Benthic Metabolism Research Articles

Influence of Potamogeton pectinatus and microphytobenthos on benthic metabolism, nutrient fluxes and denitrification in a freshwater littoral sediment in an agricultural landscape: N assimilation versus N removal

The influence of Potamogeton pectinatus colonisation on benthic nitrogen dynamics was studied in the littoral zone of a lowland pit lake with high nitrate concentration (~200 μM). Our hypothesis was that in aquatic environments where nitrogen availability is not limiting, colonisation by rooted macrophytes changes the dynamics of the benthic nitrogen cycle, stimulating N assimilation and denitrification and increasing the system capacity to take up external nitrogen loads. To test this hypothesis, we quantified and compared seasonal variations of light and dark benthic metabolism, dissolved inorganic nitrogen (DIN) fluxes, denitrification and N assimilation rates in an area colonised by P. pectinatus and a reference site colonised by microphytobenthos. In both areas, the benthic system was net autotrophic and a sink for DIN (2,241–2,644 mmol m−2 y−1). Plant colonisation increased nitrogen losses via denitrification by 30% compared to the unvegetated area. In contrast to what is generally observed in coastal marine systems, where the presence of rooted macrophytes limits denitrification rates, under the very high nitrate concentrations in the studied lake, both denitrification (1,237–1,570 mmol m−2 y−1) and N assimilation (1,039–1,095 mmol m−2 y−1) played important and comparable roles in the removal of DIN from the water column.

Impacts of Climate-Related Drivers on the Benthic Nutrient Filter in a Shallow Photic Estuary

In shallow photic systems, the benthic filter, including microphytobenthos and denitrifiers, is important in preventing or reducing release of remineralized NH4 + to the water column. Its effectiveness can be impacted by climate-related drivers, including temperature and storminess, which by increasing wind and freshwater delivery can resuspend sediment, reduce salinity and deliver nutrients, total suspended solids, and chromophoric dissolved organic matter (CDOM) to coastal systems. Increases in temperature and freshwater delivery may initiate a cascade of responses affecting benthic metabolism with impacts on sediment properties, which in turn regulate nitrogen cycling processes that either sequester (via microphytobenthos), remove (via denitrification), or increase sediment nitrogen (via remineralization, nitrogen fixation, and dissimilatory nitrate reduction to ammonium). We conducted a seasonal study at shallow stations to assess the effects of freshwater inflow, temperature, wind, light, and CDOM on sediment properties, benthic metabolism, nitrogen cycling processes, and the effectiveness of the benthic filter. We also conducted a depth study to constrain seasonally varying parameters such as temperature to better assess the effects of light availability and water depth on benthic processes. Based on relationships observed between climatic drivers and response variables, we predict a reduction in the effectiveness of the benthic filter over the long term with feedbacks that will increase effluxes of N to the water column with the potential to contribute to system eutrophication. This may push shallow systems past a tipping point where trophic status moves from net autotrophy toward net heterotrophy, with new baselines characterized by degraded water quality.

Benthic metabolism and nitrogen dynamics in an urbanised tidal creek: Domination of DNRA over denitrification as a nitrate reduction pathway

