Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient

Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France

Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?

High throughput amplicon analysis reveals potential novel ammonia oxidizing prokaryotes in the eutrophic Jiaozhou Bay

Ammonia-oxidizing prokaryotes (AOPs) are the major contributors of ammonia oxidization with widely distribution. Here we investigated the phylogenetic diversity, community composition, and regulating factors of AOPs in Jiaozhou Bay (JZB) with high-throughput sequencing of amoA gene. Phylogenetic analysis showed most of the OTUs could not be clustered with any known AOPs, indicating there might exist putative novel AOPs. With new developed protocols for AOP community analysis, we confirmed that only 3 OTUs of ammonia-oxidizing archaea (AOA) could be affiliated to known Nitrosopumilaceae and Nitrososphaera, and the other OTUs were identified as novel AOA based on the threshold. All abstained OTUs of ammonia-oxidizing bacteria (AOB) were identified as novel clusters based on the threshold. Further analysis showed the novel AOPs had different distribution characteristics related to environmental factors. The high abundance and widespread distribution of these novel AOPs indicated that they played an important role in ammonia conversion in eutrophic JZB.

Long-term integrated soil-crop management improves soil microbial community structure to reduce GHG emission and increase yield

Integrated soil-crop management (ISCM) has been shown as an effective strategy to increase efficiency and yield while its soil microbial community structure and function remain unclear. We evaluated changes in soil physicochemical factors, bacterial community structure responses, and the contributions of soil properties and bacterial communities to summer maize-winter wheat yield and GHG emissions through an ISCM experiment [T1 (local smallholder farmers practice system), T2 (improved management system), T3 (high-yield production system), and T4 (optimized management system)], which could provide scientific guidance for sustainable development of soil in summer maize-winter wheat rotation system. The results showed that the optimized ISCM could improve the soil quality, which significantly changed the soil bacterial community structure to reduce GHG emissions and increase yield. The co-occurrence network density of T3 was increased significantly. The Acidobacteria (class) and OM190 (class) were enriched in T2 and T4. The Frankiales (order) and Gaiellales (order) were enriched in T3. However, the changes in different crop growth stages were different. At the wheat jointing stage and maize mature stage, T4 could enhance carbon-related functional groups, such as aromatic hydrocarbon degradation and hydrocarbon degradation, to increase the soil organic carbon content. And at the maize tasseling stage, T4 could enhance nitrogen-related functional groups. And soil bacteria structure and function indirectly affected annual yield and GHG emission. T2 and T4 exhibited a similar soil microbial community. However, the yield and nitrogen use efficiency of T2 were reduced compared to those of T4. The yield of T3 was the highest, but the GHG emission increased and soil pH and nitrogen use efficiency decreased significantly. Therefore, T4 was a suitable management system to improve soil quality and soil bacterial community structure and function to decrease GHG emissions and increase the yield of the summer maize-winter wheat rotation system.

Instability and Stasis Among the Microbiome of Seagrass Leaves, Roots and Rhizomes, and Nearby Sediments Within a Natural pH Gradient

Seagrass meadows are hotspots of biodiversity with considerable economic and ecological value. The health of seagrass ecosystems is influenced in part by the makeup and stability of their microbiome, but microbiome composition can be sensitive to environmental change such as nutrient availability, elevated temperatures, and reduced pH. The objective of the present study was to characterize the bacterial community of the leaves, bulk samples of roots and rhizomes, and proximal sediment of the seagrass species Cymodocea nodosa along the natural pH gradient of Levante Bay, Vulcano Island, Italy. The bacterial community was determined by characterizing the 16S rRNA amplicon sequencing and analyzing the operational taxonomic unit classification of bacterial DNA within samples. Statistical analyses were used to explore how life-long exposure to different pH/pCO₂ conditions may be associated with significant differences in microbial communities, dominant bacterial classes, and microbial diversity within each plant section and sediment. The microbiome of C. nodosa significantly differed among all sample types and site-specific differences were detected within sediment and root/rhizome microbial communities, but not the leaves. These results show that C. nodosa leaves have a consistent microbial community even across a pH range of 8.15 to 6.05. The ability for C. nodosa to regulate and maintain microbial structure may indicate a semblance of resilience within these vital ecosystems under projected changes in environmental conditions such as ocean acidification.

Saltwater intrusion affecting NO2- accumulation in demersal fishery species by bacterially mediated N-cycling

To investigate the underlying effects of saltwater intrusion (SWI) on bottom aquatic ecosystems, a set of environmental parameters and the bacterial community were determined and analyzed by sampling bottom water and surface sediments at the Modaomen waterway of the Pearl River Estuary. Biodiversity of fishery species and their relationship with the environment variables were analyzed together. NO₃^- and NO₂^- concentration down-regulation and NH₄⁺ concentration up-regulation in water and sediment were observed along the resulting salinity gradient, indicating that SWI affected N-cycling. Further investigation via 16 s sequencing revealed that taxonomic and functional composition of the bacterial community in the sediment displayed greater discretization than in water, implying that SWI exerted a greater impact on the sedimentary bacterial community. Metagenomic sequencing showed that the sedimentary bacterial community was associated with NO₃^-, NO₂^-, and NH₄⁺ transformation under SWI, and that this was driven by salinity and conductivity. Nitrogen metabolism and denitrification related genes were expressed at higher levels in high salinity than in low salinity, consistent with the increased enzymatic activities of NiR and NR. The NO₂^- concentration in the muscle of six selected fishery species was significantly decreased by 11.15-65.74% (P < 0.05) along the salinity gradient, indicating that SWI reduced NO₂^- accumulation. The results suggest that SWI alleviates NO₂^- accumulation in demersal fishery species via bacterial mediation of N-cycling.

