Temperature Decouples Ammonium and Nitrite Oxidation in Coastal Waters

Influencing factors on the activity of an enriched Nitrospira culture with granular morphology

Nitrospira is a common genus of nitrite-oxidising bacteria (NOB) found in wastewater treatment plants (WWTPs). To identify the key factors influencing the composition of NOB communities, research was conducted using both sequencing batch reactor (SBR) and continuous flow reactor under different conditions. High-throughput 16S rRNA gene sequencing revealed that Nitrospira (18.79% in R1 and 25.77% in R3) was the dominant NOB under low dissolved oxygen (DO) and low nitrite (NO 2 - -N) concentrations, while Nitrobacter (21.26% in R2) was the dominant NOB under high DO and high NO 2 - -N concentrations. Flocculent and granule sludge were cultivated with Nitrospira as the dominant genus. Compared to Nitrospira flocculent sludge, Nitrospira granule sludge had higher inhibition threshold concentrations for free ammonia (FA) and free nitrous acid (FNA). It was more likely to resist adverse environmental disturbances. Furthermore, the effects of environmental factors such as temperature, pH, and DO on the activity of Nitrospira granular sludge were also studied. The results showed that the optimum temperature and pH for Nitrospira granular sludge were 36°C and 7.0, respectively. Additionally, Nitrospira granular sludge showed a higher dissolved oxygen half-saturation constant (Ko) of 3.67 ± 0.71 mg/L due to its morphological characteristics. However, the majority of WWTPs conditions do not meet the conditions for the Nitrospira granular sludge. Thus, it can be speculated that future development of aerobic partial nitrification granular sludge may automatically eliminate the influence of Nitrospira. This study provides a theoretical basis for a deeper understanding of Nitrospira and the development of future water treatment processes.

Seasonal isotopic and isotopomeric signatures of nitrous oxide produced microbially in a eutrophic estuary

Anthropogenic input of excess nutrients stimulates massive nitrous oxide (N2O) production in estuaries with distinct seasonal variations. Here, nitrogen isotopic and isotopomeric signatures were utilized to investigate the seasonal dynamics of N2O production and nitrification at the middle reach of the eutrophic Pearl River Estuary in the south of China. Elevated N2O production primarily via ammonia oxidation (> 1 nM-N d-1) occurred from April to November, along with increased temperature and decreased dissolved oxygen concentration. This consistently oxygenated water column showed active denitrification, contributing 20-40 % to N2O production. The water column microbial N2O production generally constituted a minor fraction (10-15 %) of the estuarine water-air interface efflux, suggesting that upstream transport and tidal dilution regulated the dissolved N2O inventory in the middle reach of the estuary. Nitrification (up to 3000 nM-N d-1) played a critical role in bioavailable nitrogen conversion and N2O production, albeit with N2O yields below 0.05 %.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay

Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay. Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South San Francisco Bay during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in quantitative polymerase chain reaction (PCR) data, and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Candidatus Nitrosomarinus catalina-like AOA metagenome-assembled genome that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria metagenome-assembled genome from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier metagenome-assembled genomes. This study confirms AOA are not only abundant but also highly active during blooms oxidizing large amounts of ammonia to nitrite-a key intermediate in the microbial nitrogen cycle-and producing reactive compounds that may impact other members of the microbial community.

Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation

Nitrite (NO2-) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in nitrification is a double-edged sword, i.e., a disaster in aquatic environments but a hope for innovating nitrogen removal technology in wastewater treatment. However, little information is available regarding the molecular mechanism of NOB inhibition at the cellular level. Herein, we investigate the response of NOB inhibition on NO2- accumulation established by a side-stream free ammonia treatment unit in a nitrifying reactor using integrated metagenomics and metaproteomics. Results showed that compared with the baseline, the relative abundance and activity of NOB in the experimental stage decreased by 91.64 and 68.66%, respectively, directly resulting in a NO2- accumulation rate of 88%. Moreover, RNA polymerase, translation factors, and aa-tRNA ligase were significantly downregulated, indicating that protein synthesis in NOB was interfered during NO2- accumulation. Further investigations showed that ribosomal proteins and GTPases, responsible for bindings between either ribosomal proteins and rRNA or ribosome subunits, were remarkably downregulated. This suggests that ribosome biogenesis was severely disrupted, which might be the key reason for the inhibited protein synthesis. Our findings fill a knowledge gap regarding the underlying mechanisms of NO2- accumulation, which would be beneficial for regulating the accumulation of NO2- in aquatic environments and engineered systems.

