Biodiversity and ecosystem functioning in coastal lagoons: Does microbial diversity play any role?

Estuarine, Coastal and Shelf Science 75 (2007) 4e12 www.elsevier.com/locate/ecss

Biodiversity and ecosystem functioning in coastal lagoons: Does microbial diversity play any role? Roberto Danovaro*, Antonio Pusceddu Department of Marine Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy Received 19 December 2006; accepted 26 February 2007 Available online 6 August 2007

Abstract Although prokaryotes are small in size, they are a significant biomass component in aquatic ecosystems and play a major role in biogeochemical processes. It is generally assumed that the relative importance of prokaryotes to material and energy fluxes is maximized in low-productivity (oligotrophic) ecosystems and decreases in high-productivity (eutrophic) ecosystems. Lagoon and coastal ecosystems are extremely dynamic, typically highly productive and dominated by macro-size organisms (both macrofauna and macrophytes). As such, their functional characteristics are typically evaluated from a ‘‘macrobial’’ perspective. An efficient ecosystem functioning, with fast nutrient cycling, high productivity, low C accumulation and lack of hypoxic/dystrophic crises is, however, intimately dependent on the interaction between microbial and macrobial organisms. We make here an attempt to relate prokaryote biodiversity (genotype richness, using fingerprinting techniques, ARISA) and ecosystem functioning (using a series of parameters including meiofaunal biomass, prokaryote C production and organic matter turnover rates) in different Mediterranean lagoon systems. The lagoons differed significantly with each other for all the variables. While no relationships were observed between the environmental characteristics of the lagoons and the bacterial diversity, the latter was significantly and positively correlated with the functioning and efficiency of the lagoons. The investigation of the links between microbial diversity and functioning in lagoons is still at its infancy, but these preliminary results suggest that a better understanding of the role of prokaryote diversity on ecosystem functioning and efficiency could open new perspectives for the conservation and management of these highly productive and vulnerable ecosystems. Ó 2007 Elsevier Ltd. All rights reserved. Keywords: prokaryotic biodiversity; ecosystem functioning; coastal lagoons

1. The biodiversity and ecosystem functioning (BEF) paradigm: the aquatic gap The hypothesis that a loss of biodiversity might threaten an ecosystem’s functioning (Loreau et al., 2001) has stimulated the interest of scientists on the relationship between biodiversity and ecosystem functioning (BEF) (Loreau, 2000; Petchey et al., 2004). Recent studies, indeed, have suggested that the biodiversity decrease might reduce ecosystems’ services through feedback mechanisms (Worm et al., 2006), with potentially important socio-economic consequences (Costanza

* Corresponding author. E-mail address: [email protected] (R. Danovaro). 0272-7714/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved. doi:10.1016/j.ecss.2007.02.030

et al., 1997). Marine ecosystems are experiencing impacts of unprecedented intensity and frequency, which can directly and indirectly cause alterations of biodiversity, structure and organization of marine assemblages (Worm et al., 2006). At a local scale, the loss of marine biodiversity is particularly relevant along the coastal oceans, where mangroves, coral reefs, seagrass beds and lagoons are progressively impacted (Short and Wyllie-Echeverria, 1996; Valiela et al., 2001; Duarte, 2002). Large pelagic predators and their biodiversity are also at high risk due to over-fishing (Pauly et al., 1998; Myers et al., 2000). There is still no universal consensus on how diversity would control ecosystems’ functioning (Loreau et al., 2002; Naeem et al., 2002; Cardinale et al., 2004). BEF relationships might depend on several factors including: (1) the spatial and

