
F = 3.05,
P = 0.65 [not significant]).
Median
values of RNA fluxes for the entire sampling period were
25.0, 33.0, and 47.3 µg m
2 day
1, respectively, at
1,000-, 3,000-, and 4,700-m depths.
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FIG. 4.
Seasonal and vertical changes in DNA fluxes at 1,000-, 3,000-, and 4,700-m depths. Standard deviations are reported. d, day.
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FIG. 5.
Seasonal and vertical changes in RNA fluxes at 1,000-, 3,000-, and 4,700-m depths. Standard deviations are reported. d, day.
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|
The two deepest traps displayed rather similar temporal patterns for
both DNA and RNA fluxes. Since there are no significant
quantitative
differences between nucleic acids fluxes at the 3,000-
and 4,700-m
depths, in this study we compared nucleic acid concentrations
in the
sediments with fluxes of nucleic acid from trap at the
3,000-m depth as
this trap displayed the more complete data
set.
In order to identify a pelagic-benthic coupling in nucleic acid
concentrations, sediment trap fluxes, integrated to 1 month
before
sediment sampling, were compared to sedimentary DNA and
RNA
concentrations. Significant relationships between DNA concentrations
in
the sediments and DNA fluxes (Fig.
6a)
and between RNA concentrations
and RNA fluxes (Fig.
6b) were observed.
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FIG. 6.
Relationships between nucleic acid fluxes at 3,000-m
depth and nucleic acids in the sediments in the six sampling periods.
Relationships between DNA concentrations and DNA fluxes (a) and
relationships between RNA concentrations and RNA fluxes (b) are shown.
d, day.
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|
Benthic bacteria.
Bacterial density in the sediments of the
PAP displayed highest values in the top 0 to 5 mm of sediment
[(3.2 ± 0.8) × 108 cells g1]
and lowest values in the 100- to 150-mm section [(0.6 ± 0.1) × 108 cells g1] (Table
2). Bacteria decreased significantly, up
to fivefold, from the upper 5-mm section to the 100- to 150-mm section.
Bacterial DNA from intact cells (as determined by epifluorescence
microscopy) accounted on average for 4% of the total sedimentary DNA
pools, showing limited variations along the sediment core (range, 1.8 to 6.8% in the 50- to 60- and the 60- to 100-mm sections,
respectively) (Table 2). By contrast, bacterial RNA accounted on
average for about 12% of the total RNA pool, and its importance
increased irregularly with increasing depth in the sediment core (Table 2).
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TABLE 2.
Vertical distribution of bacterial density, bacterial DNA
and RNA concentrations, and their relative contributions to the nucleic
acid pools in sediments collected in September 1996
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|
| |
DISCUSSION |
Nucleic acid concentrations in the PAP sediments.
Previous studies have shown that nucleic acid concentrations in the
sediments might vary according to changes in environmental conditions
and that higher sedimentary nucleic acid values are generally observed
in highly productive systems (5). Sedimentary DNA
concentrations reported in this study were high (ranging from 9.5 to
31.3 µg g1 in the top 0 to 5 mm of sediment) when
compared to literature data (summarized previously
[5]), indicating that this abyssal system shares
trophic conditions (i.e., organic matter accumulation) typical of
continental shelf environments. Also, RNA concentrations in the PAP
area were extremely high and comparable to those found in highly
productive systems (such as upwelling area and locations characterized
by the presence of a Posidonia bed [3]) and
about four times higher than those reported in highly oligotrophic
bathyal sediments of the Cretan Sea (5).
DNA and RNA concentrations in PAP sediments showed significant temporal
changes, whereas spatial variability of both DNA and
RNA concentrations
on mesoscale was low. Therefore, it is likely
that the observed
temporal patterns cannot be explained with spatial
heterogeneity of DNA
and RNA
pools.
DNA and RNA concentrations generally displayed opposite temporal
patterns that are likely to be dependent on the nature and
characteristics of the DNA and RNA molecules. In fact, DNA is
subjected
to lower turnover (
13) and longer degradation rates
than RNA
(
20). In this regard, RNA concentrations in the PAP
area
showed similar temporal patterns reported for bacterial secondary
production (measured as [
3H]leucine uptake rates),
determined synoptically in the same sediments
(
24). These
results suggest that RNA concentrations reflect
changes in bacterial
metabolic activity, which in turn is induced
by pulses of organic
matter sedimentation (
29).
Previous studies carried out on deep-sea sediments of the eastern
Mediterranean Sea clearly demonstrated that DNA pools were
largely
unaccounted for by DNA associated with living biomass
(detrital DNA
represented about 90% of the total DNA pool [
5]).