Spatiotemporal dynamics of ammonia-oxidizing archaea and bacteria contributing to nitrification in sediments from Bohai Sea and South Yellow Sea, China

Nitrification is a central process in nitrogen cycle in the ocean. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play significant roles in ammonia oxidation which is the first and rate-limiting step in nitrification, and their differential contribution to nitrification is an important issue, attracting extensive attention. In this study, based on the quantification of archaeal and bacterial amoA gene and the measurement of potential nitrification rate (PNR), we investigated the spatiotemporal dynamics of PNRs and the amoA gene abundance and transcript abundance of aerobic ammonia oxidizers in surface sediments collected in summer and spring across ~900 km of the Bohai Sea and Yellow Sea in China. The results revealed that the contribution of AOA to nitrification was greater than that of AOB in coastal sediments, probably due to salinity and ammonia concentration. Besides, seasons had significant effect on amoA gene abundance and transcript abundance, especially for AOA, while both seasons and sea areas had significant influence on PNR of AOA and AOB. Further analysis showed complex relationships among amoA gene abundances, transcript abundances and PNRs. More importantly, both spatial (geographic distance) and environmental factors were vital in explaining the variations of ammonia-oxidizing microorganism abundances and the PNRs.

Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient

Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.

Crab bioturbation alters nitrogen cycling and promotes nitrous oxide emission in intertidal wetlands: Influence and microbial mechanism

Intertidal wetlands provide important ecosystem functions by acting as nitrogen (N) cycling hotspots, which can reduce anthropogenic N loading from land to coastal waters. Benthic bioturbations are thought to play an important role in mediating N cycling in intertidal marshes. However, how the burrowing activity of benthos and their microbial symbionts affect N transformation and greenhouse gas nitrous oxide (N₂O) emission remains unclear in these environments. Here, we show that bioturbation of crabs reshaped the structure of intertidal microbial communities and their N cycling function. Molecular analyses suggested that the microbially-driven N cycling might be accelerated by crab bioturbation, as the abundances of most of the N related functional genes were higher on the burrow wall than those in the surrounding bulk sediments, except for genes involved in N fixation, dissimilatory nitrate reduction to ammonium (DNRA), and N₂O reduction, which were further confirmed by isotope-tracing experiments. Especially, the potential rates of the main N₂O production pathways, nitrification and denitrification, were 2-3 times higher in the burrow wall sediments. However, even higher N₂O emission rates (approximately 6 times higher) were observed in this unique microhabitat, which was due to a disproportionate increase in N₂O production over N₂O consumption driven by burrowing activity. In addition, the sources of N₂O were also significantly affected by crab bioturbation, which increased the contribution of hydroxylamine oxidation pathway. This study reveals the mechanism through which benthic bioturbations mediate N cycling and highlights the importance of considering burrowing activity when evaluating the ecological function of intertidal wetlands.

Elevation of biochar application as regulator on denitrification/NH3 volatilization in saline soils

Denitrification and NH3 volatilization are the main removal processes of nitrogen in coastal saline soils. In this incubation study, the effects of wheat straw biochar application at rates of 0, 2, 5, 10 and 15% by weight to saline soil with two salt gradients of 0 and 1‰ on denitrification and NH3 volatilization were investigated. The results showed that the denitrification rates with 2, 5 and 10% biochar amendments decreased by 25.26, 33.07 and 17.50%, respectively, under salt-free conditions, and the denitrification rates with 2 and 5% biochar amendments under 1‰ salt conditions decreased by 17.74 and 17.39%, respectively. However, the NH3 volatilization rates increased by 8.05-61.73% after biochar application. The path analysis revealed the interactions of overlying water-sediment system environmental factors in biochar-amended saline soils and their roles in denitrification and NH3 volatilization. Environmental factors in sediment exerted much greater control over denitrification than those in overlying water. In addition, environmental factors exhibited an indirect negative influence on denitrification by negatively influencing the abundance of the nosZ gene. The comprehensive effects of the environmental factors in overlying water on NH3 volatilization were greater than those in sediment. The NH4+-N content, pH of overlying water and sediment salinity were the main controlling factors for NH3 volatilization in saline soils. Biochar application effectively regulated the denitrification rate by changing the environmental factors and denitrifying functional gene abundance, but its application posed a risk of increased NH3 volatilization mainly by increasing NH4+-N, EC and pH in overlying water.

Impact of nitrogen compound variability of sewage treated water on N2O production in riverbeds

Nitrous oxide (N₂O), a strong greenhouse and ozone depleting gas, is known to be generated in the river environment. However, the impact of sewage treated water on the production mechanism has not been clarified. In this study, N₂O production in the upper reach of a river was evaluated by field survey and activity test. The results demonstrated that the N₂O production activity of the river pebbles increased with the inflow of the sewage treated water, which was supported by field survey results, such as the dissolved N₂O concentrations and water quality. The emission factors of N₂O were determined to be 0.02-0.05% in nitrification and 0.01-0.025% in denitrification. Our study shows that combining a field survey and an activity test improves the reliability of the results and leads to the appropriate quantitative evaluation. From a perspective of controlling the N₂O emissions from the sewage treatment plant, N₂O generation inside the plant is critical. However, appropriate nitrogen removal in the treatment plant is connected to the reduction of N₂O generation in the river environment.

Shifts in the relative abundance and potential rates of sediment ammonia-oxidizing archaea and bacteria along environmental gradients of an urban river-estuary-adjacent sea continuum

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in N cycling in sediments globally. However, little is known about their ammonia oxidation rates along a river-estuary-sea continuum. In this study, we investigated how the potential ammonia oxidation rates (PARs) of AOA and AOB changed spatially along a continuum comprising three habitats: the Shanghai urban river network, the Yangtze Estuary, and the adjacent East China Sea, in summer and winter. The AOA and AOB PARs (0.53 ± 0.49 and 0.72 ± 0.69 μg N g^-1 d^-1, mean ± SD, respectively) and their amoA gene abundance (0.47 ± 0.85 × 10⁶ and 2.4 ± 3.54 × 10⁶ copies g^-1, respectively) decreased along the continuum, particularly from the urban river to the estuary, driven by decreasing sediment total organic C and N and other correlated inorganic nutrients (e.g., NH₄⁺) along the gradient of anthropogenic influences. These spatial patterns were consistent between the seasons. The urban river network, where the anthropogenic influences were strongest, saw the largest seasonal differences, as both AOA and AOB had higher PARs and abundance in summer than in winter. The ratios between AOA and AOB PARs (~0.87 ± 0.51) and gene abundances (~0.25 ± 0.24), however, were predominantly <1, indicating an AOB-dominated community. Comparing the different NH₄⁺ consumption pathways, total aerobic oxidation accounted for 12-26% of the total consumption, with the largest proportion in the estuary, where the system was well oxygenated, and the lowest in the adjacent sea, where inorganic N was highly depleted. This study revealed the spatiotemporal patterns of AOA and AOB potential rates and gene abundance along gradients of human influences and identified organic matter and nutrients as key environmental factors that shaped the variation of AOA and AOB along the continuum.

