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FEMS Microbiology Ecology 33 (2000) 89^99
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MiniReview
Bacteria in the cold deep-sea benthic boundary layer and
sediment^water interface of the NE Atlantic
Carol Turley *
Plymouth Marine Laboratory, Citadel Hill, The Hoe, Plymouth PL1 2PB, UK
Received 13 March 1999; received in revised form 26 May 2000 ; accepted 14 June 2000
Abstract
This is a short review of the current understanding of the role of microorganisms in the biogeochemistry in the deep-sea benthic boundary
layer (BBL) and sediment^water interface (SWI) of the NE Atlantic, the gaps in our knowledge and some suggestions of future directions.
The BBL is the layer of water, often tens of meters thick, adjacent to the sea bed and with homogenous properties of temperature and
salinity, which sometimes contains resuspended detrital particles. The SWI is the bioreactive interface between the water column and the
upper 1 cm of sediment and can include a large layer of detrital material composed of aggregates that have sedimented from the upper mixed
layer of the ocean. This material is biologically transformed, over a wide range of time scales, eventually forming the sedimentary record. To
understand the microbial ecology of deep-sea bacteria, we need to appreciate the food supply in the upper ocean, its packaging, passage and
transformation during the delivery to the sea bed, the seasonality of variability of the supply and the environmental conditions under which
the deep-sea bacteria grow. We also need to put into a microbial context recent geochemical findings of vast reservoirs of intrinsically labile
organic material sorped onto sediments. These may well become desorped, and once again available to microorganisms, during resuspension
events caused by deep ocean currents. As biotechnologists apply their tools in the deep oceans in search of unique bacteria, an increasing
knowledge and understanding of the natural processes undertaken and environmental conditions experienced by deep-sea bacteria will
facilitate this exploitation. ß 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights
reserved.
Keywords : Deep-sea; Decomposition ; Bacterium ; Sediment; Aggregate; Biotechnology
1. Introduction
The deep-sea represents a signi¢cant long-term sink in
the global carbon budget and can e¡ectively remove carbon for hundreds to millions of years. About 75% of the
integrated bacterial biomass from surface waters to deepsea sediments is found in the top 10 cm of sediment [1].
The bacteria in oceanic and coastal sediments constitute
around 76% (ca. 3.8U1030 ) of all global bacteria (ca.
5U1030 ) with around 13% (ca. 6.6U1029 ) of the total global fraction being found in the upper 10 cm of deep-sea
sediments [2,3].
In the NE Atlantic deep-sea benthic boundary layer
(BBL) and sediment^water interface (SWI), the temperatures are low (ca. 2³C at 4500 m), pressures high (450 atm
* Tel. : +44 (1752) 633292; E-mail : [email protected]
at 4500 m) and food is severely limiting. The deep-sea SWI
can be viewed as representing the interface comprising
both water and sediment between the £ux of materials
carried through the water column and their incorporation
within the sediment record. The BBL is the layer of water
above the SWI with homogenous temperatures and salinity [4] which, at times, is enriched with resuspended detritus through increased bottom currents [5]. This detrital or
particulate organic matter (POM) raining from the richer
productive surface layer of the ocean often forms a seasonal £u¡y layer on the SWI and is the nutritional basis
for life. For this reason, it is essential to understand the
temporal and spatial processes occurring throughout the
water column from POM production, through primary
production in surface waters, to its aggregation and transformation as it sinks to the deep-sea bed. Respiration in
the SWI is dominated by bacteria [6] and they play a
major role in the decomposition of material on the deepsea bed [7,8] being able to consume at least 13^30% of the
total biological consumption of organic carbon [9]. They
0168-6496 / 00 / $20.00 ß 2000 Federation of European Microbiological Societies. Published by Elsevier Science B.V. All rights reserved.
PII: S 0 1 6 8 - 6 4 9 6 ( 0 0 ) 0 0 0 5 8 - 1
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can respond rapidly to the arrival of material, producing
enzymes that break it down to smaller fractions, which
they can incorporate to fuel their metabolism. This process
dominates the biogeochemistry of the SWI and, therefore,
the rate and nature of what gets laid down in the sediments. Residual biogenic material provides a sedimentary
record of previous changes in ocean productivity, which
can be linked to data on climate change and previous CO2
concentrations.