Benthic oxygen and nutrient fluxes and nitrate reduction rates were determined seasonally under light and dark conditions at three sites in a micro-tidal creek within an urbanised catchment (Saltwater Creek, Australia). It was hypothesized that stormwater inputs of organic matter and inorganic nitrogen would stimulate rates of benthic metabolism and nutrient recycling and preferentially stimulate dissimilatory nitrate reduction to ammonium (DNRA) over denitrification as a pathway for nitrate reduction. Stormwaters greatly influenced water column dissolved inorganic nitrogen (DIN) and suspended solids concentrations with values following a large rainfall event being 5–20-fold greater than during the preceding dry period. Seasonally, maximum and minimum water column total dissolved nitrogen (TDN) and DIN concentrations occurred in the summer (wet) and winter (dry) seasons. Creek sediments were highly heterotrophic throughout the year, and strong sinks for oxygen, and large sources of dissolved organic and inorganic nitrogen during both light and dark incubations, although micro-phytobenthos (MPB) significantly decreased oxygen consumption and N-effluxes during light incubations due to photosynthetic oxygen production and photoassimilation of nutrients. Benthic denitrification rates ranged from 3.5 to 17.7 μmol N m2 h−1, denitrification efficiencies were low (<1–15%) and denitrification was a minor process compared to DNRA, which accounted for ∼75% of total nitrate reduction.Overall, due to the low denitrification efficiencies and high rates of N-regeneration, Saltwater Creek sediments would tend to increase rather than reduce dissolved nutrient loads to the downstream Gold Coast Broadwater and Moreton Bay systems. This may be especially true during wet periods when increased inputs of particulate organic nitrogen (PON) and suspended solids could respectively enhance rates of N-regeneration and decrease light availability to MPB, reducing their capacity to ameliorate N-effluxes through photoassimilation.

Do snails facilitate bloom-forming macroalgae in a eutrophic estuary?

Blooms of macroalgae are one of the most visible and problematic results of eutrophication-driven estuarine degradation because they can smother seagrass, obstruct fishing, and close beaches to tourism. Not surprisingly, high densities of herbivores are commonly associated with these blooms. Invertebrates in other systems can facilitate macrophyte growth under equilibrium conditions by releasing nutrients or reducing competitors. Based on laboratory experiments it has been suggested that the omnivorous snail Ilyanassa obsoleta likewise facilitates bloom-forming macroalgae in estuaries of the Northeastern US. If snails enhance macroalgal blooms as suggested, it would have broad implications for nutrient retention and cycling in estuaries. We tested whether snails actually do facilitate macroalgal blooms in a natural setting through community surveys, laboratory incubations, and field experiments. We confirmed in our surveys that snail densities were positively correlated with macroalgal biomass, and in laboratory incubations that snail excreta enhanced macroalgal growth and that snail activity mobilized sediment nutrients and enhanced sediment–water column coupling. Snails thus have the potential to influence nutrient recycling and retention. However, snails did not facilitate macroalgal growth in our field manipulations of snails and bloom-forming macroalgae along an estuarine eutrophication gradient. Macroalgal growth in our experiment was highly variable across the estuarine gradient and through the growing season, suggesting that large-scale variation in physical factors such as nutrients, light, or temperature plays the dominant role in limiting macroalgal blooms. The departure of our field results from predictions of laboratory studies reinforces previous warnings that laboratory experiments can be useful tools for elucidating mechanisms that drive field patterns, but are not a substitute for field experiments where they are possible. While snails do not appear to directly influence macroalgal growth, we suggest that the potential influence of snails on benthic metabolism and nutrient cycling demands further investigation in the field.

Effects of an oil spill on benthic community production and respiration on subtropical intertidal sandflats

This study determined effects of an oil spill on subtropical benthic community production and respiration by monitoring CO2 fluxes in benthic chambers on intertidal sandflats during emersion before and after an accidental spill. The oil spill decreased sediment chlorophyll a concentrations, altered benthic macrofaunal community, and affected ecological functioning by suppressing or even stopping microalgal production, increasing bacterial respiration, and causing a shift from an autotrophic system to a heterotrophic system. Effects of the oil spill on the macrofauna were more severe than on benthic microalgae, and affected sedentary infauna more than motile epifauna. Despite the oil spill’s impact on the benthic community and carbon metabolism, the affected area appeared to return to normal in about 23days. Our results suggest that the prompt response of benthic metabolism to exposure to petroleum hydrocarbons can serve as a useful indicator of the impact of an oil spill.