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temporal scales (Chase and Leibold, 2002; Cardinale et al., 2004); (2) the species role (Petchey and Gaston, 2006); (3) the trophic interactions (The´bault and Loreau, 2003); (4) the proxies and variables utilised for investigating these relationships (Bengtsson, 1998); and (5) the experimental strategies (Emmerson and Raffaelli, 2000). Available studies suggest that the loss of biodiversity might have different consequences in different ecosystem types, being able to impair the sustainable functioning of some ecosystems, while having null or idiosyncratic effects in others (Fig. 1). Such differences indicate that results obtained on BEF interactions from terrestrial ecosystems cannot be extrapolated to the marine realm. Although investigations in marine ecosystems are much less developed than in the terrestrial ones (Cyr and Pace, 2003), available studies, mostly based on the analysis of benthic marine diversity (Duffy and Stachowicz, 2006), have reported an idiosyncratic response of ecosystems’ functioning to changes in the species number (Bolam et al., 2002), leading to the hypothesis that the effect of biodiversity loss on marine ecosystem functioning can depend upon the ecological role of the species (Pelegri and Blackburn, 1995; Banta et al., 1999; Christensen et al., 2000; Emmerson et al., 2001; Raffaelli et al., 2003; Mermillod-Blondin et al., 2005). The lack of knowledge in aquatic systems appears even more important in coastal lagoons, where investigations on the BEF relationships are almost non-existent. All available information has moreover been obtained from the study of the macroscopic (i.e. macrobenthic) components. Recent studies have pointed out that the analysis of prokaryote diversity is a priority in current ecological research (Giovannoni and Stingl, 2005) and the development of molecular tools (e.g. fingerprinting techniques) for the determination of the prokaryote diversity (Bent et al., 2007) has enhanced our ability to investigate the relationships between prokaryote’s biodiversity and ecosystem functioning not only in microcosms, but also in natural systems (Jessup et al., 2004). It has been also suggested that microorganisms (including some unicellular eukaryotes) have a cosmopolitan distribution

Ecosystem functioning

Case 1: Direct relationship

Case 4: Threshold levels

Case 5: Idiosyncratic response

Case 3: Non-linear relationship

Case 2: Negative relationship

Biodiversity

Fig. 1. Possible theoretical models of relationship between biodiversity and ecosystem functioning.

5

(Finlay and Fenchel, 2002). As such they could have a limited relevance in the performance of specific ecosystem processes. However, the discovery of endemic populations of prokaryotes, and the evidence of important changes at all spatial scales (Horner-Devine et al., 2004), has stimulated new investigations, with potentially important implication of the relationship between local prokaryote biodiversity and the ecosystem performance (Loreau, 2001; Papke et al., 2003; Whitaker et al., 2003; Hughes Martiny et al., 2006). The present work summarizes the results of new investigations and available information on the relationships between microbial diversity and ecosystem functioning in some Mediterranean coastal lagoons. This work is not intended to treat exhaustively the interactions between microbial diversity and ecosystem functioning in coastal lagoons, rather to provide ideas and scientific perspectives to address future research in this field.

2. Ecosystem functioning, services and biodiversity of coastal lagoons Transitional aquatic systems, including coastal lagoons, provide important services including: flood control, shoreline stabilization, sediment and nutrient retention, local mitigation of climate change, water quality, biodiversity and biomass reservoirs, recreation and tourism, cultural value (Levin et al., 2000; Moss, 2000) and their potential economical value has been estimated at >22,000 US dollars ha1 y1 (Costanza et al., 1997). Mediterranean coastal lagoons have been utilised historically for fisheries and extensive aquaculture practices and are presently active centres for fishery and mariculture. Mediterranean coastal lagoons are, however, also subjected to a number of anthropogenic impacts including urban, agricultural and/or industrial effluents and domestic sewage (Castel et al., 1996). Coastal lagoons are also characterised by high primary productivity levels which enter higher trophic levels sustaining locally high primary and secondary production (Viaroli et al., 1996). In addition, considerable fractions of detrital organic matter can be accumulated in the sediments or can be exported to the adjacent coastal marine areas, thus contributing to the fertilization of these systems (Barnes, 1984; Pusceddu et al., 1999, 2003). Structural changes in the morphology of coastal lagoons, related to land reclamation, changes in the bathymetry, and the construction and location of mariculture plants have made severe alterations, which are likely to persist over a long-term (Viaroli et al., 2005). In addition, these impacts are likely to be exacerbated by the present climate changes (Eisenreich, 2005). Recent reviews have pointed out that the biodiversity of transitional area can be influenced by critical alterations of ecosystem processes. Eutrophication, pollutants, species invasions, over-fishing, habitat alteration, and local climate shifts are increasingly threatening most transitional environments (Levin et al., 2000). The resulting biodiversity loss may have cascade consequences, which will further increase the diversity loss. For instance, experiments carried out by

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manipulating estuarine macrofauna have demonstrated that species loss, by making available free space for colonization, can facilitate the invasion of alien species, which in turn could cause further loss of diversity (Cohen and Carlton, 1998; Stachowicz et al., 1999). The increase in the susceptibility of these ecosystems to alterations in biodiversity is also likely to be related with the reduction of biological interactions, which are particularly important in transitional ecosystems (Levin et al., 2000). There is increasing evidence that changes in the species diversity of macrobenthic components linked to several sources of anthropogenic disturbance may lead to altered ecosystem processes in coastal lagoons (Salas et al., 2005).