Physical and biological conditions drive the fate and
residence time of this material. Important physical factors
include pressure, temperature, topography, boundary currents and advection while biological ones include degree
and timing of £ux via pelagic^benthic coupling, remineralisation, bioturbation and bioirrigation. Anthropogenic
input to the SWI will also be a¡ected by such forces.
Bacteria, which contribute the greatest biomass, hydrolytic
enzyme activity and rates of carbon turnover in this layer
[1,9,10] and contribute to all the major biogeochemical
processes (e.g. C, N, P, Mn, Fe, S, O cycling), will be
in£uenced by many of the physical and biological forcings
in the SWI and their response a¡ects the overall fate and
residence time of this material in the marine environment.
As work on the deep NE Atlantic is still relatively limited, extrapolation of results and processes found in other
marine environments may be drawn upon to highlight
areas in need of conceptual development as well as
hands-on research.
ocean [7,22]. While 10^40% of primary production may
leave the upper 100 m [20,23] of the NE Atlantic, most
gets remineralised during its decent [20,24] so that only a
few percent of the surface primary production arrives on
the deep-sea bed [20] (Fig. 2). The carbon ¢xed by primary
producers in the upper ocean is recycled to the atmosphere
within weeks. However, the carbon aggregated into sinking particles e¡ectively removes the carbon for centuries
(mid and deep waters) or millions of years (when laid
down in sediments) (Fig. 2). The £ux of particles and their
degradation during and after their decent is, therefore, of
key importance to the global carbon cycle as well as to the
delivery of food to deep-sea organisms. Particle £ux to the
sea bed can be measured, and its seasonality determined,
by sediment traps moored above the BBL (Fig. 1.4). The
seasonality of events, from surface production to arrival of
macroaggregates on the sea bed, has been captured in the
sequence of time-lapse photographs of the sea £oor at
4025 m depth in the NE Atlantic (Fig. 1.5).
Many taxa respond to this seasonal in£ux of material
such that populations of opportunist species may increase
and reproduction and growth cycles of some metazoans
may be regulated [12]. Perhaps the greatest opportunists
are bacteria re£ecting their rapid response by increased
enzyme production, DNA and protein synthesis, respiration and on occasions an increase in sediment bacterial
biomass after the seasonal in£ux of POM [1,20].
3. Life on an aggregate
2. Food supply to the deep
The supply of POM to the sea bed is the major determinant of abundance and activity of deep-sea benthic microbiota, meiofauna, macrofauna and deposit feeding
megafauna [2,10^12]. This supply of particles originates
from primary production in surface waters, such as that
seen in the satellite image in Fig. 1.1, which, in the NE
Atlantic, is mainly expressed in a phytoplankton bloom
during the spring. The macroaggregates of phytodetritus
(Fig. 1.2; commonly known as `marine snow') and faecal
pellets, which are the major components of the £ux to the
SWI, are generally produced in the upper 100 m of the
water column [13], and also exhibit strong seasonal and
diurnal variation [14]. They are comprised of a wide range
of species and sizes of living and dead phytoplankton and
zooplankton [15,16] held together by a sticky matrix of
mucopolysaccharides [17] (Fig. 1.2) produced by phytoplankton cells or mucus feeding webs of zooplankton
such as Appendicularia [18]. These sedimenting particles
also contain an enriched and active population of bacteria
(Fig. 1.3) relative to free-living bacteria [19^21] which are
grazed by bacterivorous £agellates (Fig. 1.3). Detrital material recovered from the deep-sea bed is comprised of a
similar mixture of both living and dead cells which characterised the organisms growing in the surface of the
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The aggregate microniche is recognised as an area of
nutrient enrichment containing higher concentrations of
both active and dead phototrophic and heterotrophic
planktonic cells than in the surrounding seawater [15,19].
Bacteria clearly play an important role in the remineralisation and solubilisation of the particulate organic carbon
(POC) such that many aggregates will be both formed in
the warmer euphotic zone and be recycled there. However,
many, most likely the larger, stronger ones, do escape to
the midwaters where decomposition rates may be reduced
by the cooler temperatures. Indeed, temperature variation
experienced by organisms on an aggregate can be quite
considerable. For example, temperature in the upper 20^
40 m of the NE Atlantic during summer is often around
18³C. Below this, there is an area of rapid temperature
change, the thermocline, where temperature falls to
around 12³C and then decreases gradually so that temperatures at depths of around 1000, 2000 and 4500 m are
around 5, 3 and 2³C, respectively. In addition, protein
and DNA synthesis of bacteria attached to the aggregates
in the surface waters may be drastically in£uenced by the
high pressures (100 atm every 1000 m) as well as the low
temperatures experienced during the sinking of large particles [25]. The reduced microbial activity on such particles
may contribute to the delivery of relatively undegraded
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C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
aggregates to the deep-sea bed. Molecular genetic techniques indicate that bacteria attached to oceanic macroaggregates may share few RNA types with free-living bacteria and that relatives of the attached phenotypes are
often associated with surfaces and can degrade a wide
range of polymeric compounds [26]. Attached bacteria
also tend to be substantially larger and contain more
DNA than free-living bacteria [27].
