Effects of Nitrate Availability and the Presence of Glyceria maxima on the Composition and Activity of the Dissimilatory Nitrate-Reducing Bacterial Community

Detection of Nitrate-Reducing/Denitrifying Bacteria from Contaminated and Uncontaminated Tallgrass Prairie Soil: Limitations of PCR Primers

Contamination of soil by spills of crude oil and oilfield brine is known to affect the species composition and functioning of soil microbial communities. However, the effect of such contamination on nitrogen cycling, an important biogeochemical cycle in tallgrass prairie soil, is less well known. Detecting nitrate-reducing (NR) and denitrifying (DN) bacteria via PCR amplification of the genes essential for these processes depends on how well PCR primers match the sequences of these bacteria. In this study, we enriched for NR and DN bacteria from oil/brine tallgrass prairie soil contaminated 5-10 years previously versus those cultured from uncontaminated soil, confirmed the capacity of 75 strains isolated from the enrichments to reduce nitrate and/nitrite, then screened the strains with primers specific to seven nitrogen cycle functional genes. The strains comprised a phylogenetically diverse group of NR and DN bacteria, with proportionately more γ-Proteobacteria in oil-contaminated sites and more Bacilli in brine-contaminated sites, suggesting some residual effect of the contaminants on the NR and DN species distribution. Around 82% of the strains shown to reduce nitrate/nitrite would not be identified as NR and DN bacteria by the battery of NR and DN primers used. Our results indicate an urgent need to expand the NR/DN functional gene primer database by first identifying novel NR/DN strains through their capacity to reduce nitrate/nitrite.

A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia)

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated in situ temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function

Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3--N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3--N (1.67-2.86 mg/L and 2.98-7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3--N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Effects of carbon load on nitrate reduction during riverbank filtration: Field monitoring and batch experiment

Riverbank filtration (RBF) is a well-established technique worldwide, and is critical for the maintenance of groundwater quality and production of clean drinking water. Evaluation of the decay of exogenous nitrate (NO₃^-) in river water and the enrichment of ammonium (NH₄⁺) in groundwater during RBF is important; these two processes are mainly influenced by denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) controlled by the groundwater carbon load. In this study, the effects of carbon load (organic carbon [OC]: NO₃^-) on the competing nitrate reduction (DNRA and DNF) were assessed during RBF using field monitoring and a laboratory batch experiment. Results show the groundwater OC: NO₃^- ratio did not directly affect the reaction rate of DNRA and DNF, however, it could control the competitive partitioning between the two. In the near-shore zone, the groundwater OC: NO₃^- ratio shows significant seasonal variations along the filtration path owing to the changing conditions of redox, OC-rich, and NO₃^--limited. A greater proportion of NO₃^- would be available for DNRA in the wet season with higher OC: NO₃^- ratio (> 10), resulting in a significantly NH₄⁺-N enrichment rate (from 1.43 × 10^-3 to 9.54 × 10^-4 mmol L^-1 d^-1) in the near-shore zone where the zone of Mn (IV) oxide reduction. However, the activity of DNRA was suppressed with lower OC: NO₃^- ratio (< 10) in the dry season, resulting in a stable NH₄⁺-N enrichment rate (from 3.12 × 10^-4 to 1.30 × 10^-4 mmol L^-1 d^-1). Benefiting from seasonal variation of OC-rich and NO₃^--limited conditions, DNRA bacteria outcompeted denitrifiers, which eventually led to seasonal differences in NO₃^- reduction in the near-shore zone. Overall, under the effect of DNRA induced by continuous high carbon load in RBF systems, nitrogen input is not permanently removed but rather retained in groundwater during RBF.

Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China

Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO₃^-, NH₄⁺, DOC/NO₃^-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.