Biogeography of ammonia oxidizers in New England and Gulf of Mexico salt marshes and the potential importance of comammox

Few studies have focused on broad scale biogeographic patterns of ammonia oxidizers in coastal systems, yet understanding the processes that govern them is paramount to understanding the mechanisms that drive biodiversity, and ultimately impact ecosystem processes. Here we present a meta-analysis of 16 years of data of ammonia oxidizer abundance, diversity, and activity in New England (NE) salt marshes and 5 years of data from marshes in the Gulf of Mexico (GoM). Potential nitrification rates were more than 80x higher in GoM compared to NE marshes. However, nitrifier abundances varied between regions, with ammonia-oxidizing archaea (AOA) and comammox bacteria significantly greater in GoM, while ammonia-oxidizing bacteria (AOB) were more than 20x higher in NE than GoM. Total bacterial 16S rRNA genes were also significantly greater in GoM marshes. Correlation analyses of rates and abundance suggest that AOA and comammox are more important in GoM marshes, whereas AOB are more important in NE marshes. Furthermore, ratios of nitrifiers to total bacteria in NE were as much as 80x higher than in the GoM, suggesting differences in the relative importance of nitrifiers between these systems. Communities of AOA and AOB were also significantly different between the two regions, based on amoA sequences and DNA fingerprints (terminal restriction fragment length polymorphism). Differences in rates and abundances may be due to differences in salinity, temperature, and N loading between the regions, and suggest significantly different N cycling dynamics in GoM and NE marshes that are likely driven by strong environmental differences between the regions.

Temperate southern Australian coastal waters are characterised by surprisingly high rates of nitrogen fixation and diversity of diazotrophs

Biological dinitrogen (N₂) fixation is one mechanism by which specific microorganisms (diazotrophs) can ameliorate nitrogen (N) limitation. Historically, rates of N₂ fixation were believed to be limited outside of the low nutrient tropical and subtropical open ocean; however, emerging evidence suggests that N₂ fixation is also a significant process within temperate coastal waters. Using a combination of amplicon sequencing, targeting the nitrogenase reductase gene (nifH), quantitative nifH PCR, and ¹⁵N₂ stable isotope tracer experiments, we investigated spatial patterns of diazotroph assemblage structure and N₂ fixation rates within the temperate coastal waters of southern Australia during Austral autumn and summer. Relative to previous studies in open ocean environments, including tropical northern Australia, and tropical and temperate estuaries, our results indicate that high rates of N₂ fixation (10-64 nmol L^-1 d^-1) can occur within the large inverse estuary Spencer Gulf, while comparatively low rates of N₂ fixation (2 nmol L^-1 d^-1) were observed in the adjacent continental shelf waters. Across the dataset, low concentrations of NO₃/NO₂ were significantly correlated with the highest N₂ fixation rates, suggesting that N₂ fixation could be an important source of new N in the region as dissolved inorganic N concentrations are typically limiting. Overall, the underlying diazotrophic community was dominated by nifH sequences from Cluster 1 unicellular cyanobacteria of the UCYN-A clade, as well as non-cyanobacterial diazotrophs related to Pseudomonas stutzeri, and Cluster 3 sulfate-reducing deltaproteobacteria. Diazotroph community composition was significantly influenced by salinity and SiO₄ concentrations, reflecting the transition from UCYN-A-dominated assemblages in the continental shelf waters, to Cluster 3-dominated assemblages in the hypersaline waters of the inverse estuary. Diverse, transitional diazotrophic communities, comprised of a mixture of UCYN-A and putative heterotrophic bacteria, were observed at the mouth and southern edge of Spencer Gulf, where the highest N₂ fixation rates were observed. In contrast to observations in other environments, no seasonal patterns in N₂ fixation rates and diazotroph community structure were apparent. Collectively, our findings are consistent with the emerging view that N₂ fixation within temperate coastal waters is a previously overlooked dynamic and potentially important component of the marine N cycle.

Diversity and structure of soil bacterial community in intertidal zone of Daliao River estuary, Northeast China

Soil samples from the intertidal zone of Daliao River, Northeast China, were collected in three seasons (autumn, L1; winter, L2; and spring, L3) to evaluate the diversity and structure of bacterial community using high-throughput sequencing. Soil physicochemical characteristics varied greatly with seasons, and the potential nitrification rates were detected in the range of 1.04-2.71 μg NO₃^--N·g^-1 dry soil·h^-1 with the highest rate in spring (L3). Soil bacterial communities also differed seasonally, and nitrogen nutrients were the important variables affecting the bacterial communities as demonstrated by distance-based redundancy analysis and Mantel tests. Proteobacteria was the predominant phylum in soils showing a descending trend from L1 to L3. Woeseia and Ignatzschineria, both affiliating with Gammaproteobacteria, were the two most dominant genera, but they exerted different seasonal variations. The predicted functional profiles revealed 6 major nitrogen cycling processes, and the functional genes in relation to denitrification process were dominant in intertidal soils.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Environmental Factors, More Than Spatial Distance, Explain Community Structure of Soil Ammonia-Oxidizers in Wetlands on the Qinghai-Tibetan Plateau

In wetland ecosystems, ammonia oxidation highly depends on the activity of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), which are, therefore, important for studying nitrogen cycling. However, the ammonia-oxidizer communities in the typical high-elevation wetlands are poorly understood. Here, we examined ammonia-oxidizer communities in soils from three wetland types and 31 wetland sites across the Qinghai-Tibetan Plateau. The amoA gene of AOA and AOB was widespread across all wetland types. Nitrososphaera clade (Group I.1b) overwhelmingly dominated in AOA community (90.36%), while Nitrosospira was the principal AOB type (64.96%). The average abundances of AOA and AOB were 2.63 × 104 copies g-1 and 9.73 × 103 copies g-1. The abundance of AOA amoA gene was higher in riverine and lacustrine wetlands, while AOB amoA gene dominated in palustrine wetlands. The environmental conditions, but not spatial distance, have a dominant role in shaping the pattern of ammonia-oxidizer communities. The AOA community composition was influenced by mean annual temperature (MAT) and mean annual precipitation (MAP), while MAT, conductivity and plant richness, pH, and TN influenced the AOB community composition. The net nitrification rate had a significant correlation to AOB, but not AOA abundance. Our results suggest a dominant role for climate factors (MAT and MAP) in shaping community composition across a wide variety of wetland sites and conditions.

