Sediment Ammonium Research Articles

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

BackgroundCoastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling.ResultsTaxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively.ConclusionsOur study demonstrates clear freshwater–saline and sediment–water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems.72ugw57JLuZNUPngo1htqPVideo abstract

Juvenile Oyster (Crassostrea virginica) Biodeposits Contribute to a Rapid Rise in Sediment Nutrients on Restored Intertidal Oyster Reefs (Mosquito Lagoon, FL, USA)

By filtering large volumes of water and releasing nutrient-rich biodeposits (feces and pseudofeces), oysters can locally enhance sediment biogeochemical cycling. An active Crassostrea virginica restoration program in Mosquito Lagoon, FL (USA), was leveraged to assess the immediate (first-year) effects of restoration on sediment nutrients. Measurements included extractable and total carbon, nitrogen, and phosphorus on dead, natural, and restored reefs using a before-after-control-impact design. To investigate an observed “age-nutrient paradox” in sediment nutrient concentrations, a laboratory experiment compared feeding rates and biodeposit nutrient content between juvenile and older oysters. The field study documented a 136% increase in ammonium, 78% increase in total nitrogen, 46% increase in total phosphorus, and 75% increase in organic matter concentrations 12 months post-restoration, with extractable nutrients responding more rapidly to restoration than total nutrients. Sediment nutrient increases were positively correlated with oyster density, shell length, and reef height. Moreover, the laboratory study indicated juvenile oysters had higher rates of chlorophyll-a removal and ammonium efflux and produced biodeposits with higher concentrations of dissolved organic carbon, nitrate, and ammonium than older oysters. Overall, this study documented increases in sediment nutrients on intertidal reefs within the first year of restoration, which may be explained by a greater filtration rate and more nutrient-enriched biodeposits contributed by young oysters as compared to older oysters. Sediment total nitrogen and ammonium content may be the most robust monitoring metrics for documenting the ecosystem service of enhanced biogeochemical cycling on restored oyster reefs.

Spatial distribution and factors influencing the different forms of ammonium in sediments and pore water of the aquitard along the Tongshun River, China

Nitrogen pollution of groundwater has created problems worldwide. Riparian zones form a connection hub for terrestrial and aquatic ecosystems. As a potential source of ammonium in groundwater, aquitards have an important effect on the environment of riparian zones. The spatial distribution and factors influencing the ammonium content in the riparian zone aquitard of a small watershed were analyzed through three geological boreholes with increasing distances from the river: boreholes A > B > C. The results show that the distribution of ammonium was closely related to the lithology of sediments. Under the influence of the river and floods, the average content of ion exchange form of ammonium of sediments in borehole A (stable sedimentary environment) was 94.31 mg kg−1, accounting for 21.2% of the transferable ammonium. The average proportions of ion exchange form of ammonium in the transferable ammonium of boreholes B and C (unstable sedimentary environment) were 19.1% and 17.4%, respectively. The carbonate and iron-manganese oxide forms of ammonium content of sediments in three boreholes were 0.96–15.28 mg kg−1 and 2.3–54.4 mg kg−1, respectively; this was mainly affected by the pH and Eh of the sedimentary environment. Organic sulfide, the form of transferable ammonium of sediments mainly exists in organic matter. The ammonium content in pore water generally increased with depth and was mainly derived from the mineralization of humic-like organic matter in borehole A. The ammonium in pore water in boreholes B and C mixed with ammonium from the mineralization of organic matter and the desorption of ion exchange form ammonium within sediments. The ammonium content in the pore water (up to 5.34 mg L−1) was much higher than the limit for drinking water of 0.5 mg L−1 in China. Therefore, the aquitard has a high risk of releasing ammonium and poses a certain threat to the quality of groundwater.

The potential rate and microbial communities of dissimilatory nitrate reduction to ammonium in Pearl River Estuary

Since nitrogen-related eutrophication has become a severe problem in the Pearl River Delta area in China, it is crucial to have a deep understanding of the nitrogen cycle. This study investigated the existence of dissimilatory nitrate reduction to ammonium (DNRA) in sediments of the Pearl River Estuary using the 15N isotope paring method with continuous-flow systems. The results showed that the maximum was 389.7 nmol/g in 216 h, while the maximum DNRA rate of 4.68 nmol/(g wet sediment h) occurred in 120 hours. The principal components analysis (PCA) based on community composition at the genus level was performed by the nrfA sequences distributed in the nine sites covering a salinity range of 25.3 - 30.1%º, and forming four distinct clusters. There was no significant relationship between the potential DNRA rates in the spatial distribution and salinity, but the highest potential DNRA rate occurred near the sewage discharge in the western coastal area. High contents of nrfA gene fragments were found at the same site, with values of 1159715 copies/g wet sediment, while very low contents of nrfA were found at other sites. Based on the nrfA gene pyrosequencing, Enterobacteriaceae accounts for 89.9 - 99.0% of the classified sequences.

