Contrasting degradation rates of natural dissolved organic carbon by deep-sea prokaryotes under stratified water masses and deep-water convection conditions in the NW Mediterranean Sea
Introduction
The deep sea, below 1000 m, is one of the largest ecosystems and the largest biome on Earth, yet it is the least well studied and sampled. It is a microbially dominated environment, where prokaryotes drive the most important biological processes. It is characterized by high-hydrostatic pressure, low temperature, high nutrient concentrations and low dissolved organic carbon content (around 33–45 μMC) (Nagata et al., 2010). The main source of carbon and energy is organic matter produced in the euphotic layer and transferred to depth by different processes (Boyd et al., 2019; Dall'Olmo et al., 2016; Hansell et al., 2009; Levy and Martin, 2013; Siegel et al., 2016). Hence, carbon dioxide and inorganic nutrients are converted by photosynthesis into particulate (POC) and dissolved organic carbon (DOC) in the euphotic zone, and transferred to the deeper ocean by various mechanisms including winter deep convection (Copin-Montégut and Avril, 1993), subduction (Sohrin and Sempéré, 2005; Aristegui et al., 2009; Burd et al., 2010; Hansell, 2009), fragmentation of large aggregates into small particles (Briggs et al., 2020), dissolution of sinking particles (Follett et al., 2014; Smith et al., 1992) and the vertical migration of zooplankton with release of POC/DOC by exudation and defecation (Steinberg et al., 2000; Steinberg and Landry, 2017).
DOC concentration decreases with depth (Hansell et al., 2009) and can be divided into two reservoirs of different biological lability: labile-DOC and recalcitrant DOC (Hansell et al., 2009; Carlson and Hansell, 2015). The recalcitrant fraction can be further divided in semi-labile, semi-refractory, refractory and ultra-refractory DOC (Hansell, 2013). Semi-labile DOC accumulates in the surface ocean where DOC production exceeds DOC consumption, and is transferred in the dark ocean where consumption exceeds production (Carlson et al., 1994; Carlson and Ducklow, 1996; Carlson and Hansell, 2015). However, turnover times for semi-labile DOC are largely unconstrained, and the contribution of semi-labile DOC to global prokaryotic heterotrophic production is hard to quantify (Carlson, 2002; Carlson and Hansell, 2015). From a chemical point of view, a major portion of surface high-molecular-weight-DOC (HMW-DOC) is composed of carbohydrates (acyl-polysaccharides) that have remarkably conservative spectrometric and chemical properties throughout the global ocean (Aluwihare et al., 1997; Benner et al., 1992; Repeta, 2015).
Heterotrophic prokaryotes are one of the main actors of the carbon cycle in marine ecosystems. They i) consume 10 to 50% organic matter produced by primary production in the surface waters (Azam et al., 1983), ii) facilitate particle solubilization (Aristegui et al., 2009; Cho and Azam, 1988; Panagiotopoulos et al., 2002; Sempéré et al., 2000; Tamburini et al., 2009b), iii) produce semi-labile DOC from labile DOC ( ranged 0.1 to 0.2 Gt C yr−1) (Fang et al., 2015; Jiao et al., 2010; Tamburini et al., 2003) and finally, iv) account for a large part of heterotrophic respiration in open ocean ( 20–33.3 Gt C yr−1) (Arístegui, 2003; del Giorgio et al., 1997). However, there are still significant gaps in our knowledge of prokaryotic processes that control transformation, and degradation of the organic matter in the deep sea.
Most studies of DOC degradation have targeted the labile fraction and used simple compounds coupled with radioelements or fluoregenic substrate analogs to measure uptake and turnover time (Hoppe and Ullrich, 1999; Koike and Nagata, 1997; Tamburini et al., 2009a; Tamburini et al., 2002; Teira et al., 2006a, Teira et al., 2006b). As such very little is known about the degradation of semi-labile or semi-refractory DOC fractions. In addition, most studies have not taken into account the effect of hydrostatic pressure, which is a major parameter acting on prokaryotic metabolisms (Tamburini et al., 2013a). One of the few studies of semi-labile DOC degradation under pressure was made by Boutrif et al. (2011) who used radiolabeled exopolysaccharides (3H-EPS) as a proxy semi-labile DOC and incubated their samples under in situ high-pressure conditions. Using this approach, Boutrif and colleagues were able to show (i) an increase with depth of specific-cell activity assimilating 3H-EPS and (ii) a high contribution of Euryarchaeota in driving the degradation of 3H-EPS in the deep-sea waters of the Mediterranean Sea.