Effects of 10 yr of nitrogen and phosphorus fertilization on carbon and nutrient cycling in a tidal freshwater marsh

Tidal freshwater marshes can protect downstream ecosystems from eutrophication by intercepting excess nutrient loads, but recent studies in salt marshes suggest nutrient loading compromises their structural and functional integrity. Here, we present data on changes in plant biomass, microbial biomass and activity, and soil chemistry from plots in a tidal freshwater marsh on the Altamaha River (GA) fertilized for 10 yr with nitrogen (+N), phosphorus (+P), or nitrogen and phosphorus (+NP). Nitrogen alone doubled aboveground biomass and enhanced microbial activity, specifically rates of potential nitrification, denitrification, and methane production measured in laboratory incubations. Phosphorus alone increased soil P and doubled microbial biomass but did not affect microbial processes. Nitrogen or P alone decreased belowground biomass and soil carbon (C) whereas +NP increased aboveground biomass, microbial biomass and N cycling, and N, P, and C assimilation and burial more than either nutrient alone. Our findings suggest differential nutrient limitation of tidal freshwater macrophytes by N and microbes by P, similar to what has been observed in salt marshes. Macrophytes outcompete microbes for P in response to long-term N and P additions, leading to increased soil C storage through increased inputs of belowground biomass relative to N and P added singly. The susceptibility of tidal freshwater marshes to long-term nutrient enrichment and, hence their ability to mitigate eutrophication will depend on the quantity and relative proportion of N vs. P entering estuaries and tidal wetlands.

Response of ammonia-oxidizing Bacteria and Archaea to long-term saline water irrigation in alluvial grey desert soils

Soil nitrification via ammonia oxidation is a key ecosystem process in terrestrial environments, but little is known of how increasing irrigation of farmland soils with saline waters effects these processes. We investigated the effects of long-term irrigation with saline water on the abundances and community structures of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Irrigation with brackish or saline water increased soil salinity (EC_1:5) and NH₄-N compared to irrigation with freshwater, while NO₃-N, potential nitrification rates (PNR) and amoA gene copy numbers of AOA and AOB decreased markedly under irrigation regimes with saline waters. Moreover, irrigation with brackish water lowered AOA/AOB ratios. PNR was positively correlated with AOA and AOB amoA gene copy numbers across treatments. Saline and brackish water irrigation significantly increased the diversity of AOA, as noted by Shannon index values, while saline water irrigation markedly reduced AOB diversity. In addition, irrigation with brackish or fresh waters resulted in higher proportions of unclassified taxa in the AOB communities. However, irrigation with saline water led to higher proportions of unclassified taxa in the AOA communities along with the Candidatus Nitrosocaldus genus, as compared to soils irrigated with freshwater. AOA community structures were closely associated with soil salinity, NO₃⁻N, and pH, while AOB communities were only significantly associated with NO₃⁻N and pH. These results suggest that salinity was the dominant factor affecting the growth of ammonia-oxidizing microorganisms and community structure. These results can provide a scientific basis for further exploring the response mechanism of ammonia-oxidizing microorganisms and their roles in nitrogen transformation in alluvial grey desert soils of arid areas.

Vegetation-Dependent Response to Drought in Salt Marsh Ammonia-Oxidizer Communities

We investigated the impacts of drought on ammonia-oxidizing archaea (AOA) and bacteria (AOB) in a salt marsh and compared the response to the total bacterial community. We analyzed abundance and community composition of amoA genes by QPCR and TRFLP, respectively, in three vegetation zones in 2014 (pre-drought), 2016 (drought), and 2017 (post-drought), and analyzed bacterial 16S rRNA genes by QPCR, TRFLP, and MiSeq analyses. AOA and AOB abundance in the Spartina patens zone increased significantly in 2016, while abundance decreased in the tall S. alterniflora zone, and showed little change in the short S. alterniflora zone. Total bacterial abundance declined annually in all vegetation zones. Significant shifts in community composition were detected in 2016 in two of the three vegetation zones for AOA and AOB, and in all three vegetation zones for total bacteria. Abundance and community composition of AOA and AOB returned to pre-drought conditions by 2017, while bacterial abundance continued to decline, suggesting that nitrifiers may be more resilient to drought than other bacterial communities. Finding vegetation-specific drought responses among N-cycling microbes may have broad implications for changes in N availability and marsh productivity, particularly if vegetation patterns continue to shift as predicted due to sea level rise.

Short exposure to oxygen and sulfide alter nitrification, denitrification, and DNRA activity in seasonally hypoxic estuarine sediments

Increased organic loading to sediments from eutrophication often results in hypoxia, reduced nitrification and increased production of hydrogen sulfide, altering the balance between nitrogen removal and retention. We examined the effect of short-term exposure to various oxygen and sulfide concentrations on sediment nitrification, denitrification and DNRA from a chronically hypoxic basin in Roskilde Fjord, Denmark. Surprisingly, nitrification rates were highest in the hypoxic and anoxic treatments (about 5 μmol cm⁻³ d⁻¹) and the high sulfide treatment was not significantly different than the oxic treatment. Denitrification in the hypoxic treatment was highest at 1.4 μmol cm⁻³ d⁻¹ and significantly higher than the high sulfide treatment. For DNRA, the rate in high sulfide treatment was 2 μmol cm⁻³ d⁻¹. This was significantly higher than all oxygen treatments that were near zero. In this system, nitrifiers rapidly recovered from conditions typically considered inhibiting, while denitrifiers had a more muted response. DNRA bacteria appear to depend on sulfide for nitrate reduction. Anammox was insignificant. Thus, in estuaries and coastal systems that experience short-term variations in oxygen and sulfide, capabilities of microbial communities are more diverse and tolerant of suboptimal conditions than some paradigms suggest.