Changes in N cycling induced by Ulva detritus enrichment of sediments

Macroalgal accumulation and decomposition in shallow water environments typically result in an increase in the organic matter content of the sediment, affecting both benthic metabolism and nutrient dynamics. The present study investigates how a pulse addition of Ulva detritus to estuarine sediment influences the micro-distribution of O2, NO3 and NO2 within the sediment, as well as the rates of oxygen consumption, nitrification and nitrate reduction. The micro-distributions of O2, NO3 and NO2 were monitored with microsensors in Ulva-amended sediment microcosms and in unamended controls during a 1 mo incubation experiment. Process rates were obtained from numerical modeling of the concentration profiles. Oxygen consumption and nitrate reduction were enhanced by a factor of 2 in Ulva-amended sediment compared to the control. This led to a significant reduction in the penetration depths of oxygen and nitrate. Nitrification increased significantly in response to enhanced NH4 supply from decomposition of the Ulva detritus. Aerobic ammonia oxidation exceeded rates of nitrite oxidation, leading to accumulation of NO2 in the oxic zone of the sediment. Nitrite and NO3 produced via nitrification diffused up to the sediment surface, inducing a net efflux to the water column, and downwards, supporting a high rate of denitrification coupled to nitrification. The present study shows that organic enrichment with Ulva detritus enhances sediment oxygen uptake, nitrification and denitrification, the net result being loss of nitrogen from the system. This might constitute a compensating or self-restoration mechanism counteracting an increase in N in intertidal sediment affected by eutrophication-induced macroalgal blooms.

Seasonal, daily and diel N&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; effluxes in permeable carbonate sediments

Abstract. Benthic metabolism and inorganic nitrogen and N2 flux rates (denitrification) were measured in permeable carbonate sands from Heron Island (Great Barrier Reef). Some of the N2 flux rates were among the highest measured in sediments. All benthic fluxes showed a significant difference between seasons with higher rates in summer and late summer. There was no distinct response of the benthic system to mass coral spawning. Instead, changes in benthic fluxes over 12 days in summer appear to be driven by tidal changes in water depth and associated changes in phytosynthetically active radiation reaching the sediments. Dark N2 fluxes were strongly correlated to benthic oxygen consumption across all sites and seasons (r2 = 0.63; p &lt; 0.005; slope = 0.035). However, there were seasonal differences with a steeper slope in summer than winter, reflecting either more efficient coupling between respiration and nitrification–denitrification at higher temperatures or different sources of organic matter. Adding data from published studies on carbonate sands revealed two slopes in the dark N2 flux versus benthic oxygen consumption relationship. The lower slope (0.035) was most likely due to high carbon : nitrogen (C : N) organic matter from coral reefs, and associated assimilation of nitrogen by heterotrophic bacteria including enhanced heterotrophic N-fixation, but competition by benthic microalgae or inefficient coupling between respiration and nitrification–denitrification cannot be excluded. The steeper slope (0.089) was most likely due to respiration being driven by low C : N phytodetritus. If the different slopes were driven by the sources of organic matter, then global estimates of continental shelf denitrification are probably about right. In contrast, global estimates of continental shelf denitrification may be over-estimated if the low slope was due to inefficient coupling between respiration and nitrification–denitrification and also due to reduced N2 effluxes in the light associated with competition by benthic microalgae for nitrogen and N-fixation.

Experimental Evaluation of the Response of Coastal Mediterranean Planktonic and Benthic Metabolism to Warming

The Mediterranean Sea has been identified as one of the hotspots for climate change. Intense warming in the Mediterranean Sea may have strong implications for biological activity and ecosystem functioning. To elucidate the effects of warming on planktonic and benthic metabolism, we performed experiments under different increasing temperature regimes, ranging from three to six different temperatures. The lowest range of temperatures assessed was of 2.6 A degrees C and the maximum was 7.5 A degrees C. Our results suggest that a 6 A degrees C warming of the Mediterranean waters may yield a mean increment in planktonic respiration rates of coastal communities of 24 %, higher than the mean increase expected for planktonic gross primary production (9 %). These results confirm earlier theories, and agree with previous experiments, of a higher increase in respiration rates than in primary production with warming, with the subsequent consequences for the carbon cycle, resulting in a negative feedback to climate warming, as ocean communities will capture less CO2. (Less)