Direct O<sub>2</sub> control on the partitioning between denitrification and dissimilatory nitrate reduction to ammonium in lake sediments

Abstract. Lacustrine sediments are important sites of fixed-nitrogen (N) elimination through the reduction of nitrate to N2 by denitrifying bacteria, and they are thus critical for the mitigation of anthropogenic loading of fixed N in lakes. In contrast, dissimilatory nitrate reduction to ammonium (DNRA) retains bioavailable N within the system, promoting internal eutrophication. Both processes are thought to occur under oxygen-depleted conditions, but the exact O2 concentration thresholds particularly of DNRA inhibition are uncertain. In O2 manipulation laboratory experiments with dilute sediment slurries and 15NO3- additions at low- to sub-micromolar O2 levels, we investigated how, and to what extent, oxygen controls the balance between DNRA and denitrification in lake sediments. In all O2-amended treatments, oxygen significantly inhibited both denitrification and DNRA compared to anoxic controls, but even at relatively high O2 concentrations (≥70 µmol L−1), nitrate reduction by both denitrification and DNRA was observed, suggesting a relatively high O2 tolerance. Nevertheless, differential O2 control and inhibition effects were observed for denitrification versus DNRA in the sediment slurries. Below 1 µmol L−1 O2, denitrification was favoured over DNRA, while DNRA was systematically more important than denitrification at higher O2 levels. Our results thus demonstrate that O2 is an important regulator of the partitioning between N loss and N recycling in sediments. In natural environments, where O2 concentrations change in near-bottom waters on an annual scale (e.g., overturning lakes with seasonal anoxia), a marked seasonality with regards to internal N eutrophication versus efficient benthic fixed-N elimination can be expected.

Plant traits interacting with sediment properties regulate sediment microbial composition under different aquatic DIC levels caused by rising atmospheric CO2

Rising atmospheric CO2 causes an increase in dissolved inorganic carbon (DIC) availability in aquatic ecosystems, further affecting plant growth and aquatic ecosystem production. Belowground carbon input can strongly influence microbial processes (carbon or nitrogen cycling). However, changes in sediment microbial abundance and community structure have not been thoroughly assessed in freshwater ecosystems under rising atmospheric CO2. A pot experiment was conducted using fragments of the submerged macrophyte Myriophyllum spicatum L. to study plant and sediment microbial responses to increasing aquatic carbon availability under rising atmospheric CO2. Three DIC levels of overlying water were set up by continuous bubbling with different concentrations of CO2. Higher biomass accumulation, chlorophyll content, nitrate reductase activity, and leaf N content were observed in M. spicatum under high DIC level in CO2 treatment. The increased DIC level in CO2 treatment reduced sediment ammonium nitrogen, dissolved organic nitrogen content, microbial biomass carbon content and phenol oxidase activity, but not microbial biomass nitrogen content, urease and N-acetyl-β-D-glucosaminidase activities. NifH abundance significantly decreased with the increasing DIC levels in CO2 treatment, while bacterial 16S rRNA abundance was not affected. Redundancy analysis results indicated a modest but obvious shift in sediment microbial community compositions among different levels of DIC. Variation partitioning revealed a strong interaction between plant traits and sediment properties and their regulation of sediment microbial compositions at different DIC levels. It seemed that an intensified competition for essential resources between M. spicatum and sediment microbes occurred under increased aquatic DIC availability caused by rising atmospheric CO2.

In the wake of a major hurricane: Differential effects on early vs. late successional seagrass species

AbstractAt least 18 major storms have struck the Gulf of Mexico and Caribbean in the past 50 yr including Hurricane Harvey, a Category 4 storm that passed over extensive seagrass beds in the western Gulf of Mexico and became the second‐most expensive U.S. hurricane. We sought to identify the effects of an extreme hurricane on sediment physicochemical characteristics and seagrass species with contrasting life histories and morphologies. Surprisingly, Harvey's intense wind speeds resulted in decreases in blade length, vegetative cover, and greater overall loss of Thalassia, a persistent climax species relative to Halodule, a prolific pioneer species. Sediment ammonium and grain size changed, but not organic carbon. Our results indicate that effects of wind intensity are not only restricted to the differential impacts on seagrasses, but on the physicochemical characteristics of the sediments. These changes, coupled with the slow colonization abilities of Thalassia, may prolong recovery of disturbed seagrass meadows.

Dynamics and environmental importance of anaerobic ammonium oxidation (anammox) bacteria in urban river networks

Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 106 to 3.9 × 107 copies g−1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH4+) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks.

Implications of nutrient enrichment for the conservation and management of seagrass Zostera muelleri meadows

Abstract Nutrient overenrichment in aquatic environments, or eutrophication, is increasingly affecting seagrass habitats around the world, leading to the degradation of seagrass ecosystems and the loss of associated ecosystem services. The resistance of seagrass to nutrient enrichment is believed to be site specific, yet the direct correlations between environmental factors and the resistance of seagrass meadows has not yet been adequately resolved. The response of seagrass beds to long‐term multiple‐level sediment nutrient enrichment represents a current research gap. This study therefore assessed the in situ long‐term influence of four levels of sediment urea fertilizer addition on Zostera muelleri plants using a manipulative experimental design at three sites with diverse sediment characteristics. Specifically, this study investigated the response of porewater nutrient concentration, seagrass morphology indices, and seagrass plant tissue carbon and nitrogen contents under experimental nutrient stress levels. Over a 13‐month experiment, sediment nutrient addition substantially increased the ammonium concentrations in the sediment porewater, significantly decreased seagrass morphology indices, and caused a carbon and nitrogen imbalance in plant tissues. Ammonium toxicity was more pronounced in seagrass meadows growing on sandy substrates with lower relative above‐ground biomass, which showed low resistance to eutrophication at sediment ammonium concentrations of up to 1 × 104 μM. Plants growing in muddy sand substrates with higher relative above‐ground biomass were more resistant to nutrient impacts, however, with a delayed negative response observed in response to higher nutrient concentrations (up to 1 × 105 μM). Our findings suggest that seagrasses in low‐nutrient sandy environments show more rapid responses to eutrophication, although seagrasses in both sandy and muddy substrates exhibited declines in response to a long‐term elevation of sediment nutrient concentrations. While continuing to assess the relative susceptibility of seagrass habitats across differing environments to inform coastal management, conservation efforts should allocate resources accordingly and prioritize reducing nutrient overenrichment in sensitive seagrass meadows.

Dissimilatory Nitrate/Nitrite Reduction Processes in River Sediments Across Climatic Gradient: Influences of Biogeochemical Controls and Climatic Temperature Regime

AbstractDissimilatory nitrate/nitrite reduction processes play an important role in controlling nitrogen loading in river environments. However, the relative importance of climatic temperature regime and biogeochemical controls to dissimilatory nitrate/nitrite reduction processes remains unclear. We used nitrogen isotope tracer approach to investigate geographical variabilities of denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) in river sediments from temperate to tropical climates of China. Denitrification, anammox, and DNRA varied greatly across the climatic gradient, with potential rates of 1.47–25.7, 0.54–3.4, and 0.15–7.17 nmol N g−1 h−1, respectively. Mean measured rates throughout the sampling sites were 9.73 nmol N g−1 h−1 for denitrification, 1.29 nmol N g−1 h−1 for anammox, and 1.61 nmol N g−1 h−1 for DNRA. Denitrification and DNRA rates increased significantly from temperate to tropical climates, while no significantly spatial difference was observed for anammox rates along the climatic gradient. Mean annual temperature, total organic carbon, dissolved organic carbon, pH, NH4+, NO3–, C/N, Fe2+, and functional genes were the crucial factors affecting denitrification, anammox, and DNRA. High dissolved organic carbon and NO3– availability determined nitrogen removal capacity in river sediments. Mean annual temperature was the most important factor explaining the geographical variances of denitrification and DNRA, while the critical predictor of anammox variance was sediment pH along the climatic gradient. Our results highlight that biogeochemical controls and climatic temperature regime are important coregulators affecting the geographical variabilities of dissimilatory nitrate/nitrite reduction processes in river sediments at the continental‐scale variation.