Portable Conductometric Sensing Probe for Real-Time Monitoring Ammonia Profile in Coastal Waters

An ability to real-time and continuously monitor ammonium/ammonia profiles of coastal waters over a prolonged period in a simple and maintenance-free fashion would enable economic conducting large-scale assessments, providing the needed scientific insights to better control and mitigate the impact of eutrophication on coastal ecosystems. However, this is a challenging task due to the lack of capable sensors. Here, we demonstrate the use of a membrane-based conductometric ammonia sensing probe (CASP) for real-time monitoring of ammonia levels in coastal waters. A boric acid/glycerol receiving phase is investigated and innovatively utilized to overcome the high salinity of coastal water-induced analytical errors. A calibration-free approach is used to eliminate the need for ongoing calibration, while the issues concerning practical applications, such as salinity variation, ammonia intake capability, and biofouling, are systematically investigated. The field deployment at an estuary confluence water site over a half-moon cycle period confirms that CASP is capable of continuously monitoring the ammonia profile of coastal waters in real-time with high resolution and accuracy to unveil the dynamic ammonia concentration changes over a prolonged period.

Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes

Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.

Transitions in nitrogen and organic matter form and concentration correspond to bacterial population dynamics in a hypoxic urban estuary

Nitrogen (N) inputs to developed coastlines are linked with multiple ecosystem and socio-economic impacts worldwide such as algal blooms, habitat/resource deterioration, and hypoxia. This study investigated the microbial and biogeochemical processes associated with recurrent, seasonal bottom-water hypoxia in an urban estuary, western Long Island Sound (WLIS), that receives high N inputs. A 2-year (2020-2021) field study spanned two hypoxia events and entailed surface and bottom depth water sampling for dissolved nutrients as inorganic N (DIN; ammonia-N and nitrite + nitrate (N + N)), organic N, orthophosphate, organic carbon (DOC), as well as chlorophyll a and bacterial abundances. Physical water quality data were obtained from concurrent conductivity, temperature, and depth casts. Results showed that dissolved organic matter was highest at the most-hypoxic locations, DOC was negatively and significantly correlated with bottom-water dissolved oxygen (Pearson's r = -0.53, p = 0.05), and ammonia-N was the dominant DIN form pre-hypoxia before declining throughout hypoxia. N + N concentrations showed the reverse, being minimal pre-hypoxia then increasing during and following hypoxia, indicating that ammonia oxidation likely contributed to the switch in dominant DIN forms and is a key pathway in WLIS water column nitrification. Similarly, at the most hypoxic sampling site, bottom depth bacteria concentrations ranged ~ 1.8 × 10⁴-1.1 × 10⁵ cells ml^-1 pre-hypoxia, declined throughout hypoxia, and were positively and significantly correlated (Pearson's r = 0.57; p = 0.03) with ammonia-N, confirming that hypoxia influences N-cycling within LIS. These findings provide novel insight to feedbacks between major biogeochemical (N and C) cycles and hypoxia in urban estuaries.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10533-023-01021-2.