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.

Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review

While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH₄-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.

Catchment soils supply ammonium to the coastal zone - Flood impacts on nutrient flux in estuaries

Erosion of soil from catchments during floods can deliver large quantities of sediment to the coastal zone. The transformations and processes of nutrient release from catchment soils during flooding are not well understood. To test the hypothesis that catchment soils supply nutrients to the coastal zone, we examined nutrient release and transformation following wetting of soils formed from three distinct rock types (basalt, granite and sandstone) with fresh and marine water. The soil samples were collected from eroding areas of a subtropical river catchment. We simulated runoff, transport and deposition by tumbling the fine fraction of the soils in freshwater for three days and settling in seawater for four weeks. We also collected and incubated cores from an adjacent coastal bay and added a layer of catchment soil to simulate deposition of new sediment following flood plume settling. Dissolved nutrients were measured in both simulations. Basalt soils were relatively nutrient rich and released substantial quantities of organic and inorganic dissolved nutrients, particularly phosphate. However when soils were added to estuarine sediment cores and incubated, there was a net influx of phosphate from the overlying water. All soils continually released ammonium in both experiments, indicating that catchment soils may be an important source of ammonium to fuel productivity within the coastal zone. This study provides new insights into increased nitrogen availability in a nitrogen-depauperate coastal zone and identifies catchment geology as an important influence in coastal productivity through delivery of soil nitrogen to downstream estuaries.

Niche Separation of Ammonia Oxidizers in Mudflat and Agricultural Soils Along the Yangtze River, China

Nitrification driven by ammonia oxidizers is a key step of nitrogen removal in estuarine environments. Spatial distribution characteristics of ammonia-oxidizers have been well understood in mudflats, but less studied in the agricultural soils next to mudflats, which also play an important role in nitrogen cycling of the estuarine ecosystem. In the present research, we investigated ammonia oxidizers' distributions along the Yangtze River estuary in Jiangsu Province, China, sampling soils right next to the estuary (mudflats) and the agricultural soils 100 m away. We determined the relationship between the abundance of amoA genes of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) and the potential nitrification rates of the mudflats and agricultural soils. We also identified the environmental variables that correlated with the composition of the ammonia oxidizers' communities by 16S rRNA gene pyrosequencing. Results indicated that agricultural soils have significantly higher potential nitrification rates as well as the AOA abundance, and resulted in strong phylogenetic clustering only in AOA communities. The ammonia oxidizers' community compositions differed dramatically among the mudflat and agricultural sites, and stochasticity played a dominant role. The AOA communities were dominated by the Group 1.1a cluster at the mudflat, whereas the 54D9 and 29i4 clusters were dominant in agriculture soils. The dominant AOB communities in the mudflat were closely related to the Nitrosospira lineage, whereas the agricultural soils were dominated by the Nitrosomonas lineage. Soil organic matter and salinity were correlated with the ammonia oxidizers' community compositions.

Discordance Between Resident and Active Bacterioplankton in Free-Living and Particle-Associated Communities in Estuary Ecosystem

Bacterioplankton are the major driving force for biogeochemical cycles in estuarine ecosystems, but the communities that mediate these processes are largely unexplored. We sampled in the Pearl River Estuary (PRE) to examine potential differences in the taxonomic composition of resident (DNA-based) and active (RNA-based) bacterioplankton communities in free-living and particle-associated fractions. MiSeq sequencing data showed that the overall bacterial diversity in particle-associated fractions was higher than in free-living communities. Further in-depth analyses of the sequences revealed a positive correlation between resident and active bacterioplankton communities for the particle-associated fraction but not in the free-living fraction. However, a large overlapping of OTUs between free-living and particle-associated communities in PRE suggested that the two fractions may be actively exchanged. We also observed that the positive correlation between resident and active communities is more prominent among the abundant OTUs (relative abundance > 0.2%). Further, the results from the present study indicated that low-abundance bacterioplankton make an important contribution towards the metabolic activity in PRE.

Nitrogen fate in a subtropical mangrove swamp: Potential association with seawater-groundwater exchange

Coastal mangrove swamps play an important role in nutrient cycling at the land-ocean boundary. However, little is known about the role of periodic seawater-groundwater exchange in the nitrogen cycling processes. Seawater-groundwater exchange rates and inorganic nitrogen concentrations were investigated along a shore-perpendicular intertidal transect in Daya Bay, China. The intertidal transect comprises three hydrologic subzones (tidal creek, mangrove and bare mudflat zones), each with different physicochemical characteristics. Salinity and hydraulic head measurements taken along the transect were used to estimate the exchange rates between seawater and groundwater over a spring-neap tidal cycle. Results showed that the maximum seawater-groundwater exchange occurred within the tidal creek zone, which facilitated high-oxygen seawater infiltration and subsequent nitrification. In contrast, the lowest exchange rate found in the mangrove zone caused over-loading of organic matter and longer groundwater residence times. This created an anoxic environment conducive to nitrogen loss through the anammox and denitrification processes. Potential oxidation rates of ammonia and nitrite were measured by the rapid and high-throughput method and rates of denitrification and anammox were measured by the modified membrane inlet mass spectrometry (MIMS) with isotope pairing, respectively. In the whole transect, denitrification accounted for 90% of the total nitrogen loss, and anammox accounted for the remaining 10%. The average nitrogen removal rate was about 2.07g per day per cubic meter of mangrove sediments.

Salinity is a key factor driving the nitrogen cycling in the mangrove sediment

Coastal ecosystems are hotspots for nitrogen cycling, and specifically for nitrogen removal from water and sediment through the coupled nitrification-denitrification process. Salinity is globally important in structuring bacterial and archaeal communities, but the association between salinity and microbially-mediated nitrification and denitrification remains unclear. The denitrification activity and composition and structure of microbial nitrifiers and denitrifiers were characterized across a gradient of manipulated salinity (0, 10, 20 and 30ppt) in a mangrove sediment. Salinity negatively correlated with both denitrifying activity and the abundance of nirK and nosZ denitrifying genes. Ammonia-oxidizing bacteria (AOB), which dominated nitrification, had significantly greater abundance at intermediate salinity (10 and 20ppt). However, a positive correlation between ammonia concentration and salinity suggested that nitrifying activity might also be inhibited at higher salinity. The community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nirK, nirS and nosZ denitrifying communities, were all significantly correlated with salinity. These changes were also associated with structural shifts in phylogeny. These findings provide a strong evidence that salinity is a key factor that influences the nitrogen transformations in coastal wetlands, indicating that salinity intrusion caused by climate change might have a broader impact on the coastal biospheres.

