Benthic fluxes in a tropical Estuary and their role in the ecosystem

In-situ measurements of benthic fluxes of oxygen and nutrients were made in the subtidal region of the Mandovi estuary during premonsoon and monsoon seasons to understand the role of sediment–water exchange processes in the estuarine ecosystem. The Mandovi estuary is a shallow, highly dynamic, macrotidal estuary which experiences marine condition in the premonsoon season and nearly fresh water condition in the monsoon season. The benthic flux of nutrients exhibited strong seasonality, being higher in the premonsoon compared to the monsoon season which explains the higher ecosystem productivity in the dry season in spite of negligible riverine nutrient input. NH₄⁺ was the major form of released N comprising 70–100% of DIN flux. The benthic respiration rate varied from −98.91 to −35.13 mmol m⁻² d⁻¹, NH₄⁺ flux from 5.15 to 0.836 mmol m⁻² d⁻¹, NO₃⁻ + NO₂⁻ from 0.06 to −1.06 mmol m⁻² d⁻¹, DIP from 0.12 to 0.23 mmol m⁻² d⁻¹ and SiO₄⁴⁻ from 5.78 to 0.41 mmol m⁻² d⁻¹ between premonsoon to monsoon period. The estuarine sediment acted as a net source of DIN in the premonsoon season, but changed to a net sink in the monsoon season. Variation in salinity seemed to control NH₄⁺ flux considerably. Macrofaunal activities, especially bioturbation, enhanced the fluxes 2–25 times. The estuarine sediment was observed to be a huge reservoir of NH₄⁺, PO₄³⁻ and SiO₄⁴⁻ and acted as a net sink of combined N because of the high rate of benthic denitrification as it could remove 22% of riverine DIN influx thereby protecting the eco system from eutrophication and consequent degradation. The estuarine sediment was responsible for ∼30–50% of the total community respiration in the estuary. The benthic supply of DIN, PO₄³⁻ and SiO₄⁴⁻ can potentially meet 49%, 25% and 55% of algal N, P and Si demand, respectively, in the estuary. Based on these observations we hypothesize that it is mainly benthic NH₄⁺ efflux that sustains high estuarine productivity in the NO₃⁻ depleted dry season.     

Benthic metabolism and the fate of dissolved inorganic nitrogen in intertidal sediments

We determined patterns of benthic metabolism and examined the relative importance of denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) as sinks for nitrate (NO₃⁻) in intertidal sediments in the presence and absence of benthic microalgal (BMA) activity. By influencing the activity of BMA, light regulated the metabolic status of the sediments, and, in turn, exerted strong control on sediment nitrogen dynamics and the fate of inorganic nitrogen. A pulsed addition of ¹⁵N-labeled NO₃⁻ tracked the effect and fate of dissolved inorganic nitrogen (DIN) in the system. Under illuminated conditions, BMA communities influenced benthic fluxes directly, via DIN uptake, and indirectly, by altering the oxygen penetration depth. Under dark hypoxic and anoxic conditions, the fate of water column NO₃⁻ was determined largely by three competing dissimilatory reductive processes; DNF, DNRA, and, on one occasion, anaerobic ammonium oxidation (anammox). Mass balance of the added ¹⁵N tracer illustrated that DNF accounted for a maximum of 48.2% of the ¹⁵NO₃⁻ reduced while DNRA (a minimum of 11.4%) and anammox (a minimum of 2.2%) accounted for much less. A slurry experiment was employed to further examine the partitioning between DNF and DNRA. High sulfide concentrations negatively impacted rates of both processes, while high DOC:NO₃⁻ ratios favored DNRA over DNF.     

Effects of irradiance on benthic and water column processes in a Gulf of Mexico estuary: Pensacola Bay, Florida, USA

We examined the effect of light on water column and benthic fluxes in the Pensacola Bay estuary, a river-dominated system in the northeastern Gulf of Mexico. Measurements were made during the summers of 2003 and 2004 on 16 dates distributed along depth and salinity gradients. Dissolved oxygen fluxes were measured on replicate sediment and water column samples exposed to a gradient of photosynthetically active radiation. Sediment inorganic nutrient (NH₄⁺, NO₃⁻, PO₄³⁻) fluxes were measured. The response of dissolved oxygen fluxes to variation in light was fit to a photosynthesis–irradiance model and the parameter estimates were used to calculate daily integrated production in the water column and the benthos. The results suggest that shoal environments supported substantial benthic productivity, averaging 13.6 ± 4.7 mmol O₂ m⁻² d⁻¹, whereas channel environments supported low benthic productivity, averaging 0.5 ± 0.3 mmol O₂ m⁻² d⁻¹ (±SE). Estimates of baywide microphytobenthic productivity ranged from 8.1 to 16.5 mmol O₂ m⁻² d⁻¹, comprising about 16–32% of total system productivity. Benthic and water column dark respiration averaged 15.2 ± 3.2 and 33.6 ± 3.7 mmol O₂ m⁻² d⁻¹, respectively Inorganic nutrient fluxes were generally low compared to relevant estuarine literature values, and responded minimally to light exposure. Across all stations, nutrient fluxes from sediments to the water column averaged 1.11 ± 0.98 mmol m⁻² d⁻¹ for NH₄⁺, 0.58 ± 1.08 mmol m⁻² d⁻¹ for NO₃⁻, 0.01 ± 0.09 mmol m⁻² d⁻¹ for PO₄³⁻. The results of this study illustrate how light reaching the sediments is an important modulator of benthic nutrient and oxygen dynamics in shallow estuarine systems.     