The use of double-cropping in combination with no-tillage and optimized nitrogen fertilization reduces soil N2O emissions under irrigation

The irrigation systems of the Ebro valley can lead to high N₂O emissions. The effects that crop diversification, such as double-cropping in combination with conservation tillage and different N fertilizer ratios, has on soil N₂O emissions have not been extensively studied in this region. The goal of this research was to measure N₂O soil emissions and determine the tillage practices and N fertilization rates that provide the lowest emissions when combined with double-cropping systems. The work compared monocropping maize (MC) versus legume-maize double-cropping (DC) with two tillage systems (conventional tillage, CT; and no-tillage, NT), and three mineral N fertilization rates (zero, medium and high). Pea for grain (2019), vetch for green manure (2020), and vetch for forage (2021) were the legumes employed. The N₂O emissions ranged from 0 to 15.5 mg N₂O-N m^-2 d^-1 and were concentrated in the fertilization periods. Soil temperature and water filled pore space (WFPS) content significantly influenced soil N₂O emissions. For both cropping systems, the conditions with the highest N₂O emissions were soil temperatures above 20 °C and a WFPS of 50-60 %. The use of legumes facilitated reduced N fertilization in DC without affecting crop yield and led to reduced N₂O emissions in this cropping system. DC reduced the emission factor (EF), which in all cases was lower than the default IPCC EF (1 %). With DC, a medium N fertilization rate produced similar yields to the high rate commonly applied by farmers, and also entailed lower N₂O emissions. The no-tillage system, although producing higher levels of N₂O, achieved lower yield-scaled N₂O emissions due to greater crop yields. This work underlines the advantages of using double-cropping no-tillage systems combined with medium rates of N fertilization to reduce soil N₂O emissions.

Metabolic scaling of stream dissolved oxygen across the U.S. Atlantic Coast

We investigated the hypothesis of emergent 'biogeochemical' similitude (parametric reduction) and scaling of dissolved oxygen (DO) in coastal streams across the U.S. Atlantic Coast by employing dimensional analysis methodology from fluid mechanics and hydraulic engineering. Two mechanistically meaningful dimensionless numbers were discovered as the stream 'metabolic' number and the fraction of 'DO saturation' number. The 'metabolic' number represented the synergistic control on stream DO from various climatic, hydrologic, biochemical, and ecological drivers (e.g., water temperature, atmospheric pressure, stream width and depth, total phosphorus, pH, and salinity). A graphical exploration of the 'metabolic' versus the 'DO saturation' numbers led to collapse of data during 1998-2015 from diverse coastal streams into an emergent process diagram, indicating three metabolism regimes (high, transitional, and low). The high and low metabolism regimes were, respectively, characterized by the most and least favorable environmental conditions for stream DO depletion-through reduced dissolution and reaeration, as well as increased organic decomposition, respiration, and nitrification. The emergent process diagram led to a generalized power law scaling relationship of the 'DO saturation' number as a function of the 'metabolic' number (exponent ~ 1/3; Nash-Sutcliffe Efficiency, NSE = 0.83-0.85). The metabolic scaling law was leveraged to develop a generalized empirical model to successfully predict DO in diverse streams across the U.S. Atlantic Coast (NSE = 0.83). The emergent process diagram, metabolic scaling law, and prediction model of DO would help understand and manage water quality and ecosystem health of coastal streams in the U.S. and elsewhere.

Differential Responses of the Catalytic Efficiency of Ammonia and Nitrite Oxidation to Changes in Temperature

Microbially mediated nitrification plays an important role in the nitrogen (N) cycle, and rates of activity have been shown to change significantly with temperature. Despite this, the substrate affinities of nitrifying bacteria and archaea have not been comprehensively measured and are often assumed to be static in mathematical models of environmental systems. In this study, we measured the oxidation kinetics of ammonia- (NH3) oxidizing archaea (AOA), NH3-oxidizing bacteria (AOB), and two distinct groups of nitrite (NO2 -)-oxidizing bacteria (NOB), of the genera Nitrobacter and Nitrospira, by measuring the maximum rates of apparent activity (V max(app)), the apparent half-saturation constant (K m(app)), and the overall catalytic efficiency (V max(app) /K m(app)) over a range of temperatures. Changes in V max(app) and K m(app) with temperature were different between groups, with V max(app) and catalytic efficiency increasing with temperature in AOA, while V max(app) , K m(app), and catalytic efficiency increased in AOB. In Nitrobacter NOB, V max(app) and K m(app) increased, but catalytic efficiency decreased significantly with temperature. Nitrospira NOB were variable, but V max(app) increased while catalytic efficiency and K m(app) remained relatively unchanged. Michaelis-Menten (MM) and Haldane (H) kinetic models of NH3 oxidation and NO2 - oxidation based on the collected data correctly predict nitrification potential in some soil incubation experiments, but not others. Despite previous observations of coupled nitrification in many natural systems, our results demonstrate significant differences in response to temperature strategies between the different groups of nitrifiers; and indicate the need to further investigate the response of nitrifiers to environmental changes.