Accordingly, in PAP sediments, bacterial DNA accounted for a
quasinegligible
fraction of the total DNA pool (on average, 4%). Since
bacteria
in the PAP sediments display limited temporal changes
(
22),
the concentrations and temporal changes of DNA pools
in the investigated
abyssal sediments are apparently independent of
bacterial dynamics.
As far as RNA concentrations are concerned, reports
of previous
studies of the oligotrophic eastern Mediterranean Sea
indicated
that bacteria alone accounted for about 26% of the total RNA
pool
(
5), whereas in the PAP sediments, bacterial RNA, with
the
same conversion factor, accounted for about 12%. This is not
surprising
since (i) bacteria contribute to a larger fraction of the
total
benthic biomass in oligotrophic than in eutrophic systems
(
3,
4) and (ii) detrital nucleic acids might represent a
more important
organic source to bacteria in food-limited than in
food-rich environments
(
5). Data reported here are in
agreement with these hypotheses,
indicating that the microbial loop
(reported here in terms of
bacterial capability to recycle detrital
organic compounds otherwise
lost to the benthic food webs) might play a
much more important
role in nucleic acid dynamics in oligotrophic
deep-sea sediments
than in more productive systems, such as the PAP
area.
Nucleic acid fluxes and pelagic-benthic coupling in nucleic acid
concentrations.
Previous studies have shown that large amounts of
DNA and RNA may be supplied to the benthos from particle sedimentation
(1, 11, 12, 28). Temporal changes in DNA concentrations in
deep-sea sediments have been hypothesized to be related to DNA inputs
from the photic layer (5), but a direct pelagic-benthic
coupling between nucleic acid fluxes and nucleic acid concentrations in the sediments has never been demonstrated. In the PAP area, nucleic acid fluxes were high and displayed clear seasonal fluctuations apparently coupled with seasonal pulses of primary production (23). However, while median values of DNA fluxes were
relatively constant in all sediment traps, median values of RNA fluxes
almost doubled from 1,000- to 4,700-m depths, suggesting an increased microbial metabolic activity associated with particles during sinking.
These results might suggest that RNA fluxes are subjected, more than
DNA, to changes related to microbial growth and colonization of the
settling particles.
The relationships between nucleic acid concentrations in the sediments
and nucleic acid vertical fluxes indicate the presence
of a clear
pelagic-benthic coupling. Such relationships are not
spurious, as DNA
and RNA concentrations followed opposite temporal
patterns and provide,
to our knowledge, the first direct evidence
on the relationships
between changes of sedimentary nucleic acid
concentrations and nucleic
acid inputs from the photic
layer.
Assuming that measured DNA fluxes represent the input of DNA to the
benthos, we tentatively estimated the amount of DNA utilized
by benthic
heterotrophs. In about 2 years (from September 1996
to September 1998),
24 mg of DNA m
2 reached the sediments through particulate
fluxes. In the absence
of heterotrophic uptake, this input of DNA would
accumulate in
the sediments, but, conversely, DNA concentrations in the
0- to
150-mm sediment layer decreased (from September 1996 to October
1998) to about 141 mg of DNA m
2. Given the low
contribution of living biomass to the total sedimentary
DNA pool, DNA
decrease could be dependent upon a progressive utilization
of detrital
DNA by benthic heterotrophs. Since total organic carbon
flux was low
when compared to measurements in situ of CO
2 and
dissolved
organic carbon release by benthic activities (
14),
the
utilization of labile compounds (such as detrital DNA) would
represent
an important trophic source to sustain benthic metabolic
requirements.
The total amount of DNA potentially removed from
the system during the
study period was equivalent to 165 mg of
DNA m
2. This
result suggests that detrital DNA is utilized by deep-sea
benthic
organisms, but the pathway of utilization (as nucleotides
or N and P
source) and turnover rates of sedimentary DNA pools
are as yet
unknown.
Vertical distribution of nucleic acid concentrations in the PAP
sediments.
Vertical profiles of DNA and RNA concentrations
revealed a significant decrease with depth in the sediments. This is
obvious and expected since most benthic parameters follow similar
patterns and there are no reasons for enhanced nucleic acid synthesis
in deeper sediment layers. Since living biomass accounted for an almost
negligible fraction of the total sedimentary DNA pool, vertical
distribution of DNA is likely to be dependent on three main factors:
(i) quantity of the DNA reaching the seafloor, (ii) sediment mixing,
and (iii) DNA utilization rates along the sediment core. In all
sampling periods, DNA concentrations in deeper sediment layers seem to
reach an asymptotic value of about 5 µg g1. Mayer
(17), describing vertical distribution of organic carbon in
marine sediments, assumed this asymptotic value to represent the
refractory fraction throughout the sediment core. Since extracellular DNA bound to mineral particles and to highly refractory organic compounds (i.e., humic acids) is resistant to DNase degradation (2, 16, 25), such a DNA fraction recalcitrant to enzymatic degradation (i.e., refractory DNA) might persist in the sediments (19).