Ammonium Transformation in 14 Lakes along a Trophic Gradient

Ammonia is a widespread pollutant in aquatic ecosystems originating directly and indirectly from human activities, which can strongly affect the structure and functioning of the aquatic foodweb. The biological oxidation of NH4+ to nitrite, and then nitrate is a key part of the complex nitrogen cycle and a fundamental process in aquatic environments, having a profound influence on ecosystem stability and functionality. Environmental studies have shown that our current knowledge of physical and chemical factors that control this process and the abundance and function of involved microorganisms are not entirely understood. In this paper, the efficiency and the transformation velocity of ammonium into oxidised compounds in 14 south-alpine lakes in northern Italy, with a similar origin, but different trophic levels, are compared with lab-scale experimentations (20 °C, dark, oxygen saturation) that are performed in artificial microcosms (4 L). The water samples were collected in different months to highlight the possible effect of seasonality on the development of the ammonium oxidation process. In four-liter microcosms, concentrations were increased by 1 mg/L NH4+ and the process of ammonium oxidation was constantly monitored. The time elapsed for the decrease of 25% and 95% of the initial ion ammonium concentration and the rate for that ammonium oxidation were evaluated. Principal Component Analysis and General Linear Model, performed on 56 observations and several chemical and physical parameters, highlighted the important roles of total phosphorus and nitrogen concentrations on the commencement of the oxidation process. Meanwhile, the natural concentration of ammonium influenced the rate of nitrification (µg NH4+/L day). Seasonality did not seem to significantly affect the ammonium transformation. The results highlight the different vulnerabilities of lakes with different trophic statuses.

Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China

Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg^-1 dry sediments d^-1, respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.

Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China

Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA) gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla) and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring

Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2-10 and 0.2-2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW). The gene copy numbers of AOA-amoA were higher than those of AOB-amoA in ECS. The relative abundance of amoA to the total 16S rRNA gene level reached approximately 15% in KBW and CKBW for the free-living fraction of AOA, whereas the level was less than 0.01% throughout ECS for the AOB. A cluster analysis of the AOA-amoA-DGGE band pattern showed distinct genotype compositions in CSW in both the size fractions and in the surface of the TCSKB and KBW. Sequences of the DGGE bands were assigned to two clades. One of the clades exclusively consisted of sequences derived from the 2-10-µm fraction. This study revealed that AOA-amoA abundance dominated over AOB-amoA throughout the ECS, whereas the genotype composition of AOA-amoA were distributed heterogeneously across the water masses. Additionally, this is the first report showing the distribution of AOA-amoA genotypes characteristic to particle-associated AOA in the offshore of the East China Sea.

Effects of aerobic respiration and nitrification on dissolved inorganic nitrogen and carbon dioxide in human-perturbed eastern Jiaozhou Bay, China

Aerobic respiration and nitrification are important processes for dissolved inorganic nitrogen (DIN) composition change and CO₂ production in human-perturbed coastal waters. On-site incubations and field investigations were conducted in the eastern Jiaozhou Bay, a high-urbanization region, from May to August 2014. Results show that aerobic respiration rates reached 15.58μmolO₂L^-1d^-1, and NH₄⁺ and NO₂^- oxidation rates were 0.53 and 0.13μmolNL^-1d^-1, respectively, in the human-perturbed northeastern area. The intense aerobic respiration there contributed to high-concentration NH₄⁺, and meanwhile caused a pH decrease of 0.042units and a pCO₂ increase of 166μatm per day. Moreover, the linear relationship between excess CO₂ and apparent oxygen utilization suggested that the excess CO₂ in the entire eastern Jiaozhou Bay was mainly from the aerobic respiration. This study may help us better understand the role of aerobic respiration in DIN composition and CO₂ sink/source pattern in coastal waters.

Small-scale variation of ammonia oxidisers within intertidal sediments dominated by ammonia-oxidising bacteria Nitrosomonas sp. amoA genes and transcripts

While numerous studies have investigated the abundance of ammonia oxidising bacteria and archaea (AOB/AOA) via the ammonia monooxygenase gene amoA, less is known about their small-scale variation and if amoA gene abundance equates to activity. Here we present a spatial and temporal study of ammonia oxidation in two small intertidal bays, Rusheen and Clew bay, Ireland. Potential Nitrification Rate (PNR) was ten-fold higher in Rusheen bay (Clew: 0.27 ± SD 0.55; Rusheen: 2.46 ± SD 3.4 NO2- µg-1 g-1 day-1, P < 0.001) than in Clew bay but amoA gene abundances were similar between bays, and comparable to those in other coastal ecosystems. Within bays AOB genes increased towards the muddy sediments and were positively correlated with PNR and pH. Less spatial variation was observed in AOA abundances which nevertheless positively correlated with pH and temperature and negatively with salinity and ammonia. Transcriptionally active AOB and AOA were quantified from all sites in Rusheen bay, February 2014, following the general trends observed at DNA level. AOB phylotypes predominantly from the known Nitrosomonas group were distributed across the bay, while Nitrosomonas group B phylotypes were absent from low salinity sites. AOA genes and transcripts were primarily affiliated with Thaumarchaeota group I.1a.