Wetland buffer zones for nitrogen and phosphorus retention: Impacts of soil type, hydrology and vegetation

Wetland buffer zones (WBZs) are riparian areas that form a transition between terrestrial and aquatic environments and are well-known to remove agricultural water pollutants such as nitrogen (N) and phosphorus (P). This review attempts to merge and compare data on the nutrient load, nutrient loss and nutrient removal and/or retention from multiple studies of various WBZs termed as riparian mineral soil wetlands, groundwater-charged peatlands (i.e. fens) and floodplains. Two different soil types ('organic' and 'mineral'), four different main water sources ('groundwater', 'precipitation', 'surface runoff/drain discharge', and 'river inundation') and three different vegetation classes ('arboraceous', 'herbaceous' and 'aerenchymous') were considered separately for data analysis. The studied WBZs are situated within the temperate and continental climatic regions that are commonly found in northern-central Europe, northern USA and Canada. Surprisingly, only weak differences for the nutrient removal/retention capability were found if the three WBZ types were directly compared. The results of our study reveal that for example the nitrate retention efficiency of organic soils (53 ± 28%; mean ± sd) is only slightly higher than that of mineral soils (50 ± 32%). Variance in load had a stronger influence than soil type on the N retention in WBZs. However, organic soils in fens tend to be sources of dissolved organic N and soluble reactive P, particularly when the fens have become degraded due to drainage and past agricultural usage. The detailed consideration of water sources indicated that average nitrate removal efficiencies were highest for ground water (76 ± 25%) and lowest for river water (35 ± 24%). No significant pattern for P retention emerged; however, the highest absolute removal appeared if the P source was river water. The harvesting of vegetation will minimise potential P loss from rewetted WBZs and plant biomass yield may promote circular economy value chains and provide compensation to land owners for restored land now unsuitable for conventional farming.

Microbial community composition of sediments influenced by intensive mariculture activity

Marine aquaculture is a major industry that supports the economy in many countries, including the Philippines. However, excess feeds and fish waste generated by mariculture activities contribute an immense nutrient load to the environment that can affect the underlying sediment. To better understand these impacts, we compared the physicochemical characteristics and microbial community composition of sediments taken at a fish cage and an off cage site in Bolinao, Philippines. Sediments and pore water at the fish cage site showed evidence of greater organic enrichment relative to the off cage site. Under these conditions, we found lower relative abundance of dissimilatory sulfate reductase and nitrite reductase genes, suggesting shifts in prevalent nutrient cycling processes. This is further supported by 16S rRNA gene sequencing that revealed differences in the community composition between sites. Fish cage sediments favored the growth of taxa that thrive in anaerobic, organic carbon-enriched environments, such as members of class Anaerolineae, which can potentially serve as bioindicators of eutrophication in sediments. This study demonstrates that intensive mariculture activity can cause eutrophic sediment conditions that influence microbial community structure and function.

Role of organic carbon, nitrate and ferrous iron on the partitioning between denitrification and DNRA in constructed stormwater urban wetlands

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed wetlands. An important factor that controls DNRA in an aquatic ecosystem is the electron donor, commonly organic carbon (OC) or alternatively ferrous iron and sulfide. In this study, we investigated the role of natural organic carbon (NOC) and acetate at different OC/NO₃^- ratios and ferrous iron on the partitioning between DNF and DNRA using the ¹⁵N-tracer method in slurries from four constructed stormwater urban wetlands in Melbourne, Australia. The carbon and nitrate experiments revealed that DNF dominated at all OC/NO₃^- ratios. The higher DNF and DNRA rates observed after the addition of NOC indicates that nitrate reduction was enhanced more by NOC than acetate. Moreover, addition of NOC in slurries stimulated DNRA more than DNF. Interestingly, slurries amended with Fe²⁺ showed that Fe²⁺ had significant control on the balance between DNF and DNRA. From two out of four wetlands, a significant increase in DNRA rates (p < .05) at the cost of DNF in the presence of available Fe²⁺ suggests DNRA is coupled to Fe²⁺ oxidation. Rates of DNRA increased 1.5-3.5 times in the Fe²⁺ treatment compared to the control. Overall, our study provides direct evidence that DNRA is linked to Fe²⁺ oxidation in some wetland sediments and highlights the role of Fe²⁺ in controlling the partitioning between removal (DNF) and recycling (DNRA) of bioavailable N in stormwater urban constructed wetlands. In our study we also measured anammox and found that it was always <0.05% of total nitrate reduction in these sediments.