Physical and Biological Controls on the Carbonate Chemistry of Coral Reef Waters: Effects of Metabolism, Wave Forcing, Sea Level, and Geomorphology

We present a three-dimensional hydrodynamic-biogeochemical model of a wave-driven coral-reef lagoon system using the circulation model ROMS (Regional Ocean Modeling System) coupled with the wave transformation model SWAN (Simulating WAves Nearshore). Simulations were used to explore the sensitivity of water column carbonate chemistry across the reef system to variations in benthic reef metabolism, wave forcing, sea level, and system geomorphology. Our results show that changes in reef-water carbonate chemistry depend primarily on the ratio of benthic metabolism to the square root of the onshore wave energy flux as well as on the length and depth of the reef flat; however, they are only weakly dependent on channel geometry and the total frictional resistance of the reef system. Diurnal variations in pCO2, pH, and aragonite saturation state (Ωar) are primarily dependent on changes in net production and are relatively insensitive to changes in net calcification; however, net changes in pCO2, pH, and Ωar are more strongly influenced by net calcification when averaged over 24 hours. We also demonstrate that a relatively simple one-dimensional analytical model can provide a good description of the functional dependence of reef-water carbonate chemistry on benthic metabolism, wave forcing, sea level, reef flat morphology, and total system frictional resistance. Importantly, our results indicate that any long-term (weeks to months) net offsets in reef-water pCO2 relative to offshore values should be modest for reef systems with narrow and/or deep lagoons. Thus, the long-term evolution of water column pCO2 in many reef environments remains intimately connected to the regional-scale oceanography of offshore waters and hence directly influenced by rapid anthropogenically driven increases in pCO2.

Carbon cycling hysteresis in permeable carbonate sands over a diel cycle: Implications for ocean acidification

Dissolved inorganic carbon, dissolved oxygen, H+, and alkalinity fluxes from permeable carbonate sediments at Heron Island (Great Barrier Reef) were measured over one diel cycle using benthic chambers designed to induce advective pore‐water exchange. A complex hysteretic pattern between carbonate precipitation and dissolution in sands and the aragonite saturation state (ΩAr) of the overlying chamber water was observed throughout the incubations. During the day, precipitation followed a hysteretic pattern based on the incidence of photosynthetically active radiation with lower precipitation rates in the morning than in the afternoon. The observed diel hysteresis seems to reflect a complex interaction between photosynthesis and respiration rather than ΩAr of the overlying water as the main driver of carbonate precipitation and dissolution within these permeable sediments. Changes in flux rates over a diel cycle demonstrate the importance of taking into account the short‐term variability of benthic metabolism when calculating net daily flux rates. Based on one diel cycle, the sediments were a net daily source of alkalinity to the water column (5.13 to 8.84 mmol m−2 d−1, depending on advection rates), and advection had a net stimulatory effect on carbonate dissolution. The enhanced alkalinity release associated with benthic metabolism and pore‐water advection may partially buffer shallow coral reef ecosystems against ocean acidification on a local scale.

