# Diagenesis and benthic fluxes of nutrients and metals during experimentally induced anoxia in the Gulf of Trieste (northern Adriatic Sea)

Neža Koron, Nives Ogrinc, E. Metzger, Bettina Riedel, Jadran Faganeli

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Neža Koron, Nives Ogrinc, E. Metzger, Bettina Riedel, Jadran Faganeli. Diagenesis and benthic fluxes of nutrients and metals during experimentally induced anoxia in the Gulf of Trieste (northern Adriatic Sea). Biogeosciences Discussions, 2013, 10 (7), pp.11729-11755. 10.5194/bgd-10-11729-2013 . hal-03278280

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# Diagenesis and benthic fluxes of nutrients and metals during experimentally induced anoxia in the Gulf of Trieste (northern Adriatic Sea)

N. Koron<fnref n="1" />, N. Ogrinc<fnref n="2" />, E. Metzger<fnref n="3" />, B. Riedel<fnref n="4" />, and J. Faganeli<fnref n="1" />

Received: 30 June 2013 – Accepted: 2 July 2013 – Published: 15 July 2013

Correspondence to: N. Ogrinc (nives.ogrinc@ijs.si)

Published by Copernicus Publications on behalf of the European Geosciences Union.

<footnote n="1">¹National Institute of Biology, Marine Biological Station, Fornače 41, 6330 Piran, Slovenia</footnote>

<footnote n="2">²Jožef Stefan Institute, Department of Environmental Sciences, Jamova 39, 1000 Ljubljana, Slovenia</footnote>

<footnote n="3">³LUNAM Université, Université d'Angers, UMR CNRS 6112 LPGN-BIAF-Laboratoire des Bio-Indicateurs Actuels et Fossiles, 2 Boulevard Lavoisier, 49045 Angers Cedex, France</footnote>

<footnote n="4">⁴University of Vienna, Department of Limnology and Oceanography, Althanstrasse 14, 1090 Vienna, Austria</footnote>
Sequential nutrient regeneration and organic matter (OM) degradation in surface sediments of the Gulf of Trieste (northern Adriatic Sea) were examined using in situ benthic chambers under normoxic, anoxic and reoxic conditions. Intensive NH₄⁺ and PO₄³⁻ anoxic regeneration was subsequently slower in prolonged anoxia. NH₄⁺ production was probably also a consequence of dissimilatory nitrate reduction to NH₄⁺. The presence of anammox and laterally pumping of oxygenated water by benthic infauna explained the presence of NO₃⁻ in anoxia. Anoxic phases were characterized by enhanced dissolution of Siᵢₗᵢₗ, decreasing pore water Ca and Mg concentrations indicating carbonate precipitation and higher Fe and Mn concentrations as a result of reduction/respiration. Reoxygenation was characterized by enhanced bioturbation. Nitrification caused NH₄⁺ decrease and P precipitated quickly as carbonate fluorapatite and FePO₄. In addition adsorption of P onto Fe-hydroxides could also occur since Fe (and Mn) reoxidized quickly. Increased Ca levels suggested enhanced carbonate dissolution. Diffusive fluxes at the sediment-water interface (SWI), calculated from pore water modelling using diffusion-reaction model, revealed high anoxic NH₄⁺ effluxes and Ca (and Mg) influxes. PO₄³⁻ fluxes were very low and high NH₄⁺/PO₄³⁻ flux ratios in anoxic and reoxic phases suggested an excess of benthic inorganic N. Nutrient budgets at the SWI showed intensive anoxic recycling of inorganic N but low P and Si cycling in all redox phases.

# 1 Introduction

The Gulf of Trieste is an example of shallow coastal marine environments that are characterized by relatively low organic matter (OM) contents in sediments (Ogrinc et al., 2005). The largest fraction of sedimentary OM originates from the pelagic production, which escapes degradation in the water column and settles on the sediment bed. The remainder originates from benthic primary production, which represents a significant

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source of easily degradable OM in this environment due to the euphotic zone reaching the bottom (Kemp et al., 1999; Welker et al., 2001). The autochthonous (marine) origin of OM is confirmed by its $\delta^{13}C_{org}$ values (Faganeli et al., 1991; Ogrinc et al., 2005). The Gulf, becoming recently oligotrophic, experiences two phytoplankton blooms yearly occurring in spring and autumn (Mozetič et al., 2012). The first is a consequence of increased nutrient-rich fresh water inflow into the Gulf, whereas the autumn bloom follows disruption of the stratified summer water column, and thus releases of the trapped nutrients. Benthic microalgae exhibit summer peaks due to the highest release of nutrients from pore waters (Welker et al., 2002).

Vertical stratification of water masses in the gulf lead to $O_2$ depletion in the bottom water layers causing hypoxia and even anoxia (Kemp et al., 1999). Coastal hypoxia and anoxia are widespread and increasingly common events that can result in seasonal or even persistent “dead zones” (Diaz and Rosenberg, 2008), which are also known in the Gulf of Trieste (Faganeli et al., 1985; Stachowitsch, 1991; Riedel et al., 2008). These can influence the biogeochemical processes taking place in sediment by marine microorganisms and influenced by activities of benthic infauna. The latter include changes in sediment burrowing and reworking by benthic invertebrates (Aller, 1982). In sediments of the Gulf of Trieste, the most important macrofauna are sea urchins, brittle stars and polychaetes (Ogorelec et al., 1991; Stachowitsch et al., 2007). Their activities influence nutrient release and the redox cycling of elements at the sediment-water interface (SWI) (Hunter et al., 2012). With the occurrence of hypoxia or even anoxia, the activity of sediment infauna decreases limiting the sediment reworking and reoxidation of reduced chemical species originating from deeper sediment layers where anoxic OM mineralization takes place (Aller and Yingst, 1988; Hines et al., 1997). This leads to a migration of reductive layers upwards and enhances the importance of sulfate reduction in the topmost sediment layers. Due to the accumulation of toxic hydrogen sulfide, the mortality of benthic macrofauna increases and the decaying biomass acts as an additional source of “fresh” easily degradable OM.
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The aim of this study was to simulate anoxia and reoxidation for variable amount of time in order to investigate the consequences of shifts in benthic biogeochemical processes using the changes of pore water composition of nutrients and metals encompassing oxic and anoxic conditions and subsequent recovery. Since the composition of pore water serves as a sensitive indicator of early diagenetic reactions (Berner, 1980), it was the primary focus of this research. This study was a part of a broader project entitled "Low dissolved oxygen events in the Northern Adriatic: in situ experimental insights into multi-level responses before, during and post-anoxia" with its main objectives being a behavior, mortality and regeneration of infauna community in extreme conditions. The recovery of deteriorated marine environment, which experiences severe anoxia events is usually slow. Sedimentary biogeochemical data were used also as a proxy for evaluating environmental status in such extreme conditions and as a tool for projection of environmental consequences induced by anoxia. The results also allow us to discuss the consequences of advanced remineralization in a relatively organic poor sedimentary environment.

## 2 Materials and methods

### 2.1 Study area

The study site was located 2.3 km off Piran (Slovenia) in the southern part of the Gulf of Trieste (northern Adriatic Sea) at the Marine Biological Station hydrographic buoy Vida (45°32.300' N, 13°33.000' E). This northernmost part of the Adriatic Sea is covering an area of 500 km² with a maximal depth of 25 m and is isolated from the rest of northern Adriatic by a shoal. The salinity of bottom waters ranges from 36 to 38.5 and bottom water temperatures range from 8 °C in winter and 20 °C in summer. A density gradient in late summer can result in bottom water layer hypoxia and even anoxia (Faganeli et al., 1985). Sediment in the southern part of the Gulf is composed mainly of silty sand that is high in biogenic carbonate, populated mostly by brittle stars, sponges and
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tunicates and actively bioturbated by polychaetes and bivalves (Ogorelec et al., 1991). The sedimentation rate, determined using $^{210}$Pb, is approximately 1.2 mm yr$^{-1}$ in the central part of the gulf increasing up to 3 mm yr$^{-1}$ towards the shore (Ogorelec et al., 1991). The sediment surface is populated by microalgae composed mostly of diatoms (Welker et al., 2002).

## 2.2 Experimental design and sampling procedure

Benthic experiments, conducted from 2009 to 2011, included a simulation of different episodes of anoxia using benthic chambers with each simulation experiment consisting of three separate phases. The first phase, called normoxic, represented conditions that governed the environment at the time of sampling. This phase was followed by the anoxic phase, in which the system inside the benthic chamber slowly became anoxic due to benthic respiration and limited contact with outer environment. The anoxic phase was followed by the recovery phase, in which the benthic chamber was removed and the system was left to recover for at least 7 days. Various durations of anoxia were simulated throughout the project. In 2009, anoxia only 7 days in length was mimicked. In the following year a greater number of experiments were performed, with anoxia lasting 7 days, 1 month, 2 months and 10 months. The recovery phase in all, except the 10 months experiment, lasted 7 days, while in the last phase it lasted 3 months. Samplings of 1 yr anoxia and the 1 yr recovery phase were performed in 2011.

In an experiment conducted in 2010, with anoxia onset lasting 7 days, a benthic chamber called Experimental Anoxia Generating Unit (EAGU) were equipped with sensors for dissolved oxygen ($O_2$) and sulphide ($H_2S$) and cameras primarily used for studying the behavior and survival/mortality of benthic infauna since each group of organisms showed different tolerance on changing $O_2$ levels (Reider et al., 2013; Grego et al., 2013a,b; DeTroch et al., 2013; Langlet et al., 2013a,b). The other chambers used were simpler lacking sensors and cameras. They were however designed with special rubber-closed openings used for sample manipulations inside the chamber.
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All benthic chamber deployments and sediment core samplings were performed by SCUBA divers after careful and thorough planning of correct positioning of all utensils. Firstly, before the deployment of chambers, 4 cores (normoxic) were sampled using Plexiglass tubes (6 cm i.d., 12 cm length) and sealed with rubber stoppers underwater. The chambers were pushed approximately 2 cm into the sediment and carefully sealed to avoid any leakage of ambient water into or experimental water out of the chambers. In the experiment using EAGU, O₂ and H₂S sensors were used to monitor the evolution of anoxia inside the chamber (Riedel et al., 2013). After the elapsed time set by the experiment outline SCUBA divers again performed core sampling. After sampling, the benthic chamber was carefully removed to avoid any further disturbance of the sediment. The area previously covered by the benthic chamber and anoxic water column became exposed to ambient seawater and the recovery period began. The sampling of the “recovery” sediments was performed after 7 days, following same sampling protocol as before. The sampling procedure was the same in every experiment, except with 2 months anoxia, which lacked the recovery phase. Recovery cores of 7 days and 1 month anoxia experiment were sampled after a 7 day period, whereas in the 1 yr experiment they were collected after 3 months period.