Challenges, solutions and prospects of mainstream anammox-based process for municipal wastewater treatment

Anaerobic ammonia oxidation (anammox) process has a promising application prospect for the mainstream deammonification of municipal wastewater due to its high efficiency and low energy consumption. In this paper, challenges and solutions of mainstream anammox-based process are summarized by analyzing the literature of recent ten years. Slow growth rate of anammox bacteria is a main challenge for mainstream anammox-based process, and enhancement of bacteria retention has been recognized to be necessary. Compared with directly increasing sludge retention time (SRT) with membrane bioreactors or sequencing batch reactors, culturing anammox bacteria in the form of biofilm or granule sludge is more promising for its feasibility of eliminating nitrite oxidizing bacteria (NOB). Besides, adding external electron donors or conductive materials and enriching the concentration of ammonia with absorption materials have also been proved helpful to improve the activity of anammox bacteria. Other challenges include the elimination of NOB and achieving ideal ratio of NH₄⁺ and NO₂^-. To solve these problems and achieve stable partial nitrification, composite control strategies based on low SRT and limited aeration are needed based on the special characteristics of ammonia oxidizing bacteria (AOB) and NOB. When treating actual wastewater, interference of low temperature and components in the influent is another problem. Relatively high activity of anammox bacteria has been realized after artificial acclimation at low temperature and the mechanism was also preliminary explored. Different pre-treatment sections have been designed to reduce the concentration of COD and S^2- from the influent. As for the nitrate produced by the anammox reaction, coupling processes are useful to reduce the concentration of nitrate in the effluent. In brief, suitable reactor and coupling process should be selected according to the temperature, influent quality and discharge targets of different regions. The future prospects of the mainstream anammox-based process are also put forward.

Analysis of nitrite oxidation process and nitrification performance by nitrogen and oxygen isotope fractionation effect

The N and O isotope fractionation effects in NO₂^--N oxidation and nitrification performance of an activated sludge system treating municipal wastewater are unknown. The nitrifying sludge was cultured under different temperature (33 ± 1 °C, 25 ± 1 °C,and 18 ± 1 °C) and dissolved oxygen (DO: 0.5-1 mg/L, 3-4 mg/L, and 7-8 mg/L). The inverse kinetic isotope effects of N and O (¹⁵ε_NO2 and ¹⁸ε_NO2) were -0.62‰ to -7.08‰ and -0.87‰ to -1.68‰ in the process of NO₂^--N oxidation, respectively. ¹⁵ε_NO3 gradually increased with increasing of temperature (¹⁵ε_NO3-33°C (14.49‰) > ¹⁵ε_NO3-25°C (10.43‰) > ¹⁵ε_NO3-18°C (7.3‰)), while the ¹⁵ε_NO3:¹⁸ε_NO3 was maintained at 1.02-5.32. The increase of temperature improved the nitrification activity, which promoted the fractionation effect, but the change of DO did not highlight this difference. The exchange of NO₂^--N and H₂O (X_NOB) was 32.5 ± 1.5%, and the kinetic isotope effect of H₂O participating in the reaction (¹⁸ε_{k, H2O, 2}) was 22.57 ± 1.79‰, indicating that H₂O was involved in the NO₂^--N oxidation rather than DO. In summary, the elevated temperature enhanced the fractionation effect of NO₂^--N oxidation. This study provides a new perspective to reveal the mechanism of NO₂^--N oxidation, optimize the process of nitrogen removal from wastewater and further control water eutrophication.