Benthic metabolism and nitrogen dynamics in a sub-tropical coastal lagoon: Microphytobenthos stimulate nitrification and nitrate reduction through photosynthetic oxygen evolution

Benthic oxygen and nutrient fluxes, and rates of nitrate reduction, were determined seasonally under light and dark conditions at four sites within a sub-tropical coastal lagoon (Coombabah Lake, Australia). Sediments at all sites were strongly heterotrophic acting as strong oxygen sinks and sources of dissolved inorganic nitrogen (DIN) in all seasons during both light and dark incubations. Sediment oxygen demand (SOD) and DIN effluxes were greatest during summer, but showed only a relatively small degree of seasonal variation. In contrast, there was a strong spatial trend in SOD and DIN effluxes, which were consistently greater at the sites with fine grained compared to the coarser sediments. Microphytobenthos (MPB) directly influenced SOD and DIN effluxes, with lower SOD and DIN effluxes measured during all light incubations. Strong correlations were found between sediment chlorophyll-a content and light–dark shifts in oxygen and ammonium fluxes (ΔO2 and ΔNH4+), and between ΔO2 and ΔNH4+. Rates of total nitrate reduction were relatively low ranging from 3 to 26 μmol N m−2 h−1 and exhibited only minor seasonal variations. Dissimilatory nitrate reduction to ammonium (DNRA) was the dominant pathway for nitrate reduction, accounting for on average, 65 and 68% of total nitrate reduction during light and dark incubations, respectively. Nitrification was the dominant source of nitrate fuelling nitrate reduction processes, accounting for approximately 90% of total nitrate supply. In contrast to typical MPB colonised sediments, rates of nitrification and, as a consequence, nitrate reduction rates were consistently stimulated in the light, indicating that MPB primarily influenced these processes through photosynthetic oxygen evolution rather than through competition for inorganic N-species.

Impacts of shrimp farm effluent on water quality, benthic metabolism and N-dynamics in a mangrove forest (New Caledonia)

Water quality parameters, sediment oxygen demand (SOD), dissolved organic and inorganic nutrient fluxes, and N-cycle processes (nitrification; denitrification; dissimilatory nitrate reduction to ammonium (DNRA)) were determined in a New Caledonian mangrove receiving shrimp farm effluent and a natural mangrove. Effluent was enriched in nutrients and organic matter, and significantly stimulated SOD and nutrient regeneration rates in the receiving sediments. All N-cycling processes were stimulated between ∼2 and 12-fold in the sediments receiving effluents compared to the natural mangrove. However, due to the preferential enhancement of DNRA compared to denitrification, there was no significant increase in net nitrogen elimination compared to the significant increase in sediment nutrient regeneration rates. These results indicate that the mangroves are only a partial filter for the shrimp farm effluent, as confirmed by the elevated nutrient concentrations measured in an external, marine creek of the effluent receiving mangrove.

Depositional fluxes and sources of particulate carbon and nitrogen in natural lakes and a young boreal reservoir in Northern Québec

We investigated the depositional trends of total particles, carbon and nitrogen in a newly created, 600-km2 hydroelectric reservoir in Northern Quebec, and compared the results with those observed in lakes of the surrounding region. We show that particulate fluxes exhibit a large degree of spatial heterogeneity in both the reservoir (68–548 mg POC m−2 d−1 and 5–33 mg PN m−2 d−1) and the natural lakes (30–150 mg POC m−2 d−1 and 3–12 mg PN m−2 d−1) and that on average, settling fluxes of the reservoir (211 ± 46 mg POC m−2 d−1 and 14 ± 3 mg PN m−2 d−1) exceeded lake deposition (79 ± 13 mg POC m−2 d−1 and 7 ± 1 mg PN m−2 d−1) by approximately two-fold. Our results also show that the nature of the organic matter reaching the sediments was significantly different between lakes and the reservoir, which can have consequences for benthic metabolism and the long-term storage. We found that sinking fluxes in the reservoir were mostly regulated by local morphological and hydrological conditions, with higher fluxes along or in the vicinity of the old riverbed (average 400 ± 73 mg POC m−2 d−1 and 24 ± 5 mg PN m−2 d−1) and lower fluxes in calmer zones such as side bays (average 106 ± 10 mg POC m−2 d−1 and 8 ± 1 mg PN m−2 d−1). In lakes, where settling fluxes were not linked to the trophy, or dissolved organic carbon, the actual nature of the sedimenting organic material was influenced by lake morphometry and the relative contribution of algal versus terrestrial sources. We conclude that re-suspension and erosion play a major role in shaping the reservoir sinking fluxes which explain both, the higher reservoir deposition and also some of the qualitative differences between the two systems. Despite all these differences, sinking particulate organic carbon fluxes were small and surprisingly similar relative to the surface carbon dioxide emissions in both the reservoir and lakes, representing approximately 16–17 % of the carbon efflux estimated for these same systems in 2008.