Potential effects of rainwater-borne hydrogen peroxide on pollutants in stagnant water environments

Microcosm experiments were conducted to examine the effects of rainwater-borne H₂O₂ on inactivation of water-borne coliforms, oxidation of ammonia and nitrite, and degradation of organic pollutants in canal and urban lake water. The results show that the soluble iron in the investigated water samples was sufficiently effective for reaction with H₂O₂ in the simulated rainwater-affected stagnant water to produce OH (Fenton reaction), which inactivated coliform bacteria even at a H₂O₂ dose as low as 5 μM within just 1 min of contact time. Coliform inhibition could last for at least 1 h and repeated input of H₂O₂ at a 30 min interval allowed maintenance of microbial inhibition for at least 3 h. Nitrification was also impeded by the Fenton process. The resulting inhibition of ammonia-oxidizing microbes reduced the removal rate of NH₄⁺ and the emission of gaseous N species. In the presence of H₂O₂ at a dose of 20 μM, Fenton-driven chemical oxidation appeared to outplay the impediment of biodegradation caused by inhibited microbial activities in terms of removing total polycyclic aromatic hydrocarbons from the water column. The findings point to a potential research direction that may help to explain the dynamics of water-borne pollutants in ambient water environments.

Spatial Abundance, Diversity, and Activity of Ammonia-Oxidizing Bacteria in Coastal Sediments of the Liaohe Estuary

Ammonia-oxidizing bacteria (AOB) play an important role in nitrification in estuaries. The aim of this study was to examine the spatial abundance, diversity, and activity of AOB in coastal sediments of the Liaohe Estuary using quantitative PCR, high-throughput sequencing of the amoA gene coding the ammonia monooxygenase enzyme active subunit, and sediment slurry incubation experiments. AOB abundance ranged from 8.54 × 10⁴ to 5.85 × 10⁶ copies g^-1 of wet sediment weight and exhibited an increasing trend from the Liaohe Estuary to the open coastal zone. Potential nitrification rates (PNRs) ranged from 0.1 to 336.8 nmol N g^-1 day^-1 along the estuary to the coastal zone. Log AOB abundance and PNRs were significantly positively correlated. AOB richness decreased from the estuary to the coastal zone. High-throughput sequencing analysis indicated that the majority of amoA gene sequences fell within the Nitrosomonas and Nitrosomonas-like clade, and only a few sequences were clustered within the Nitrosospira clade. This finding indicates that the Nitrosomonas-related lineage may be more adaptable to the specific conditions in this estuary than the Nitrosospira lineage. Sites with high nitrification rates were located in the southern open region and were dominated by the Nitrosomonas-like lineage, whereas the Nitrosospira lineage was found primarily in the northern estuary mouth sites with low nitrification rates. Thus, nitrification potentials in Liaohe estuarine sediments in the southern open region were greater than those in the northern estuary mouth, and the Nitrosomonas-related lineage might play a more important role than the Nitrosospira lineage in nitrification in this estuary.

Archaea Dominate the Ammonia-Oxidizing Community in Deep-Sea Sediments of the Eastern Indian Ocean-from the Equator to the Bay of Bengal

Ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) oxidize ammonia to nitrite, and therefore play essential roles in nitrification and global nitrogen cycling. To better understand the population structure and the distribution of AOA and AOB in the deep Eastern Indian Ocean (EIO), nine surface sediment samples (>3,300 m depth) were collected during the inter-monsoon Spring 2013. One sediment sample from the South China Sea (SCS; 2,510 m) was also included for comparison. The community composition, species richness, and diversity were characterized by clone libraries (total 1,238 clones), and higher diversity of archaeal amoA genes than bacterial amoA genes was observed in all analyzed samples. Real time qPCR analysis also demonstrated higher abundances (gene copy numbers) of archaeal amoA genes than bacterial amoA genes, and the ratios of AOA/AOB ranged from 1.42 to 8.49 among sites. In addition, unique and distinct clades were found in both reconstructed AOA and AOB phylogeny, suggesting the presence of niche-specific ammonia-oxidizing microorganisms in the EIO. The distribution pattern of both archaeal and bacterial amoA genes revealed by NMDS (non-metric multidimensional scaling) showed a distinct geographic separation of the sample from the SCS and most of the samples from the EIO following nitrogen gradients. Higher abundance and diversity of archaeal amoA genes indicated that AOA may play a more important role than AOB in the deep Indian Ocean. Environmental parameters shaping the distribution pattern of AOA were different from that of AOB, indicating distinct metabolic characteristics and/or adaptation mechanisms between AOA and AOB in the EIO, especially in deep-sea environments.

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill

The recent oil spill in the Gulf of Mexico had significant effects on microbial communities in the Gulf, but impacts on nitrifying communities in adjacent salt marshes have not been investigated. We studied persistent effects of oil on ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities and their relationship to nitrification rates and soil properties in Louisiana marshes impacted by the Deepwater Horizon oil spill. Soils were collected at oiled and unoiled sites from Louisiana coastal marshes in July 2012, 2 years after the spill, and analyzed for community differences based on ammonia monooxygenase genes (amoA). Terminal Restriction Fragment Polymorphism and DNA sequence analyses revealed significantly different AOA and AOB communities between the three regions, but few differences were found between oiled and unoiled sites. Community composition of nitrifiers was best explained by differences in soil moisture and nitrogen content. Despite the lack of significant oil effects on overall community composition, we identified differences in correlations of individual populations with potential nitrification rates between oiled and unoiled sites that help explain previously published correlation patterns. Our results suggest that exposure to oil, even 2 years post-spill, led to subtle changes in population dynamics. How, or if, these changes may impact ecosystem function in the marshes, however, remains uncertain.

Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the diversity of the responsible microorganisms is regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated in the surface waters along an environmental gradient of the Yong River in Ningbo, East China. Water samples were collected from three pelagic zones: (1) freshwaters in the urban canals of Ningbo, (2) brackish waters in the downstream Yong River, and (3) coastal marine water of Hangzhou Bay. Shifts in activity and diversity of the ammonia-oxidizing microorganisms occurred simultaneously with changes in environmental factors, among which salinity and the availabilities of ammonium and oxygen. The AOA abundance was always higher than that of AOB and was related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and the AOB from brackish and marine waters mainly belonged to Nitrosospira.

Anaerobic ammonium oxidation and its contribution to nitrogen removal in China's coastal wetlands

Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China’s coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China’s coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8–10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China’s coastal wetland ecosystems.