The phylogenetic composition and metabolic capabilities of marine microbial communities change with depth (Delong et al., 2006; Nagata et al., 2010), as does metabolic capabilities of the microbial communities that regulate carbon export (Giovannoni and Stingl, 2005; McCarren et al., 2010). Delong et al. (2006) identified a great number of genes, putatively involved in polysaccharide degradation, in deep microbial populations compared to those found in the surface. More recently, using comparative metaproteomics, Bergauer et al. (2018) found that deep-sea microorganisms produce transporters not only for substrate such as amino acids and carbohydrates, but also for osmolytes. These osmolyte transporters increase with depth, reaching 39% of protein sequences identified in the bathypelagic zone. Recently, Saw et al. (2020) described the enzymatic repertoire of resident mesopelagic and bathypelagic SAR202 that appear to favor remineralization of recalcitrant DOC. Moreover, under high hydrostatic pressure, piezophile deep-sea microorganisms display unique metabolisms (Lauro and Bartlett, 2008; Vezzi et al., 2005). As an example, piezophilic Photobacterium profondum SS9 have shown its ability to degrade complex organic matter. The regulation of metabolic pathways for the degradation of different polymers such as chitin, pullulan, and cellulose is controlled by pressure, being activated at 28 MPa and turned off at 0.1 MPa (Vezzi et al., 2005). Fieldwork investigation using 3H-labeled extracellular polymeric substance labeled (3H-EPS), done at in situ high pressure conditions, showed that prokaryotes increased their ability to use 3H-EPS with depth (Boutrif et al., 2011).
The Mediterranean Sea is a semi-enclosed sea, with a deep warm temperature (~13 °C), and very short ventilation and residence times for deep waters of ~70–126 years (Schlitzer et al., 1991). The NW Mediterranean Sea is one of the few regions in the world's ocean where both dense shelf water cascading and open-sea convection take place (Canals et al., 2006; Durrieu de Madron et al., 2017; Durrieu de Madron et al., 2011; Mertens and Schott, 2002; Santinelli et al., 2010; Tamburini et al., 2013b). These sinking water masses carry POC and DOC, as well as significant numbers of organisms from the surface layer into the deep sea (Avril, 2002; Marshall and Schott, 1999; Martín et al., 2010; Testor and Gascard, 2006; Vidal et al., 2009; Santinelli et al., 2010; Santinelli, 2015). Depending on the preconditioning phase different volumes of surface water are exported (in a more cold and dry winter, more water will sink; Durrieu de Madron et al., 2017), driving a larger amount of dissolved oxygen, semi-labile DOC (Canals et al., 2006; Lefèvre et al., 1996; Santinelli, 2015; Santinelli et al., 2010; Powley et al., 2017) and surface-prokaryotic communities (Luna et al., 2016; Severin et al., 2016; Tamburini et al., 2013a) from surface to deep-sea layers.
This paper investigates the utilization of HMW-DOC on the short temporal scale (10–15 days) by deep-sea prokaryotes maintained at in situ high-pressure conditions. Deep-sea prokaryotic natural assemblages were collected in the Mediterranean Sea in two contrasting hydrological conditions including water column stratification and deep-water formation period conditions. Here, the experimental results were coupled with a cell-quota model (Droop, 1968), in order to quantify the kinetics of HMW-DOC degradation and its impact on the prokaryotic assemblages under these two contrasting hydrological conditions.