Interaction of benthic microalgae and macrofauna in the control of benthic metabolism, nutrient fluxes and denitrification in a shallow sub-tropical coastal embayment (western Moreton Bay, Australia)

Benthic biogeochemistry and macrofauna were investigated six times over 1 year in a shallow sub-tropical embayment. Benthic fluxes of oxygen (annual mean −918 μmol O2 m−2 h−1), ammonium (NH4 +), nitrate (NO3 −), dissolved organic nitrogen, dinitrogen gas (N2), and dissolved inorganic phosphorus were positively related to OM supply (N mineralisation) and inversely related to benthic light (N assimilation). Ammonium (NH4 +), NO3 − and N2 fluxes (annual means +14.6, +15.9 and 44.6 μmol N m−2 h−1) accounted for 14, 16 and 53 % of the annual benthic N remineralisation respectively. Denitrification was dominated by coupled nitrification–denitrification throughout the study. Potential assimilation of nitrogen by benthic microalgae (BMA) accounted for between 1 and 30 % of remineralised N, and was greatest during winter when bottom light was higher. Macrofauna biomass tended to be highest at intermediate benthic respiration rates (−1,000 μmol O2 m−2 h−1), and appeared to become limited as respiration increased above this point. While bioturbation did not significantly affect net fluxes, macrofauna biomass was correlated with increased light rates of NH4 + flux which may have masked reductions in NH4 + flux associated with BMA assimilation during the light. Peaks in net N2 fluxes at intermediate respiration rates are suggested to be associated with the stimulation of potential denitrification sites due to bioturbation by burrowing macrofauna. NO3 − fluxes suggest that nitrification was not significantly limited within respiration range measured during this study, however comparisons with other parts of Moreton Bay suggest that limitation of coupled nitrification–denitrification may occur in sub-tropical systems at respiration rates exceeding −1,500 μmol O2 m−2 h−1.

Interactive influences of the marine yabby (Trypaea australiensis) and mangrove (Avicennia marina) leaf litter on benthic metabolism and nitrogen cycling in sandy estuarine sediment

A previous study has demonstrated that in sandy sediment the marine yabby (Trypaea australiensis) stimulated benthic metabolism, nitrogen regeneration and nitrification, but did not stimulate denitrification, as the intense bioturbation of the yabbies eliminated anoxic microzones amenable to denitrification. It was hypothesised that organic matter additions would alleviate this effect as the buried particles would provide anoxic microniches for denitrifiers. To test this hypothesis a 55-day microcosm (75 cm × 36 cm diameter) experiment, comprising four treatments: sandy sediment (S), sediment + yabbies (S + Y), sediment + A. marina litter (S + OM) and sediment + yabbies + A. marina litter (S + Y + OM), was conducted. Trypaea australiensis significantly stimulated benthic metabolism, nitrogen regeneration, nitrification and nitrate reduction in the presence and the absence of litter additions. In contrast, the effects of litter additions alone were more subtle, developed gradually and were only significant for sediment oxygen demand. However, there was a significant interaction between yabbies and litter with rates of total nitrate reduction and denitrification being significantly greater in the S + Y + OM than all other treatments, presumably due to the decaying buried litter providing anoxic micro-niches suitable to nitrate reduction. In addition, both T. australiensis and litter significantly decreased rates of DNRA and its contribution to nitrate reduction.