Factors Influencing Soil Nitrification Process and the Effect on Environment and Health

To meet the global demand for food, several factors have been deployed by agriculturists to supply plants with nitrogen. These factors have been observed to influence the soil nitrification process. Understanding the aftermath effect on the environment and health would provoke efficient management. We review literature on these factors, their aftermath effect on the environment and suggest strategies for better management. Synthetic fertilizers and chemical nitrification inhibitors are the most emphasized factors that influence the nitrification process. The process ceases when pH is <5.0. The range of temperature suitable for the proliferation of ammonia oxidizing archaea is within 30 to 37oC while that of ammonia oxidizing bacteria is within 16 to 23oC. Some of the influencing factors excessively speed up the rate of the nitrification process. This leads to excess production of nitrate, accumulation of nitrite as a result of decoupling between nitritation process and nitratation process. The inhibition mechanism of chemical nitrification inhibitors either causes a reduction in the nitrifying micro-organisms or impedes the amoA gene's function. The effects on the environment are soil acidification, global warming, and eutrophication. Some of the health effects attributed to the influence are methemoglobinemia, neurotoxicity, phytotoxicity and cancer. Biomagnification of the chemicals along the food chain is also a major concern. The use of well-researched and scientifically formulated organic fertilizers consisting of microbial inoculum, well-treated organic manure and good soil conditioner are eco-friendly. They are encouraged to be used to efficiently manage the process. Urban agriculture could promote food production, but environmental sustainability should be ensured.

Genome-Resolved Metagenomic Insights into Massive Seasonal Ammonia-Oxidizing Archaea Blooms in San Francisco Bay

Ammonia-oxidizing archaea (AOA) are key for the transformation of ammonia to oxidized forms of nitrogen in aquatic environments around the globe, including nutrient-rich coastal and estuarine waters such as San Francisco Bay (SFB). Using metagenomics and 16S rRNA gene amplicon libraries, we found that AOA are more abundant than ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB), except in the freshwater stations in SFB. In South SFB, we observed recurrent AOA blooms of “Candidatus Nitrosomarinus catalina” SPOT01-like organisms, which account for over 20% of 16S rRNA gene amplicons in both surface and bottom waters and co-occur with weeks of high nitrite concentrations (>10 μM) in the oxic water column. We observed pronounced nitrite peaks occurring in the autumn for 7 of the last 9 years (2012 to 2020), suggesting that seasonal AOA blooms are common in South SFB. We recovered two high-quality AOA metagenome-assembled genomes (MAGs), including a Nitrosomarinus-like genome from the South SFB bloom and another Nitrosopumilus genome originating from Suisun Bay in North SFB. Both MAGs cluster with genomes from other estuarine/coastal sites. Analysis of Nitrosomarinus-like genomes show that they are streamlined, with low GC content and high coding density, and harbor urease genes. Our findings support the unique niche of Nitrosomarinus-like organisms which dominate coastal/estuarine waters and provide insights into recurring AOA blooms in SFB.

IMPORTANCE Ammonia-oxidizing archaea (AOA) carry out key transformations of ammonia in estuarine systems such as San Francisco Bay (SFB)—the largest estuary on the west coast of North America—and play a significant role in both local and global nitrogen cycling. Using metagenomics and 16S rRNA gene amplicon libraries, we document a massive, recurrent AOA bloom in South SFB that co-occurs with months of high nitrite concentrations in the oxic water column. Our study is the first to generate metagenome-assembled genomes (MAGs) from SFB, and through this process we recovered two high-quality AOA MAGs, one of which originated from bloom samples. These AOA MAGs yield new insight into the Nitrosopumilus and Nitrosomarinus-like lineages and their potential niches in coastal and estuarine systems. Nitrosomarinus-like AOA are abundant in coastal regions around the globe, and we highlight the common occurrence of urease genes, low GC content, and range of salinity tolerances within this lineage.