Impact of Seabed Resuspension on Oxygen and Nitrogen Dynamics in the Northern Gulf of Mexico: A Numerical Modeling Study

AbstractResuspension affects water quality in coastal environments by entraining seabed organic matter into the water column, which can increase remineralization, alter seabed fluxes, decrease water clarity, and affect oxygen and nutrient dynamics. Nearly all numerical models of water column biogeochemistry, however, simplify seabed and bottom boundary layer processes and neglect resuspension. Here we implemented HydroBioSed, a coupled hydrodynamic‐sediment transport‐biogeochemical model to examine the role of resuspension in regulating oxygen and nitrogen dynamics on timescales of a day to a month. The model was implemented for the northern Gulf of Mexico, where the extent of summertime hypoxia is sensitive to seabed and bottom boundary layer processes. Results indicated that particulate organic matter remineralization in the bottom water column increased by an order of magnitude during resuspension events. This increased sediment oxygen consumption and ammonium production, which were defined as the sum of seabed fluxes of oxygen and ammonium, plus oxygen consumption and ammonium production in the water column due to resuspended organic matter. The increases in remineralization impacted biogeochemical dynamics to a greater extent than resuspension‐induced seabed fluxes and oxidation of reduced chemical species. The effect of resuspension on bottom water biogeochemistry increased with particulate organic matter availability, which was modulated by sediment transport patterns. Overall, when averaged over the shelf and on timescales of a month in the numerical model, cycles of erosion and deposition accounted for about two thirds of sediment oxygen consumption and almost all of the sediment ammonium production.

Eco-exergy based self-organization of the macrobenthic faunal assemblage during mangrove succession in Zhanjiang, China

Eco-exergy (ecological exergy) has been used to evaluate the health and self-organization of aquatic and wetland ecosystems following perturbation or natural succession. Although macrobenthic fauna are important components of mangrove ecosystems, their self-organization during mangrove succession is unclear. In this study, eco-exergy was used to quantify the self-organization processes of macrobenthic faunal assemblages in a mangrove chronosequence that included a primary (unvegetated shoal), early (Avicennia marina), middle (Aegiceras corniculatum), and late (Bruguiera gymnorrhiza + Rhizophora stylosa) community in Zhanjiang, China. Eco-exergy and biomass of the macrobenthic faunal community tended to decrease in the wet season during mangrove succession. The specific eco-exergy of the macrobenthic faunal community, in contrast, remained relatively constant in both wet and dry seasons during mangrove succession, although mollusk eco-exergy tended to decrease and arthropod eco-exergy tended to increase. Statistical analyses indicated that the self-organization of the macrobenthic faunal community during mangrove succession was mainly associated with the development of a suite of vegetation characteristics and sediment physicochemical properties, e.g., plant crown breadth, plant density, sediment ammonium nitrogen and sediment total nitrogen. Unlike the diversification trends of species richness and functional groups, this study confirmed the decreased self-organization trend of macrobenthic fauna assemblage mainly derived from biomass and genetic information. These results highlight the importance of conserving the macrobenthic faunal community in mangrove forests, especially in the late successional stages.

Sulfide production kinetics and model of stormwater retention ponds.

Stormwater retention ponds can play a critical role in mitigating the detrimental effects of urbanization on receiving waters that result from increases in polluted runoff. However, the benthic oxygen demand of stormwater facilities may cause significant hypoxia and trigger the production of hydrogen sulfide (H2S). This process is not well-documented and further research is needed to characterize benthic processes in stormwater retention ponds in order to improve their design and operation. In this study, sediment oxygen demand (SOD), sediment ammonia release (SAR) and sediment sulfide production (SSP) kinetics were characterized in situ and in the laboratory. In situ SOD and SSP data were utilized to develop a stormwater retention pond water sulfide concentration model which demonstrates strong correlation with sulfide concentrations observed in situ (r = 0.724, N = 91, p < 0.001) and in laboratory experiments (r = 0.691, N = 38, p < 0.001). At 4 °C, in situ rates of SOD, SAR and SSP were higher than those measured in laboratory. Sulfate-reducing bacteria (SRB) represented 4.99% of the bacteria present in the top 30 cm of the pond sediment, with Desulfobulbaceae spp., Desulfobacteraceae spp. and Desulfococcus spp. being the dominant SRB taxa identified.

Bacterial Communities and Their Predicted Functions Explain the Sediment Nitrogen Changes Along with Submerged Macrophyte Restoration.

Submerged vegetation biomass fluctuation usually occurs during the preliminary stage of vegetation restoration in shallow lakes, which impacts the final status and duration for achieving a macrophyte-dominant state. This study uncovered the sediment N characteristics and the sediment bacterial community and their predicted functions during the preliminary stage of vegetation recovery in the West Lake, a typical subtropical degenerated shallow lake in China. Results showed increased amounts of sediment TN and NH4-N, reaching 3425.76 and 345.5mgkg-1, respectively, when the vegetation biomass decreased from its maximum to its minimum. The maximum concentration of sediment NH4-N reached 508.60mgkg-1 with the decline in vegetation, which might restrict further growth of the submerged macrophytes. The bacterial community structure during the high macrophyte biomass (HMB) period was distinct from that observed during the low macrophyte biomass (LMB) period. Specific taxa such as the phyla Chloroflexi and Acidobacteria and the genus Anaerolineaceae that are related to organic carbon degradation were significantly higher during the LMB period. Potential denitrifiers, such as Lactococcus and Bacillus genera decreased during the LMB period. Accumulation of sediment ammonia could be attributed to the enhanced production by assimilatory nitrate reduction, organic N degradation, and/or the decreased consumption by nitrification. Our findings highlight that the unstable preliminary stage of vegetation restoration brings drastic fluctuation of sediment N loading, of which NH4-N accumulation caused by bacterial communities prevents further growth of the submerged macrophytes. Therefore, extra management measures for the vegetation recovery areas should be taken to avoid excess NH4-N accumulation in sediments.

Marine Macrophyte Detritus and Degradation: the Role of Intraspecific Genetic Variation

Intraspecific genetic diversity influences the primary production and biomass of coastal marine foundation plants. The majority of their primary production ends up as detritus, yet the relationship between their intraspecific genetic diversity and detritus-based functions has rarely been considered. We addressed the relationship between these functions (detritus standing stock, degradation, sediment ammonium production) and genotypic diversity (richness, evenness, relatedness) in eelgrass (Zostera marina L.), a widely distributed coastal foundation plant, grown in the field at different levels of genotypic richness and relatedness. The functions were largely insensitive to the genotypic diversity, density, and biomass of the living plants in a plot, which suggests that changes in eelgrass genotypic diversity have minimal effects on these important functions and their consequences ranging from trophic support to carbon sequestration. Instead, detritus-based functions are perhaps more related to the sediment environment, the genotypic composition of the detritus itself, and macro- and microscopic detritus consumers.

Push‐pull incubation method reveals the importance of denitrification and dissimilatory nitrate reduction to ammonium in seagrass root zone

In this study, we developed a push-pull incubation method to measure denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in subsurface sediments of subtidal seagrass meadows. This subtidal push-pull technique, adapted from a push-pull method developed for intertidal salt marshes, used mini-piezometers to directly sample pore water in the root zone of the seagrass during an in situ incubation. The pore water was amended with 15 NO3− and with Ar(g) as a tracer gas, and the denitrification products (28N2(g), 29N2(g), and 30N2(g)) were measured with membrane inlet mass spectrometry (MIMS), using the Ar tracer to correct for dilution and gas loss. Production of 15 NH4+ was also measured using hypobromite oxidation and MIMS to determine rates of DNRA. Using this new technique, subsurface rates of denitrification and DNRA were determined to be 17.5 μmol N m−2 h−1 and 14.7 μmol N m−2 h−1, respectively, for a restored Zostera meadow. Rates showed substantial spatial variability, likely due to both heterogeneous conditions in the root zone sediment and variable in situ conditions. When compared to traditional core and slurry incubations, push-pull rates were greater and more variable, suggesting that the push-pull technique more accurately captures heterogeneity and the natural range of denitrification and DNRA in subsurface sediments under field conditions. In vegetated systems with low water column nitrate concentrations, the majority of denitrification and DNRA occurs below the sediment surface, and the subtidal push-pull technique provides an effective method to assess these subsurface rates.

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH communities were also shaped by indicators of subsurface groundwater influence. These results show that interactions between the mats and sediments are crucial for sustaining this hot spot of biological diversity and biogeochemical cycling.