Benthic fluxes of oxygen, carbon and nutrients in the Marano and Grado Lagoon (northern Adriatic Sea, Italy)

Benthic metabolism and carbon and nutrient cycling at the sediment–water interface were studied seasonally in the Marano (sites MB and MC) and Grado Lagoon (sites ART and BAR), northern Adriatic Italy, using porewater vertical profiles and daily fluxes of O2, DIC, DOC, NO3−, NH4+, PO43− and SiO44− measured in situ deployed transparent and dark benthic chambers. Diffusive and benthic fluxes of solutes were evaluated on a seasonal basis. Sites MC and ART were characterized by higher Corg. contents due to input of riverine organic matter and mariculture, respectively. The Corg., Ntot., Ptot., Porg. and Sibiog. contents decreased along the sediment cores while porewater concentrations of DIC, DOC, NO3−, NH4+, PO43− and SiO44− increased along the sediment cores at all study sites due to the degradation of labile sedimentary matter. Higher concentrations of all porewater solutes and higher diffusive fluxes were observed in warmer periods. Benthic fluxes of O2, DIC, NO3−, NH4+, PO43− and SiO44− showed intensive seasonal variations. Based on O2 and DIC metabolism, the lagoon sediments were highly heterotrophic except at BAR being in trophic balance or weakly heterotrophic. NO3− and SiO44− exhibited influxes due to intense microphytobenthic assimilation, mostly by diatoms, and denitrification while extremely low PO43− fluxes suggest P as a limiting factor. The great difference observed between the diffusive and the in situ benthic fluxes suggests the importance of bioturbation and that the pertinent processes occur at the sediment–water interface. Tentative annual budgets of carbon and nutrients in surface sediments of studied sites indicate that their cycling, compared to burial flux, is more intensive at the sediment–water interface. These basic benthic biogeochemical processes can be important to better understand the trace metal cycling, especially Hg mobilization and sequestration, in the lagoon environment.

Benthic ciliate and meiofaunal communities in two contrasting habitats of an intertidal estuarine wetland

Annual variations in benthic meiofaunal and ciliated protozoan communities were investigated using monthly samplings from June 2006 to May 2007 in two habitats characterized by different vegetal coverage in an estuarine intertidal wetland of Qingdao Jiaozhou Bay, China. The sediment composition was stable at each site: sediments densely covered with seagrass (Suaeda glauca) in the lower estuarine site (Station S) were finer, with higher content of organic matter, phaeopigments and water than sediments at the upper estuarine site (Station S-P) which was unvegetated other than for patches of S. glauca and common reed (Phragmites australis). Chlorophyll a exhibited a similar distribution in the two habitats. A total of 14 meiofaunal groups, and 249 species of ciliates belonging to 37 genera, 28 families and 16 orders, were isolated from the two sites. Univariate and multivariate measures of the communities were significantly different between the two habitats. There were higher abundances of ciliates and meiofauna, and a greater diversity of ciliates, at Station S than Station S-P (223 vs. 61 species). Herbivorous ciliates were numerically predominant in ciliate communities at both sites. The representative ciliates at Station S-P belonged to the Cyrtophorida and appeared to be a reduced subset of the assemblage at Station S, which was characterized by members of the Prostomatida, Cyrtophorida, Hypotrichida and Scuticociliatida. More than 96% of the total meiofauna were nematodes, accounting for 93% of the differences in the abundance compositions of the meiofaunal communities between habitats. The average individual weights of nematodes were nearly 3 times greater at Station S than Station S-P, indicating a distinctive species composition at each site. Temperature, salinity and food availability were key factors that regulated the ciliate and meiofaunal community structure. Nematodes were the dominant group in terms of the combined abundance, biomass and benthic metabolism of ciliates and meiofauna. With respect to the dominance of herbivorous ciliates and epistrate-feeder nematodes in seagrass sediment, predator–prey relationships and competition for food resources between nematodes and ciliates are likely to be important factors in controlling the abundances of these groups.