Refractory DNA in the top sediment layer would account, depending upon
the different seasons and ecological conditions, for
16 to 40% of the
total DNA pool (in September 1996 and March 1998,
respectively).
Available data are too limited to draw general
conclusions, but the
different contributions of the refractory
DNA fraction in the two
periods are likely to be related to the
increasing time lag between DNA
input in the sediments and sediment
collection and/or different
utilization rates of detrital DNA
in different periods. Further studies
are needed to fully understand
the bioavailability and pathways of
detrital DNA utilization in
marine
sediments.
| |
ACKNOWLEDGMENTS |
This research has been undertaken in the framework of the
BENGAL programme. We acknowledge the support from 60% of
University of Bari and the European Commission's Marine Science
and Technology Program (MAST III) under contract MAS3-CT-950018.
Two anonymous referees contributed to improve the quality of the manuscript.
| |
FOOTNOTES |
*
Corresponding author. Mailing address: Institute of
Marine Science, University of Ancona, Via Brecce Bianche, 60131 Ancona, Italy. Phone: 39 71 220 4654. Fax: 39 71 220 4650. E-Mail:
danovaro{at}popcsi.unian.it.
| |
REFERENCES |
| 1.
|
Bailiff, D. M., and D. M. Karl.
1991.
Dissolved and particulate DNA dynamics during a spring bloom in the Antarctic Peninsula region, 1986-87.
Deep-Sea Res.
38:1077-1095.
|
| 2.
|
Blum, S. A. E.,
M. G. Lorenz, and W. Wackernagel.
1997.
Mechanisms of retarded DNA degradation and prokaryotic origin of DNases in non-sterile soil.
Syst. Appl. Microbiol.
20:513-521.
|
| 3.
|
Danovaro, R.,
N. Della Croce, and M. Fabiano.
1993.
Labile organic matter and microbial biomasses in deep-sea sediments (E-Mediterranean).
Deep-Sea Res.
40:953-965.
|
| 4.
|
Danovaro, R.,
A. Dell'Anno, and N. Della Croce.
1997.
Lack or evidence for a pelagic-benthic coupling in the Eastern Mediterranean Sea?
Mediterr. Target Project Newsl.
5:14-15.
|
| 5.
|
Danovaro, R.,
A. Dell'Anno,
A. Pusceddu, and M. Fabiano.
1999.
Nucleic acid concentrations (DNA, RNA) in the continental and deep-sea sediments of the eastern Mediterranean: relationships with seasonally varying organic inputs and bacterial dynamics.
Deep-Sea Res.
46:1077-1094.
|
| 6.
|
Dell'Anno, A.,
M. Fabiano,
G. C. A. Duineveld,
A. Kok, and R. Danovaro.
1998.
Nucleic acid (DNA, RNA) quantification and RNA/DNA ratio determination in marine sediments: comparison of spectrophotometric, fluorometric and high-performance liquid chromatography methods and estimation of detrital DNA.
Appl. Environ. Microbiol.
64:3238-3245[Abstract/Free Full Text].
|
| 7.
|
Fabiano, M.,
P. Povero, and R. Danovaro.
1996.
Particulate organic matter composition in Terra Nova Bay (Ross Sea, Antarctica) during summer 1990.
Antarct. Science
8:7-13.
|
| 8.
|
Fuhrman, J. A., and F. Azam.
1982.
Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters: evaluation and field results.
Mar. Biol.
66:109-120.
|
| 9.
|
Gardner, W. D.,
K. R. Hinga, and J. Marra.
1983.
Observation on the degradation of biogenic material in the deep ocean with implication on accuracy of sediment trap fluxes.
J. Mar. Res.
41:195-214.
|
| 10.
|
Heussner, S.,
C. Ratti, and J. Carbenne.
1990.
The PPS 3 time-series sediment trap and the sample processing technique used during the ECOMARGE experiment.
Continental Shelf Res.
10:943-958.
|
| 11.
|
Karl, D. M., and G. A. Knauer.
1984.
Vertical distribution, transport, and exchange of carbon in the northeast Pacific Ocean: evidence for multiple zones of biological activity.