Upon arrival on the sea bed, the particulate organic £ux
can support a fast growing population of deep-sea bacteria
[7,8]. However, free-living bacterial populations change
with depth [28] and it is possible that scavenging of freeliving bacteria, which may be adapted to life in the deepsea, occurs during the decent of the particles. In addition,
phytodetrital enrichment experiments carried out under in
situ pressure and temperature show that deep-sea bacteria
associated with the SWI can respond to enrichment within
hours or days [8,29] and contribute substantially to its
decomposition. Turley and Lochte [8] found that 28% of
detrital carbon was degraded in the ¢rst 23 days after
decomposition started. The aggregates may also be resuspended into the BBL because of bottom currents and be
redeposited [5]. Whether such events stimulate or inhibit
microbial activity in the deep-sea remains unknown but
laboratory experiments on shallow water aggregates have
shown their continued suspension results in higher microbial production and respiration [30].
4. Solubilisation of POM
Bacteria produce hydrolytic enzymes prior to POM decomposition so that POM is cleaved into smaller molecules, which can support bacterial metabolism [31]. Studies
on deep-sea sediment bacterial exoenzymes indicate that
their production is regulated by the supply of substrates
and nutrients, some enzymes being induced and some repressed, but in general POM induced higher enzyme production than dissolved organic matter (DOM) [32,33], suggesting that bacteria in the SWI respond directly to the
seasonal fall of detritus. These enzymes and other measures of activity are highest in the upper 1 cm of the sediment [10] and in the overlying detrital or `£u¡' layer [34].
In continental slope sediments, glycosidase activity was
positively correlated to the £ux of phytodetritus, while
peptidase activity increased with water column depth
and reduced food availability [35]. Boetius and Lochte
[33] suggest that high peptidase activity may be indicative
of oligotrophic (food limiting) conditions. Addition of organic nitrogen resulted in signi¢cant bacterial growth and
indicated that nitrogen may be limiting growth of sediment bacteria [33]. Large additions of glucose provided
enough energy for bacterial growth presumably using sedimentary nitrogen [33]. It therefore seems that the supply
of organic nitrogen in sinking detritus will be an important
control on bacterial growth while input of labile carbon
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91
may facilitate a greater decomposition of sedimentary organic compounds [33]. These observations demonstrate the
importance of nutrient cycling (and therefore availability)
in controlling the microbial response to changes in their
environment, and the importance of enzyme production
and regulation on the survival of bacteria in the deepsea SWI [31].
Rates of POM degradation and the e¤ciency at which
this is converted into biomass depend largely on the proportion of labile material [1,8]. Under in situ pressure and
temperature, conversion e¤ciency decreases from around
50% on relatively fresh material to around 10%, with increasing age of the material and there is evidence that
deep-sea adapted bacteria are more e¡ective at degrading
the less labile material than their upper water column
counterparts [1,8]. It may not be totally surprising, therefore, that activity of an extracellular protease produced by
a bacterium isolated from 6500 m was enhanced under
high hydrostatic pressure [36], suggesting that the protease
may be adapted to the high pressure found in the deepsea. The metabolic versatility of deep-sea bacteria may,
therefore, enable the breakdown of compounds that are
unavailable to other organisms [37]. Deming and Yager [2]
compiled the few existing deep-sea sediment datasets and
found a signi¢cant relationship between both bacterial biomass and bacterial dissolved organic carbon (DOC) utilisation and vertical POC £ux. Typically, 90% of
[14 C]amino acids fed to sediment bacteria was respired
over 2^5 days, leaving the remaining small amount for
cell maintenance and growth. This can decrease to ca.