In situ denitrification and DNRA rates in groundwater beneath an integrated constructed wetland

Evaluation of the environmental benefits of constructed wetlands (CWs) requires an understanding of their impacts on the groundwater quality under the wetlands. Empirical mass-balance (nitrogen in/nitrogen out) approaches for estimating nitrogen (N) removal in CWs do not characterise the final fate of N; where nitrate (NO₃^--N) could be reduced to either ammonium (NH₄⁺-N) or N₂ with the potential for significant production of N₂O. Herein, in situ denitrification and DNRA (dissimilatory nitrate reduction to ammonium) rates were measured in groundwater beneath cells of an earthen lined integrated constructed wetland (ICW, used to remove the nutrients from municipal wastewater) using the ¹⁵N-enriched NO₃^--N push-pull method. Experiments were conducted utilising replicated (n = 3) shallow (1 m depth) and deep (4 m depth) piezometers installed along two control planes. These control planes allowed for the assessment of groundwater underlying high (Cell 2, septic tank waste) and low (Cell 3) load cells of the ICW. Background piezometers were also installed off-site. Results showed that denitrification (N₂O-N + N₂-N) and DNRA were major NO₃^--N consumption processes accounting together for 54-79% of the total biochemical consumption of the applied NO₃^--N. Of which 14-16% and 40-63% were consumed by denitrification and DNRA, respectively. Both processes differed significantly across ICW cells indicating that N transformation depends on nutrient loading rates and were significantly higher in shallow compared to the deep groundwater. In such a reduced environment (low dissolved oxygen and low redox potential), higher DNRA over the denitrification rate can be attributed to the high C concentration and high TC/NO₃^--N ratio. Low pH (6.5-7.1) in this system might have limited denitrification to some extent to an incomplete state, evidenced by a high N₂O-N/(N₂O-N+N₂-N) ratio (0.35 ± 0.17, SE). A relatively higher N₂O-N/(N₂O-N+N₂-N) ratio and higher DNRA rate over denitrification, suggest that the end products of N transformations are reactive. This N₂O can be consumed to N₂ and/or emitted to the atmosphere. The DNRA rate and accumulation of NH₄⁺-N indicated that the ICW created a suitable groundwater biogeochemical environment that enhanced NO₃^--N reduction to NH₄⁺-N. This study showed that CWs significantly influence NO₃^--N attenuation to reactive forms of N in the groundwater beneath them and that solely focusing on within wetland NO₃^--N attenuation can underestimate the environmental benefits of wetlands.

Planting richness affects the recovery of vegetation and soil processes in constructed wetlands following disturbance

The resilience of constructed wetland ecosystems to severe disturbance, such as a mass herbivory eat-out or soil disturbance, remains poorly understood. In this study, we use a controlled mesocosm experiment to examine how original planting diversity affects the ability of constructed freshwater wetlands to recover structurally and functionally after a disturbance (i.e., aboveground harvesting and soil coring). We assessed if the planting richness of macrophyte species influences recovery of constructed wetlands one year after a disturbance. Mesocosms were planted in richness groups with various combinations of either 1, 2, 3, or 4 species (RG 1-4) to create a gradient of richness. Structural wetland traits measured include morphological regrowth of macrophytes, soil bulk density, soil moisture, soil %C, and soil %N. Functional wetland traits measured include above ground biomass production, soil potential denitrification, and soil potential microbial respiration. Total mesocosm cover increased along the gradient of plant richness (43.5% in RG 1 to 84.5% in RG 4) in the growing season after the disturbance, although not all planted individuals recovered. This was largely attributed to the dominance of the obligate annual species. The morphology of each species was affected negatively by the disturbance, producing shorter, and fewer stems than in the years prior to the disturbance, suggesting that the communities had not fully recovered one year after the disturbance. Soil characteristics were almost uniform across the planting richness gradient, but for a few exceptions (%C, C:N, and non-growing season soil moisture were higher slightly in RG 2). Denitrification potential (DEA) increased with increasing planting richness and was influenced by the abundance and quality of soil C. Increased open space in unplanted mesocosms and mesocosms with lower species richness increased labile C, leading to higher C mineralization rates.

Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO3(-)/NO2(-) reduction pathways in Shewanella loihica strain PV-4

Denitrification and respiratory ammonification are two competing, energy-conserving NO3(-)/NO2(-) reduction pathways that have major biogeochemical consequences for N retention, plant growth and climate. Batch and continuous culture experiments using Shewanella loihica strain PV-4, a bacterium possessing both the denitrification and respiratory ammonification pathways, revealed factors that determine NO3(-)/NO2(-) fate. Denitrification dominated at low carbon-to-nitrogen (C/N) ratios (that is, electron donor-limiting growth conditions), whereas ammonium was the predominant product at high C/N ratios (that is, electron acceptor-limiting growth conditions). pH and temperature also affected NO3(-)/NO2(-) fate, and incubation above pH 7.0 and temperatures of 30 °C favored ammonium formation. Reverse-transcriptase real-time quantitative PCR analyses correlated the phenotypic observations with nirK and nosZ transcript abundances that decreased up to 1600-fold and 27-fold, respectively, under conditions favoring respiratory ammonification. Of the two nrfA genes encoded on the strain PV-4 genome, nrfA0844 transcription decreased only when the chemostat reactor received medium with the lowest C/N ratio of 1.5, whereas nrfA0505 transcription occurred at low levels (≤3.4 × 10(-2) transcripts per cell) under all growth conditions. At intermediate C/N ratios, denitrification and respiratory ammonification occurred concomitantly, and both nrfA0844 (5.5 transcripts per cell) and nirK (0.88 transcripts per cell) were transcribed. Recent findings suggest that organisms with both the denitrification and respiratory ammonification pathways are not uncommon in soil and sediment ecosystems, and strain PV-4 offers a tractable experimental system to explore regulation of dissimilatory NO3(-)/NO2(-) reduction pathways.

Identification and quantification of a novel nitrate-reducing community in sediments of Suquía River basin along a nitrate gradient

We evaluated the molecular diversity of narG gene from Suquía River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 x 10(2) to 5.0 x 10(4) copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times.

Changes in denitrifier abundance, denitrification gene mRNA levels, nitrous oxide emissions, and denitrification in anoxic soil microcosms amended with glucose and plant residues

In agricultural cropping systems, crop residues are sources of organic carbon (C), an important factor influencing denitrification. The effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mRNA levels, nitrous oxide (N(2)O) emissions, and denitrification rates were quantified in anoxic soil microcosms for 72 h. nosZ gene abundances and mRNA levels significantly increased in response to all organic carbon treatments over time. In contrast, the abundance and mRNA levels of Pseudomonas mandelii and closely related species (nirS(P)) increased only in glucose-amended soil: the nirS(P) guild abundance increased 5-fold over the 72-h incubation period (P < 0.001), while the mRNA level significantly increased more than 15-fold at 12 h (P < 0.001) and then subsequently decreased. The nosZ gene abundance was greater in plant residue-amended soil than in glucose-amended soil. Although plant residue carbon-to-nitrogen (C:N) ratios varied from 15:1 to 30:1, nosZ gene and mRNA levels were not significantly different among plant residue treatments, with an average of 3.5 x 10(7) gene copies and 6.9 x 10(7) transcripts g(-1) dry soil. Cumulative N(2)O emissions and denitrification rates increased over 72 h in both glucose- and plant-tissue-C-treated soil. The nirS(P) and nosZ communities responded differently to glucose and plant residue amendments. However, the targeted denitrifier communities responded similarly to the different plant residues under the conditions tested despite changes in the quality of organic C and different C:N ratios.