Intermediate conditions: high organic load

Accumulation of organic material: limited transfer to higher trophic levels

0.04

0.02

0.05 0.05

Goro

Lesina

Limited OM accumulation: high transfer to higher trophic levels

Prokaryote: Flagellate: Meiofaunal biomass ratio

6

2.0 1.5 1.0 0.5 0.0

Prokaryotes

Shallow coastal environments with salt-marsh components, such as coastal lagoons, are highly productive ecosystems often dominated by macrophytes (e.g. Spartina spp. and Zostera spp.) and macroalgae (e.g. Ulva spp.). Primary production from these components typically exceeds the consumption by herbivores, so that most of such primary organic matter becomes available to the consumers as detritus (Newell, 1982). Moreover, when the inputs of organic matter to the sediment exceed the capacity of the consumers’ web to manage these inputs (e.g. under dystrophic conditions), the fraction of organic matter potentially available for consumers (loss due to anoxic crises) tends to progressively accumulate in the sediment. Because of its mainly refractory composition, only a minor fraction of this detritus is directly available to the consumers (Pusceddu et al., 2003), whereas the largest fraction needs to be fragmented and processed through prokaryotes to enter higher trophic levels (Tibbles et al., 1992; Fiordelmondo et al., 2003; Manini et al., 2003). In these environments prokaryotes are key players, and their role appears to be even more relevant in areas characterised by large organic C accumulation. Benthic prokaryotes in coastal lagoons are indeed key components of the remineralization process allowing the recycling of the nutrients needed to sustain primary production (Alongi, 1994), guaranteeing a buffer system against sulphide accumulation under dystrophic conditions (de Wit et al., 2001) and representing an important trophic source for benthic deposit feeders (Alongi, 1994). One important factor controlling the efficiency in the transfer of detritus towards higher trophic levels is represented by prokaryote activity. The accumulation of organic substrates typically decreases the efficiency of organic C transfer to higher trophic levels (Fig. 2; redrawn after Manini et al., 2003). However, data reported here suggest that, in coastal lagoons, shifts in the ecosystem functioning (de Wit et al., 2001), such as those leading to the accumulation of labile organic C in the sediments, can increase the efficiency of heterotrophic prokaryotes in transforming organic detritus pools into biomass (Fig. 3).

Heterotrophic flagellates

Meiofauna

Fig. 2. Energy transfer efficiency in different coastal lagoons. Illustrated is the benthic microbial loop efficiency in channelling energy and material to higher trophic levels. Energy transfer efficiency is reported here as the biomass of prokaryotes, flagellates and meiofauna normalised to the prokaryote biomass (modified from Manini et al., 2003). A much higher meiofaunal biomass per unit of prokaryote biomass, in Goro than in Lesina and Marsala, is evident.

4. Environmental setting Recent investigations conducted in several Mediterranean lagoons have provided new insights, which can be used to investigate the relationships between prokaryote diversity and lagoon ecosystem functioning and efficiency (Manini et al., 2003; Pusceddu et al., 2003). Benthic prokaryote diversity and community structure were investigated in different coastal lagoons (Table 1; Fig. 4) characterised by differences in terms of ecosystem functioning: Goro, Lesina and Venice. Also the Marsala lagoon was investigated for some variables. The Goro lagoon, the southern most basin of the wider Po deltaic system (average water depth of 1.5 m), is subjected to continuous natural subsidence phenomena and large anthropogenic loads. The basin is connected to the sea by means of both natural and artificial canals and, during summer, may experience 30

Prokaryote C conversion efficiency (%)

3. The key role of benthic prokaryotes in the functioning of coastal lagoons

Marsala

25 20 15 10 R2 = 0.97

5 0 0.0

2.0

4.0

6.0

8.0

Bioavailable organic C (mg C g-1) Fig. 3. The relationship between bioavailable organic C (sensu Pusceddu et al., 2003) and the prokaryote C conversion efficiency determined as the ratio of prokaryote C production and the amount of C degraded enzymatically and expressed as percentage.

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Table 1 Environmental features of the investigated lagoons’ sediments in summer Lagoon

Sediment type

Eh (mV)

Depth (m)

Salinity

Temperature ( C)

Vegetation

Goro Lesina Venice Marsala

Mud Sandy-mud Sandy-mud Sandy-gravel

85.4 265 228 141.1

1.4 1.0 1.0 1.0

24.00 16.75 29.67 34.15

24.5 24.6 21.2 25.4

Macroalgae (Ulva sp.) Non-vegetated Macroalgae (Ulva sp.) Seagrass (Posidonia oceanica)

sub-oxic/anoxic conditions with dystrophic crises related with macroalgae blooms (Ulva sp. and Gracilaria sp.). The Lesina lagoon, characterised by shallow depths (on average 0.8 m depth), is connected to the sea through two channels and receives freshwater from two minor rivers. Lesina lagoon is experiencing an increasing eutrophication and occasional dystrophic crises related with Valonia utricularis blooms. Large parts of the lagoon are also covered by Zostera noltii and Ruppia sp. The Venice lagoon has a mean depth of ca. 1 m and communicates with the northern Adriatic Sea through three main inlets: Chioggia, Malamocco and Lido. The lagoon exchanges ca. 60% of its waters at any tidal cycle (ca. 12 h) and receives sewage from the cities of Venice, Mestre and the Marghera industrial districts. The Marsala lagoon is connected to the sea by means of two large channels allowing a large mixing with seawaters (Pusceddu et al., 2003). No major continental inputs are present. The average water depth is ca. 1 m and most of the lagoon is characterised by a seagrass meadow (Posidonia oceanica). 5. Relationship between prokaryote’s biodiversity and ecosystem functioning in different Mediterranean lagoons The analysis of community structure carried out using the fluorescent in situ hybridization (FISH) technique allowed

toclarify that the accumulation of organic matter in the sediment, as observed during dystrophic phenomena, was associated with relevant shifts in prokaryote diversity and community structure. For instance, the benthic prokaryote assemblages displayed the tendency of increasing the relevance of sulphate-reducing bacteria (Fig. 5). The ecological role of prokaryotes, which reduce the excess of organic loads, and produce biomass that can be used by consumers, represents an example of feedback mechanisms, which enables the lagoon systems to prevent the collapse of their functioning. This example points out that the efficient functioning of benthic prokaryotes is tightly connected with the global lagoon functioning and ecosystem efficiency. However, it does not allow clarifying whether the shift in microbial community composition and structure is associated or not with changes in biodiversity (as species richness), so that it is unclear whether a change in prokaryote biodiversity can influence the functioning of the lagoon ecosystem or its resilience after a dystrophic crisis. The bacterial diversity of Mediterranean coastal lagoons, determined by a fingerprinting technique, is comparable to that reported for coastal marine sediments and, quite surprisingly, can be significantly higher than that observed in tropical coral reef sediments (Fig. 6). These results indicate that despite the large accumulation of organic matter, typical of

d)

a) N

Adriatic Sea Adriatic Sea

Adriatic Sea

Adriatic Sea

Mediterranean Sea

c)

Lesina

Tyrrhenian Sea

N

b)

N

Fig. 4. Location of the four investigated lagoons: (a) Goro; (b) Lesina; (c) Marsala; and (d) Venice.

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Table 2 Results of one-way analysis of variance applied to test for differences in prokaryote biodiversity and ecosystem functioning between three Mediterranean lagoons. Reported are also the results of the post hoc Tukey’s test (a ¼ 0.05) carried out to ascertain the actual differences among the three lagoons.***p-Level < 0.001

% of total prokaryote abundance

100% 80% 60% 40% 20% 0% Lesina

Goro

Sulphate reducing Bacteria

Venice Other bacteria

Variable

F

p-Level Tukey’s test

Ribotype richness Meiofaunal biomass Prokaryote C conversion efficiency Sediment protein turnover rate

19.6 43.8 27.4 53.2

*** *** *** ***

[Goro, Lesina] > Marsala Goro > Lesina > Marsala Goro > Lesina > Marsala Goro > [Lesina, Marsala]

Archaea

Fig. 5. Mean percentage contribution of Archaea, sulphate-reducing bacteria and other bacteria to the total prokaryotic abundance in the sediments of Mediterranean coastal lagoons. Sulphate-reducing bacteria, other bacteria, and Archaea were enumerated by fluorescence in situ hybridization (FISH) on replicate (n ¼ 3) samples using the SRB385, EUB338 and ARC915 probes, respectively. Since sulphate-reducing bacteria are a subgroup of the domain bacteria, their percentage was calculated by subtracting their numbers from the total bacterial number.