30% at high latitudes and may well be due to an increase
in both quantity and quality of the sedimenting particles
leaving more for maintenance and growth [2]. Indeed,
some seasonal increase in benthic bacterial biomass was
observed by Lochte [1] in the N Atlantic, where phytodetritus had also been observed and bacteria were seen to
double rapidly [7]. This can be attributed to a response of
the benthic bacteria to the seasonal vertical £ux of POM
[20]. Stimulation of bacterial [3 H]leucine incorporation
and enzymatic activity occurs in deep-sea sediment cores
when enriched with detritus. Furthermore, Pfannkuche [6]
compared sediment community oxygen consumption with
bacterial growth and respiration in the NE Atlantic and
found that 60^80% of the doubling in respiration between
April (before detritus arrived) and July/August (after detritus arrived) is due to microorganisms inhabiting the
SWI.
In addition, a signi¢cant positive, exponential relationship between bacterial thymidine incorporation rates (a
measure of bacterial production) and POC concentrations
was found in the NE Atlantic SWI (upper 1 cm sediment
and overlying detrital layer) [34]. When comparable data
from the Soloman and Coral Seas were superimposed on
this, the relationship held (P s 0.001). Should this relationship hold for other oceanic sediments, then prediction of
deep-sea sediment bacterial production and their role in
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early sediment diagenesis may be possible from more simple measurements of sediment or detrital POC. All of
these investigations indicate that the bacterial growth in
the deep-sea of the NE Atlantic is food-limited.
Hence, bacteria are implicated in a major way in decomposition in the deep-sea SWI. The large-scale consequences of this decomposition are produced by processes occurring at very small spatial and temporal scales. In
addition, the delivery of labile material to the sea bed is
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not homogenous but rather packaged in the form of discrete aggregates and faecal pellets. The in£uence of such
small-scale heterogenous processes and their impact on
large-scale processes on the SWI has been shown to be
important in the Norwegian^Greenland Sea [38] at depths
of ca. 1750 m but received little attention in deeper waters.
Since many of the enzymes produced by bacteria are attached to the bacterial membrane, bacteria must come in
contact with POM to hydrolyse it. There is evidence that
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C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
93
Fig. 1. 1: SeaWiFS surface colour image of the NE Atlantic on 10 May 1998 showing the development of the seasonal spring phytoplankton bloom o¡
Ireland. Chlorophyll is blue when concentrations are low, increasing through green and yellow to high concentrations at orange and red. Black is cloud
cover. Images captured and archived by the NERC Satellite Receiving Station, Dundee, and processed by the Remote Sensing Group, Plymouth Marine
Laboratory. Data courtesy of the NASA SeaWiFS Project and Orbital Science Corporation. 2: Epi£uorescent photomicrograph of a macroaggregate
from the surface waters in the NE Atlantic, showing a range of red auto£uorescing (excitation at 450^490 nm) phytoplankton cells containing chlorophyll. Scale bar = 200 Wm. Taken by Dr C. Turley. 3: Epi£uorescent photomicrograph under blue excitation (450^490 nm) of dispersed detritus collected
from the deep-sea bed at 4500 m in the NE Atlantic, stained with the DNA £uorochrome AO showing small orange rod-shaped bacteria and the larger,
yellow £uorescing bacterivorous £agellates. Scale bar = 10 Wm. Taken by Dr C. Turley. 4: Time-series of sediment trap collecting cups. The cone shape
of the trap funnels sedimenting particles into the cups which have been previously ¢lled with a preservative. The sequence of cups shown here containing settled material are from sediment traps deployed in the NE Atlantic in 1989 at 3200 and 4400 m water depth. The seasonality of sedimentation is
clearly visible and is due to the £ux of material from the increased productivity during the spring bloom in the surface waters about 4 weeks previously.