Methane emission from natural wetlands: interplay between emergent macrophytes and soil microbial processes. A mini-review

BACKGROUND

According to the Intergovernmental Panel on Climate Change (IPCC) 2007, natural wetlands contribute 20-39 % to the global emission of methane. The range in the estimated percentage of the contribution of these systems to the total release of this greenhouse gas is large due to differences in the nature of the emitting vegetation including the soil microbiota that interfere with the production and consumption of methane.

SCOPE

Methane is a dominant end-product of anaerobic mineralization processes. When all electron acceptors except carbon dioxide are used by the microbial community, methanogenesis is the ultimate pathway to mineralize organic carbon compounds. Emergent wetland plants play an important role in the emission of methane to the atmosphere. They produce the carbon necessary for the production of methane, but also facilitate the release of methane by the possession of a system of interconnected internal gas lacunas. Aquatic macrophytes are commonly adapted to oxygen-limited conditions as they prevail in flooded or waterlogged soils. By this system, oxygen is transported to the underground parts of the plants. Part of the oxygen transported downwards is released in the root zone, where it sustains a number of beneficial oxidation processes. Through the pores from which oxygen escapes from the plant into the root zone, methane can enter the plant aerenchyma system and subsequently be emitted into the atmosphere. Part of the oxygen released into the root zone can be used to oxidize methane before it enters the atmosphere. However, the oxygen can also be used to regenerate alternative electron acceptors. The continuous supply of alternative electron acceptors will diminish the role of methanogenesis in the anaerobic mineralization processes in the root zone and therefore repress the production and emission of methane. The role of alternative element cycles in the inhibition of methanogenesis is discussed.

CONCLUSIONS

The role of the nitrogen cycle in repression of methane production is probably low. In contrast to wetlands particularly created for the purification of nitrogen-rich waste waters, concentrations of inorganic nitrogen compounds are low in the root zones in the growing season due to the nitrogen-consuming behaviour of the plant. Therefore, nitrate hardly competes with other electron acceptors for reduced organic compounds, and repression of methane oxidation by the presence of higher levels of ammonium will not be the case. The role of the iron cycle is likely to be important with respect to the repression of methane production and oxidation. Iron-reducing and iron-oxidizing bacteria are ubiquitous in the rhizosphere of wetland plants. The cycling of iron will be largely dependent on the size of the oxygen release in the root zone, which is likely to be different between different wetland plant species. The role of the sulfur cycle in repression of methane production is important in marine, sulfate-rich ecosystems, but might also play a role in freshwater systems where sufficient sulfate is available. Sulfate-reducing bacteria are omnipresent in freshwater ecosystems, but do not always react immediately to the supply of fresh sulfate. Hence, their role in the repression of methanogenesis is still to be proven in freshwater marshes.

Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions

Competition between different isogenic mutants of Pseudomonas fluorescens unable to carry out the first steps of the denitrification pathway was compared in soil micro-columns non-planted or planted with maize. A new isogenic mutant of P. fluorescens YT101 affected in both nitrate and nitrite respirations was constructed and used as a model of non-denitrifying strain (FM69MS strain). The outcome of the selection exerted by the plant after co-inoculation of FM69MS at the same ratio either with an isogenic denitrifier unable to reduce nitrate (Nar(-) mutant) or with an isogenic NO2 (-) accumulator (Nir(-) mutant) was investigated in non-limiting NO3 (-) conditions. Regardless of the inoculated mixture, both strains were able to grow in both rhizosphere and non-planted soil. The proportion of Nar(-) or Nir(-) strain in the Nar(-)+FM69MS or Nir(-)+FM69MS total introduced population remained stable in non-planted soil. In the rhizosphere, we observed a higher competitiveness of the Nir(-) mutant compared with FM69MS, whereas the latter showed the same competitiveness as the Nar(-) mutant. These results provide the first demonstration that NO3 (-) reduction is the main nitrogen-dissimilating step controlling the competitiveness of P. fluorescens in the rhizosphere.