Fig. 6. Comparison between the bacterial community structures in marine coastal and lagoon sediments. Different tones represent different genotypes obtained using ARISA analysis carried out on the ITS1 region located between the 16S rRNA and the 23S rRNA genes. DNA was extracted from triplicate sediment samples, quantified and amplified using PCR. Details on the complete procedure are reported in Luna et al. (2006) and Danovaro et al. (2006). S ¼ number of ribotypes (standard deviation on triplicate sediment samples).

coastal lagoons, prokaryote diversity, conversely to macrobial counterparts, can be extremely high. Moreover, the different investigated lagoons displayed significant differences in bacterial biodiversity (Table 2), with genotype numbers in the Goro lagoon much higher than those in the Lesina and Venice lagoons (Fig. 7). These findings suggest that any lagoon, having different environmental settings and trophic conditions, is characterised by bacterial assemblages, which differ both in terms of absolute number of genotypes and in their composition. By using a set of samples collected synoptically, which ensured consistency in the data analysis, these measures of biodiversity were compared with the performance of the lagoon systems. Ecosystem functioning involves several processes which can be summarized as production, consumption and transfer to higher trophic levels, organic matter decomposition and nutrient regeneration. In this study we utilised the following independent indicators of ecosystem functioning: (1) prokaryote C conversion efficiency, which enables to estimate the efficiency of energy transfer towards higher levels; (2) meiofaunal biomass, which regulates the transfer of prokaryote biomass to higher trophic levels, represents a key component of lagoons’ benthic trophic webs; and (3) organic matter decomposition rates, measured by the rates of enzymatic activities in the sediment, which is a crucial step in the nutrient regeneration processes. As mentioned above, the different lagoons displayed significant differences in a number of parameters describing their functioning (Table 2). Despite the high biopolymeric C concentrations in the sediment, extracellular enzymatic activities in the lagoons were low when compared with values reported in the literature for coastal sediments (Manini et al., 2003), and the protein turnover rates (calculated as the ratio between the quantity of proteins mobilised enzymatically and the sediment protein content) in the Goro lagoon are ca. three times faster than in Lesina and Venice lagoons (Manini et al., 2003). All parameters describing lagoon ecosystem functioning or their performance were not significantly correlated with any environmental variable, but were higher where prokaryote biodiversity displayed higher values (Fig. 8). This is confirmed by the significant and positive (n ¼ 9; p < 0.01) relationships observed between the bacterial genotype richness and the three

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Fig. 7. Bacterial diversity in different Mediterranean lagoons determined by ARISA. Diagrams illustrate the electropherograms of purified ITS1 products: each peak represents a different genotype. ARISA analysis was carried out on the ITS1 region located between the 16S rRNA and the 23S rRNA genes. DNA was extracted from triplicate sediment samples, quantified and amplified using PCR. Details on the complete procedure are reported in Luna et al. (2006) and Danovaro et al. (2006). S ¼ number of ribotypes (standard deviation).

different ecosystem functioning proxies used in this study (Fig. 9). These preliminary results allow identifying, for the first time, of a positive relationship between microbial (i.e. prokaryote) diversity and ecosystem functioning. In benthic ecosystems, a higher prokaryote diversity can promote ecosystem processes in different ways: (1) a higher diversity may increase the efficiency in the utilization of complex organic substrates, which require a large number of enzymatic functions; (2) a higher number of prokaryote ribotypes can react more promptly to changing environmental conditions, ensuring higher rates of ecosystem processes than that ensured by a few species; and (3) higher ribotype richness can also promote higher rates of detritus processing, determined by a complementary role in the decomposition process. In this regard, Loreau (2001) proposed that under the assumption that any microbial species is specialised on the exploitation of different organic compounds, the effect of microbial diversity on nutrient recycling efficiency and ecosystem functioning can be positive. Moreover, in hypoxic conditions, although sedimentary carbon cycling is depressed, a higher prokaryote diversity can maintain some functions thus enhancing ecosystem resilience after cessation of the causes inducing the dystrophic crisis. Since nutrient recycling and ecosystem efficiency are key steps for the sustainable maintenance of the primary and secondary productivity of these systems, the results of this study, though limited to a comparative approach, would suggest that prokaryote biodiversity and ecosystem