The Enzymology of Ocean Global Change

A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.

Microbial community analysis of biopiles in Antarctica provides evidence of successful hydrocarbon biodegradation and initial soil ecosystem recovery

Microorganisms comprise the bulk of biodiversity and biomass in Antarctic terrestrial ecosystems. To effectively protect and manage the Antarctic environment from anthropogenic impacts including contamination, the response and recovery of microbial communities should be included in soil remediation efficacy and environmental risk assessments. This is the first investigation into the microbial dynamics associated with large scale bioremediation of hydrocarbon contaminated soil in Antarctica. Over five years of active management, two significant shifts in the microbial community were observed. The initial shift at 12-24 months was significantly correlated with the highest hydrocarbon degradation rates, increased microbial loads, and significant increases in alkB gene abundances. ANCOM analysis identified bacterial genera most likely responsible for the bulk of degradation including Alkanindiges, Arthrobacter, Dietzia and Rhodococcus. The second microbial community shift occurring from 36 to 60 months was associated with further reductions in hydrocarbons and a recovery of amoA nitrification genes, but also increasing pH, accumulation of nitrite and a reduction of oligotrophic bacterial species. Over time, the addition of inorganic fertilisers altered the soil chemistry and led to a disruption of the nitrogen cycle, most likely decoupling ammonia oxidisers from nitrite oxidisers, resulting in nitrite accumulation. The results from this study provide key insights to the long-term management of hydrocarbon bioremediation in Antarctic soils.

Physical mixing in coastal waters controls and decouples nitrification via biomass dilution

Changes in both quantity and speciation of nitrogen in coastal waters impact phytoplankton communities, contributing to eutrophication and harmful algal blooms. Multidisciplinary oceanographic time series of high resolution are rare but crucial for identifying complex mechanisms that underlie such anthropogenic impacts. Analysis and modeling of such a time series from a seasonally stratified fjord showed that dilution of nitrifier biomass by variable winter mixing altered the timing and rates of nitrification, which converts ammonia to nitrite and nitrate. This reveals a link among climate-sensitive physical dynamics, nitrifier abundance, and diversity, with controls on phytoplankton ecology. The findings imply that explicit measurement and modeling of microbial communities will be required to project impacts of climate change on coastal ecosystems.

Nitrification is a central process of the aquatic nitrogen cycle that controls the supply of nitrate used in other key processes, such as phytoplankton growth and denitrification. Through time series observation and modeling of a seasonally stratified, eutrophic coastal basin, we demonstrate that physical dilution of nitrifying microorganisms by water column mixing can delay and decouple nitrification. The findings are based on a 4-y, weekly time series in the subsurface water of Bedford Basin, Nova Scotia, Canada, that included measurement of functional (amoA) and phylogenetic (16S rRNA) marker genes. In years with colder winters, more intense winter mixing resulted in strong dilution of resident nitrifiers in subsurface water, delaying nitrification for weeks to months despite availability of ammonium and oxygen. Delayed regrowth of nitrifiers also led to transient accumulation of nitrite (3 to 8 μmol · kg_sw⁻¹) due to decoupling of ammonia and nitrite oxidation. Nitrite accumulation was enhanced by ammonia-oxidizing bacteria (Nitrosomonadaceae) with fast enzyme kinetics, which temporarily outcompeted the ammonia-oxidizing archaea (Nitrosopumilus) that dominated under more stable conditions. The study reveals how physical mixing can drive seasonal and interannual variations in nitrification through control of microbial biomass and diversity. Variable, mixing-induced effects on functionally specialized microbial communities are likely relevant to biogeochemical transformation rates in other seasonally stratified water columns. The detailed study reveals a complex mechanism through which weather and climate variability impacts nitrogen speciation, with implications for coastal ecosystem productivity. It also emphasizes the value of high-frequency, multiparameter time series for identifying complex controls of biogeochemical processes in aquatic systems.