Influence of plant communities on denitrification in a tidal freshwater marsh of the Potomac River, United States

We investigated whether marsh surface elevation, plant community composition (annuals vs. perennials), and organic matter quantity/quality were associated with differences in denitrification rates in an urban tidal freshwater marsh of the Potomac River, United States. We measured denitrification rates using both denitrification enzyme activity (DEA) with acetylene inhibition (June: n = 38, 3234 +/- 303; October: n = 38, 1557 +/- 368 ng N g dry soil(-1) h(-1)) and direct N(2) flux measurements with membrane inlet mass spectrometry (MIMS) (November: n = 6, 147 +/- 24 mumol m(-2) h(-1)). Organic carbon content and nitrate concentrations in soil, and plant community composition were correlated with elevation, but DEA rates did not differ across marsh surface elevation. Soil organic carbon was highest in plots dominated by perennial graminoids, but DEA rates did not differ across plant community types. The DEA rates increased with increasing soil ammonium concentrations and total N content, and DEA rates differed between summer and fall sampling. The MIMS rates did not differ across plant community types, but were correlated with soil organic N content. Denitrification rates suggest that potential N removal at the site could be substantial. In addition, denitrification rates measured in Dyke Marsh were higher than rates for sediments measured in the adjacent Potomac River. Tidal freshwater marshes can represent an important site for denitrification, and factors fostering denitrification should be considered when restoring urban tidal freshwater wetlands as they are faced with pressures from increasing land use change and sea level rise.

Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments

Dissimilatory nitrate reduction is catalyzed by a membrane-bound and a periplasmic nitrate reductase. We set up a real-time PCR assay to quantify these two enzymes, using the narG and napA genes, encoding the catalytic subunits of the two types of nitrate reductases, as molecular markers. The narG and napA gene copy numbers in DNA extracted from 18 different environments showed high variations, with most numbers ranging from 2 x 10(2) to 6.8 x 10(4) copies per ng of DNA. This study provides evidence that, in soil samples, the number of proteobacteria carrying the napA gene is often as high as that of proteobacteria carrying the narG gene. The high correlation observed between narG and napA gene copy numbers in soils suggests that the ecological roles of the corresponding enzymes might be linked.

Rapid removal of nitrate and sulfate in freshwater wetland sediments

Anaerobic microbial processes play particularly important roles in the biogeochemical functions of wetlands, affecting water quality, nutrient transport, and greenhouse gas fluxes. This study simultaneously examined nitrate and sulfate removal rates in sediments of five southwestern Michigan wetlands varying in their predominant water sources from ground water to precipitation. Rates were estimated using in situ push-pull experiments, in which 500 mL of anoxic local ground water containing ambient nitrate and sulfate and amended with bromide was injected into the near-surface sediments and subsequently withdrawn over time. All wetlands rapidly depleted nitrate added at ambient ground water concentrations within 5 to 20 h, with the rate dependent on concentration. Sulfate, which was variably present in porewaters, was also removed from injected ground water in all wetlands, but only after nitrate was depleted. The sulfate removal rate in ground water-fed wetlands was independent of concentration, in contrast to rates in precipitation-fed wetlands. Sulfate production was observed in some sites during the period of nitrate removal, suggesting that the added nitrate either stimulated sulfur oxidation, possibly by bacteria that can utilize nitrate as an oxidant, or inhibited sulfate reduction by stimulating denitrification. All wetland sediments examined were consistently capable of removing nitrate and sulfate at concentrations found in ground water and precipitation inputs, over short time and space scales. These results demonstrate how a remarkably small area of wetland sediment can strongly influence water quality, such as in the cases of narrow riparian zones or small isolated wetlands, which may be excluded from legal protection.