Section snippets
Recovering and preparation of HMW-DOC
HMW-DOC was obtained from seawater that was drawn from the 600 m depth at the Natural Energy laboratory of Hawaii Authority NEHLA (19° 43′ 42.7“N; 156° 03’ 33.2” W) in December 2003. Samples were filtered in-line, and the <0.2 μm fraction concentrated using a custom crossflow ultrafiltration system fitted with a GE-osmonics “GE series” membrane. The membrane has a pore size of ~1 nm and nominally retains organic matter of molecular weight > 1 kDa (>99% rejection of vitamin B12 in laboratory
Bulk and molecular composition characteristics of HMW-DOC throughout the experiment
At 2000 m-depth, DOC concentration significantly increased from 42 μM in December 2009, prior to a deep-water convection period, to 63 μM in March and 72 μM in May 2010 when the new deep water mass occupied the ANTARES site, concurrently with higher oxygen concentration in the bottom waters between March and mid-June 2010 (see for details Tamburini et al., 2013a and Durrieu de Madron et al., 2017). The in situ DOC concentrations for Strat. and Conv. experiments were 42 and 72 μM, respectively;
HMW-DOC compositional changes during degradation
The monosaccharide composition of the samples after addition of HMW-DOC (samples retrieved at 2000 m at DEC and HP conditions) resembled that generally reported for deep waters (Table 1) (Kaiser and Benner, 2008; Panagiotopoulos et al., 2014; Skoog and Benner, 1997). Our results showed distinct differences in the initial and final sugar composition during the biodegradation experiments for both Strat. and Conv. conditions (Table 1). This finding was more pronounced for glucose (45% decrease of
Conclusion and perspectives
Our results demonstrate that the degradation of DOC under stratified and deep convective mixing conditions depends on the origin and the history of the prokaryotic communities, which were controlled by the origin of the water masses in the NW Mediterranean Sea. Depending on the hydrological conditions, the proportion of allochthonous and autochthonous prokaryotes in deep-sea microflora can vary, with surface bacteria increasing in deep-sea waters during deep-sea convection (Luna et al., 2016;
Declaration of Competing Interest
None.
Acknowledgments
This research is endorsed by the national French program MERMEX and funded by the National Research Agency under the grant POTES [grant number ANR ANR-05-BLAN-0161-01, 2007] and the French LEFE-Cyber program [DORADE project]. Part of the equipment used in this work was funded by European Regional Development Fund (ERDF). The project associated to this publication has received funding from European ERDF Fund under project 1166-39417. This work is a contribution to the Mediterranean Institute of
References (109)
DOC dynamics in the northwestern Mediterranean Sea (DYFAMED site)
Deep Sea Res. Part II Top. Stud. Oceanogr.
(2002)- et al.
Assessing the apparent imbalance between geochemical and biochemical indicators of meso- and bathypelagic biological activity: what the @$♯! is wrong with present calculations of carbon budgets?
Deep Sea Res. Part II Top. Stud. Oceanogr.
(2010) Production and removal processes
- et al.
DOM sources, sinks, reactivity, and budgets
- et al.
Vertical distribution and temporal variation of dissolved organic carbon in the North-Western Mediterranean Sea
Deep Sea Res. Part I Oceanogr. Res. Pap.
(1993) - et al.
Comparison of Niskin vs. in situ approaches for analysis of gene expression in deep Mediterranean Sea water samples
Deep Sea Res. Part II top. Stud. Oceanogr
(2016) - et al.
An investigation of the physiology and potential role of components of the deep ocean bacterial community (of the NE Atlantic) by enrichments carried out under minimal environmental change
Deep Sea Res. Part I Oceanogr. Res. Pap.
(2012) - et al.
A novel protocol for determining the concentration and composition of sugars in particulate and in high molecular weight dissolved organic matter (HMW-DOM) in seawater
Mar. Chem.
(2011) - et al.
Biochemical composition and size distribution of organic matter at the Pacific and Atlantic time-series stations
Mar. Chem.
(2009) - et al.
High potential activity of extracellular alkaline phosphatase in deep waters of the Central Pacific
Deep Sea Res. Part II Top. Stud. Oceanogr.
(1997)
Is DOC the main source of organic matter remineralization in the ocean water column?
J. Mar. Syst.
Major biochemical composition of dissolved high molecular weight organic matter in seawater
Mar. Chem.
Distribution and composition of dissolved and particulate organic carbon in northern San Francisco Bay during low flow conditions
Estuar. Coast. Shelf Sci.
Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry, and genomics
Deep Sea Res. Part II Top. Stud. Oceanogr.
Sub-ambient temperature effects on the separation of monosaccharides by high-performance anion-exchange chromatography with pulse amperometric detection - application to marine chemistry
Journal of Chromatography A. pp
Composition and distribution of dissolved carbohydrates in the Beaufort Sea Mackenzie margin (Arctic Ocean)
Mar. Chem.