Temporal Dynamics of Active Prokaryotic Nitrifiers and Archaeal Communities from River to Sea

To test if different niches for potential nitrifiers exist in estuarine systems, we assessed by pyrosequencing the diversity of archaeal gene transcript markers for taxonomy (16S ribosomal RNA (rRNA)) during an entire year along a salinity gradient in surface waters of the Charente estuary (Atlantic coast, France). We further investigated the potential for estuarine prokaryotes to oxidize ammonia and hydrolyze urea by quantifying thaumarchaeal amoA and ureC and bacterial amoA transcripts. Our results showed a succession of different nitrifiers from river to sea with bacterial amoA transcripts dominating in the freshwater station while archaeal transcripts were predominant in the marine station. The 16S rRNA sequence analysis revealed that Thaumarchaeota marine group I (MGI) were the most abundant overall but other archaeal groups like Methanosaeta were also potentially active in winter (December-March) and Euryarchaeota marine group II (MGII) were dominant in seawater in summer (April-August). Each station also contained different Thaumarchaeota MGI phylogenetic clusters, and the clusters' microdiversity was associated to specific environmental conditions suggesting the presence of ecotypes adapted to distinct ecological niches. The amoA and ureC transcript dynamics further indicated that some of the Thaumarchaeota MGI subclusters were involved in ammonia oxidation through the hydrolysis of urea. Our findings show that ammonia-oxidizing Archaea and Bacteria were adapted to contrasted conditions and that the Thaumarchaeota MGI diversity probably corresponds to distinct metabolisms or life strategies.

Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.

Bacterial domination over archaea in ammonia oxidation in a monsoon-driven tropical estuary

Autotrophic ammonia oxidizing microorganisms, which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon-driven estuary in India opening into the southeast Arabian Sea. CE receives surplus quantities of ammonia through industrial and domestic discharges. The distribution of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and anaerobic ammonia-oxidizing bacteria (anammox) were studied using fluorescence in situ hybridization (FISH) and their relative contribution to the process as well as the governing factors were examined and reported for the first time from CE. The order of occurrence of these assemblages was β-proteobacteria (0.79 to 2 × 10(5) cells ml(-1)) > γ-proteobacteria (0.9 to 4.6 × 10(4) cells ml(-1)) > anammox (0.49 to 1.9 × 10(4) cells ml(-1)) > AOA (0.56 to 6.3 × 10(3) cells ml(-1)). Phylogenetic analysis of DGGE bands showed major affiliation of AOB to β-proteobacteria, while AOA was affiliated to Crenarchaeota. The abundance of AOB was mostly influenced by ammonia concentrations. The recovered ammonia oxidation rate of AOB was in the range of 45-65%, whereas for AOA, it was 15-45%, indicating that AOB were mostly responsible for the ammonia oxidation in CE during the study period. Overall, the present study provides an insight into the relevance and contribution of different groups of ammonia oxidizing bacteria in CE and emphasizes the need for further in depth studies across space and on season scale.

Long-term impacts of disturbance on nitrogen-cycling bacteria in a New England salt marsh

Recent studies on the impacts of disturbance on microbial communities indicate communities show differential responses to disturbance, yet our understanding of how different microbial communities may respond to and recover from disturbance is still rudimentary. We investigated impacts of tidal restriction followed by tidal restoration on abundance and diversity of denitrifying bacteria, ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in New England salt marshes by analyzing nirS and bacterial and archaeal amoA genes, respectively. TRFLP analysis of nirS and betaproteobacterial amoA genes revealed significant differences between restored and undisturbed marshes, with the greatest differences detected in deeper sediments. Additionally, community patterns indicated a potential recovery trajectory for denitrifiers. Analysis of archaeal amoA genes, however, revealed no differences in community composition between restored and undisturbed marshes, but we detected significantly higher gene abundance in deeper sediment at restored sites. Abundances of nirS and betaproteobacterial amoA genes were also significantly greater in deeper sediments at restored sites. Porewater ammonium was significantly higher at depth in restored sediments compared to undisturbed sediments, suggesting a possible mechanism driving some of the community differences. Our results suggest that impacts of disturbance on denitrifying and ammonia-oxidizing communities remain nearly 30 years after restoration, potentially impacting nitrogen-cycling processes in the marsh. We also present data suggesting that sampling deeper in sediments may be critical for detecting disturbance effects in coastal sediments.

Spatiotemporal relationships between the abundance, distribution, and potential activities of ammonia-oxidizing and denitrifying microorganisms in intertidal sediments

The primary objective of this study was to gain an understanding of how key microbial communities involved in nitrogen cycling in estuarine sediments vary over a 12-month period. Furthermore, we sought to determine whether changes in the size of these communities are related to, or indicative of, seasonal patterns in fixed nitrogen dynamics in Elkhorn Slough--a small, agriculturally impacted estuary with a direct connection to Monterey Bay. We assessed sediment and pore water characteristics, abundance of functional genes for nitrification (bacterial and archaeal amoA, encoding ammonia monooxygenase subunit A) and denitrification (nirS and nirK, encoding nitrite reductase), and measurements of potential nitrification and denitrification activities at six sites. No seasonality in the abundance of denitrifier or ammonia oxidizer genes was observed. A strong association between potential nitrification activity and the size of ammonia-oxidizing bacterial communities was observed across the estuary. In contrast, ammonia-oxidizing archaeal abundances remained relatively constant in space and time. Unlike many other estuaries, salinity does not appear to regulate the distribution of ammonia-oxidizing communities in Elkhorn Slough. Instead, their distributions appear to be governed over two different time scales. Long-term niche characteristics selected for the gross size of archaeal and bacterial ammonia-oxidizing communities, yet covariation in their abundances between monthly samples suggests that they respond in a similar manner to short-term changes in their environment. Abundances of denitrifier and ammonia oxidizer genes also covaried, but site-specific differences in this relationship suggest differing levels of interaction (or coupling) between nitrification and denitrification.

amoA Gene abundances and nitrification potential rates suggest that benthic ammonia-oxidizing bacteria and not Archaea dominate N cycling in the Colne Estuary, United Kingdom

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (amoA) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw](-1) day(-1) in June, increasing to 37.4 μmol N gdw(-1) day(-1) in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw(-1) day(-1) in June, increasing to 11.7 μmol N gdw(-1) day(-1) in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB amoA gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally. Nitrosomonas spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA amoA gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly Nitrosomonas spp.) were of major significance in nitrification.

Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms

Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes.