Temperature response of denitrification and anaerobic ammonium oxidation rates and microbial community structure in Arctic fjord sediments

Removal efficiency and abundance of nitrogen cycling microorganism in three bio-matrix materials to treat swine wastewater

A bio-matrix material (BMM) system is used to pretreat swine wastewater and reduce the nitrogen (N) concentration to the tolerance range of plants in constructed wetlands. In this study, rice straw (RS), wheat straw (WS), and corn stalk (CS) were applied to treat pollutants from swine wastewater, respectively. This one year-long field experiment make up for the lack of long-term experiments and mechanistic investigations of BMM. The pollutant removal efficiency, degradation process of crop straw, and the abundance of nitrogen cycling genes were determined in different BMM systems. The results showed that the removal efficiency of COD, TN, NH4+, and NO3- was the best in the initial 6 months. Furthermore, RS and WS exhibited favorable annual removal efficiency of TN and NH4+, which were 32.81% and 32.99%, 35.3% and 34.97%, respectively. Moreover, the removal efficiency of COD was 30.81% in three BMM systems. Meanwhile, it was found that the dry matter (DM) degradation of crop straws was fast in the first 4-5 months. The degradation rates of cellulose, hemicellulose, and lignin were 94.19%, 94.36%, and 87.32%, respectively, in 1 year. The abundance of nitrogen cycling genes significantly increased by adding BMM, compared with CK (P < 0.05). This showed the abundance of the hzsB gene in RS was the highest, while nirK, nirS, AOA, and AOB were the highest in WS. The addition of RS and WS was better than that of CS in promoting the abundance of nitrogen cycling microorganisms. The results indicated that adding BMM could enhance the anaerobic ammonia oxidation, nitrification, and denitrification. This study not only extends our comprehension of BMM mechanisms in swine wastewater treatment but also serves as a guiding light for numerous farms in similar climate regions.

Relationship between denitrification and anammox rates and N2 production with substrate consumption and pH in a riparian zone

Denitrification and anaerobic ammonium oxidation (anammox) are the key processes to quantitatively remove nitrate (NO3-) and balance the nitrogen (N) budget of the ecosystem. In this paper, a slurry-based 15N tracer approach was used to study the correlation and quantitative relation of substrate consumption and pH with rates of denitrification and anammox in a riparian zone. The results showed that the fastest rates of 0.93 µg N h-1 and 0.32 µg N h-1 for denitrification (Denitrif-N2) and anammox (Denitrif-N2), respectively. N2 produced by denitrification occupied 74.04% and produced by anammox occupied 25.96% of the total N2, proving denitrification is the dominant process to remove NO3-. The substrate content (NO3-, NH4+ and TOC) and pH varied during incubation and were significantly correlated with Dentrif-N2 and Anammox-N2. Nitrate and TOC as the substrates of denitrification demonstrated a significant correlation with Anammox-N2, which was associated with the products of denitrification involved in the anammox process. This proved a coupling of denitrification and anammox. A quantitative relationship was observed between Dentrif-N2 and Anammox-N2 in the range of 2.75-2.90 when TOC, NH4+ and NO3- consumption per unit mass or pH changed per unit. Nitrogen mass balance analysis showed that 1 mg N substrate (NO3-+NH4+) consumption in the denitrification and anammox can produce 1.05 mg N2 with a good linear relationship (r2 = 0.9334). This could be related to other processes that produced extra N2 in denitrification and anammox system.

Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica

Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3-) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3- via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.

Sources and seasonal variations of nitrate in the coastal multiple-aquifer groundwater of Beihai, southern China

Elevated nitrate (NO3-) loadings in groundwater may cause health effects in drinking water and nutrient enrichment of aquatic ecosystems. To reveal the sources and seasonal variations of NO3- in the coastal groundwater of Beihai, southern China, we carried out hydrochemical and isotopic (δ15N-δ18O in NO3-) investigations in the summer and winter, respectively, concerning multiple-aquifer groundwater, rainwater, seawater, and surface water. The sources of the main elements present in the waters were interpreted by ionic ratios. NO3- sources were identified by combined use of the δ15N values and δ18O values or NO3-/Na+ molar ratios, with estimations of the proportional contribution by the Bayesian stable isotope mixing model. Denitrification was interpreted along the flow paths. The results show groundwater main elements are originated primarily from silicate weathering, and secondarily from anthropogenic inputs and carbonate dissolution. Its qualities are largely affected by seawater intrusion along the coastline. Because of difference in the predominant minerals within the aquifers and in scale and extent of seawater intrusion, the groundwater displays distinct ionic ratio characters. NO3- concentrations are up to 33.9 mg/L, with higher loadings in the plains relative to along the coastline. Soil N, domestic sewage, rainwater, chemical fertilizers, and algae are NO3- sources, with average proportional contributions of 0.255, 0.221, 0.207, 0.202, and 0.116, respectively. In relation to the winter, higher production of NO3- from nitrification of soil N- and algae-derived ammonium induced by higher temperatures in the summer accounts for increases in groundwater NO3- loadings. In the rural areas, elevated loadings of NO3- in the winter may be due to larger infiltration fractions of sewage. Seasonal variations of atmospheric NO3- deposition and farming may also cause the dynamics. Our results improve the understanding of sources and seasonal dynamics of NO3- in coastal groundwater.

A pilot study of situ sludge fermentation-driven multiple biological nitrogen removal pathways (SFBNR): Revealing microbial synergy mechanism based on co-occurrence network analysis

The sludge fermentation-driven biological nitrogen removal (SFBNR) has garnered increasing attention due to its efficient carbon resource utilization from waste activated sludge (WAS). This study successfully extended the application of this technique to a 38 m3 reactor, facilitating a daily ultra-low carbon to nitrogen ratio (<1) wastewater treatment capacity of 16 tons and a WAS capacity of 500 L. After 185-days operation, the system demonstrated commendable performance with a denitrification efficiency (DNE) of 93.22 % and a sludge reduction efficiency (SRE) of 72.07 %. To better understand the potential mechanisms, various functional bacteria interactions were revealed by co-occurrence network analysis. The results unveiled module hubs (e.g., Anaerolineaceae, Denitratisoma, and Candidatus Brocadia) and connectors (e.g., Tuaera and Candidatus Alysiosphaera) in the network exhibited synergistic relationships facilitated by carbon metabolism and nitrogen cycling. Furthermore, the interaction between biofilm sludge (BS) and suspended sludge (SS) contributed to the in-situ enrichment of anaerobic ammonium oxidizing bacteria (AnAOB), whose abundance in BS reached 1.8 % (200-times higher than in SS) after six months, and the suspend-biofilm interface served as a hotspot for anammox activity.

Dynamics of Benthic Nitrate Reduction Pathways and Associated Microbial Communities Responding to the Development of Seasonal Deoxygenation in a Coastal Mariculture Zone

Intensive mariculture activities result in eutrophication and enhance coastal deoxygenation. Deoxygenation profoundly influences nitrate reduction processes and further the fate of nitrogen (N) in coastal systems. Herein, 15N isotope labeling, real-time PCR, and high-throughput sequencing techniques were jointly used to investigate the participation and seasonal dynamics of sediment nitrate reduction pathways and the succession of functional microbial communities during the development of seasonal deoxygenation in a coastal aquaculture zone. Denitrification dominated benthic nitrate reduction (46.26-80.91%). Both denitrification and dissimilatory nitrate reduction to ammonium were significantly enhanced by summer deoxygenation (dissolved oxygen levels fell to 2.94 ± 0.28 mg L-1), while anammox remained unchanged. The abundance of the nitrous oxide reductase gene nosZ increased during deoxygenation. The community of the nosZ gene was sensitive to deoxygenation, with Azospirillum and Ruegeria accounting for the majority. Pelobacter was overwhelming in the nrfA gene (encoding dissimilatory nitrite reductase) community, which was less affected by deoxygenation. The variations of benthic nitrate reduction processes were driven by bottom water oxygen combined with temperature, chlorophyll a, and microbial gene abundances and community compositions. Our results implicated that seasonal oxygen-deficient zones could be substantial N sinks of coastal ecosystems and important for N balance. Effective management measures need to be developed to avoid further exacerbation of coastal deoxygenation and maintain the sustainable development of mariculture.

Modified microbiology through enhanced denitrification by addition of various organic substances-temperature effect

Worldwide, the environmental nitrate (NO₃^-) problem is increasingly coming into focus. These increases in NO₃^- concentration result mainly from agricultural inputs and are further exacerbated by decreasing and finite geogenic NO₃^- degradation capacity in aquifers. Thus, treatment methods are becoming more and more important. In this study, the effects of enhanced denitrification with addition of organic carbon (C) on thereby autochthonous occurring microbiology and compared at room temperature as well as 10 °C were investigated. Incubation of bacteria and fungi was carried out using natural sediments without degradation capacity and groundwater with high NO₃^- concentrations. Addition of the four applied substrates (acetate, glucose, ascorbic acid, and ethanol) results in major differences in microbial community. Cooling to 10 °C changes the microbiology again. Relative abundances of bacteria are strongly influenced by temperature, which is probably the explanation for different denitrification rates. Fungi are much more sensitive to the milieu change with organic C. Different fungi taxa preferentially occur at one of the two temperature approaches. Major modifications of the microbial community are mainly observed whose denitrification rates strongly depend on the temperature effect. Therefore, we assume a temperature optimum of enhanced denitrification specific to each substrate, which is influenced by the microbiology.

The Study of Soil Bacterial Diversity and the Influence of Soil Physicochemical Factors in Meltwater Region of Ny-Ålesund, Arctic

Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH₄⁺-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH₄⁺-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH₄⁺-N. Our findings suggest that NH₄⁺-N plays an important role in soil bacterial community structure in the Arctic meltwater areas.

Bacterial Metabolic Potential in Response to Climate Warming Alters the Decomposition Process of Aquatic Plant Litter—In Shallow Lake Mesocosms

Increased decomposition rates in shallow lakes with global warming might increase the release of atmospheric greenhouse gases, thereby producing positive feedback for global warming. However, how climate warming affects litter decomposition is still unclear in lake ecosystems. Here, we tested the effects of constant and variable warming on the bacterial metabolic potential of typically submerged macrophyte (Potamogeton crispus L.) litters during decomposition in 18 mesocosms (2500 L each). The results showed that warming reduced main chemoheterotrophic metabolic potential but promoted methylotrophy metabolism, which means that further warming may alter methane-cycling microbial metabolism. The nitrate reduction function was inhibited under warming treatments, and nitrogen fixation capability significantly increased under variable warming in summer. The changes in dissolved oxygen (DO), pH, conductivity and ammonium nitrogen driven by warming are the main environmental factors affecting the bacteria’s metabolic potential. The effects of warming and environmental factors on fermentation, nitrate reduction and ammonification capabilities in stem and leaf litter were different, and the bacterial potential in the stem litter were more strongly responsive to environmental factors. These findings suggest that warming may considerably alter bacterial metabolic potential in macrophyte litter, contributing to long-term positive feedback between the C and N cycle and climate.

Sediment Nitrate Dissimilatory Reduction Processes along a Salinity Gradient in an Estuarine and Coastal Wetland, China

Nitrate (NO3−) dissimilatory reduction processes (denitrification, anammox and dissimilatory NO3− reduction to ammonium (DNRA)) in estuarine and coastal ecosystems play a crucial role in regulating reactive nitrogen loadings. However, nitrate reduction process rates and relative proportions along the estuarine salinity gradient remain poorly understood. Here, denitrification, anammox and DNRA were explored simultaneously along a salinity gradient in Yangtze Estuary based on nitrogen isotope-tracing experiments. Measured denitrification, anammox and DNRA process rates were in the range of 2.33–28.21 nmol g−1 h−1, 0.43–1.87 nmol g−1 h−1 and 0.28–0.74 nmol g−1 h−1, respectively, with a large spatio-temporal variation. The changes in these nitrate reduction process rates were mainly affected by the TOC, TN, NH4+ and NOx− concentrations, rather than salinity and related functional gene abundance. Denitrification dominated the total NO3− reduction process (67.52 to 93.85%), while anammox (3.67 to 25.01%) and DNRA (2.48 to 11.21%) also played a substantially important role in nitrate reduction. The proportions of denitrification to gross nitrate reduction in high-salinity areas were generally lower than those in freshwater, but the opposite was true for DNRA. Overall, our study reported the simultaneous observation of nitrate dissimilatory reduction processes along the salinity gradient of the estuary and highlighted that changes in sediment environmental variables affected by human activities can alter the distribution patterns of NO3− reduction processes.

Microbial Biogeochemical Cycling of Nitrogen in Arid Ecosystems

Arid ecosystems cover ∼40% of the Earth's terrestrial surface and store a high proportion of the global nitrogen (N) pool. They are low-productivity, low-biomass, and polyextreme ecosystems, i.e., with (hyper)arid and (hyper)oligotrophic conditions and high surface UV irradiation and evapotranspiration. These polyextreme conditions severely limit the presence of macrofauna and -flora and, particularly, the growth and productivity of plant species. Therefore, it is generally recognized that much of the primary production (including N-input processes) and nutrient biogeochemical cycling (particularly N cycling) in these ecosystems are microbially mediated. Consequently, we present a comprehensive survey of the current state of knowledge of biotic and abiotic N-cycling processes of edaphic (i.e., open soil, biological soil crust, or plant-associated rhizosphere and rhizosheath) and hypo/endolithic refuge niches from drylands in general, including hot, cold, and polar desert ecosystems. We particularly focused on the microbially mediated biological nitrogen fixation, N mineralization, assimilatory and dissimilatory nitrate reduction, and nitrification N-input processes and the denitrification and anaerobic ammonium oxidation (anammox) N-loss processes. We note that the application of modern meta-omics and related methods has generated comprehensive data sets on the abundance, diversity, and ecology of the different N-cycling microbial guilds. However, it is worth mentioning that microbial N-cycling data from important deserts (e.g., Sahara) and quantitative rate data on N transformation processes from various desert niches are lacking or sparse. Filling this knowledge gap is particularly important, as climate change models often lack data on microbial activity and environmental microbial N-cycling communities can be key actors of climate change by producing or consuming nitrous oxide (N₂O), a potent greenhouse gas.

Denitrification and dissimilatory nitrate reduction to ammonia in long-term lake sediment microcosms with iron(II)

Nitrate is an abundant pollutant in aquatic environments. Competition between the nitrate reduction processes, denitrification, which converts nitrate into nitrogen gas, and dissimilatory nitrate reduction to ammonia (DNRA), which converts nitrate into ammonia, decides whether an ecosystem removes or retains nitrogen. The presence of iron was previously reported to stimulate DNRA while sometimes inhibiting denitrification in in-situ studies, but long-term effect of iron(II) inputs on the competition is unknown. Here we inoculated long-term microcosms with sediments from two freshwater lakes. During 540 days of incubations, the microcosms with nitrate and Fe(II) additions of both lakes were able to sustain high nitrate reduction rates. Lepidocrocite was produced as a product of iron oxidation. We found both denitrification and DNRA were stimulated by nitrate and iron in the absence of external organic carbon addition. Phylogenetic analysis of denitrification genes, nirK and nirS, and DNRA genes, nirB and nrfA, was performed with metagenomic sequencing results. Enrichment was shown for reported Fe(II)-dependent nitrate reducers associated with nirS and nirB. Most of these bacteria are affiliated with Betaproteobacteria. From 16S rRNA gene analysis, Betaproteobacteria was enriched as well. In parallel, heterotrophic denitrifiers and methanotrophic DNRA archaea increased in abundance. Our results suggested heterotrophic and Fe(II)-dependent nitrate reducers both contributed to denitrification and DNRA in long-term microcosm incubations provided with iron.

Disproportionate variations in denitrification and anaerobic ammonium oxidation across freshwater-oligohaline wetlands in Min River Estuary, Southeast China

Spatial and temporal variations in soil denitrification and anaerobic ammonium oxidation (anammox) across the freshwater-oligohaline wetlands in subtropical estuary have not been well understood. In this study, continuous-flow soil core incubation combined with nitrogen isotope tracer was used to determine denitrification and anammox rates across freshwater-oligohaline tidal wetlands in Min River Estuary, Southeast China. Areal rates of denitrification and anammox varied from 3.89 to 19.0 μmol m^-2 h^-1 and from 0.15 to 1.11 μmol m^-2 h^-1, respectively, across these wetlands and throughout sampling months. Denitrification rates were higher in warm months (July, September) than in cool months (November, January), whereas anammox did not vary significantly across the sampling months. Average denitrification rates throughout the sampling months were higher in freshwater than in oligohaline wetlands, while anammox rates did not vary among the wetlands. Relative contribution of anammox (R_a) to N₂ production (including denitrification and anammox) varied from 1.03 to 18.3% across the sampling months and wetlands. Denitrification rates differed significantly across the wetlands and sampling months. Anammox rates and R_a did not vary significantly among the sampling months. Denitrification rates were positively correlated with water content, total organic carbon (TOC), total nitrogen, dissolved organic nitrogen, NH₄⁺, NO_x^-, Fe²⁺, and Fe²⁺/Fe³⁺, but negatively related to pH. Anammox rates showed negative relationships with water content and TOC. Water content, temperature, and pH were crucial for organic carbon and Fe²⁺ availability with important implications on denitrification and anammox. Therefore, denitrification rates vary significantly, whereas anammox rates do not vary significantly across freshwater-oligohaline wetlands in the Min River Estuary.

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

Nitrogen loads alter the N2 production between denitrification and anammox in Min River Estuary, a highly impacted estuary in southeast China

Estuarine sediment denitrification and anammox in response to increased nitrogen (N) loads remain poorly understood. In this study, we used N isotope tracer approach to investigate the spatial distribution of denitrification and anammox and identified the crucial controls on the partitioning of dinitrogen gas (N₂) production along the Min River Estuary (MRE), a highly impacted estuary in southeast China. The results indicated that denitrification and anammox rates ranged from 10.5 to 70.7 nmol g^-1 h^-1 and from 0.44 to 4.31 nmol g^-1 h^-1, respectively. Relative contribution of anammox to N₂ production (R_a) was in a range of 1.04-15.1%, tending to increase toward estuary mouth. Denitrification rates were significantly higher in upper (high N loads) than in lower estuary (low N loads), while anammox rates and R_a showed inverse distributions along the MRE. Wastewater discharge caused the N point pollution triggering denitrification but inhibiting anammox. The best predictor of the variations in denitrification rates was total nitrogen, whereas pH and NH₄⁺ could explained the variations in anammox rates across the estuary. The crucial predictors for the partitioning of N₂ production between denitrification and anammox were NH₄⁺ and NO_x^-. These results suggest that the increase in human activities intensity can alter the partitioning of N₂ production between denitrification and anammox, and the magnitude of this switch can be predicted by N loads in MRE and other highly impacted estuaries.

Effects of Sea Animal Activities on Tundra Soil Denitrification and nirS- and nirK-Encoding Denitrifier Community in Maritime Antarctica

In maritime Antarctica, sea animals, such as penguins or seals, provide a large amount of external nitrogen input into tundra soils, which greatly impact nitrogen cycle in tundra ecosystems. Denitrification, which is closely related with the denitrifiers, is a key step in nitrogen cycle. However, effects of sea animal activities on tundra soil denitrification and denitrifier community structures still have received little attention. Here, the abundance, activity, and diversity of nirS- and nirK-encoding denitrifiers were investigated in penguin and seal colonies, and animal-lacking tundra in maritime Antarctica. Sea animal activities increased the abundances of nirS and nirK genes, and the abundances of nirS genes were significantly higher than those of nirK genes (p < 0.05) in all tundra soils. Soil denitrification rates were significantly higher (p < 0.05) in animal colonies than in animal-lacking tundra, and they were significantly positively correlated (p < 0.05) with nirS gene abundances instead of nirK gene abundances, indicating that nirS-encoding denitrifiers dominated the denitrification in tundra soils. The diversity of nirS-encoding denitrifiers was higher in animal colonies than in animal-lacking tundra, but the diversity of nirK-encoding denitrifiers was lower. Both the compositions of nirS- and nirK-encoding denitrifiers were similar in penguin or seal colony soils. Canonical correspondence analysis indicated that the community structures of nirS- and nirK-encoding denitrifiers were closely related to tundra soil biogeochemical processes associated with penguin or seal activities: the supply of nitrate and ammonium from penguin guano or seal excreta, and low C:N ratios. In addition, the animal activity-induced vegetation presence or absence had an important effect on tundra soil denitrifier activities and nirK-encoding denitrifier diversities. This study significantly enhanced our understanding of the compositions and dynamics of denitrifier community in tundra ecosystems of maritime Antarctica.

Human activities aggravate nitrogen-deposition pollution to inland water over China

In the past three decades, China has built more than 87 000 dams with a storage capacity of ≈6560 km3 and the total surface area of inland water has increased by 6672 km2. Leaching of N from fertilized soils to rivers is the main source of N pollution in China, but the exposure of a growing inland water area to direct atmospheric N deposition and N leaching caused by N deposition on the terrestrial ecosystem, together with increased N deposition and decreased N flow, also tends to raise N concentrations in most inland waters. The contribution of this previously ignored source of  N deposition to freshwaters is estimated in this study, as well as mitigation strategies. The results show that the annual amounts of N depositions ranged from 4.9 to 16.6 kg · ha-1 · yr-1 in the 1990s to exceeding 20 kg · ha-1 · yr-1 in the 2010s over most of regions in China, so the total mass of ΔN (the net contribution of N deposition to the increase in N concentration) for lakes, rivers and reservoirs change from 122.26 Gg N · yr-1 in the 1990s to 237.75 Gg N · yr-1 in the 2010s. It is suggested that reducing the N deposition from various sources, shortening the water-retention time in dams and decreasing the degree of regulation for rivers are three main measures for preventing a continuous increase in the N-deposition pollution to inland water in China.

Nitrate reduction in the reed rhizosphere of a riparian zone: From functional genes to activity and contribution

The increased nitrogen (N) fertilizer usage caused substantial nitrate (NO₃^-) leaching into groundwater and eutrophication in downstream aquatic systems. Riparian zones positioned as the link interfaces of terrestrial and aquatic environments are effective in NO₃^- removal. However, the microbial mechanisms regulating NO₃^- reduction in riparian zones are still unclear. In this study, four microbial NO₃^- reduction processes were explored in fine-scale riparian soil horizons by isotopic tracing technique, qPCR of functional gene, high-throughput amplicon sequencing, and phylogenetic molecular ecological network analysis. Interestingly, anaerobic ammonium oxidation (anammox) contributed to NO₃^- removal of up to 48.2% only in waterward sediments but not in landward soil. Denitrification was still the most significant contributor to NO₃^- reduction (32.0-91.8%) and N-losses (51.7-100%). Additionally, dissimilatory nitrate reduction to ammonium (DNRA) played a key role in NO₃^- reduction (4.4-67.5%) and was even comparable to denitrification. Community structure analysis of denitrifying, anammox, and DNRA bacterial communities targeting the related functional gene showed that spatial heterogeneity played a greater role than both temporal and soil type (rhizosphere and non-rhizosphere soil) variability in microbial community structuring. Denitrification and DNRA communities were diverse, and their activities did not depend on gene abundance but were significantly related to organic matter, suggesting that gene abundance alone was insufficient in assessing their activity in riparian zones. Based on networks, DNRA plays a keystone role among the microbial NO₃^- reducers. As the last line of defense in the interception of terrestrial NO₃^-, these findings contribute to our understanding of NO₃^- removal mechanisms in riparian zones, and could potentially be exploited to reduce the diffusion of NO₃^- pollution.

Nitrogen purification potential limited by nitrite reduction process in coastal eutrophic wetlands

Coastal wetlands accumulate enormous quantities of nitrogen due to their position at the interface between land and sea and high trapping capacity. Fortunately, they have high nitrogen (N) purifying (removal) capacity, which means that they likely play an important role in mitigating against coastal eutrophication. However studies that empirically measure the degree to which wetlands purify nitrogen and their removal pathways (e.g. denitrification, anammox, plant uptake, microbial immobilization, etc.) are rare. In this study, the N purification potential (denitrification and anammox) and enzyme activities related to denitrification in different subtropical wetlands types were conducted in nitrogen-enriched wetlands of Daya Bay, Southern China. We found the average N purification rate was 11.4 μmol N·kg^-1·h^-1, with denitrification accounting for 84.2%-100% of the total N₂ production in the wetlands of Daya Bay. The N purification potential in the wet season, subtidal areas and mangrove forests were generally observed to be higher than that in the dry season, high and low tidal areas, barren and estuary habitats, respectively. Correspondingly, these differences were mainly driven by the temperature, Eh and NH₄-N, respectively. Additionally, the nitrate reductase (Nar) and nitrite reductase (Nir) activities tended to be similar among different seasons and tidal areas, however, Nir activity in mangrove forest was 1.5-fold and 2-fold of the estuarine and barren areas, respectively. Meanwhile, Nir showed a positive correlation with denitrification rate. These results indicate that NO₂-N reduction, the key control mechanism for N purification, should be the rate-limiting step of the denitrification process in Daya Bay wetlands. Notably, mangroves could improve N removal rates by 48.0% compared to other wetlands. Therefore, protecting and restoring mangrove ecosystems could be an effective way to reduce the risk of coastal eutrophication.

Effects of shrimp-aquaculture reclamation on sediment nitrate dissimilatory reduction processes in a coastal wetland of southeastern China

The conversion of natural saltmarshes to shrimp aquaculture ponds can potentially influence the biogeochemical cycling of nutrients in coastal wetlands, but its impact on the dynamics of sediment dissimilatory nitrate (NO₃^-) reduction remains poorly understood. In this study, three sediment NO₃^- reduction processes including denitrification (DNF), anaerobic ammonium oxidation (ANAMMOX), and dissimilatory NO₃^- reduction to ammonium (DNRA) were examined simultaneously in a natural saltmarsh and two shrimp culture ponds (5- and 18-year-old) in July and November, using nitrogen (N) isotope-tracing experiments. Our results showed that sediment potential DNF, ANAMMOX and DNRA rates were generally higher in the shrimp culture ponds than the natural saltmarsh in the two seasons. The rates of all three processes generally increased with the age of shrimp ponds, with the magnitude of increase being less pronounced for DNF and ANAMMOX than DNRA. The contribution of DNRA to total NO₃^- reduction increased significantly following saltmarsh conversion to shrimp ponds, suggesting that DNRA became an increasingly important biogeochemical process under shrimp culture. DNRA competed with DNF and limited reactive N loss to some extent after natural saltmarshes converted to shrimp culture ponds. The results of redundancy analysis revealed that the availability of substrates and sulfides in sediments, rather than the bacteria gene abundance, were the most important factor influencing the NO₃^- reduction processes. Overall, our findings highlighted that shrimp-aquaculture reclamation may aggravate nitrogen loading in coastal wetlands by promoting the production of bioavailable ammonium.

The core seafloor microbiome in the Gulf of Mexico is remarkably consistent and shows evidence of recovery from disturbance caused by major oil spills

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in > 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies.

Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics

Lakes of meltwater in the Artic have become one of the transforming landscape changes under global warming. We herein compared microbial communities between sediments and bank soils at an arctic lake post land submergence using geochemistry, 16S rRNA amplicons, and metagenomes. The results obtained showed that each sample had approximately 2,609 OTUs on average and shared 1,716 OTUs based on the 16S rRNA gene V3-V4 region. Dominant phyla in sediments and soils included Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Nitrospirae; sediments contained a unique phylum, Euryarchaeota, with the phylum Thaumarchaeota being primarily present in bank soils. Among the top 35 genera across all sites, 17 were more abundant in sediments, while the remaining 18 were more abundant in bank soils; seven out of the top ten genera across all sites were only from sediments. A redundancy analysis separated sediment samples from soil samples based on the components of nitrite and ammonium. Metagenome results supported the role of nitrite because most of the genes for denitrification and methane metabolic genes were more abundant in sediments than in soils, while the abundance of phosphorus-utilizing genes was similar and, thus, was not a significant explanatory factor. We identified several modules from the global networks of OTUs that were closely related to some geochemical factors, such as pH and nitrite. Collectively, the present results showing consistent changes in geochemistry, microbiome compositions, and functional genes suggest an ecological mechanism across molecular and community levels that structures microbiomes post land submergence.

Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass

Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m², J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m², J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH₄⁺-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO₃^--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH₄⁺-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.

Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry

Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Globally, marine sediments are a vast repository of organic matter, which is degraded through various microbial pathways, including polymer hydrolysis and monomer fermentation. The sources, abundances, and quality (i.e., labile or recalcitrant) of the organic matter and the composition of the microbial assemblages vary between sediments. Here, we examine new and previously published sediment metagenomes from the Baltic Sea and the nearby Kattegat region to determine connections between geochemistry and the community potential to degrade organic carbon. Diverse organic matter hydrolysis encoding genes were present in sediments between 0.25 and 67 meters below seafloor and were in higher relative abundances in those sediments that contained more organic matter. New analysis of previously published metatranscriptomes demonstrated that many of these genes were transcribed in two organic-rich Holocene sediments. Some of the variation in deduced pathways in the metagenomes correlated with carbon content and depositional conditions. Fermentation-related genes were found in all samples and encoded multiple fermentation pathways. Notably, genes involved in alcohol metabolism were amongst the most abundant of these genes, indicating that this is an important but underappreciated aspect of sediment carbon cycling. This study is a step towards a more complete understanding of microbial food webs and the impacts of depositional facies on present sedimentary microbial communities.

IMPORTANCE Sediments sequester organic matter over geologic time scales and impact global climate regulation. Microbial communities in marine sediments drive organic matter degradation, but the factors controlling their assemblages and activities, which in turn impact their role in organic matter degradation, are not well understood. Hence, determining the role of microbial communities in carbon cycling in various sediment types is necessary for predicting future sediment carbon cycling. We examined microbial communities in Baltic Sea sediments, which were deposited across various climatic and geographical regimes to determine the relationship between microbial potential for breakdown of organic matter and abiotic factors, including geochemistry and sediment lithology. The findings from this study will contribute to our understanding of carbon cycling in the deep biosphere and how microbial communities live in deeply buried environments.

Can cold-season macrophytes at the senescence stage improve nitrogen removal in integrated constructed wetland systems treating low carbon/nitrogen effluent?

Cold-season macrophytes were configured in a system of stabilization ponds (SPs) and batch operation constructed wetlands (BCWs) to supply a carbon source for low carbon/nitrogen (C/N) effluent in spring and summer without generating secondary pollution during the decomposition process. For eutrophic water, the macrophyte configuration increased the average removal efficiency (RE) from 41.6% to 68.6% and from 70.2% to 83.7% for NO₃^--N and TN in the final BCW effluent, respectively, with the concentrations decreasing from 3.08 mg/L to 1.04 mg/L and from 4.94 mg/L to 3.12 mg/L, respectively. In the early decomposition stages, the RE and concentrations were 82.9% and 0.53 mg/L and 89.4% and 2.38 mg/L for NO₃^--N and TN, respectively. Thus, cold-season macrophytes can improve N removal in SP-BCW systems at the senescence stage, especially at the early decomposition stage.

Warming intensify CO2 flux and nutrient release from algal wrack subsidies on sandy beaches

Algal wrack subsidies underpin most of the food web structure of exposed sandy beaches and are responsible of important biogeochemical processes that link marine and terrestrial ecosystems. The response in decomposition of algal wrack deposits to global warming has not been studied in ocean-exposed sandy beaches to date. With this aim, passive open top chambers (OTCs) were used to increase soil temperature within the range predicted by the IPCC for western Europe (between 0.5 and 1.5°C), following the hypothesis that the biogeochemical processing of macroalgal wrack subsidies would accelerate in response to temperature increase. The effect of temperature manipulation on three target substrates: fresh and aged macroalgae, and bare sand, was tested. Results indicated that a small warming (<0.5°C) affected the wrack decomposition process through traceable increases in soil respiration through CO2 flux, inorganic nutrients within the interstitial environment (N and P), sediment organic contents measured through the amount of proteins and microbial pool through the total soil DNA. The different responses of soil variables in the studied substrates indicated that the decomposition stage of stranded macroalgae influences the biogeochemical processing of organic matter in sandy beaches. Thus, CO2 fluxes, releases of organic and inorganic nutrients and microbial activity intensify in aged wrack deposits. Our results predict that expected global warming will increase the release of inorganic nutrients to the coastal ocean by 30% for the N (21 Gg/year) and 5.9% for P (14 Gg/year); that increase for the flow of C to the atmosphere as CO2 was estimated in 8.2% (523 Gg/year). This study confirms the key role of sandy beaches in recycling ocean-derived organic matter, highlighting their sensitivity to a changing scenario of global warming that predicts significant increases in temperature over the next few decades.

Bacterial interactions during sequential degradation of cyanobacterial necromass in a sulfidic arctic marine sediment

Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation. Sequential 16S rRNA gene and transcript amplicon sequencing and fluorescence in situ hybridization combined with Raman microspectroscopy revealed that only few bacterial species were the main degraders of 13 C-spirulina necromass. Psychrilyobacter, Psychromonas, Marinifilum, Colwellia, Marinilabiaceae and Clostridiales species were likely involved in the primary hydrolysis and fermentation of spirulina. VFAs, mainly acetate, produced from spirulina degradation were mineralized by sulfate-reducing bacteria and an Arcobacter species. Cellular activity of Desulfobacteraceae and Desulfobulbaceae species during acetoclastic sulfate reduction was largely decoupled from relative 16S rRNA gene abundance shifts. Our findings provide new insights into the identities and physiological constraints that determine the population dynamics of key microorganisms during complex OM degradation in arctic marine sediments.© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

The cycle of nitrogen in river systems: sources, transformation, and flux

Nitrogen is a requisite and highly demanded element for living organisms on Earth. However, increasing human activities have greatly altered the global nitrogen cycle, especially in rivers and streams, resulting in eutrophication, formation of hypoxic zones, and increased production of N2O, a powerful greenhouse gas. This review focuses on three aspects of the nitrogen cycle in streams and rivers. We firstly introduce the distributions and concentrations of nitrogen compounds in streams and rivers as well as the techniques for tracing the sources of nitrogen pollution. Secondly, the overall picture of nitrogen transformations in rivers and streams conducted by organisms is described, especially focusing on the roles of suspended particle-water surfaces in overlying water, sediment-water interfaces, and riparian zones in the nitrogen cycle of streams and rivers. The coupling of nitrogen and other element (C, S, and Fe) cycles in streams and rivers is also briefly covered. Finally, we analyze the nitrogen budget of river systems as well as nitrogen loss as N2O and N2 through the fluvial network and give a summary of the effects and consequences of human activities and climate change on the riverine nitrogen cycle. In addition, future directions for the research on the nitrogen cycle in river systems are outlined.

Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process

Temperature and energy resources (e.g., iron, sulfur and organic matter) usually undergo dynamic changes, and play important roles during industrial bioleaching process. Thus, it is essential to investigate their synergistic effects and the changes of their independent effects with simultaneous actions of multi-factors. In this study, we explored the synergistic effects of temperature and original mineral compositions (OMCs, energy resources) on the sphalerite bioleaching process. The microbial community structure was monitored by 16S rRNA gene sequencing technology and showed clear segregation along temperature gradients and Shannon diversity decreased at high temperature. On the contrary, the physicochemical parameters (pH and [Fe³⁺]) in the leachate were significantly affected by the OMCs. Interestingly, the influence of temperature on zinc recovery was greater at relatively simpler OMCs level, whereas the influence of OMCs was stronger at lower temperature. In addition, using [Fe³⁺], pH, relative abundances of dominant OTUs of microbial community and temperature as variable parameters, several models were constructed to predict zinc leaching efficiency, providing a possibility to predict the metal recovery efficiency under temperature change and variable energy resources.

Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L⁻¹ d⁻¹, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L⁻¹ oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification.

Ecological Energetic Perspectives on Responses of Nitrogen-Transforming Chemolithoautotrophic Microbiota to Changes in the Marine Environment

Transformation and mobilization of bioessential elements in the biosphere, lithosphere, atmosphere, and hydrosphere constitute the Earth’s biogeochemical cycles, which are driven mainly by microorganisms through their energy and material metabolic processes. Without microbial energy harvesting from sources of light and inorganic chemical bonds for autotrophic fixation of inorganic carbon, there would not be sustainable ecosystems in the vast ocean. Although ecological energetics (eco-energetics) has been emphasized as a core aspect of ecosystem analyses and microorganisms largely control the flow of matter and energy in marine ecosystems, marine microbial communities are rarely studied from the eco-energetic perspective. The diverse bioenergetic pathways and eco-energetic strategies of the microorganisms are essentially the outcome of biosphere-geosphere interactions over evolutionary times. The biogeochemical cycles are intimately interconnected with energy fluxes across the biosphere and the capacity of the ocean to fix inorganic carbon is generally constrained by the availability of nutrients and energy. The understanding of how microbial eco-energetic processes influence the structure and function of marine ecosystems and how they interact with the changing environment is thus fundamental to a mechanistic and predictive understanding of the marine carbon and nitrogen cycles and the trends in global change. By using major groups of chemolithoautotrophic microorganisms that participate in the marine nitrogen cycle as examples, this article examines their eco-energetic strategies, contributions to carbon cycling, and putative responses to and impacts on the various global change processes associated with global warming, ocean acidification, eutrophication, deoxygenation, and pollution. We conclude that knowledge gaps remain despite decades of tremendous research efforts. The advent of new techniques may bring the dawn to scientific breakthroughs that necessitate the multidisciplinary combination of eco-energetic, biogeochemical and “omics” studies in this field.

Temperature response of sulfide/ferrous oxidation and microbial community in anoxic sediments treated with calcium nitrate addition

Nitrate-driven sulfide oxidation has been proved a cost-effective way to control sediments odor which has long been a universal problem for urban rivers in south China areas. In this work, sediments treatment experiments under a dynamic variation of temperature from 5 °C to 35 °C with 3% of calcium nitrate added were conducted to reveal the influence of temperature variation on this process. The results showed that microbial community was remarkably restructured by temperature variation. Pseudomonas (15.56-29.31%), Sulfurimonas (26.81%) and Thiobacillus (37.99%) were dominant genus at temperature of ≤15 °C, 25 °C and 35 °C, respectively. It seemed that species enrichment occurring at different temperature gradient resulted in the distinct variation of microbial community structure and diversity. Moreover, nitrate-driven sulfide and ferrous oxidation were proportionally promoted only when temperature increased above 15 °C. The dominant bacteria at high temperature stage were those genus that closely related to autotrophic nitrate-driven sulfide and ferrous oxidizing bacteria (e.g.Thiobacillus, Sulfurimonas and Thermomonas), revealing that promotion of sulfide/ferrous oxidation could be attributed to the change of dominant bacteria determined by temperature variation. Thus, a higher treatment efficiency by calcium nitrate addition for odor control would be achieved in summer than any other seasons in south China areas.

Potential role of anammox in nitrogen removal in a freshwater reservoir, Jiulonghu Reservoir (China)

Currently, the nitrogen removal potential of anaerobic ammonium oxidation (anammox) and its regulating factors in reservoir systems remain uncertain. Here, we provided the molecular and isotopic evidence for anammox in the freshwater sediment of Jiulonghu Reservoir that is located in Quzhou, Zhejiang Province, China. Diverse 16S rRNA gene sequences related to Candidatus Kuenenia and Candidatus Brocadia were detected by using high-throughput (Illumina MiSeq) sequencing of total bacterial 16S rRNA genes, and the Candidatus Brocadia was the most frequently detected anammox bacterial genus. The anammox bacterial abundance was determined based on quantitative PCR on hzsA (the alpha subunit of the hydrazine synthase) genes and varied from 3.1 × 10⁵ to 1.1 × 10⁶ copies g^-1 dry sediment. Homogenized sediments were further incubated with ¹⁵NO₃^- amendments to measure the potential anammox rates and determine the contribution of this process to dinitrogen gas (N₂) production. The potential rates of anammox ranged between 8.1 and 30.8 nmol N₂ g^-1 dry sediment day^-1, and anammox accounted for 7.7-20.5% of total N₂ production in sediment. Higher levels of anammox bacterial diversity, abundance, and activity were observed in the downstream with greater human disturbance than those in the upstream with less human disturbance. Correlation analyses suggested that the inorganic nitrogen level in sediment could be a key factor for the anammox bacterial abundance and activity. The results showed that the nitrogen removal via anammox may not be negligible in the examined reservoir and indicated that human activities could influence the anammox process in reservoir systems.

Similar temperature responses suggest future climate warming will not alter partitioning between denitrification and anammox in temperate marine sediments

Removal of biologically available nitrogen (N) by the microbially mediated processes denitrification and anaerobic ammonium oxidation (anammox) affects ecosystem N availability. Although few studies have examined temperature responses of denitrification and anammox, previous work suggests that denitrification could become more important than anammox in response to climate warming. To test this hypothesis, we determined whether temperature responses of denitrification and anammox differed in shelf and estuarine sediments from coastal Rhode Island over a seasonal cycle. The influence of temperature and organic C availability was further assessed in a 12-week laboratory microcosm experiment. Temperature responses, as characterized by thermal optima (T_opt ) and apparent activation energy (E_a ), were determined by measuring potential rates of denitrification and anammox at 31 discrete temperatures ranging from 3 to 59 °C. With a few exceptions, T_opt and E_a of denitrification and anammox did not differ in Rhode Island sediments over the seasonal cycle. In microcosm sediments, E_a  was somewhat lower for anammox compared to denitrification across all treatments. However, T_opt  did not differ between processes, and neither E_a  nor T_opt  changed with warming or carbon addition. Thus, the two processes behaved similarly in terms of temperature responses, and these responses were not influenced by warming. This led us to reject the hypothesis that anammox is more cold-adapted than denitrification in our study system. Overall, our study suggests that temperature responses of both processes can be accurately modeled for temperate regions in the future using a single set of parameters, which are likely not to change over the next century as a result of predicted climate warming. We further conclude that climate warming will not directly alter the partitioning of N flow through anammox and denitrification.

Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea

Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies.

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.

Dissimilatory nitrate reduction processes in sediments of urban river networks: Spatiotemporal variations and environmental implications

Urbanizations have increased the loadings of reactive nitrogen in urban riverine environments. However, limited information about dissimilatory nitrate reduction processes and associated contributions to nitrogen removal is available for urban riverine environments. In this study, sediment slurry experiments were conducted with nitrogen isotope-tracing technique to investigate the potential rates of denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) and their contributions to nitrate reduction in sediments of urban river networks, Shanghai. The potential rates of denitrification, anammox and DNRA measured in the study area ranged from 0.193 to 98.7 nmol N g^-1 h^-1 dry weight (dw), 0.0387-23.7 nmol N g^-1 h^-1 dw and 0-10.3 nmol N g^-1 h^-1 dw, respectively. Denitrification and DNRA rates were higher in summer than in winter, while anammox rates were greater in winter than in summer for most sites. Dissolved oxygen, total organic carbon, nitrate, ammonium, sulfide, Fe(II) and Fe(III) were found to have significant influence on these nitrate reduction processes. Denitrification contributed 11.5-99.5%% to total nitrate reduction, as compared to 0.343-81.6% for anammox and 0-52.3% for DNRA. It is estimated that nitrogen loss of approximately 1.33 × 10⁵ t N year^-1 was linked to both denitrification and anammox processes, which accounted for about 20.1% of total inorganic nitrogen transported annually into the urban river networks of Shanghai. Overall, these results show the potential importance of denitrification and anammox in nitrogen removal and provide new insight into the mechanisms of nitrogen cycles in urban riverine environments.

Biotic and abiotic controls on co-occurring nitrogen cycling processes in shallow Arctic shelf sediments

The processes that convert bioavailable inorganic nitrogen to inert nitrogen gas are prominent in continental shelf sediments and represent a critical global sink, yet little is known of these pathways in the Arctic where 18% of the world's continental shelves are located. Moreover, few data from the Arctic exist that separate loss processes like denitrification and anaerobic ammonium oxidation (anammox) from recycling pathways like dissimilatory nitrate reduction to ammonium (DNRA) or source pathways like nitrogen fixation. Here we present measurements of these co-occurring processes using ¹⁵N tracers. Denitrification was heterogeneous among stations and an order of magnitude greater than anammox and DNRA, while nitrogen fixation was undetectable. No abiotic factors correlated with interstation variability in biogeochemical rates; however, bioturbation potential explained most of the variation. Fauna-enhanced denitrification is a potentially important but overlooked process on Arctic shelves and highlights the role of the Arctic as a significant global nitrogen sink.

Arctic continental shelves could store a significant amount of nitrogen, yet the specific nitrogen transformation pathways in these sediments remain unknown. Using nitrogen tracers, McTigue et al. simultaneously measure multiple pathways in the Chukchi Sea, confirming the Arctic as a major nitrogen sink.

Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics

Genes encoding dissimilatory sulfite reductase (DsrAB) are commonly used as diagnostic markers in ecological studies of sulfite- and sulfate-reducing microorganisms. Here, we developed new high-coverage primer sets for generation of reductive bacterial-type dsrA and dsrB polymerase chain reaction (PCR) products for highly parallel amplicon sequencing and a bioinformatics workflow for processing and taxonomic classification of short dsrA and dsrB reads. We employed two diverse mock communities that consisted of 45 or 90 known dsrAB sequences derived from environmental clones to precisely evaluate the performance of individual steps of our amplicon sequencing approach on the Illumina MiSeq platform. Although PCR cycle number, gene-specific primer mismatches and stringent filtering for high-quality sequences had notable effects on the observed dsrA and dsrB community structures, recovery of most mock community sequences was generally proportional to their relative input abundances. Successful dsrA and dsrB diversity analysis in selected environmental samples further proved that the multiplex amplicon sequencing approach is adequate for monitoring spatial distribution and temporal abundance dynamics of dsrAB-containing microorganisms. Although tested for reductive bacterial-type dsrAB, this method is readily applicable for oxidative-type dsrAB of sulfur-oxidizing bacteria and also provides guidance for processing short amplicon reads of other functional genes.

Cold Temperature Effects on Long-Term Nitrogen Transformation Pathway in a Tidal Flow Constructed Wetland

The present study investigated long-term treatment performance and nitrogen transformation mechanisms in tidal flow constructed wetlands (TFCWs) under 4, 8, and 12 °C temperature regimes. High and stable ammonium (NH4(+)-N) removal efficiency (93-96%) was achieved in our TFCWs, whereas nitrate (NO3(-)-N) was accumulated at different levels under different temperatures. Quantitative response relationships showed anammox/amoA, (narG+napA)/amoA, and (narG+napA)/bacteria were the respective key functional gene groups determining 4, 8, and 12 °C NO3(-)-N reduction. Pathway analysis revealed the contribution of these functional gene groups along a depth gradient. In addition, denitrification process increased, while anammox process decreased consistent with a rise in temperature from 4 to 12 °C. Furthermore, cold temperatures exhibited different effects on anammox and denitrification and their long-term acclimatization capacities changed with temperature.

Bacterial biogeography influenced by shelf-basin exchange in the Arctic surface sediment at the Chukchi Borderland

It has been known that continental shelves around the Arctic Ocean play a major role in the ventilation of the deep basins as a consequence of shelf-basin exchange. In the present study, we found that bacterial assemblage of the surface sediment was different from that of seawater while seawater harboured local bacterial assemblages in response to the Arctic hydrography. This finding suggests that the Arctic seafloor sediments may have distinctive bacterial biogeography. Moreover, the distribution of bacterial assemblages and physicochemical properties in surface sediments changed gradually from the Arctic continental shelf to deep-sea basin. Based on the results, bacterial biogeography in the Arctic seafloor sediments may be influenced by winnowing and re-deposition of surface sediments through the sediment gravity flow. The present study offers a deeper understanding of shelf convection and its role for the construction of bacterial assemblages in the Arctic Ocean.