After each campaign, all samples were carefully transported to the lab where the cores were extruded and sectioned into 0.5 cm thick slices for the upper 2 cm, and 1 cm slices for next 5 cm. All core sample manipulations, including pore water, were performed in an N₂-filled glove bag or box. Core slices were put into sterile 50 mL centrifuge tubes (Corning Inc.) to allow the pore water extraction. This was performed by centrifugation at 3500 rpm for 20 min at in situ temperature measured at the sea bottom at the time of sampling. Pore waters from matching depths were filtered through 0.2 µm Millipore-HA filters in an inert atmosphere and combined three or four cores to obtain enough sample for all required analyses. Where necessary pore waters were acidified and refrigerated until analyses. Sediments devoid of pore waters (solid phase) were kept frozen until analyses.
## 2.3 Analyses

### 2.3.1 Solid phase

Sediment samples for C<sub>org</sub> and N<sub>tot</sub> analyses were freeze-dried, ground in an agate mortar and sieved through 200 µm mesh to remove coarse shell debris. C<sub>org</sub> was determined in sediments acidified with 1 M HCl to quantitatively remove carbonates (Hedges and Stern, 1984), whereas N<sub>tot</sub> was determined in non-acidified samples using a CHN analyzer (Elementar varioMICRO CUBE; Elementar Analysensysteme GmbH, Hanau, Germany). Total P was analyzed by extraction with 1 M HCl after ignition and P<sub>org</sub> was calculated from the difference in P contents of 1 M HCl extracts before and after ignition of the samples (Aspila et al., 1976), whereas Si<sub>biog</sub> was extracted with Na<sub>2</sub>CO<sub>3</sub> (DeMaster, 1981) and dissolved Si(OH)<sub>4</sub> determined colorimetrically (Grasshoff et al., 1999).

A small sediment core was also sampled to determine the porosity of sediments at the experimental site according to Čermelj et al. (1997).

### 2.3.2 Pore waters

Nutrient concentrations in pore waters were determined using standard analytical methods (Grasshoff et al., 1999). Detection limits for nutrients were: 0.5 µmol L<sup>-1</sup> for NO<sub>3</sub><sup>-</sup> + NO<sub>2</sub><sup>-</sup>, 0.4 µmol L<sup>-1</sup> for NH<sub>4</sub><sup>+</sup> and 0.01 µmol L<sup>-1</sup> for PO<sub>4</sub><sup>3-</sup>. Concentrations of Si, Fe, Mn, Ca and Mg in filtered and acidified samples were determined using ICP-OES (Perkin-Elmer Optima 5300 DV). NASS-6 certified reference material was used for quality control. All samples were available in only one replicate, so the reproducibility of the method was determined based on multiple measurements of the standard solutions and reference material, whereas limit of detection and limit of quantification were determined based on three and ten standard deviations of the blank samples measurements, respectively. The method detection limit (MDL) for ICP-OES was cal-

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culated based on the t-statistics calculated at two different confidence intervals (99% and 95%) multiplied by average standard deviation in mgL⁻¹.

### 2.3.3 Pore water and benthic flux modelling

The fluxes of PO₄³⁻, NH₄⁺, dissolved silicon (dSi), Ca, Mg, Mn and Fe across the sediment-water interface (SWI) were determined using Fick's first law of diffusion and advection (Lerman, 1979):

$$F_{z=0} = -\phi D_s \left(\frac{\partial C}{\partial z}\right) + \phi \omega C|_{z=0} \quad (1)$$

where F is the rate of flux [mol m⁻² s⁻¹], Φ is sediment porosity, D_s is the effective diffusion coefficient [m⁻² yr⁻¹], C/z is the concentration gradient across the SWI [mol dm⁻⁴], sedimentation rate [cm s⁻¹]. The measured Φ was 0.55, while D_s were corrected for temperature and average porosity (Lerman, 1979). C/z was estimated from a profile of concentrations plotted against depth using the diffusion-reaction model for PO₄³⁻, NH₄⁺ and dSi, while Ca, Mg, Mn and Fe depth profiles were described by a curve fitting routine of a polynomial function.

The diffusion–advection–reaction model included the degradation of OM via first-order kinetics, equilibrium adsorption from pore water onto sediment particles and dissolution precipitation reactions using the following equation (Lerman, 1979):

$$\frac{\partial C}{\partial t} = 0 = D \frac{\partial^2 C}{\partial z^2} - \omega \frac{\partial C}{\partial z} - kC + J + R_0 \exp(-\beta z) \quad (2)$$

where k is the reaction rate constant, J is the rate of reaction, R₀ is the production rate at the SWI [mol dm⁻³ s⁻¹], is the depth attenuation constant [cm⁻¹]. The change of PO₄³⁻, NH₄⁺ and dSi with depth and time in the model was described for every species separately depending on the processes influencing their distribution: decomposition of OM to NH₄⁺ and PO₄³⁻; equilibrium adsorption for NH₄⁺, PO₄³⁻ following a simple linear
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isotherm; precipitation of PO₄³⁻ to form authigenic minerals and dissolution of biogenic silica assuming first-order reaction. Thus, the change of nutrient concentrations with depth can be described by the following steady-state differential equations.

For NH₄⁺:

$$ \frac{\partial C}{\partial t} = 0 = \frac{D_s}{1 + K_N} \frac{\partial^2 C}{\partial z^2} - \omega(1 + K_N) \frac{\partial C}{\partial z} + R_0 \exp(-\beta z) \quad (3) $$

where K_N is the equilibrium adsorption constant for NH₄⁺.

For PO₄³⁻:

$$ \frac{\partial C}{\partial t} = 0 = \frac{D_s}{1 + K_p} \frac{\partial^2 C}{\partial z^2} - \omega(1 + K_p) \frac{\partial C}{\partial z} - \frac{k_m(C - C_{eq})}{1 + K_p} + R_0 \exp(-\beta z) \quad (4) $$

where K_p is the equilibrium adsorption constant for PO₄³⁻, Cₐeq concentration at saturation with the authigenic precipitate dependent on T and k_m authigenic mineral precipitation rate constant.

For dSi:

$$ \frac{\partial C}{\partial t} = 0 = D_s \frac{\partial^2 C}{\partial z^2} - \omega \frac{\partial C}{\partial z} + k_m(C_{\infty} - C) \quad (5) $$

where k_m is the rate constant for Si dissolution and C_∞ is asymptotic concentration at z → ∞. The equations were solved using the following boundary conditions at:

at z = 0 : C = C_{z=0}

at z → ∞ : C → C_∞ for NH₄⁺ and dSi and C → Cₐeq for PO₄³⁻.

The parameters used in the diffusion-advection-reaction model together with the model output data are collected in Table 1.
# 3 Results

## 3.1 Solid phase

Results on C<sub>org</sub>, N<sub>tot</sub>, P<sub>tot</sub>, P<sub>inorg</sub>, P<sub>org</sub> and Si<sub>biog</sub> results and C<sub>org</sub>/N<sub>tot</sub> and C<sub>org</sub>/P<sub>org</sub> ratios (molar) in the sediment solid phase during anoxia are presented in Fig. 1. Our C<sub>org</sub>, N<sub>tot</sub>, P<sub>tot</sub>, P<sub>inorg</sub>, P<sub>org</sub> and Si<sub>biog</sub> results (Fig. 1) from normoxic phase agreed with previously reported values from surficial sediment at this study site (Čermelj et al., 1997; Ogrinc et al., 2005). Little vertical variation of concentrations in all measured parameters was observed except those of P<sub>tot</sub> and Si<sub>biog</sub>, which decreased with depth. The C<sub>org</sub>/N<sub>tot</sub> ratios (molar) ranged from 6 to 12 and C<sub>org</sub>/P<sub>org</sub> ratios (molar) averaged about 200 both roughly corroborating with the values typical for OM of marine origin (Ogrinc et al., 2005).

During the 1 month and 2 months anoxic phases the C<sub>org</sub>/N<sub>tot</sub> ratios rose to values from 12 to 15 and 11 to 21, respectively, due to the dropping of N<sub>tot</sub> levels. Interestingly, the results of 1 yr anoxia showed relatively high values of N<sub>tot</sub>, comparable to those in normoxia, with C<sub>org</sub> values being higher than in all short-term experiments. Only changes in the pool of P<sub>org</sub> were observed and the degradation of P<sub>org</sub> was most noticeable in the 2 months anoxia experiment reflecting in higher C<sub>org</sub>/P<sub>org</sub> ratios. Si<sub>biog</sub> levels increased in the 7 days anoxia but were somewhat lower in the longer anoxic conditions. In the recovery phases, the C<sub>org</sub> and P<sub>tot</sub> and P<sub>org</sub> values remained approximately unchanged in 7 days recovery but were higher in 1 month recovery. Conversely, N<sub>tot</sub> values in both phases were much lower than in normoxia.

## 3.2 Nutrients

Concentrations of NH<sub>4</sub><sup>+</sup> and PO<sub>4</sub><sup>3-</sup>, during normoxia (Fig. 2), were low and relatively constant throughout the whole sediment core, reaching values between 20 and 115 µmol L<sup>-1</sup> for NH<sub>4</sub><sup>+</sup> and 2 and 40 µmol L<sup>-1</sup> for PO<sub>4</sub><sup>3-</sup>, respectively. Concentrations in overlaying water were lower, around 1 µmol L<sup>-1</sup> for NH<sub>4</sub><sup>+</sup> and 0.1 µmol L<sup>-1</sup> for PO<sub>4</sub><sup>3-</sup>.

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Pore water $NO_3^-$ concentrations (not presented) in the normoxic phase ranged from 5 to 35 µmol L$^{-1}$, whereas the concentration in overlaying water was around 0.1 µmol L$^{-1}$. The profile of dSi showed lower concentrations at SWI and uniform levels at about 100 µmol L$^{-1}$ at all analyzed depths. Normoxic pore water profiles are comparable to those previously reported for the same sampling point (Čermelj et al., 1997; Ogrinc and Faganeli, 2006; Faganeli and Ogrinc, 2009).

Pore water profiles of $NH_4^+$, $PO_4^{3-}$ and dSi during anoxia are presented in Fig. 2. Concentrations of $NH_4^+$ in the 7 days anoxia experiment were much higher compared to normoxic concentrations (Fig. 2) and ranged from 100 to 200 µmol L$^{-1}$ showing two distinct peaks at depths between 1.5 and 2 cm and between 4 and 5 cm, respectively. In 1 month anoxia, the concentrations of $NH_4^+$ were even higher reaching maximum values of 700 µmol L$^{-1}$. There was a noticeable increase in concentrations at the depths between 0.5 and 4 cm. In the 2 months and 1 yr anoxia experiment, the concentrations of $NH_4^+$ dropped and stabilized around 300 µmol L$^{-1}$ and 200 µmol L$^{-1}$, respectively. Concentrations of $NO_3^-$ (not presented) in the 7 days and 1 month anoxia experiments did not change much and were comparable to those in normoxic conditions, ranging from 10 to 40 µmol L$^{-1}$, with peaks overlapping those of $NH_4^+$ profiles. In the 2 months and 1 yr anoxia experiments, its concentrations rose reaching values up to 100 µmol L$^{-1}$. The 7 days anoxia $PO_4^{3-}$ profile was similar to $NH_4^+$ profile. Concentrations rose only in two active layers reaching values of 20 and 40 µmol L$^{-1}$, respectively. In the $PO_4^{3-}$ depth profiles in the 1 month, 2 months and 1 yr anoxia experiments, the concentrations remained nearly constant throughout the sediment cores. Concentrations ranged from 0.5 to 9 µmol L$^{-1}$, and therefore, did not exceed the values observed in the normoxia or 7 days anoxia experiments. Concentrations of dSi during all anoxia experiments (Fig. 2) increased to levels > 200 µmol L$^{-1}$. High pore water dSi levels, around 150 µmol L$^{-1}$, also remained during reoxidation phases. Observed irregular ("disrupted") depth profiles of $NH_4^+$ after 1 month recovery and $PO_4^{3-}$ and dSi observed after 1 yr of recovery indicate the importance of enhanced bioturbation.
Vertical pore water profiles of Ca and Mg concentrations (Fig. 3) showed lower values in anoxic phases, particularly for Mg during 7 days and 1 month anoxia. In 1 month and 1 yr recovery experiments, pore water Ca concentrations increased to higher values than observed in normoxia while Mg concentrations reached levels approximately those encountered in normoxia. Changing of dissolved Fe and Mn (Fe(II) and Mn(II)) concentrations during anoxia experiments are shown in Fig. 3. In 7 days anoxia, there was a notable increase of Fe and Mn concentrations in pore waters compared to values under normoxic conditions. Concentrations increased from values of less than 5 µmol L⁻¹ for Fe and 35 µmol L⁻¹ for Mn, to 35 µmol L⁻¹ for Fe and 110 µmol L⁻¹ for Mn. Two distinct vertical peaks can be seen, one at depth of 0–0.5 cm and other at 2–4 cm. In the 1 month, 2 months and 1 yr anoxia experiments, the concentrations of Fe were notably lower compared to 7 days anoxia, but still higher than in normoxia. Peaks of increased Fe(II) release into pore waters remain noticeable. Mn profiles in the 7 days and 1 yr anoxia experiments were almost identical to profiles of Fe. Profiles of Mn from 1 month and 2 months anoxia experiments did not show any concentration changes throughout the sediment core. However, the concentrations of dissolved Mn in prolonged anoxia dropped from 150 to 5 µmol L⁻¹.

The comparison between depth profiles of model calculated and measured NH₄⁺, PO₄³⁻ and dSi concentrations are presented in Fig. 2. The diagenetic model gave quite a good description of the distribution of nutrients in pore water of 1 month and 1 yr anoxia and 1 month recovery experiments, however, the 1 yr recovery experiment conditions were not reproduced well, since no clear pattern in the measured distribution of nutrient concentrations was observed probably due to enhanced bioturbation. Furthermore, it was also observed that the depth attenuation coefficient increased with the increasing time of the anoxic condition present for both NH₄⁺ and PO₄³⁻ from 2.0 to 6.3 and from

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1.6 to 3.8, respectively. These data show a more pronounced release of both nutrients due to more intense remineralization processes.

Based on the diagenetic models, the diffusive fluxes were calculated and the data are presented in Table 2. The calculated $NH_4^+$ benthic fluxes ranged from -34 to 513 $\mu mol m^{-2} day^{-1}$ and those of $PO_4^{3-}$ from 1.3 to 13.8 $\mu mol m^{-2} day^{-1}$. The highest $NH_4^+$ efflux was observed after one month of anoxia. On the other hand, the influx of $NH_4^+$ into sediments was observed after one year of recovery. The dSi fluxes ranged from -140 to 286 $\mu mol m^{-2} day^{-1}$. Fe and Mn exhibited the highest effluxes in 7 days and 1 month anoxia reaching values of 16.6 and 20.1 $\mu mol m^{-2} day^{-1}$, respectively. In these experiments, the influx of Ca into sediment was mainly observed ranging from -10 to -700 $\mu mol m^{-2} day^{-1}$ except after 7 days and 1 month recovery. Similar dynamics was found for Mg.

## 4 Discussion

Our study documents the sequential biogeochemical changes occurring during the OM degradation and nutrient regeneration in relatively OM poor coastal surface sediments of the Gulf of Trieste under various redox conditions: normoxic, anoxic and reoxic. It can be seen that the longer the span of anoxia the less pronounced is the rise of concentrations of $NH_4^+$ and $PO_4^{3-}$ in pore waters. The majority of $NH_4^+$ and $PO_4^{3-}$ regeneration in anoxic marine environments likely results from hydrolytic and/or fermentative processes that produce low molecular weight molecules from complex sedimentary OM (Burdige, 2002). The utilization of these compounds by sulphate reducing bacteria then results in the complete mineralization of sedimentary OM (Burdige, 2002). Consequently, the sedimentary $C_{org}/N_{org}$ ratios and $C_{org}/P_{org}$ ratios generally increase with depth in surface coastal marine and estuarine sediments (Hedges and Keil, 1995). This is usually considered as an indication of preferential mineralization of organic nitrogen and phosphorus in sediments and that the more labile fractions have lower $C_{org}/N_{org}$
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and C<sub>org</sub>/P<sub>org</sub> ratios than the bulk sedimentary OM (Hedges and Keil, 1995; Ingall and Jahnke, 1997). In anoxic conditions, higher pore water NH<sub>4</sub><sup>+</sup> and PO<sub>4</sub><sup>3-</sup> levels can be also related with the higher density of decaying infaunal organisms providing additional easily degradable “fresh” OM to microbes (Riedel et al., 2013). It was demonstrated, using <sup>15</sup>N incubations, that in the deep Skagerrak sediments the pore water NH<sub>4</sub><sup>+</sup> is the main end product of anoxic N mineralization (Thamdrup and Dalsgaard, 2000). A build-up of NH<sub>4</sub><sup>+</sup> in pore waters can also be a consequence of other processes in the N cycle, which can be important in anoxic environments and can simultaneously proceed in microniches. One of them is dissimilatory nitrate reduction to ammonium (DNRA) (Gardner et al., 2006) which can supersede respiratory denitrification as a process of NO<sub>3</sub><sup>-</sup> removal from the system, when labile organic matter is more available, redox potential and ambient NO<sub>3</sub><sup>-</sup> concentrations are low, and when H<sub>2</sub>S production is high (Canfield et al., 2005). The NO<sub>3</sub><sup>-</sup> behaviour in sediments of the Gulf of Trieste was somewhat unusual since it was expected to decrease in anoxic pore waters due to denitrification, which rapidly removes NO<sub>3</sub><sup>-</sup>. Results of the 2 months anoxia experiment indicated a possible breach in anoxia, since increased concentrations of NO<sub>3</sub><sup>-</sup> were seen at two separate depths suggesting that there was an active sediment re-working (outside chamber) and laterally pumping of overlying oxygenated water into deeper layers of chamber sediment (Čermelj et al., 1997). Anamox (anaerobic ammonium oxidation), another important nitrogen process, might be running simultaneously (Dalsgaard et al., 2005) and might explain the increased values of NO<sub>3</sub><sup>-</sup> in anoxic conditions, which is probably formed as a byproduct in CO<sub>2</sub> reduction, especially in the 2 months and 1 yr anoxia experiments (van de Graaf et al., 1997). Within the current knowledge of N cycling in marine sediments, it is suggested that in environments with relatively high C<sub>org</sub> concentrations and high free H<sub>2</sub>S concentrations, respiratory denitrification is suppressed (because of enzyme inhibition), therefore making DNRA and anammox more important processes for N recycling (Burgin and Hamilton, 2007). Bottom water hypoxia and anoxia typically lead to increased regeneration of P from sediments and thus increased recycling of P in the system (Conley et al., 2009). Significant
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amount of P is released from Fe-(oxy)hydroxides upon transition from oxic to anoxic conditions (Ogrinc and Faganeli, 2006; Faganeli and Ogrinc, 2009). Enhanced microbial and chemical dissolution of Si<sub>biog</sub> (opal) proceeded in anoxic conditions (Canfield et al., 2005; Belias et al., 2007) and remained high in recovery phases.

Distribution of Mn, Fe, Ca and Mg in pore waters (Fig. 3) further support the thesis of an active microbial metabolism in sediments. Results of Fe and Mn in the 7 days anoxia experiment show an enhanced release of these species to the water column indicating an active Fe and Mn reduction/respiration in these layers. The results clearly show Fe and Mn reduction processes since the concentrations of dissolved species notably rise. When the system is subjected to prolonged anoxic conditions, the importance of Fe and Mn reduction from our set of results (Fig. 3) becomes less evident. These processes are energetically more favourable than sulphate reduction (Froelich et al., 1979) and even though the DET results (Metzger et al., 2013) indicate that sulphate reduction is the preferential anaerobic microbial process in early diagenesis in these coastal sediments, Fe and Mn reduction can proceed in some microniches. DET results of SO<sub>4</sub><sup>2-</sup> concentrations during anoxia experiments (Metzger et al., 2013) also clearly showed the migration of redox layers towards SWI and the increasing importance of sulphate reduction over prolonged anoxia spans. The prevalence of sulphate reduction, as a major anaerobic path of early OM diagenesis in coastal marine sediments, over other electron acceptors, was demonstrated for surface sediments in the Gulf of Trieste (Hines et al., 1997). In anoxic conditions, Ca and Mg pore water concentrations indicate lower carbonate dissolution or even carbonate precipitation as previously postulated for surface anoxic sediments of the Gulf of Trieste (Čermelj et al., 2001; Ogrinc et al., 2003).

In the recovery experiments, the normoxic biogeochemical conditions of metals were almost completely restored in 7 days even though this was not completely true for higher organisms (infauna). Reoxygenation of previously anoxic sediments promotes OM remineralization (Hulthe et al., 1998; Bastviken et al., 2004). Unfortunately, data on pore water nutrient concentrations in 7 days recovery period following an O<sub>2</sub> water
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penetration are missing. We observed, however, a peak of NO₃⁻ at a depth of 4–5 cm in the 7 days reoxygenation phase, which may be a consequence of enhanced bioturbation also clearly evident in NH₄⁺, dSi and Fe pore water profiles especially in the 1 yr recovery experiment. Nitrification was a likely cause of relative NH₄⁺ depletion. When oxic conditions reappears P precipitates quickly as authigenic carbonate fluorapatite, FePO₄ or it is adsorbed onto Fe-hydroxides (Ogrinc and Faganeli, 2006), most probably onto goethite having a large sorption capacity for phosphate (Arčon et al., 1999). This is confirmed by the rapid decrease of pore water Fe concentrations after 7 days of recovery precipitating as Fe-oxyhydroxides. Increased pore water Ca concentrations in longer recovery experiments reflect enhanced carbonate dissolution in oxic conditions (Ogrinc et al., 2003).

The differences between N, P and Si cycling in oxic, anoxic and reoxic phases can be estimated by comparing their benthic diffusive fluxes and burial. The amount of N<sub>tot</sub>, P<sub>tot</sub> and Si<sub>biog</sub> buried in sediment was calculated from the sedimentation rate (ω) and the concentration (C) of sedimentary N<sub>tot</sub>, P<sub>tot</sub> and Si<sub>biog</sub> in the deepest measured sediment layer (approximately 7 cm), since they are nearly constant and less affected by bioturbation, using the following equation:

$$ \text{Burial} = \omega C \rho (1 - \Phi) \quad (6) $$

ρ is the dry density (2.5 g cm⁻³; Ogorelec et al., 1991), Φ porosity (0.55) and ω sedimentation rate (1.2 mm yr⁻¹) estimated from ²¹⁰Pb measurements (Faganeli et al., 1991). Burial fluxes of N<sub>tot</sub>, P<sub>tot</sub> and Si<sub>biog</sub> amounted to 170, 30 and 6800 µmol m⁻² day⁻¹, respectively. Comparison between benthic fluxes (Table 2) and burial revealed that the intensive recycling of dissolved inorganic N at the SWI is enhanced in anoxic conditions while P benthic fluxes appear extremely low even in anoxic phases despite the evident increase of Fe (and Mn) fluxes particularly in early anoxic stages (Table 2). This suggests an important role of P precipitation as authigenic carbonate fluoroapatite (Ingall and Jahnke, 1997). Si recycling appears much less intensive compared to burial flux in all redox phases indicating rather low Si<sub>biog</sub> solubility.
5

Conversely, carbonates seem more reactive showing precipitation (Ca and Mg influx) in anoxic conditions. The comparison between diffusive and laboratory incubated benthic fluxes in oxic and anoxic conditions, reported previously for the same sampling point (Faganeli and Ogrinc, 2009), reveals lower values of $NH_4^+$ and $PO_4^{3-}$ diffusive fluxes for both conditions which can be attributed to the presence of bioturbation, not included in modelling approach, and differences in experimental approach. Benthic fluxes integrate the processes in the whole sedimentary column while diffusive fluxes consider changes at SWI.

## 5 Conclusions

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1. The study of sequential nutrient regeneration and OM degradation in surface sediments of the Gulf of Trieste under normoxic, anoxic and reoxic conditions were primarily focused into variations of pore water composition. $NH_4^+$ and $PO_4^{3-}$ regeneration was more intensive in anoxic phases but prolonged span of anoxia reduced their increase. Consequently, the solid phase $N_{tot}$ and $P_{org}$ contents decreased increasing $C_{org}/N_{tot}$ and $C_{org}/P_{org}$ ratios. Higher pore water $NH_4^+$ levels were presumably also a consequence of dissimilatory nitrate reduction to $NH_4^+$ that is a concurrent process of denitrification in removing $NO_3^-$. The presence of $NO_3^-$ in anoxic phases can be explained by the presence of anammox and laterally pumping of oxygenated water by benthic infauna. Enhanced dissolution of $Si_{biog}$ was also observed in anoxic phases. Anoxic phases were characterized by higher pore water Fe and Mn concentrations as a result of reduction/respiration which is prevailed by sulphate reduction. The decreased pore water Ca and Mg concentrations compared to normoxia indicated carbonate precipitation.

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2. Reoxygenation was characterized by enhanced bioturbation. Nitrification caused $NH_4^+$ decrease and $P$ precipitated quickly as carbonate fluorapatite, $FePO_4$ and it

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is adsorbed onto Fe-hydroxides since Fe (and Mn) reoxidized quickly. Increased Ca levels suggested enhanced carbonate dissolution.

3. Diffusive benthic fluxes at the SWI, calculated from pore water modelling using diffusion-reaction model, showed high anoxic $NH_4^+$ effluxes and Ca (and Mg) in-fluxes according to described processes. $PO_4^{3-}$ fluxes were very low despite pro-nounced anoxic Fe and Mn effluxes. High $NH_4^+/PO_4^{3-}$ flux ratios in anoxic and reoxic phases suggest an excess of N in the benthos. Nutrient budgets at the SWI, i.e. comparison between diffusive benthic and burial fluxes, showed intensive anoxic recycling of inorganic N but low P and Si recycling in all redox phases.

*Acknowledgements.* The research was conducted in the framework of the Austrian Science Fund (FWF) project P21542-B17 entitled "Low dissolved oxygen events in the Northern Adriatic: in situ experimental insights into benthic responses before, during and post-anoxia". This part of the research was also financially supported by the Research Programme P1-0143 and the Young Researcher Programme of the Slovenian Research Agency (ARRS). We thank M. Stachowitsch, M. Zuschin, I. Gallmetzer and A. Haselmair for technical and diving support.

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<table><caption>**Table 1.** Parametres used in the diffusion-advection-reaction model. Values marked with <sup>a</sup> were measured values, the others were output model data.</caption><thead><tr><th>Parameters</th><th>Units</th><th>Value</th><th>Description</th></tr></thead><tbody><tr><td>D<sub>s</sub> (NH<sub>4</sub><sup>+</sup>)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>9.06–10.9</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (PO<sub>4</sub><sup>3-</sup>)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>2.78–3.40</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (dSi)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>4.54–5.56</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (Ca)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>3.72–4.56</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (Mg)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>3.17–3.81</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (Mn)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>3.05–3.73</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>D<sub>s</sub> (Fe)</td><td>10<sup>-6</sup> cm<sup>2</sup> s<sup>-1</sup></td><td>2.76–3.37</td><td>Sediment diffusion coefficient<sup>a</sup></td></tr><tr><td>Ω</td><td>Cm yr<sup>-1</sup></td><td>0.15</td><td>Sedimentation rate<sup>a</sup></td></tr><tr><td>Φ</td><td></td><td>0.49–0.62</td><td>Porosity in sediments<sup>a</sup></td></tr><tr><td>k<sub>m</sub></td><td>10<sup>-7</sup> s<sup>-1</sup></td><td>17–1083</td><td>Rate constant for silicate dissolution</td></tr><tr><td>K<sub>N</sub></td><td></td><td>1.3</td><td>Equilibrium constant for NH<sub>4</sub><sup>+</sup></td></tr><tr><td>K<sub>P</sub></td><td></td><td>2</td><td>Equilibrium constant for PO<sub>4</sub><sup>3-</sup></td></tr><tr><td>β<sub>N</sub></td><td>cm<sup>-1</sup></td><td>1.81–6.32</td><td>Attenuation depth constant for NH<sub>4</sub><sup>+</sup></td></tr><tr><td>β<sub>P</sub></td><td>cm<sup>-1</sup></td><td>0.73–3.88</td><td>Attenuation depth constant for PO<sub>4</sub><sup>3-</sup></td></tr><tr><td>C<sub>z</sub> = 0</td><td>μmol L<sup>-1</sup></td><td>0.31–1.56</td><td>Concentration of NH<sub>4</sub><sup>+</sup></td></tr><tr><td>C<sub>z</sub> = 0</td><td>μmol L<sup>-1</sup></td><td>0.98–55.5</td><td>Concentration of PO<sub>4</sub><sup>3-</sup></td></tr></tbody></table>
<table><caption>**Table 2.** Diffusive benthic fluxes of nutrients and metals from different experiments calculated from diffusion–advection–reaction model and pore water concentration gradients.</caption><thead><tr><th>Date</th><th>Eksperiment</th><th>T<br>°C</th><th>NH<sub>4</sub><sup>+</sup></th><th>PO<sub>4</sub><sup>3-</sup><br>µmol m<sup>-2</sup> day<sup>-1</sup></th><th>dSi</th><th>Mn</th><th>Fe</th><th>Ca<br>mmol m<sup>-2</sup> day<sup>-1</sup></th><th>Mg</th></tr></thead><tbody><tr><td>3 Aug 2010</td><td>normoxia</td><td>23.0</td><td>108</td><td>13.4</td><td>36.5</td><td>3.69</td><td>-0.21</td><td>-0.07</td><td>-0.40</td></tr><tr><td>11 Aug 2010</td><td>7d anoxia</td><td>25.2</td><td>194</td><td>13.8</td><td>-140</td><td>8.17</td><td>16.6</td><td>-0.19</td><td>-1.09</td></tr><tr><td>18 Aug 2010</td><td>7d recovery</td><td>24.5</td><td></td><td></td><td>61.5</td><td>0.45</td><td>3.14</td><td>0.07</td><td>0.07</td></tr><tr><td>25 Aug 2010</td><td>1mo anoxia</td><td>25.5</td><td>513</td><td>4.72</td><td>97.8</td><td>20.1</td><td>7.66</td><td>-0.70</td><td>-2.63</td></tr><tr><td>22 Sep 2010</td><td>1mo recovery</td><td>20.5</td><td>47.9</td><td>7.51</td><td>181</td><td>-2.87</td><td>7.75</td><td>0.37</td><td>0.12</td></tr><tr><td>23 Sep 2010</td><td>2mo anoxia</td><td>21.5</td><td>343</td><td>7.39</td><td>78.7</td><td>5.64</td><td>-0.05</td><td>-0.45</td><td>0.31</td></tr><tr><td>5 Aug 2011</td><td>1y anoxia</td><td>24.7</td><td>196</td><td>1.32</td><td>286</td><td>1.87</td><td>3.17</td><td>-0.35</td><td>-1.05</td></tr><tr><td>22 Oct 2011</td><td>1y recovery</td><td>17.0</td><td>-34.0</td><td>2.24</td><td>75.7</td><td>7.11</td><td>2.32</td><td>-0.01</td><td>-0.98</td></tr></tbody></table>

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Interactive Discussion
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<figure><img src="image_101.png" /><figcaption>**Fig. 1.** Distribution of C<sub>org</sub>, N<sub>tot</sub>, P<sub>tot</sub>, P<sub>inorg</sub>, P<sub>org</sub>, C/N and C<sub>org</sub>/P<sub>org</sub> ratios together with Si<sub>biog</sub> in sediment solid phase during normoxic-anoxic-reoxic experiments performed in the Gulf of Trieste.</figcaption></figure>
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<figure><img src="image_106.png" /><figcaption>**Fig. 2.** Depth profiles of pore water $NH_4^+$, $PO_4^{3-}$ and dSi together with model calculation data during various experiments in the Gulf of Trieste. Measured data – white dots; model calculation data – black dots.</figcaption></figure>
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<figure><img src="image_111.png" /><figcaption>**Fig. 3.** Depth profiles of Ca, Mg, Mn and Fe in pore waters during normoxic–anoxic–reoxic experiments performed in the Gulf of Trieste.</figcaption></figure>