Deep-Sea Res.
31:221-243.
|
| 12.
|
Karl, D. M., and G. A. Knauer.
1984.
Detritus-microbe interactions in the marine pelagic environment: selected results from the vertex experiment.
Bull. Mar. Sci.
35:550-565.
|
| 13.
|
Karl, D. M., and J. A. Novitsky.
1988.
Dynamics of microbial growth in surface layers of a coastal marine sediment ecosystem.
Mar. Ecol. Prog. Ser.
50:169-176.
|
| 14.
|
Lampitt, R. S.
1998.
BENGAL Workshop Gif Sur Yvette (France) 26-28 October.
Personal communication.
|
| 15.
|
Lochte, K., and C. M. Turley.
1988.
Bacteria and cyanobacteria associated with phytodetrituts in the deep-sea.
Nature
333:67-69.
|
| 16.
|
Lorenz, M. G., and W. Wackernagel.
1987.
Adsorption of DNA to sand and variable degradation rates of adsorbed DNA.
Appl. Environ. Microbiol.
53:2948-2952[Abstract/Free Full Text].
|
| 17.
|
Mayer, L. M.
1989.
The nature and determination of living sedimentary organic matter as food source for deposit-feeders, p. 98-113.
In
G. Lopez, G. Tagon, and J. Levinton (ed.), Ecology of marine deposit-feeders, lecture notes on coastal and estuarine studies. Springer-Verlag, New York, N.Y.
|
| 18.
|
Newton, P. R.,
R. S. Lampitt,
T. D. Jickells,
P. King, and C. Boutle.
1994.
Temporal and spatial variability of biogenic particle fluxes during the JGOFS NE Atlantic Process studies at 47°N 20°W.
Deep-Sea Res.
41:1617-1642.
|
| 19.
|
Nielsen, K. M.,
A. M. Bones,
K. Smalla, and J. D. van Elsas.
1998.
Horizontal gene transfer from transgenic plants to terrestrial bacteria a rare event.
FEMS Microbiol. Rev.
22:79-103[Medline].
|
| 20.
|
Novitsky, J. A.
1986.
Degradation of dead microbial biomass in a marine sediment.
Appl. Environ. Microbiol.
52:504-509[Abstract/Free Full Text].
|
| 21.
|
Paul, J. H.,
W. H. Jeffrey, and M. F. DeFlaun.
1987.
Dynamics of extracellular DNA in the marine environment.
Appl. Environ. Microbiol.
53:170-179[Abstract/Free Full Text].
|
| 22.
|
Patching, J. W.
1998.
BENGAL Workshop Gif Sur Yvette (France) 26-28 October.
Personal communication.
|
| 23.
|
Rice, A. L.,
M. H. Thurston, and B. J. Bett.
1994.
The IOSDL DEEPSEAS programme: introduction and photographic evidence for the presence and absence of a seasonal input of phytodetritus at contrasting abyssal sites in the northeastern Atlantic.
Deep-Sea Res.
41:1305-1320.
|
| 24.
|
Rice, A. L.
1998.
High resolution temporal and spatial study of the benthic biology and geochemistry of a north-eastern atlantic abyssal locality, p. 1-130.
In
Annual Report BENGAL. Southampton Oceanography Centre, Southampton, England.
|
| 25.
|
Romanowski, G.,
M. G. Lorenz, and W. Wackernagel.
1991.
Adsorption of plasmid DNA to mineral surfaces and protection against DNase I.
Appl. Environ. Microbiol.
57:1057-1061[Abstract/Free Full Text].
|
| 26.
|
Simon, M., and F. Azam.
1989.
Protein content and protein synthesis rates of planktonic bacteria.
Mar. Ecol. Prog. Ser.
51:201-213.
|
| 27.
|
Turley, C. M., and K. Lochte.
1990.
Microbial response to the input of fresh detritus to the deep-sea bed.
Paleogeog. Paleoclim. Paleoecol. (Global and Planetary Change Section)
89:3-23.
|
| 28.
|
Turley, C. M., and P. J. Mackie.
1995.
Bacterial and cyanobacterial flux to the deep NE Atlantic on sedimenting particles.
Deep-Sea Res.
42:1453-1474.
|
| 29.
|
Van Duyl, F. C., and A. J. Kop.
1994.
Bacterial production in North Sea sediments: clues to seasonal and spatial variations.
Mar. Biol.
120:323-337.
|
Applied and Environmental Microbiology, October 1999, p. 4451-4457, Vol. 65, No. 10
0099-2240/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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Abstract
Introduction