In-depth Spatiotemporal Characterization of Planktonic Archaeal and Bacterial Communities in North and South San Francisco Bay

Despite being the largest estuary on the west coast of North America, no in-depth survey of microbial communities in San Francisco Bay (SFB) waters currently exists. In this study, we analyze bacterioplankton and archaeoplankton communities at several taxonomic levels and spatial extents (i.e., North versus South Bay) to reveal patterns in alpha and beta diversity. We assess communities using high-throughput sequencing of the 16S rRNA gene in 177 water column samples collected along a 150-km transect over a 2-year monthly time-series. In North Bay, the microbial community is strongly structured by spatial salinity changes while in South Bay seasonal variations dominate community dynamics. Along the steep salinity gradient in North Bay, we find that operational taxonomic units (OTUs; 97% identity) have higher site specificity than at coarser taxonomic levels and turnover ("species" replacement) is high, revealing a distinct brackish community (in oligo-, meso-, and polyhaline samples) from fresh and marine end-members. At coarser taxonomic levels (e.g., phylum, class), taxa are broadly distributed across salinity zones (i.e., present/abundant in a large number of samples) and brackish communities appear to be a mix of fresh and marine communities. We also observe variations in brackish communities between samples with similar salinities, likely related to differences in water residence times between North and South Bay. Throughout SFB, suspended particulate matter is positively correlated with richness and influences changes in beta diversity. Within several abundant groups, including the SAR11 clade (comprising up to 30% of reads in a sample), OTUs appear to be specialized to a specific salinity range. Some other organisms also showed pronounced seasonal abundance, including Synechococcus, Ca. Actinomarina, and Nitrosopumilus-like OTUs. Overall, this study represents the first in-depth spatiotemporal survey of SFB microbial communities and provides insight into how planktonic microorganisms have specialized to different niches along the salinity gradient.

Change of abundance and correlation of Nitrospira inopinata-like comammox and populations in nitrogen cycle during different seasons

Complete-nitrifying bacteria (comammox) play important roles in nitrogen-overloading aquatic systems. However, the understanding of the environmental relevance is still limited. Here, we studied the responses of comammox bacteria (Nitrospira inopinata) in a tributary of the Yellow River, with the water and sediment, microbial, seasonal, and chemical variations considered. Illumina sequencing indicated that the predominant phyla in the river sediment were Proterobacteria, Bacteroidetes, Actinobacteria, and Chloroflex. Quantitative PCR revealed that N. inopinata-like comammox were approximately twice as abundant in the water during the wet season and in the sediment during the dry season than that of other conditions. Significant correlations were found between the abundance of N. inopinata-like comammox and pH (r = 0.58), temperature (r = 0.63), and dissolved oxygen (r = - 0.77). The abundance of N. inopinata-like comammox was higher than that of ammonia oxidizing archaea (AOA), and lower than that of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Furthermore, a significant correlation was discovered between N. inopinata-like comammox and NOB (r = 0.60), and so was anammox bacteria (r = 0.358). Interestingly, N. inopinata-like comammox also showed positive relationships with denitrifying microbes (r = 0.559).

Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA)

Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations. Notably, four MAGs are archaea, with two Thaumarchaeota and two marine group II Euryarchaeota.

Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta

Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.

Anthropogenic impact on nitrification dynamics in coastal waters of the Mediterranean Sea

The anthropogenic alteration of the nitrogen cycle results in the modification of the whole food web. And yet, the impact caused on nitrogen dynamics in marine systems is still very uncertain. We propose a workflow to evaluate changes to coastal nitrification by modelling nitrite dynamics, the intermediary compound. Nitrite concentrations were estimated with a simple steady state nitrification model, which was calibrated in 9 NW Mediterranean coastal sites with different anthropogenic pressures, located within 250 km. The results obtained indicate that nitrite peaks are observed in winter and explained by nitrification response to temperature, but these dynamics are altered in impacted coastal waters. We found the second step of nitrification to be more sensitive to temperature, which entails a significant impact of climate change on the decoupling of the two steps of nitrification. The results could be extrapolated to numerous coastal regions of the Mediterranean Sea with similar characteristics.