functioning in coastal lagoons can be directly and positively related. 6. Conclusions and perspectives The intensified disruption of the natural settings of many aquatic ecosystems is altering the benthic biota worldwide, and the consequences of this are expected to accelerate the biodiversity loss (Lake et al., 2000). While the loss of macroscopic species represents the main focus of studies investigating the impact of biodiversity decrease on ecosystem functioning, the role of microbial diversity is still to be properly evaluated. Our results provide evidence that coastal lagoons displaying higher performances are characterised by higher prokaryote diversity. These results stimulate new questions on the role of prokaryote biodiversity on ecosystems’ functioning, and among the others: which are the factors controlling benthic prokaryote biodiversity in different aquatic ecosystems? Are global changes affecting aquatic prokaryote biodiversity? Is the prokaryote biodiversity coupled with metazoan diversity or the two display idiosyncratic relationships? Which is, among the numerous functional roles of prokaryotes, the most important for enhancing ecosystem performance? Are specific ribotypes more important than others, and if so are they the same in all systems? The investigation of the links between microbial diversity and the functioning of lagoons is still at its infancy, but responding to some of these questions could open new perspective for the conservation and management of these highly productive and vulnerable ecosystems.

Goro

Lesina

Venice

Ecosystem functioning

R. Danovaro, A. Pusceddu / Estuarine, Coastal and Shelf Science 75 (2007) 4e12

10

1000 100 R2 = 0.78

10

R2 = 0.82

1 0.1 0.01

R2 = 0.58

0.001 0

Sediment protein turnover rate

20

40

60

80

100

120

Bacterial genotype richness (S)

0.08 0.07

Prokaryote C conversion efficiency

0.06

Sediment protein turnover

Meiofaunal biomass

d-1

0.05

Fig. 9. Relationships between bacterial diversity and prokaryote C conversion efficiency (%), sediment protein turnover rates (d1) and meiofaunal biomass (mg C g1). Y-axis is in log scale. Reported are the linear regression coefficients ( p-level is <0.01 for the three relationships).

0.04 0.03 0.02 0.01 0.00

Prokaryote C conversion efficiency % of C mobilised enzymatically

12 10 8 6 4 2 0

Meiofaunal biomass

COFIN-PRIN program NITIDA (New indicators of trophic state and environmental quality of lagoon ecosystems, Italian Ministry of Research), by the PR/1 Project (Italian Agency for the Protection of the Environment, APAT) and by SESAME (‘‘Southern European Seas: Assessing and Modelling Ecosystem changes’’) program under the FP6 EU contract no. 036949-2. Thanks to Dr. Gian Marco Luna (Polytechnic University of Marche, Ancona, Italy) and Elena Manini (ISMAR-CNR, Ancona, Italy) for providing data and support to this research and to two anonymous reviewers for valuable suggestions on an early version of the manuscript.

160 140

References

µg g-1

120 100 80 60 40 20 0

GORO

LESINA

VENICE

Fig. 8. Ecosystem functioning and efficiency vs bacterial biodiversity in Mediterranean coastal lagoons. C conversion efficiency is calculated as the ratio of prokaryotic C production (determined by 3H-leucine incorporation mg C g1 sediment h1) and organic C degraded enzymatically and expressed as percentage. Sediment protein turnover rates are calculated as the ratio of protein degradation (by aminopeptidase activity) to concentration of sedimentary protein in the sediment of different Mediterranean coastal lagoons (d1; Fabiano and Danovaro, 1998). The pie charts represent the bacterial community structure of the three lagoons. Different tones represent different genotypes obtained using ARISA analysis carried out on the ITS1 region located between the 16S rRNA and the 23S rRNA genes. DNA was extracted from triplicate sediment samples, quantified and amplified using PCR. Details on the complete procedure are reported in Luna et al. (2006) and Danovaro et al. (2006). S ¼ number of ribotypes (standard deviation).

Acknowledgements This work has been carried out within the framework of the network of excellence MARBEF (Marine Biodiversity and Ecosystem Functioning) and was financially supported by

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