Courtesy of Dr P. Williamson, University of East Anglia. 5: `Bathysnap' time-lapse photographs of the sea bed at 4025 m depth in the NE Atlantic between 1 May and 10 August 1983. Initially, there is a progressive build-up of detrital material covering the sea bed, visible as dark patches overlying
the lighter sediment. After 14 July, there is a progressive decrease. The mound in the centre is 18 cm across. Courtesy of Dr R. Lampitt, Southampton
Oceanography Centre. 6: The Dunsta¡nage Marine Laboratory (DML) benthic lander (made by KC Denmark), which has the capability of sampling
microscale variations in pore-water chemistry in pro¢le mode or of determining benthic £uxes when ¢tted with a box core benthic chamber. Oxygen
electrodes in the chamber measure benthic community respiration. Syringes can sample water in the chamber to enable estimates of chemical benthic
£uxes (e.g. DOC and inorganic nutrients). It can be deployed on the sea bed for several days or weeks and released from the ballast weight by an
acoustically operated mechanism. A hydraulically operated shovel captures and retains the sediment for shipboard analysis and buoyancy spheres at the
top carry the entire mooring to the surface after activation of the release. The lander is 4 m high. Courtesy of Dr K. Black, DML. 7: A mega corer
(manufactured by Bowers and Connelly, Oban, a hydraulically damped multiple corer) during retrieval with eight, 10 cm internal diameter, plastic core
tubes containing relatively undisturbed deep-sea sediment cores and overlying water. The photograph was taken during May 1998 in the NE Atlantic
during a BENBO cruise during the surface water spring bloom (1) prior to the sedimentation of detritus to the sea bed. Taken by Dr C. Turley.
6
deep-sea bacteria from the SWI colonise aggregates prior
to decomposition [8]. It is likely that contact with the
bacteria-rich sediments and movement of the phytodetrital
layer may result in faster incorporation of bacteria into
the detritus. High sediment enzymatic activity has been
associated with foraminifera in the deep waters (ca. 1750
m) of the Norwegian^Greenland Sea and it has been proposed that these Protozoa may contribute signi¢cantly to
the total pool of hydrolytic enzymes [38], increasing DOM
concentrations and stimulating bacterial growth. However,
on incubating agglutinated foraminifera from the NE Atlantic in ¢ltered seawater, I have observed no increase in
enzymatic activity until after the organisms died and decomposition commenced. An alternative explanation to
the observations by Meyer-Reil and Ko«ster [38] may be
that both bacteria and foraminifera had responded to an
organic input by increasing their numbers and/or activity
[12] or that the foraminifera are grazing the dense populations of bacteria [39]. Such conjectures demand further
work on the deep-sea microbial food web and trophodynamics.
5. The sediment reservoir, resuspension and desorption
Deep-sea sediments contain a vast reservoir of organic
carbon and are a possible source of the old (4^6000 years)
refractory DOC found in deep water [40]. There are substantial gradients of DOC and dissolved inorganic carbon
(DIC) across the SWI implying their di¡usion from the
sediment to the water column [41]. However, compared
to the overlying water, the DOC in the sediment is greatly
enriched in 14 C, indicating that the DOC supplied by the
sediments to the water must be relatively young and that
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its remnant ages in the water column itself [41]. The upper
(6 1 cm) sediment microlayer at the SWI is known to
harbour the highest bacterial productivity and highest
concentration of bacteria and their enzymes [10,38,
42,43], so this is the likely region of intensive microbiological processing of the DOC di¡using from the underlying
sediment. This would also explain the DIC gradients
across this interface through intensive conversion of
DOC to DIC via bacterial respiration.
A recent study has revealed that a large proportion of
organic matter (OM) in marine sediments from ca. 650 m
water depth, is intrinsically labile material stabilised
through sorption onto mineral matrices [44]. This, presumably, makes it inaccessible to bacterial enzymatic hydrolysis. Once desorped, s 70% of the OM, having been
present in the sediment for up to 500 years, was remineralised by bacteria within 6 days [44]. Such desorption may
also occur in the deep-sea through increased particle^solute interaction during resuspension events caused by bottom currents and storms in the BBL [5]. This could make
OM available for bacterial utilisation in the BBL as well as
in the SWI once deposition reoccurs. Such desorption
events have not yet, to my knowledge, been studied in
deep-sea sediments but, should they occur, may result in
organic enrichment. This may be particularly important
during periods when there is little or no £ux of material
from surface waters and, therefore, desorped OM may act
as a food supply to bacteria in the SWI in otherwise extensive `lean' periods. The question of survival mechanisms of bacteria during these potentially long periods,
perhaps through dormancy and shifts in metabolism, remains unresolved [45]. Tantilisingly, pressure-dependent
membrane proteins and lipids have been found in isolated
barophiles from the deep-sea, which may enable the cells
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C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
to have greater substrate a¤nity when nutrient concentrations decrease [45^48].
The hydrodynamics of the BBL may therefore a¡ect the
rates of OM decomposition through mixing, resuspension
[49] and desorption of organic inputs, both of which may
in£uence colonisation of the particles and incorporation of
particles into the sediment. For example, resuspension
events in the NE Atlantic were measured by sediment
traps moored in the BBL at 4465 m, 90 m above the sea
bed, and were found to comprise of recently deposited
resuspended material and geological sediment [5]. This
was greatly enhanced during winter and was related to
near-bottom currents [5]. There is evidence that this deeper
trap received bacteria from resuspended sediments and
colonised macroaggregates and that there may be enhanced growth of these deep-sea bacteria [24].
6. Adaptation to the cold, deep ocean
The low temperature and elevated hydrostatic pressure
found in the deep NE Atlantic are only extreme to those
organisms that have not evolved there over time, e.g. those
carried there on particles and currents. The natural residents of this extensive environment are so well adapted
that many are well suited to growth at high pressure and
low temperature, many of these are barophilic (pressureloving), some of which can be obligate barophiles [50].
Barophilic bacteria have been found to play a predominant role in the turnover of radiolabelled glutamic acid in
sediment box core samples [51]. However, for bacteria
from sediment trap samples from above the BBL, highest
turnover rates were found at surface pressures implying
that barophilic bacteria do not contribute substantially
to decomposition in the deep-sea until after the particle
£ux arrives on the sea bed. Lochte and Turley [7] found
that bacterial growth rates were similar at in situ and surface pressures on naturally occurring phytodetritus recovered from the deep-sea bed. This implies that both deepsea adapted and surface-originating bacteria may play a
role in decomposition after the particle has arrived on the
deep-sea bed. Up to 3U109 cells m31 day31 can be carried
to the deep-sea bed on sedimenting particles in this region
[24]. What remains unquanti¢ed is the degree to which the
bacteria originating from surface waters on the particles
are able to contribute to decomposition in the SWI and
whether genetic exchange with indigenous deep-sea bacteria can occur [24,45]. Pressure inducible genes which pressure-acclimatise bacteria experiencing such large vertical
changes have been proposed [52]. Experimental work on
cultures implies that there may be a tendency for increased
barophily and oligotrophy with depth (synonymous with
increasing pressure and decreasing food supply) [11]. However, growth rates of deep-sea bacterial assemblages under
non-limiting nutrient conditions at in situ pressure and
temperatures are similar to those of shallow water assem-
FEMSEC 1154 21-8-00
blages [7,8,53], indicating that food resources are an important factor controlling growth.
Free-living bacterial concentrations in the BBL (ca. 0.3^
1.6U105 ml31 seawater) are several fold lower than those
in the SWI (1^5U109 ml31 sediment) [42]. Rates of bacterial thymidine incorporation in the BBL and SWI also
re£ect these sorts of di¡erence [54]. Bacteria in the SWI
are, in general, larger (some s 10 Wm long) than those in
the BBL with a greater frequency of dividing cells (per
observation). Detrital enrichment experiments, carried
out on free-living bacteria in the NE Atlantic BBL from
4500 m, under in situ pressure and temperature, showed
that their mean cell volume increased from 0.065 Wm3 to
0.231 Wm3 in 5.5 days [8] with colonisation of the detritus
very obvious. It, therefore, seems that small cell size of
free-living bacteria in the BBL may be a response to starvation and, at least, some of the population were able to
respond rapidly when food in the form of detritus became
available. It may be a valuable exercise to relate mean cell
volume to oligotrophy in the deep NE Atlantic and other
oceans but I am unaware of such a study. The e¡ects of
size reduction on cell viability and the e¡ects of other
strategies for surviving starvation, such as attachment,
are important issues in this extremely oligotrophic environment [45].
Barophilic bacterial populations also exist in the hindguts of holothurians (sea cucumbers), which feed opportunistically on phytodetritus and sur¢cal sediments. These
bacteria may convert refractory organic compounds, not
absorbed in the animal's foregut, into molecules that can
be easily taken up by the host [55].
A range of di¡erent bacterivorous micro£agellates with
a range of pressure tolerances have been isolated from
sinking particles in the NE Atlantic [56]. Even at a depth
of 4500 m, a barophilic £agellate of the genus Bodo has
been isolated [42]. It grazed bacteria growing on phytodetritus and had a growth rate of 0.3 day31 under 450 atm
and 2³C. The presence and rapid growth of these £agellates indicate that the microbial loop may well exist in the
deep-sea. Bacteria may also be an important food resource
for another important group of deep-sea organisms, the
foraminifera [12].