Frequency and diversity of nitrate reductase genes among nitrate-dissimilating Pseudomonas in the rhizosphere of perennial grasses grown in field conditions

A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatment.

Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR

Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR(R) Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08x10(8) and 1.12x10(11) copies per gram of dry weight of environmental sample. Environmental real-time PCR products were cloned and sequenced. Data was used to generate a phylogenetic tree showing that all environmental products belonged to the target group. Moreover, 16S rDNA copy number was quantified in the different environments by real-time PCR using universal primers for Eubacteria. 16S rDNA copy number was similar or slightly higher than that of narG, between 7.12x10(9) and 1.14x10(11) copies per gram of dry weight of environmental sample. Therefore, the yet uncultivated nitrate-reducing group targeted in this study seems to be numerically important in the environment, as revealed by narG high absolute and relative densities across various environments. Further analysis of the density of the nitrate-reducing community as a whole by real-time PCR may provide insights into the correlation between microbial density, diversity and activity.

Influence of maize mucilage on the diversity and activity of the denitrifying community

In order to understand the effect of the maize rhizosphere on denitrification, the diversity and the activity of the denitrifying community were studied in soil amended with maize mucilage. Diversity of the denitrifying community was investigated by polymerase chain reaction (PCR) amplification of total community DNA extracted from soils using gene fragments, encoding the nitrate reductase (narG) and the nitrous oxide reductase (nosZ), as molecular markers. To assess the underlying diversity, PCR products were cloned and 10 gene libraries were obtained for each targeted gene. Libraries containing 738 and 713 narG and nosZ clones, respectively, were screened by restriction fragment analysis, and grouped based on their RFLP (restriction fragment length polymorphism) patterns. In all, 117 and 171 different clone families have been identified for narG and nosZ and representatives of RFLP families containing at least two clones were sequenced. Rarefaction curves of both genes did not reach a clear saturation, indicating that analysis of an increasing number of clones would have revealed further diversity. Recovered NarG sequences were related to NarG from Actinomycetales and from Proteobacteria but most of them are not related to NarG from known bacteria. In contrast, most of the NosZ sequences were related to NosZ from alpha, beta, and gammaProteobacteria. Denitrifying activity was monitored by incubating the control and amended soils anaerobically in presence of acetylene. The N2O production rates revealed denitrifying activity to be greater in amended soil than in control soil. Altogether, our results revealed that mucilage addition to the soil results in a strong impact on the activity of the denitrifying community and minor changes on its diversity.

Genetic characterization of the nitrate reducing community based on narG nucleotide sequence analysis

The ability of facultative anerobes to respire nitrate has been ascribed mainly to the activity of a membrane-bound nitrate reductase encoded by the narGHJI operon. Respiratory nitrate reduction is the first step of the denitrification pathway, which is considered as an important soil process since it contributes to the global cycling of nitrogen. In this study, we employed direct PCR, cloning, and sequencing of narG gene fragments to determine the diversity of nitrate-reducing bacteria occurring in soil and in the maize rhizosphere. Libraries containing 727 clones in total were screened by restriction fragment analysis. Phylogenetic analysis of 128 narG sequences separated the clone families into two main groups that represent the Gram-positive and Gram-negative nitrate-reducing bacteria. Novel narG lineages that branch distinctly from all currently known membrane bound nitrate-reductase encoding genes were detected within the Gram-negative branch. All together, our results revealed a more complex nitrate-reducing community than did previous culture-based studies. A significant and consistent shift in the relative abundance of the nitrate-reducing groups within this functional community was detected in the maize rhizosphere. Thus a substantially higher abundance of the dominant clone family and a lower diversity index were observed in the rhizosphere compared to the unplanted soil, suggesting that a bacterial group has been specifically selected within the nitrate-reducing community. Furthermore, restriction fragment length polymorphism analysis of cloned narG gene fragments proved to be a powerful tool in evaluating the structure and the diversity of the nitrate-reducing community and community shifts therein.

Molecular analysis of the nitrate-reducing community from unplanted and maize-planted soils

Microorganisms that use nitrate as an alternative terminal electron acceptor play an important role in the global nitrogen cycle. The diversity of the nitrate-reducing community in soil and the influence of the maize roots on the structure of this community were studied. The narG gene encoding the membrane bound nitrate reductase was selected as a functional marker for the nitrate-reducing community. The use of narG is of special interest because the phylogeny of the narG gene closely reflects the 16S ribosomal DNA phylogeny. Therefore, targeting the narG gene provided for the first time a unique insight into the taxonomic composition of the nitrate-reducing community in planted and unplanted soils. The PCR-amplified narG fragments were cloned and analyzed by restriction fragment length polymorphism (RFLP). In all, 60 RFLP types represented by two or more clones were identified in addition to the 58 RFLP types represented by only one clone. At least one clone belonging to each RFLP type was then sequenced. Several of the obtained sequences were not related to the narG genes from cultivated bacteria, suggesting the existence of unidentified nitrate-reducing bacteria in the studied soil. However, environmental sequences were also related to NarG from many bacterial divisions, i.e., Actinobacteria and alpha, beta, and gamma proteobacteria. The presence of the plant roots resulted in a shift in the structure of the nitrate-reducing community between the unplanted and planted soils. Sequencing of RFLP types dominant in the rhizosphere or present only in the rhizosphere revealed that they are related to NarG from the Actinobacteria in an astonishingly high proportion.

Dissimilatory nitrate reduction in anaerobic sediments leading to river nitrite accumulation

Recent studies on Northern Ireland rivers have shown that summer nitrite (NO(inf2)(sup-)) concentrations greatly exceed the European Union guideline of 3 (mu)g of N liter(sup-1) for rivers supporting salmonid fisheries. In fast-flowing aerobic small streams, NO(inf2)(sup-) is thought to originate from nitrification, due to the retardation of Nitrobacter strains by the presence of free ammonia. Multiple regression analyses of NO(inf2)(sup-) concentrations against water quality variables of the six major rivers of the Lough Neagh catchment in Northern Ireland, however, suggested that the high NO(inf2)(sup-) concentrations found in the summer under warm, slow-flow conditions may result from the reduction of NO(inf3)(sup-). This hypothesis was supported by field observations of weekly changes in N species. Here, reduction of NO(inf3)(sup-) was observed to occur simultaneously with elevation of NO(inf2)(sup-) levels and subsequently NH(inf4)(sup+) levels, indicating that dissimilatory NO(inf3)(sup-) reduction to NH(inf4)(sup+) (DNRA) performed by fermentative bacteria (e.g., Aeromonas and Vibrio spp.) is responsible for NO(inf2)(sup-) accumulation in these large rivers. Mechanistic studies in which (sup15)N-labelled NO(inf3)(sup-) in sediment extracts was used provided further support for this hypothesis. Maximal concentrations of NO(inf2)(sup-) accumulation (up to 1.4 mg of N liter(sup-1)) were found in sediments deeper than 6 cm associated with a high concentration of metabolizable carbon and anaerobic conditions. The (sup15)N enrichment of the NO(inf2)(sup-) was comparable to that of the NO(inf3)(sup-) pool, indicating that the NO(inf2)(sup-) was predominantly NO(inf3)(sup-) derived. There is evidence which suggests that the high NO(inf2)(sup-) concentrations observed arose from the inhibition of the DNRA NO(inf2)(sup-) reductase system by NO(inf3)(sup-).