Cyanobacterial life at low O2: community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat

Cyanobacteria are renowned as the mediators of Earth's oxygenation. However, little is known about the cyanobacterial communities that flourished under the low-O(2) conditions that characterized most of their evolutionary history. Microbial mats in the submerged Middle Island Sinkhole of Lake Huron provide opportunities to investigate cyanobacteria under such persistent low-O(2) conditions. Here, venting groundwater rich in sulfate and low in O(2) supports a unique benthic ecosystem of purple-colored cyanobacterial mats. Beneath the mat is a layer of carbonate that is enriched in calcite and to a lesser extent dolomite. In situ benthic metabolism chambers revealed that the mats are net sinks for O(2), suggesting primary production mechanisms other than oxygenic photosynthesis. Indeed, (14)C-bicarbonate uptake studies of autotrophic production show variable contributions from oxygenic and anoxygenic photosynthesis and chemosynthesis, presumably because of supply of sulfide. These results suggest the presence of either facultatively anoxygenic cyanobacteria or a mix of oxygenic/anoxygenic types of cyanobacteria. Shotgun metagenomic sequencing revealed a remarkably low-diversity mat community dominated by just one genotype most closely related to the cyanobacterium Phormidium autumnale, for which an essentially complete genome was reconstructed. Also recovered were partial genomes from a second genotype of Phormidium and several Oscillatoria. Despite the taxonomic simplicity, diverse cyanobacterial genes putatively involved in sulfur oxidation were identified, suggesting a diversity of sulfide physiologies. The dominant Phormidium genome reflects versatile metabolism and physiology that is specialized for a communal lifestyle under fluctuating redox conditions and light availability. Overall, this study provides genomic and physiologic insights into low-O(2) cyanobacterial mat ecosystems that played crucial geobiological roles over long stretches of Earth history.

Novel use of burrow casting as a research tool in deep-sea ecology

Although the deep sea is the largest ecosystem on Earth, its infaunal ecology remains poorly understood because of the logistical challenges. Here we report the morphology of relatively large burrows obtained by in situ burrow casting at a hydrocarbon-seep site and a non-seep site at water depths of 1173 and 1455 m, respectively. Deep and complex burrows are abundant at both sites, indicating that the burrows introduce oxygen-rich sea water into the deep reducing substrate, thereby influencing benthic metabolism and nutrient fluxes, and providing an oxic microhabitat for small organisms. Burrow castings reveal that the solemyid bivalve Acharax johnsoni mines sulphide from the sediment, as documented for related shallow-water species. To our knowledge, this is the first study to examine in situ burrow morphology in the deep sea by means of burrow casting, providing detailed information on burrow structure which will aid the interpretation of seabed processes in the deep sea.

Benthic metabolism and nitrogen transformations affected by fish cage farming in the tropical Nha Phu estuary (Vietnam)

Effects of organic-waste loading from fish farming on benthic metabolism and nitrogen (N) cycling were studied in the tropical Nha Phu Estuary, Vietnam. The loading of fish excreta and feed waste enhanced benthic oxygen (O2) uptake two times and total carbon dioxide (TCO2) release three times, compared with the reference station. NH4+ was the major form of released N, comprising 94–100% of dissolved inorganic N (DIN) flux below and near fish cages. Only 3% and 1% of organic carbon (OC) and organic N (ON) deposited from the fish farm was degraded in the sediment, whereas the rest was dispersed to adjacent areas via tidal currents or buried into the sediment. Coupled nitrification–denitrification were almost 0 under fish cages but increased at distances greater than 10 m from fish cages. Consequently, biologically available N was not removed permanently near fish cages as the excess N deposited under cages were mineralised and released as DIN. The nutrient efflux could therefore potentially be a source for pelagic primary production in the vicinity of cages. However, the water currents and low water residence time may have distributed and diluted the nutrient effect of cages to the entire estuary and the adjacent ocean.