Application of the isotope pairing technique in sediments where anammox, denitrification, and dissimilatory nitrate reduction to ammonium coexist

The 15N isotope pairing technique is widely used to quantify anammox, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) in sediments. However, the effects of DNRA on anammox and denitrification in slurry incubations and on genuine N2 production in intact core incubations have not been fully explored. We developed a mathematical model describing these effects of DNRA, and tested this model in field and computational studies. Our model calculations revealed that for slurry incubations the presence of DNRA tends to under -and overestimate the actual anammox and denitrification rates, respectively, when calculated according to Thamdrup and Dalsgaard (2002). We found this underestimate of anammox to be proportional to the 15 NH4+ mole fraction (FA), and the overestimate of denitrification to be related to both FA and the relative contribution of anammox to the total N2 production (ra). We propose three alternative procedures to better quantify anammox and denitrification rates in slurry incubations and two procedures for intact core incubations. Our model calculations also revealed that for intact core incubations, the presence of DNRA leads to an overestimate of the genuine N2 production rate when calculated according to Risgaard-Petersen et al. (2003). This overestimate depends on the ra and the mole fractions of 15 NH4+ and 15 NO3− in intact core incubations. The results of our field experiments and numerical modeling indicated that the overestimate of the genuine N2 production was less than 1% at two sites in the East China Sea.

Microbial nitrogen processing in hard clam ( Mercenaria mercenaria ) aquaculture sediments: the relative importance of denitrification and dissimilatory nitrate reduction to ammonium (DNRA)

As bivalve aquaculture expands worldwide, an understanding of its role in nutrient cycling is necessary to ensure ecological sustainability and determine the potential of using bivalves for nutrient mitigation. Whereas several studies, primarily of epifaunal bivalves, have assessed denitrification, few have considered nutrient regeneration processes such as dissimilatory nitrate reduction to ammonium (DNRA), which competes with denitrification for nitrate and results in nitrogen retention rather than loss. This study compares sediment nitrogen cycling including mineralization, DNRA, and denitrification within U.S. clam aquaculture sediments to nearby uncultivated sediments, seasonally. Clam aquaculture significantly increased sediment ammonium and phosphate effluxes relative to uncultivated sediments. Both DNRA and denitrification were significantly enhanced at clam beds compared to uncultivated sediments in July and November, while in May only DNRA was increased. The ratio of DNRA to denitrification was significantly higher at clam beds compared to uncultivated sediments, demonstrating that DNRA may be favored due to a ready supply of labile organic carbon relative to nitrate and perhaps sulfidic conditions. Functional gene abundances, nrfA (DNRA) and nirS (denitrification) followed similar patterns to nitrate respiration rates with highest nrfA abundances in the clam sediments and similar nirS abundances across seasons and sediment type. Ultimately clam sediments were found to be a significant source of nutrients to the water column whereas uncultivated sediments retained ammonium produced by microbial mineralization. Thus, clam cultivation may promote local eutrophication (i.e., increased primary production) by facilitating nutrient regeneration and retention of ammonium in the sediments.

Warming increases nutrient mobilization and gaseous nitrogen removal from sediments across cascade reservoirs

Increases in water temperature, as a result of climate change, may influence biogeochemical cycles, sediment-water fluxes and consequently environmental sustainability. Effects of rising temperature on dynamics of nitrate, nitrite, ammonium, dissolved inorganic nitrogen (DIN), dissolved reactive phosphorus (DRP), dissolved organic carbon (DOC) and gaseous nitrogen (N2 and N2O) were examined in a subtropical river (the Jiulong River, southeast China) by microcosm experiments. Slurry sediments and overlying water were collected from three continuous cascade reservoirs, and laboratory incubations were performed at four temperature gradients (5 °C, 15 °C, 25 °C and 35 °C). Results indicated: (1) warming considerably increased sediment ammonium, DIN and DOC fluxes to overlying water; (2) warming increased retention of nitrate, and to a lesser extent, nitrite, corresponding to increases in N2 and N2O emission; (3) DRP was retained but released from Fe/Al-P enriched sediments at high temperature (35 °C) due to enhanced coupled transformation of carbon and nitrogen with oxygen deficiency. Using relationships between sediment fluxes and temperature, a projected 2.3°C-warming in future would increase ammonium flux from sediment by 7.0%–16.8%, while increasing nitrate flux into sediment by 8.9%–28.6%. Moreover, substrates (e.g., grain size, carbon availability) influenced nutrient delivery and cycling across cascade reservoirs. This study highlights that warming would increase bioreactive nutrient (i.e., ammonium and phosphate) mobilization with limited gaseous N removal from sediments, consequently deteriorating water quality and increasing eutrophication with future climate change.