Ecological control of nitrite in the upper ocean

Microorganisms oxidize organic nitrogen to nitrate in a series of steps. Nitrite, an intermediate product, accumulates at the base of the sunlit layer in the subtropical ocean, forming a primary nitrite maximum, but can accumulate throughout the sunlit layer at higher latitudes. We model nitrifying chemoautotrophs in a marine ecosystem and demonstrate that microbial community interactions can explain the nitrite distributions. Our theoretical framework proposes that nitrite can accumulate to a higher concentration than ammonium because of differences in underlying redox chemistry and cell size between ammonia- and nitrite-oxidizing chemoautotrophs. Using ocean circulation models, we demonstrate that nitrifying microorganisms are excluded in the sunlit layer when phytoplankton are nitrogen-limited, but thrive at depth when phytoplankton become light-limited, resulting in nitrite accumulation there. However, nitrifying microorganisms may coexist in the sunlit layer when phytoplankton are iron- or light-limited (often in higher latitudes). These results improve understanding of the controls on nitrification, and provide a framework for representing chemoautotrophs and their biogeochemical effects in ocean models.

Nitrite tends to peak at the base of the sunlit zone in the ocean, but the ecological drivers of the local and global distributions of nitrite are not known. Here, Zakem et al. use a marine ecosystem model to show how the interactions of nitrifying microbes mediate nitrite accumulation.

Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight

Mid-summer peaks in the abundance of Thaumarchaeota and nitrite concentration observed on the Georgia, USA, coast could result from in situ activity or advection of populations from another source. We collected data on the distribution of Thaumarchaeota, ammonia-oxidizing betaproteobacteria (AOB), Nitrospina, environmental variables and rates of ammonia oxidation during six cruises in the South Atlantic Bight (SAB) from April to November 2014. These data were used to examine seasonality of nitrification in offshore waters and to test the hypothesis that the bloom was localized to inshore waters. The abundance of Thaumarchaeota marker genes (16S rRNA and amoA) increased at inshore and nearshore stations starting in July and peaked in August at >10⁷ copies L^-1. The bloom did not extend onto the mid-shelf, where Thaumarchaeota genes ranged from 10³ to 10⁵ copies L^-1. Ammonia oxidation rates (AO) were highest at inshore stations during summer (to 840 nmol L^-1 d^-1) and were always at the limit of detection at mid-shelf stations. Nitrite concentrations were correlated with AO (R = 0.94) and were never elevated at mid-shelf stations. Gene sequences from samples collected at mid-shelf stations generated using Archaea 16S rRNA primers were dominated by Euryarchaeota; sequences from inshore and nearshore stations were dominated by Thaumarchaeota. Thaumarchaeota were also abundant at depth at the shelf-break; however, this population was phylogenetically distinct from the inshore/nearshore population. Our analysis shows that the bloom is confined to inshore waters during summer and suggests that Thaumarchaeota distributions in the SAB are controlled primarily by photoinhibition and secondarily by water temperature.

Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969-2015

The U.S. Geological Survey (USGS) maintains a place-based research program in San Francisco Bay (USA) that began in 1969 and continues, providing one of the longest records of water-quality measurements in a North American estuary. Constituents include salinity, temperature, light extinction coefficient, and concentrations of chlorophyll-a, dissolved oxygen, suspended particulate matter, nitrate, nitrite, ammonium, silicate, and phosphate. We describe the sampling program, analytical methods, structure of the data record, and how to access all measurements made from 1969 through 2015. We provide a summary of how these data have been used by USGS and other researchers to deepen understanding of how estuaries are structured and function differently from the river and ocean ecosystems they bridge.

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.