Chemical characterization and cycling of dissolved organic matter
Biodegradation of Emiliania huxleyi aggregates by a natural Mediterranean prokaryotic community under increasing hydrostatic pressure
Prog. Oceanogr.
DOC in the Mediterranean Sea
DOC dynamics in the meso and bathypelagic layers of the Mediterranean Sea
Deep. Res. Part II Top. Stud. Oceanogr.
Influence of stratification on marine dissolved organic carbon (DOC) dynamics: the Mediterranean Sea case
Prog. Oceanogr.
Chlorofluoromethane and oxygen in the eastern Mediterranean
Deep Sea Res. Part A. Oceanogr. Res. Pap.
Zooplankton vertical migration and the active transport of dissolved organic and inorganic carbon in the Sargasso Sea
Deep Sea Res. Part I Oceanogr. Res. Pap.
Biopolymer hydrolysis and bacterial production under ambient hydrostatic pressure through a 2000 m water column in the NW Mediterranean
Deep Sea Res. Part II Top. Stud. Oceanogr.
Distribution and activity of Bacteria and archaea in the different water masses of the Tyrrhenian Sea
Deep Sea Res. Part II Top. Stud. Oceanogr.
Effects of hydrostatic pressure on microbial alteration of sinking fecal pellets
Deep Sea Res. Part II Top. Stud. Oceanogr.
Mediterranean Sea response to climate change in an ensemble of twenty first century scenarios
Clim. Dyn.
A major biopolymeric component to dissolved organic carbon in surface sea water
Nature.
Respiration in the dark ocean
Geophys. Res. Lett.
Microbial oceanography of the dark ocean’s pelagic realm
Limnol. Ocean.
Dilution limits dissolved organic carbon utilization in the deep ocean
Science (80-. )
The ecological role of water-column microbes in the sea
Mar. Ecol. Prog. Ser.
Bulk chemical characteristics of dissolved organic matter in the ocean
Science (80-. )
Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics
Proc. Natl. Acad. Sci. U. S. A.
Assimilation of marine extracellular polymeric substances by deep-sea prokaryotes in the NW Mediterranean Sea
Environ. Microbiol. Rep.
Multi-faceted particle pumps drive carbon sequestration in the ocean
Nature
Major role of particle fragmentation in regulating biological sequestration of CO2 by the oceans
Science
Flushing submarine canyons
Nature
Growth of bacterioplankton and consumption of dissolved organic carbon in the Sargasso Sea
Aquat. Microb. Ecol.
Annual flux of dissolved organic carbon from the euphotic zone in the northwestern Sargasso Sea
Nature
Interactions among dissolved organic carbon, microbial processes, and community structure in the mesopelagic zone of the northwestern Sargasso Sea
Limnol. Oceanogr.
Major role of bacteria in biogeochemical fluxes in the ocean’s interior
Nature
Contribution of major bacterial groups to bacterial biomass production (thymidine and leucine incorporation) in the Delaware estuary
Limnol. Oceanogr.
Substantial energy input to the mesopelagic ecosystem from the seasonal mixed-layer pump
Nat. Geosci.
Bacterial growth efficiency in natural aquatic systems
Annu. Rev. Ecol. Syst.
Respiration rates in bacteria exceed phytoplankton production in un prroductive aquatic systems
Nature
Genomic perspectives in microbial oceanography
Nature
Community genomics among stratified microbial assemblages in the Ocean’s interior
Science (80-. )
Vitamin B 12 and marine ecology. IV. The kinetics of uptake, growth and inhibition in Monochrysis Lutheri
J. Mar. Biol. Assoc. United Kingdom
Cited by (11)
Dynamics of organic matter in the changing environment of a stratified marine lake over two decades
2023, Science of the Total EnvironmentIncreased prokaryotic diversity in the Red Sea deep scattering layer
2023, Environmental MicrobiomeImpact of Water Mass Mixing on the Composition and Mineralization of Dissolved Organic Matter in the Deep Labrador Sea
2023, Journal of Geophysical Research: OceansExploring the hidden treasures: Deep-sea bacterial community structure in the Bay of Bengal and their metabolic profile
2023, Frontiers in Marine Science