Impact of a flood event on benthic and pelagic coupling in a sub-tropical east Australian estuary (Brunswick)

We examined the impact of a 1:3 year return period flood on benthic and pelagic coupling in the river-dominated sub-tropical Brunswick Estuary. The flood had a significant impact on the study site flushing it with freshwater, reducing the flushing time 0.6 days, increasing nutrient concentrations in the water column and scouring the sediment surface. In the three weeks post-flood the benthic and pelagic systems alternated between being coupled and un-coupled via dissolved, particulate and living material pathways. Immediately post-flood benthic and pelagic coupling via the deposition of phyto-detritus and viable algal cells was reduced due to the scouring of the top sediment layers, and benthic respiration and productivity and NH₄⁺ effluxes all decreased correspondingly. In contrast, benthic and pelagic coupling was enhanced via the uptake and denitrification of NO₃⁻ due to elevated NO₃⁻ concentrations in the water column. Some of the NO₃⁻ consumed by the sediments may have also been converted to DON. Two weeks post-flood benthic and pelagic coupling was significantly enhanced via the deposition of phyto-detritus and viable algal cells associated with a phytoplankton bloom in the water column. This increased supply of phyto-detritus and viable algal cells rapidly increased benthic respiration and productivity and NH₄⁺ efflux. The depletion of water column DIN by the phytoplankton bloom resulted in a de-coupling of the benthic and pelagic systems via the uptake and denitrification of NO₃⁻. However, benthic and pelagic coupling was enhanced via the uptake of NH₄⁺ by benthic microalgae. Three weeks post-flood the phytoplankton bloom had collapsed and the coupling between the benthic and pelagic systems via the deposition of phyto-detritus and living algal cells had diminished. Again benthic and pelagic coupling was enhanced via the uptake and denitrification of NO₃⁻ due to elevated NO₃⁻ concentrations in the water column associated with the recycling of bloom material. Overall the sediments became less heterotrophic (increasing benthic productivity/respiration ratio) following the flood. Floods can cause rapid and complex changes in the coupling between benthic and pelagic systems in sub-tropical estuaries.     

Tidal time-scale variation in nutrient flux across the sediment–water interface of an estuarine tidal flat

We determined the range of the tidal variations in nutrient flux across the sediment–water interface and elucidated mechanisms of the flux variation in two estuarine intertidal flats (one sand, one mud) in northeastern Japan. Nutrient flux was measured using in situ light and dark chambers, which were incubated for 2 h, 2–6 times per day. Results showed that nutrient concentration in overlying water varied by tide and was also affected by sewage-treated water inflow. The nutrient fluxes responded quickly to the tidal variation in overlying water chemistry and the range of the variation in flux was as large as the seasonal-scale variation reported in previous studies. In the sand flat, salinity increase likely enhanced benthos respiration and led to increases in both O₂ consumption and PO₄³⁻ regeneration under low illumination, while benthic microalgae were likely to actively generate O₂, uptake PO₄³⁻ and suppress PO₄³⁻ release under high illumination (>900 μmol photons m⁻² s⁻¹). Also in the mud flat, PO₄³⁻ flux was related with O₂ flux, although the range of temporal variation in PO₄³⁻ flux was small. In both the flats, NH₄⁺ flux was always governed by NH₄⁺ concentration in the overlying water; either an increase in NH₄⁺ uptake or a decrease in NH₄⁺ release was observed as the NH₄⁺ concentration rose due to inflow of river water or input of sewage-treated water. Although NO₃⁻ tended to be released in both tidal flats when low NO₃⁻ concentration seawater dominated, their relationship was likely to be weakened under conditions of low oxygen consumption and suppressed denitrification. It is likely that tidal variation in nutrient flux is governed more by the nutrient concentration than other factors, such as benthic biological processes, particularly in the case where nutrient concentration in the overlying water is relatively high and with wide amplitude.     

Benthic fluxes in a tidal salt marsh creek affected by fish farm activities: Río San Pedro (Bay of Cádiz,SW Spain)

Benthic fluxes of dissolved inorganic carbon, total alkalinity, oxygen, nutrients, nitrous oxide and methane were measured in situ at three sites of Río San Pedro salt marsh tidal creek (Bay of Cádiz, SW Spain) during three seasons. This system is affected by the discharges of organic carbon and nutrients from the surrounding aquaculture installations. Sediment oxygen uptake rates and inorganic carbon fluxes ranged respectively from 16 to 79 mmol O₂ m^? 2 d^? 1 and from 48 to 146 mmol C m^? 2 d^? 1. Benthic alkalinity fluxes were corrected for the influence of NH₄⁺ and NO₃^? + NO₂^? fluxes, and the upper and lower limits for carbon oxidation rates were inferred by considering two possible scenarios: maximum and minimum contribution of CaCO₃ dissolution to corrected alkalinity fluxes. Average C_ox rates were in all cases within ± 25% of the upper and lower limits and ranged from 40 to 122 mmol C m^? 2 d^? 1. Whereas carbon mineralization did not show significant differences among the sites, C_ox rates varied seasonally and were correlated with temperature (r² = 0.72). During winter and spring denitrification was estimated to account for an average loss of 46% and 75%, respectively, of the potentially recyclable N, whereas during the summer no net removal was observed. A possible shift from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) during this period is argued. Dissolved CH₄ and N₂O fluxes ranged from 5.7 to 47 μmol CH₄ m^? 2 d^? 1 and 4.3 to 49 μmol N–N₂O m^? 2 d^? 1, respectively, and represented in all cases a small fraction of total inorganic C and N flux. Overall, about 60% of the total particulate organic matter that is discharged into the creek by the main fish farm facility is estimated to degrade in the sediments, resulting in a significant input of nutrients to the system.     