7. Sampling the deep-sea and methods application
One reason the data are sparse in the deep-sea is the
problem of sampling and maintaining the samples under
in situ conditions. Pressure retaining samplers for retrieving undecompressed water have been designed and operated successfully [57]. However, retrieving sediment samples in a similar fashion is a more di¤cult problem
currently requiring the use of manned submersibles or
benthic `landers' (Fig. 1.6) resulting in few, but expensive
data. A `lander' is an autonomous, unmanned vehicle that
free-falls to the sea bed and then works independently on
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C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
95
Fig. 2. A schematic diagram showing the £ux of carbon through the NE Atlantic water column to the deep-sea sediments. Amended from Dr P. Williamson [66].
the sea £oor [58]. More usually, researchers have worked
on sediments retrieved using samplers (such as the corer
seen in Fig. 1.7) where the sample gradually decompresses
during retrieval and once on board ship, are recompressed
in pressure vessels with a wide range of substrates added
(see below) to investigate microbial metabolic rate processes.
The e¡ects of decompression during retrieval have received little attention although laboratory cultures seem to
be able to withstand brief periods of compression [57].
However, Bianchi and Garcin [59] have found a decrease
in metabolic activity of deep-sea bacteria within the strati¢ed deep and warm (13³C) waters of the Mediterranean.
FEMSEC 1154 21-8-00
What seems to be most critical is maintaining the very low
temperatures characteristic of the majority of the deep-sea
(ca. 2^5³C) [37,57,60]. Once the samplers are on deck, the
samples need to be immediately removed to a constant
temperature laboratory running at in situ temperature.
In addition, all sample manipulation and incubation
must be carried out at in situ temperatures prior to incubation under in situ pressure and temperature. All these
requirements make the logistics and working conditions of
deep-sea microbiology at the very least challenging.
Bacteria in the deep-sea SWI are important in the transformation of organic material but due to their high respiration and low growth e¤ciency are often [53], but not
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C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
always [1,20], non-growing. Thus there is often, but not
always [10], a constancy of bacterial abundance [61] and
following only incremental increase in bacterial biomass is
not always an e¡ective method of determining their biogeochemical impact and can be misleading. That is, they
may be expending the majority of their energy in enzyme
production, respiration and cell maintenance rather than
increasing their cell numbers. It is essential therefore to
study a range of rate processes to get a more realistic
understanding of the role of bacteria in biogeochemical
transformations. Each method has limitations and assumptions associated with them [2,33,62] and measures a
di¡erent aspect of microbial growth but their combined
use may give a greater understanding of the microbial
contribution to OM transformation in the SWI.
Bacterial numbers and biomass can be determined by
4P6-diamidino-2-phenylindole and Acridine Orange (AO)staining epi£uorescent microscopy but a sonication and
detergent step needs to be used to free bacteria from particles [24,63]. Microbial growth rates can be estimated by
increase in bacterial counts [7] (but see caution above),
bacterial respiration and incorporation rates of dissolved
material by the [14 C]amino acid method [51,64] and remineralisation of model particulate material by 14 C-labelled
algal cells [1]. The relative contribution of bacteria to total
community respiration can be estimated from total community oxygen consumption using a benthic lander (Fig.
1.6) and bacterial respiration.
Bacterial DNA and protein synthesis in seawater and
detritus has been determined for some years by the
addition of high speci¢c activity [3 H]thymidine and
[3 H]leucine, respectively. Application of these two radioisotope techniques in seawater is now widely accepted.
However, in sediments they are the best available methods
although there are many unresolved problems in sediments
[62]. These include potential non-incorporation by subsets
of the sediment population, use of conversion factors from
incorporation to production, e¡ects of slurrying the sediment, adsorption of the label to the sediments, extraction
e¤ciency of the radiolabel and unmeasurable isotope dilution. However, there has been a recent attempt to resolve some of these problems in deep-sea calcium carbonate sediments [54].
To determine how bacteria achieve hydrolysis of the
POM, the hydrolysis of a range of model £uorogenic substrates [32,65] can be measured. For example, 4-methylcoumarinyl-7-amide-labelled leucine hydrolysis, an analogue for measuring protease activity, will be an
indicator of extracellular enzyme activity of relatively labile material. In contrast, methylumbelliferone (MUF)-labelled glucosaminide hydrolysis, an analogue for chitinaselike activity, will indicate enzymatic hydrolysis of more
refractory substrates. Similarly, MUF-labelled K- and
L-glucoside may be useful model substrates for carbohydrates which may be important components of macroaggregates arriving intact on the deep-sea bed. The ¢ndings
FEMSEC 1154 21-8-00
of Boetius and Lochte [32,33] using these methods indicate
that peptidase activity may be a useful indicator of food
supply.
The relative fraction of active, dormant and dead cells,
as with other habitats, remains unquanti¢ed in the BBL
and SWI but an important question. It is likely that, consistent with other aquatic and terrestrial environments,
only a minor fraction of deep-sea bacteria have been obtained in culture and these may not be representative. The
relative sparcity of such studies in the cold deep-sea, sampling di¤culties and the diversity of habitat found there
may make culture of a larger proportion and representative species an even greater challenge than in other habitats. There are already many examples of active bacteria
from the cold deep-sea that remain uncultured [45].
8. Outlook
In my mind there are two important areas for future
research in the cold deep-sea. Firstly, we need to understand more fully the role of microorganisms in the cycling
of OM and early diagenesis. This understanding is required on both small and large temporal and spatial
scales. For instance, we need to determine the importance
of microbial processes in the SWI and within aggregates or
animal burrows and the di¡erences in rates of microbial
processes between oceans and ocean regions of di¡erent
depth and degree of oligotrophy. We need to try to
achieve this understanding in an unobtrusive way introducing the minimal artifacts through sampling. In addition, the role of environmental conditions (e.g. seasonal
£uxes, deep-sea storms and resuspension events and interannual variations) needs to be incorporated in our understanding and conceptual and mathematical models of the
microbial role in the biogeochemistry of the deep-sea and
hence the cycling of carbon on a global scale [66].
Secondly, the deep oceans, the largest and perhaps earliest biosphere on Earth, are an enormous reservoir of
bacteria and a source of unique microorganisms that
may have evolved some 3.5 billion years ago. As yet this
wealth is largely unexplored and certainly untapped. Perhaps one of the most tantalising ideas is that through the
molecular study of deep-sea bacteria we may get an important insight into the origin of life and its evolution. For
instance, a high pressure regulated system for gene expression has been found not only in deep-sea adapted bacteria
but also in bacteria, such as Escherichia coli, adapted to
growth at atmospheric pressure and foreign to the deep
oceans. One suggestion to explain this is that the systems
developed in a high pressure environment and may be
conserved in organisms adapted to atmospheric pressure
and may indicate that life emerged from the deep-sea
[36,67], the earliest inhabitants being fueled by hydrothermal vents [68,69].
However, the future may lie in combining our new
Cyaan Magenta Geel Zwart
C. Turley / FEMS Microbiology Ecology 33 (2000) 89^99
changed perceptions of the deep-sea environment, consisting of a myriad of micro-habitats containing vast numbers
of bacteria capable of a wide range of biogeochemical
activities under `extreme' conditions, with our new found
biotechnological tools so that we will meet the challenge of
exploring more fully the oceans s 2000 m deep which,
after all, comprise about 60% of the Earth's surface.
Already, the application of molecular techniques to the
deep-sea has resulted in huge advances in our understanding of phylogenetic diversity. For example, one recent and
remarkable discovery, using rRNA sequences of marine
microbial diversity, is the importance of widespread occurrence of Archaea in the World's oceans [70]. These prokaryotes have been found to be important members of
bacterioplankton communities in the deep ocean, in cold
pelagic waters, in hydrothermal vents and in guts of deepsea deposit feeders [71,72].
The cold deep-sea has enormous biodiversity with estimates around 5^10 million species [73]. A case for high
bacterial biodiversity in deep-sea sediments due to wide
ranges in temperature, pressure and food resources has
also been proposed [45]. With such potential microbial
phylogenetic diversity, it is not surprising then that more
countries are investing substantially in both the collection
and culture of bacteria from the deep oceans to explore
and exploit their metabolic diversity through biotechnological applications [45,74] by, for example, the development of high pressure or low temperature bioreactors,
degradation of organic solvents and for producing steroids
[36,75].
[5]
[6]
[7]
[8]
[9]
[10]
[11]
[12]
[13]
[14]
[15]
[16]
Acknowledgements
This is publication Number 4 of the Thematic Research
Programme BENBO, carried out under award GST/02/
1761 from the UK Natural Environment Research Council. My thanks to those who supplied the images and to
J. Shackleford for compiling them and for typing the
manuscript.
[17]
[18]
[19]
[20]
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