Benthic fluxes of nitrogen in the tidal reaches of a turbid, high-nitrate sub-tropical river

Benthic fluxes of dissolved inorganic nitrogen (NO₃⁻ and NH₄⁺), dissolved organic nitrogen (DON), N₂ (denitrification), O₂ and TCO₂ were measured in the tidal reaches of the Bremer River, south east Queensland, Australia. Measurements were made at three sites during summer and winter. Fluxes of NO₃⁻ were generally directed into the sediments at rates of up to −225 μmol N m⁻² h⁻¹. NH₄⁺ was mostly taken up by the sediments at rates of up to −52 μmol N m⁻² h⁻¹, its ultimate fate probably being denitrification. DON fluxes were not significant during winter. During summer, fluxes of DON were observed both into (−105 μmol m⁻² h⁻¹) and out of (39 μmol m⁻² h⁻¹) the sediments. Average N₂ fluxes at all sampling sites were similar during summer (162 μmol N m⁻² h⁻¹) and winter (153 μmol N m⁻² h⁻¹). Denitrification was fed both by nitrification within the sediment and NO₃⁻ from the water column. Sediment respiration rates played an important role in the dynamics of nitrification and denitrification. NO₃⁻ fluxes were significantly related to TCO₂ fluxes (p<0.01), with a release of NO₃⁻ from the sediment only occurring at respiration rates below 1000 μmol C m⁻² h⁻¹. Rates of denitrification increased with respiration up to TCO₂ fluxes of 1000 μmol C m⁻² h⁻¹. At sediment respiration rates above 1000 μmol C m⁻² h⁻¹, denitrification rates increased less rapidly with respiration in winter and declined during summer. On a monthly basis denitrification removed about 9% of the total nitrogen and 16% of NO₃⁻ entering the Bremer River system from known point sources. This is a similar magnitude to that estimated in other tidal river systems and estuaries receiving similar nitrogen loads. During flood events the amount of NO₃⁻ denitrified dropped to about 6% of the total river NO₃⁻ load.     

Nitrogen cycling in deep-sea sediments of the Porcupine Abyssal Plain, NE Atlantic

Rates of transformation, recycling and burial of nitrogen and their temporal and spatial variability were investigated in deep-sea sediments of the Porcupine Abyssal Plain (PAP), NE Atlantic during eight cruises from 1996 to 2000. Benthic fluxes of ammonium (NH₄) and nitrate (NO₃) were measured in situ using a benthic lander. Fluxes of dissolved organic nitrogen (DON) and denitrification rates were calculated from pore water profiles of DON and NO₃, respectively. Burial of nitrogen was calculated from down core profiles of nitrogen in the solid phase together with ¹⁴C-based sediment accumulation rates and dry bulk density. Average NH₄ and NO₃-effluxes were 7.4 ± 19 μmol m⁻² d⁻¹ (n = 7) and 52 ± 30 μmol m⁻² d⁻¹ (n = 14), respectively, during the period 1996–2000. During the same period, the DON-flux was 11 ± 5.6 μmol m⁻² d⁻¹ (n = 5) and the denitrification rate was 5.1 ± 3.0 μmol m⁻² d⁻¹ (n = 22). Temporal and spatial variations were only found in the benthic NO₃ fluxes. The average burial rate was 4.6 ± 0.9 μmol m⁻² d⁻¹. On average over the sampling period, the recycling efficiency of the PON input to the sediment was 94% and the burial efficiency hence 6%. The DON flux constituted 14% of the nitrogen recycled, and it was of similar magnitude as the sum of burial and denitrification. By assuming the PAP is representative of all deep-sea areas, rates of denitrification, burial and DON efflux were extrapolated to the total area of the deep-sea floor (>2000 m) and integrated values of denitrification and burial of 8 ± 5 and 7 ± 1 Tg N year⁻¹, respectively, were obtained. This value of total deep-sea sediment denitrification corresponds to 3–12% of the global ocean benthic denitrification. Burial in deep-sea sediments makes up at least 25% of the global ocean nitrogen burial. The integrated DON flux from the deep-sea floor is comparable in magnitude to a reported global riverine input of DON suggesting that deep-sea sediments constitute an important source of DON to the world ocean.     

Use of inhibitors for coastal bacteria and phytoplankton: Application to nitrogen uptake measurement

For several decades, prokaryotic and eukaryotic inhibitors have been used to exclude bacteria from microalgal cultures and for investigating prey-predator relationships. Recently there has been considerable interest in using specific inhibitors for studying the interactions between bacteria and phytoplankton, by selective repression of either organism’s activity. The effectiveness of chemical inhibitors must be tested before applying them to natural communities to partition metabolic activities between functional groups. Six different antibiotics selected from the most commonly reported in the literature were tested, at concentrations varying from 12.5 to 100 mg L⁻¹, for their effect on bacterial growth and functional diversity of natural communities from Mediterranean coastal waters. Penicillin and streptomycin each at a final concentration of 100 mg L⁻¹ significantly reduced bacterial growth within 2 h. There was a greater impact on bacterial functional diversity when both antibiotics were mixed together. This mixture did not have any significant effect on the growth of selected cultured phytoplankton strains, whereas the eukaryote inhibitor cycloheximide at 100 mg L⁻¹ reduced growth within 2 h of incubation. The penicillin–streptomycin mixture and cycloheximide alone successfully partitioned NH₄⁺ and NO₃⁻ uptake between bacteria and phytoplankton bi-weekly sampled in a coastal lagoon in Autumn, where bacterial contribution to total NH₄⁺ and NO₃⁻ uptake averaged 46 and 41%, respectively. The use of specific inhibitors may be a valuable method for studying interactions, such as competition and mutualism, or lack of interaction between the different components of microbial communities and could be used to study their relative importance in biogeochemical fluxes.     

Close coupling between ammonium uptake by phytoplankton and excretion by Antarctic krill, Euphausia superba

In this study we examined the hypothesis that, under conditions of replete macronutrients and iron in the Southern Ocean, phytoplankton abundance and specific N uptake rates are influenced strongly by the processes of grazing and NH₄ regeneration. NH₄ and NO₃ uptake rates by marine phytoplankton were measured to the northeast and northwest of the island of South Georgia during January-February 1998. Mean specific uptake rate for NO₃ (vNO₃) was 0.0026 h⁻¹ (range 0.0013-0.0065 h⁻¹) and for NH₄ (vNH₄) was 0.0097 h⁻¹ (0.0014-0.0376 h⁻¹). vNH₄ was related positively with NH₄ availability, which ranged from 0.1 to 1.5 mmol m⁻³ within the upper mixed layer. Ambient NH₄ concentrations and vNH₄ were both positively related to local krill biomass values, computed from mean values along acoustic transect segments within 2 km of the uptake measurement stations. These biomass values ranged from ∼1 g krill fresh mass m⁻² in the northwest to >4 kg krill wet mass m⁻² in the northeast. In contrast to the variability found with NH₄ concentrations and uptake rates, vNO₃ was more uniform across the sampling sites. Under these conditions, increasing NH₄ concentration appeared to represent an additional N resource. However, high vNH₄ tended to be found for stations with lower phytoplankton standing stocks, across a total range of 0.24-20 mg chlorophyll a m⁻³. These patterns suggest a coupling between phytoplankton biomass, vNH₄ and krill in this region of variable but high krill biomass. Locally high concentrations of krill in parts of the study area appeared to have two opposing effects. On the one hand they could graze down phytoplankton stocks, but on the other hand, their NH₄ excretion supported enhanced uptake rates by the remaining, ungrazed cells.     

In vitro simulation of oxic/suboxic diagenesis in an estuarine fluid mud subjected to redox oscillations

Estuarine turbidity maxima (ETMs) are sites of intense mineralisation of land-derived particulate organic matter (OM), which occurs under oxic/suboxic oscillating conditions owing to repetitive sedimentation and resuspension cycles at tidal and neap-spring time scales. To investigate the biogeochemical processes involved in OM mineralisation in ETMs, an experimental set up was developed to simulate in vitro oxic/anoxic oscillations in turbid waters and to follow the short timescale changes in oxygen, carbon, nitrogen, and manganese concentration and speciation. We present here the results of a 27-day experiment (three oxic periods and two anoxic periods) with an estuarine fluid mud from the Gironde estuary. Time courses of chemical species throughout the experiment evidenced the occurrence of four distinct characteristic periods with very different properties. Steady oxic conditions were characterised by oxygen consumption rates between 10 and 40 μmol L⁻¹ h⁻¹, dissolved inorganic carbon (DIC) production of 9–12 μmol L⁻¹ h⁻¹, very low NH₄⁺ and Mn²⁺ concentrations, and constant NO₃⁻ production rates (0.4 - 0.7 μmol L⁻¹ h⁻¹) due to coupled ammonification and nitrification. The beginning of anoxic periods (24 h following oxic to anoxic switches) showed DIC production rates of 2.5–8.6 μmol L⁻¹ h⁻¹ and very fast NO₃⁻ consumption (5.6–6.3 μmol L⁻¹ h⁻¹) and NH₄⁺ production (1.4–1.5 μmol L⁻¹ h⁻¹). The latter rates were positively correlated to NO₃⁻ concentration and were apparently caused by the predominance of denitrification and dissimilatory nitrate reduction to ammonia. Steady anoxic periods were characterised by constant and low NO₃⁻ concentrations and DIC and NH₄⁺ productions of less than 1.3 and 0.1 μmol L⁻¹ h⁻¹, respectively. Mn²⁺ and CH₄ were produced at constant rates (respectively 0.3 and 0.015 μmol L⁻¹ h⁻¹) throughout the whole anoxic periods and in the presence of nitrate. Finally, reoxidation periods (24–36 h following anoxic to oxic switches) showed rapid NH₄⁺ and Mn²⁺ decreases to zero (1.6 and 0.8–2 μmol L⁻¹ h⁻¹, respectively) and very fast NO₃⁻ production (3 μmol L⁻¹ h⁻¹). This NO₃⁻ production, together with marked transient peaks of dissolved organic carbon a few hours after anoxic to oxic switches, suggested that particulate OM mineralisation was enhanced during these transient reoxidation periods. An analysis based on C and N mass balance suggested that redox oscillation on short time scales (day to week) enhanced OM mineralisation relative to both steady oxic and steady anoxic conditions, making ETMs efficient biogeochemical reactors for the mineralisation of refractory terrestrial OM at the land-sea interface.     

Rates of C,N, P and Si recycling and denitrification at the US Mid-Atlantic continental slope depocenter

Benthic fluxes of O₂, titration alkalinity (TA), total inorganic carbon (TIC), Ca²⁺, NO₃⁻, NH₄⁺, PO₄³⁻, and Si(OH)₄ were measured by in situ benthic flux chamber incubations at 13 locations on the North Carolina continental slope. The majority of measurements were made at water depths of approximately 700–850 m, in the previously identified upper slope depocenter. This region is characterized by extremely high organic matter deposition rates and near saturation bottom water oxygen concentrations. Measured benthic fluxes of TA are reasonably correlated with O₂ benthic fluxes. Because bottom waters are supersaturated with respect to calcite and aragonite at these shallow water depths, these results demonstrate the importance of metabolically driven dissolution in this region. Subtraction of the calcium carbonate dissolution contributions from the TIC benthic fluxes suggests rates of organic matter remineralization ranging from 0.97 to 3.9 mol C m⁻² yr⁻¹ at the depocenter sites, a factor of 3–10 greater than estimated for the adjacent continental rise and upper slope areas. Because biological primary production in the overlying waters does not follow this pattern, these extremely high values are most likely supported by lateral inputs of highly reactive organic matter. Mass balance calculations indicate that despite the oxygenated bottom water conditions, 68% of the organic nitrogen released during organic matter remineralization processes is ultimately denitrified. The release of PO₄³⁻ from the depocenter sediments is equivalent to or larger than that predicted from the remineralization of Redfield organic matter. This implies either that PO₄³⁻ is preferentially released in this setting and that the accumulating sediments must be depleted in PO₄³⁻ relative to organic carbon or that another, non-organic, phase is contributing PO₄³⁻ to the system. The molar ratio of the Si benthic flux and organic carbon remineralization rate ranges from 0.30 to 0.86. This is significantly greater than the ratio reported for most pelagic diatoms. Possible reasons for this high ratio include the deposition of benthic diatoms that may have a larger Si : C ratio than pelagic diatoms, the near-bottom lateral input of partially reworked organic matter that may have an elevated Si : C ratio relative to fresh diatoms, preferential loss of carbon in sinking particulates or the release of Si from non-opaline materials.     

Nitrogen dynamics during the Arabian Sea Northeast Monsoon

This investigation focused on the weaker and less well understood of the two Arabian Sea monsoonal wind phases, the NE Monsoon, which persists for 3–4 months in the October to February period. Historically, this period has been characterized as a time of very low nutrient availability and low biological production. As part of the US JGOFS Arabian Sea Process Study, 17 stations were sampled on a cruise in January 1995 (late NE Monsoon) and, 15 stations were sampled on a cruise in November 1995 (early NE Monsoon). Only the southern most stations (10° and 12°N) and one shallow coastal station were as nutrient-depleted as had been expected from the few relevant prior studies in this region. Experiments were conducted to ascertain the relative importance of different nitrogenous nutrients and the sufficiency of local regeneration processes in supplying nitrogenous nutrients utilized in primary production. Except for the southern oligotrophic stations, the euphotic zone concentrations of NO₃⁻ were typically 5–10-fold greater than those of NO₂⁻ and NH₄⁺. There was considerable variation (20–40-fold) in nutrient concentration both within and between the two sections on each cruise. All nitrogenous nutrients were more abundant (2–4-fold) later in the NE Monsoon. Strong vertical gradients in euphotic zone NH₄⁺ concentration, with higher concentrations at depth, were common. This was in contrast to the nearly uniform euphotic zone concentrations for both NO₃⁻ and NO₂⁻. Half-saturation constants for uptake were higher for NO₃⁻ (1.7 μmol kg⁻¹ (s.d.=0.88, n=8)) than for NH₄⁺ (0.47 μmol kg⁻¹ (s.d.=0.33, n=5)). Evidence for the suppressing effect of NH₄⁺ on NO₃⁻ uptake was widespread, although not as severe as has been noted for some other regions. Both the degree of sensitivity of NO₃⁻ uptake to NH₄⁺ concentration and the half-saturation constant for NO₃⁻ uptake were correlated with ambient NO₃⁻ concentration. The combined effect of high affinity for low concentrations of NH₄⁺ and the effect of NH₄⁺ concentration on NO₃⁻ uptake resulted in similarly low f-ratios, 0.15 (s.d.=0.07, n=15) and 0.13 (s.d.=0.08, n=17), for early and late observations in the NE Monsoon, respectively. Stations with high f-ratios had the lowest euphotic zone NH₄⁺ concentrations, and these stations were either very near shore or far from shore in the most oligotrophic waters. At several stations, particularly early in the NE Monsoon, the utilization rates for NO₂⁻ were equal to or greater than 50% the utilization rates for NO₃⁻. When converted with a Redfield C : N value of 6.7, the total N uptake rates measured in this study were commensurate with measurements of C productivity. While nutrient concentrations at some stations approached levels low enough to limit phytoplankton growth, light was shown to be very important in regulating N uptake at all stations in this study. Diel periodicity was observed for uptake of all nitrogenous nutrients at all stations. The amplitude of this periodicity was positively correlated with nutrient concentration. The strongest of these relationships occurred with NO₃⁻. Ammonium concentration strongly influenced the vertical profiles for NO₃⁻ uptake as well as for NH₄⁺ uptake. Both NO₂⁻ and NH₄⁺ were regenerated within the euphotic zone at rates comparable to rates of uptake of these nutrients, and thus maintenance of mixed layer concentrations did not require diffusive or advective fluxes from other sources. Observed turnover times for NH₄⁺ were typically less than one day. Rapid turnover and the strong light regulation of NH₄⁺ uptake allowed the development and maintenance of vertical structure in NH₄⁺ concentration within the euphotic zone. In spite of the strong positive effect of light on NO₂⁻ uptake and its strong negative effect on NO₂⁻ production, the combined effects of much longer turnover times for this nutrient and mixed layer dynamics resulted in nearly uniform NO₂⁻ concentrations within the euphotic zone. Responses of the NE Monsoon planktonic community to light and nutrients, in conjunction with mixed layer dynamics, allowed for efficient recycling of N within the mixed layer. As the NE Monsoon evolved and the mixed layer deepened convectively, NO₂⁻ and NO₃⁻ concentrations increased correspondingly with the entrainment of deeper water. Planktonic N productivity increased 2-fold, but without a significant change the new vs. recycled N proportionality. Consequently, NO₃⁻ turnover time increased from about 1 month to greater than 3 months. This reflected the overriding importance of recycling processes in supplying nitrogenous nutrients for primary production throughout the duration of the NE Monsoon. As a result, NO₃⁻ supplied to the euphotic zone during the NE Monsoon is, for the most part, conserved for utilization during the subsequent intermonsoon period.     

Nitrogen dynamics within a wind-driven eddy

Wind-driven cyclonic eddies are hypothesized to relieve nutrient stress and enhance primary production by the upward displacement of nutrient-rich deep waters into the euphotic zone. In this study, we measured nitrate (NO₃⁻), particulate carbon (PC), particulate nitrogen (PN), their stable isotope compositions (δ¹⁵N-NO₃⁻, δ¹³C-PC and δ¹⁵N-PN, respectively), and dissolved organic nitrogen (DON) within Cyclone Opal, a mature wind-driven eddy generated in the lee of the Hawaiian Islands. Sampling occurred in March 2005 as part of the multi-disciplinary E-Flux study, approximately 4–6 weeks after eddy formation. Integrated NO₃⁻ concentrations above 110 m were 4.8 times greater inside the eddy (85.8±6.4 mmol N m⁻²) compared to the surrounding water column (17.8±7.8 mmol N m⁻²). Using N-isotope derived estimates of NO₃⁻ assimilation, we estimated that 213±59 mmol m⁻² of NO₃⁻ was initially injected into the upper 110 m Cyclone Opal formation, implying that NO₃⁻ was assimilated at a rate of 3.75±0.5 mmol N m⁻² d⁻¹. This injected NO₃⁻ supported 68±19% and 66±9% of the phytoplankton N demand and export production, respectively. N isotope data suggest that 32±6% of the initial NO₃⁻ remained unassimilated. Self-shading, inefficiency in the transfer of N from dissolved to particulate export, or depletion of a specific nutrient other than N may have led to a lack of complete NO₃⁻ assimilation. Using a salt budget approach, we estimate that dissolved organic nitrogen (DON) concentrations increased from eddy formation (3.8±0.4 mmol N m⁻²) to the time of sampling (4.0±0.09 mmol N m⁻²), implying that DON accumulated at rate of 0.83±1.3 mmol N m⁻² d⁻¹, and accounted for 22±15% of the injected NO₃⁻. Interestingly, no significant increase in suspended PN and PC, or export production was observed inside Cyclone Opal relative to the surrounding water column. A simple N budget shows that if 22±15% of the injected NO₃⁻ was shunted into the DON pool, and 32±6% is unassimilated, then 46±16% of the injected NO₃⁻ remains undocumented. Alternative loss processes within the eddy include lateral exchange of injected NO₃⁻ along isopycnal surfaces, remineralization of PN at depth, as well as microzooplankton grazing. A 9-day time series within Cyclone Opal revealed a temporal depletion in δ¹⁵N-PN, implying a rapid change in the N source. A change in NO₃⁻ assimilation, or a shift from NO₃⁻ fueled growth to assimilation of a ¹⁵N-deplete N source, may be responsible for such observations.     

The cycling and oxidation pathways of organic carbon in a shallow estuary along the Texas Gulf Coast

The cycling and oxidation pathways of organic carbon were investigated at a single shallow water estuarine site in Trinity Bay, Texas, the uppermost lobe of Galveston Bay, during November 2000. Radio-isotopes were used to estimate sediment mixing and accumulation rates, and benthic chamber and pore water measurements were used to determine sediment-water exchange fluxes of oxygen, nutrients and metals, and infer carbon oxidation rates. Using ⁷Be and ²³⁴Th_XS, the sediment-mixing coefficient (D_b) was 4.3 ± 1.8 cm² y⁻¹, a value that lies at the lower limit for marine environments, indicating that mixing was not important in these sediments at this time. Sediment accumulation rates (S_a), estimated using ¹³⁷Cs and ²¹⁰Pb_XS, were 0.16 ± 0.02 g cm⁻² y⁻¹. The supply rate of organic carbon to the sediment-water interface was 30 ± 3.9 mmol C m⁻² d⁻¹, of which ∼10% or 2.9 ± 0.44 mmol C m⁻² d⁻¹was lost from the system through burial below the 1-cm thick surface mixed layer. Measured fluxes of O₂ were 26 ± 3.8 mmol m⁻² d⁻¹ and equated to a carbon oxidation rate of 20 ± 3.3 mmol C m⁻² d⁻¹, which is an upper limit due to the potential for oxidation of additional reduced species. Using organic carbon gradients in the surface mixed layer, carbon oxidation was estimated at 2.6 ± 1.1 mmol C m⁻² d⁻¹. Independent estimates made using pore water concentration gradients of ammonium and C:N stoichiometry, equaled 2.8 ± 0.46 mmol C m⁻² d⁻¹. The flux of DOC out of the sediments (DOC_efflux) was 5.6 ± 1.3 mmol C m⁻² d⁻¹. In general, while mass balance was achieved indicating the sediments were at steady state during this time, changes in environmental conditions within the bay and the surrounding area, mean this conclusion might not always hold. These results show that the majority of carbon oxidation occurred at the sediment-water interface, via O₂ reduction. This likely results from the high frequency of sediment resuspension events combined with the shallow sediment mixing zone, leaving anaerobic oxidants responsible for only ∼10–15% of the carbon oxidized in these sediments.     

Evaluation of spatial correlation between nutrient exchange rates and benthic biota in a reef-flat ecosystem by GIS-assisted flow-tracking

A Geographic Information System (GIS)-aided flow-tracking technique was adopted to investigate nutrient exchange rates between specific benthic communities and overlying seawater in a fringing reef of Ishigaki Island, subtropical Northwestern Pacific. Net exchange rates of NO₃ ⁻, NO₂ ⁻, NH₄ ⁺, PO₄ ³⁻, Total-N and Total-P were estimated from concentration changes along the drogue trajectories, each of which was tracked by the Global Positioning System and plotted on a benthic map to determine the types of benthic habitat over which the drogue had passed. The observed nutrient exchange rates were compared between 5 typical benthic zones (branched-coral (B) and Heliopora communities (H), seaweed-reefrock zone (W), bare sand area (S), and seagrass meadow (G)). The dependence of nutrient exchange rates on nutrient concentrations, physical conditions and benthic characteristics was analyzed by multiple regression analysis with the aid of GIS. The spatial correlation between nutrient exchange rates and benthic characteristics was confirmed, especially for NO₃ ⁻ and PO₄ ³⁻, which were usually absorbed in hydrographically upstream zones B and W and regenerated in downstream zones H and G. NO₃ ⁻ uptake in zones B and W was concentration-dependent, and the uptake rate coefficient was estimated to be 0.58 and 0.67 m h⁻¹, respectively. Both nutrient uptake in zone W and regeneration in zone H were enhanced in summer. The net regeneration ratio of NO₃ ⁻/PO₄ ³⁻ in zone H in summer ranged 5.2 to 34 (mean, 17.4), which was somewhat higher than previously measured NO₃ ⁻/PO₄ ³⁻ for sediment pore waters around this zone (1.1–8.5). Nutrient exchanges in zone S were relatively small, indicating semi-closed nutrient cycling at the sediment-water interface of this zone. NH₄ ⁺ efflux from sediments was suggested in zone G. The data suggest that the spatial pattern of nutrient dynamics over the reef flat community was constrained by zonation of benthic biota, and that abiotic factors such as nutrient concentrations and flow rates, influenced nutrient exchange rates only in absorption-dominated communities such as zones B and W.     

Aerobic ammonium oxidation in the oxycline and oxygen minimum zone of the eastern tropical South Pacific off northern Chile (∼20°S)

Aerobic NH₄⁺ oxidation rates were measured along the strong oxygen gradient associated with the oxygen minimum zone (OMZ) of the eastern tropical South Pacific off northern Chile (∼20°S) during 2000, 2003, and 2004. This process was examined by comparing NH₄⁺ rates of change during dark incubations, with and without the addition of allylthiourea, a classical inhibitor of the ammonia monooxygenase enzyme of ammonium-oxidizing bacteria. The contribution of aerobic NH₄⁺ oxidation in dark carbon fixation and NO₂⁻ rates of change were also explored. Thirteen samples were retrieved from the oxycline (252 to ⩽5 μM O₂; 15 to ∼65 m depth) and three from the oxygen minimum core (⩽5 μM O₂; 100–200 m depth). Aerobic NH₄⁺ oxidation rates were mainly detected in the upper part (15–30 m depth) of the oxycline, with rates ranging from 0.16 to 0.79 μM d⁻¹, but not towards the oxycline base (40–65 m depth). In the oxygen minimum core, aerobic NH₄⁺ oxidation was in the upper range and higher than in the upper part of the oxycline (0.70 and 1.0 μM d⁻¹). Carbon fixation rates through aerobic NH₄⁺ oxidation ranged from 0.18 to 0.43 μg C L⁻¹ d⁻¹ and contributed between 33% and 57% of the total dark carbon fixation, mainly towards the oxycline base and, in a single experiment, in the upper part of the oxycline. NO₂⁻ consumption was high (up to 10 μM d⁻¹) towards the oxycline base and OMZ core, but was significantly reduced in experiments amended with allylthiourea, indicating that aerobic NH₄⁺ oxidation could contribute between 8% and 76% of NO₂⁻ production, which in turn could be available for denitrifiers. Overall, these results support the important role of aerobic NH₄⁺ oxidizers in the nitrogen and carbon cycling in the OMZ and at its upper boundary.     

Denitrification in coastal Louisiana: A spatial assessment and research needs

By transforming fixed nitrogen (N) into nitrogen gas, the biochemical processes that support denitrification provide a function critical to maintaining the integrity of ecosystems subjected to increased loading of N from anthropogenic sources. The Louisiana coastal region receives high nitrate (NO₃^?) concentrations (> 100 µM) from the Mississippi–Ohio–Missouri River Basin and is also an area undergoing high rates of wetland loss. Ongoing and anticipated changes in the Louisiana coastal region promise to alter biogeochemical cycles including the net rate of denitrification by ecosystems. Projecting what these changes could mean for coastal water quality and natural resources requires an understanding of the magnitude and patterns of variation in denitrification rates and their connection to estuarine water quality at large temporal and spatial scales under current conditions. We compile and review denitrification rates reported in 32 studies conducted in a variety of habitats across coastal Louisiana during the period 1981– 2008. The acetylene inhibition and ¹⁵N flux were the preferred techniques (95%); most of the studies used sediment slurries rather than intact sediment cores. There are no estimates of denitrification rates using the N₂/Ar ratio and isotope pairing techniques, which address some of the problems and limitations of the acetylene inhibition and ¹⁵N flux techniques. These studies have shown that sediments from estuaries, lakes, marshes, forested wetlands, and the coastal shelf region are capable of high potential denitrification rates when exposed to high NO₃^? concentrations (> 100 µM). Maximum potential denitrification rates in experimental and natural settings can reach values > 2500 µmol m² h^? 1. The lack of contemporary studies to understand the interactions among critical nitrogen transformations (e.g., organic matter mineralization, immobilization, aquatic plant assimilation, nitrification, nitrogen fixation, dissimilatory nitrate reduction to ammonium (DNRA) and anaerobic ammonium oxidation (annamox) limits our understanding of nitrogen cycling in coastal Louisiana, particularly the role of respiratory and chemolithoautotrophic denitrification in areas undergoing wetland restoration.     

Tidal variability in benthic silicic acid fluxes and microphytobenthos uptake in intertidal sediment

Silicic acid (DSi) benthic fluxes play a major role in the benthic–pelagic coupling of coastal ecosystems. They can sustain microphytobenthos (MPB) development at the water–sediment interface and support pelagic diatoms when river DSi inputs decrease. DSi benthic fluxes have been studied at the seasonal scale but little is known about their dial variations. This study measured the amplitude of such variations in an intertidal area over an entire tidal cycle by following the alteration of DSi pore water concentrations at regular intervals over the flood/ebb period. Furthermore we independently estimated the potential DSi uptake by benthic diatoms and compared it to the variations of DSi pore water concentrations and fluxes. The microphytobenthos DSi demand was estimated from primary production measurements on cells extracted from the sediment. There were large changes in DSi pore water concentration and a prominent effect of tidal pumping: the DSi flushed out from the sediment at rising tide, occurs in a very short period of time, but plays a far more important role in fueling the ecosystem (800 μmol-Si m⁻² d⁻¹), than diffusive fluxes occurring throughout the rest of the tidal cycle (2 μmol-Si m⁻² d⁻¹). This process is not, to our knowledge, currently considered when describing the DSi cycling of intertidal sediments. Moreover, there was a large potential MPB requirement for DSi (812 μmol-Si m⁻² d⁻¹), similar to the advective flow periodically pumped by the incoming tide, and largely exceeded benthic diffusive fluxes. However, this DSi uptake by benthic diatoms is almost undetectable given the variation of DSi concentration profiles within the sediment.     

Benthic nitrate biogeochemistry affected by tidal modulation of Submarine Groundwater Discharge (SGD) through a sandy beach face, Ria Formosa, Southwestern Iberia

To investigate both the role of tides on the timing and magnitude of Submarine Groundwater Discharge (SGD), and the effect on benthic nitrogen biogeochemistry of nitrate-enriched brackish water percolating upwards at the seepage face, we conducted a study of SGD rates measured simultaneously with seepage meters and mini-piezometers, combined with sets (n = 39) of high resolution in-situ porewater profiles describing NH₄⁺, NO₃⁻, Si(OH)₄ and salinity distribution with depth (0–20 cm). Sampling took place during two consecutive spring tidal cycles in four different months (November 2005, March, April and August 2006) at a backbarrier beach face in the Ria Formosa lagoon, southern Portugal. Our results show that the tide is one of the major agents controlling the timing and magnitude of SGD into the Ria Formosa. Intermittent pumping of brackish, nitrate-bearing water at the beach face through surface sediments changed both the magnitudes and depth distributions of porewater NH₄⁺ and NO₃⁻ concentrations. The most significant changes in nitrate and ammonium concentrations were observed in near-surface sediment horizons coinciding with increased fraction of N in benthic organic matter, as shown by the organic C:N ratio. On the basis of mass balance calculations executed on available benthic profiles, providing ratios of net Ammonium Production Rate (APR) to Nitrate Reduction Rate (NRR), coupled to stoichiometric calculations based on the composition of organic matter, potential pathways of nitrogen transformation were speculated upon. Although the seepage face occasionally contributes to reduce the groundwater-borne DIN loading of the lagoon, mass balance analysis suggests that a relatively high proportion of the SGD-borne nitrogen flowing into the lagoon may be enhanced by nitrification at the shallow (1–3 cm) subsurface and modulated by dissimilatory nitrate reduction to ammonium (DNRA).