Dynamics of Soil Denitrifier Populations: Relationships between Enzyme Activity, Most-Probable-Number Counts, and Actual N Gas Loss

Biodiversity breakpoints along stress gradients in estuaries and associated shifts in ecosystem interactions

Denitrification in coastal sediments can provide resilience to eutrophication in estuarine ecosystems, but this key ecosystem function is impacted directly and indirectly by increasing stressors. The erosion and loading of fine sediments from land, resulting in sedimentation and elevated sediment muddiness, presents a significant threat to coastal ecosystems worldwide. Impacts on biodiversity with increasing sediment mud content are relatively well understood, but corresponding impacts on denitrification are uncharacterised. Soft sediment ecosystems have a network of interrelated biotic and abiotic ecosystem components that contribute to microbial nitrogen cycling, but these components (especially biodiversity measures) and their relationships with ecosystem functions are sensitive to stress. With a large dataset spanning broad environmental gradients this study uses interaction network analysis to present a mechanistic view of the ecological interactions that contribute to microbial nitrogen cycling, showing significant changes above and below a stressor (mud) threshold. Our models demonstrate that positive biodiversity effects become more critical with a higher level of sedimentation stress, and show that effective ecosystem management for resilience requires different action under different scenarios.

Controls on denitrification potential in nitrate-rich waterways and riparian zones of an irrigated agricultural setting

Denitrification, the microbial conversion of NO₃^- to N gases, is an important process contributing to whether lotic and riparian ecosystems act as sinks for excess NO₃^- from agricultural activities. Though agricultural waterways and riparian zones have been a focus of denitrification research for decades, almost none of this research has occurred in the irrigated agricultural settings of arid and semiarid climates. In this study, we conducted a broad survey of denitrification potential in riparian soils and channel sediments from 79 waterway reaches in the irrigated agricultural landscape of California's Central Valley. With this approach, we sought to capture the wide range of variation that arose from diverse waterway management and fluctuating flow conditions, and use this variation to identify promising management interventions. We explored associations of denitrification potentials with surface water NO₃^- -N, organic matter, flow conditions, vegetation cover, near-channel riparian bank slope, and channel geomorphic features using generalized linear mixed models. We found strong associations of sediment denitrification potentials with reach flow conditions, which we hypothesize was the result of variation in microbial communities' tolerance to dry-wet cycles. Denitrification potentials in riparian soils, in contrast, did not appear affected by flow conditions, but instead were associated with organic matter, vegetation cover, and bank slope in the riparian zone. These results suggest a strong need for further work on how denitrification responds to varying flow conditions and dry-wet cycles in non-perennial lotic ecosystems. Our findings also demonstrate that denitrifier communities respond to key features of waterway management, which can therefore be leveraged to control denitrification through a variety of management actions.

Competition between Two Isolates of Denitrifying Bacteria Added to Soil

We examined the competitive relationship between two isolates of denitrifying bacteria, both of which grow well under aerobic conditions but differ in their ability to grow under denitrifying conditions. The growth and persistence of the two isolates, added to sterile soil or added to soil previously colonized by the other isolate, were monitored under aerobic and denitrifying (anaerobic) conditions. When isolates were added together to sterile soil, the isolate added at the higher density reduced the growth of the isolate added at the lower density. The magnitude of the growth reduction varied depending on the competitive abilities of the individual isolates and the aeration state of the soil. Prior colonization of soil with one of the isolates conferred a competitive advantage on the colonized isolate but did not lead to the disappearance of the challenging isolate. Fluctuations in aeration state caused large changes in the population density of one isolate and altered the competitive relationship between the two isolates. The competitive effectiveness of each isolate varied with cell density, the degree of prior colonization of the soil by the other isolate, and the aeration state of the soil.

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

The effects of nitrate availability and the presence of Glyceria maxima on the composition and activity of the dissimilatory nitrate-reducing bacterial community were studied in the laboratory. Four different concentrations of NO(inf3)(sup-), 0, 533, 1434, and 2,905 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), were added to pots containing freshwater sediment, and the pots were then incubated for a period of 69 days. Upon harvest, NH(inf4)(sup+) was not detectable in sediment that received 0 or 533 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1). Nitrate concentrations in these pots ranged from 0 to 8 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1) at harvest. In pots that received 1,434 or 2,905 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), final concentrations varied between 10 and 48 (mu)g of NH(inf4)(sup+)-N g of dry sediment(sup-1) and between 200 and 1,600 (mu)g of NO(inf3)(sup-)-N g of dry sediment(sup-1), respectively. Higher input levels of NO(inf3)(sup-) resulted in increased numbers of potential nitrate-reducing bacteria and higher potential nitrate-reducing activity in the rhizosphere. In sediment samples from the rhizosphere, the contribution of denitrification to the potential nitrate-reducing capacity varied from 8% under NO(inf3)(sup-)-limiting conditions to 58% when NO(inf3)(sup-) was in ample supply. In bulk sediment with excess NO(inf3)(sup-), this percentage was 44%. The nitrate-reducing community consisted almost entirely of NO(inf2)(sup-)-accumulating or NH(inf4)(sup+)-producing gram-positive species when NO(inf3)(sup-) was not added to the sediment. The addition of NO(inf3)(sup-) resulted in an increase of denitrifying Pseudomonas and Moraxella strains. The factor controlling the composition of the nitrate-reducing community when NO(inf3)(sup-) is limited is the presence of G. maxima. In sediment with excess NO(inf3)(sup-), nitrate availability determines the composition of the nitrate-reducing community.

Silver (Ag+) reduces denitrification and induces enrichment of novelnirKgenotypes in soil

The use of silver ions in industry to prevent microbial growth is increasing and silver is a new and an overlooked heavy-metal contaminant in sewage sludge-amended soil. The denitrifying community was the model used to assess the dose-dependent effects of silver ions on microorganisms overtime in soil microcosms. Silver caused a sigmoid dose-dependent reduction in denitrification activity, and no recovery was observed during 90 days. Dentrifiers with nirK, which encodes the copper nitrite reductase, were targeted to estimate abundance and community composition for some of the concentrations. The nirK copy number decreased by the highest addition (100 mg Ag kg(-1) soil), but the nirK diversity increased. Treatment-specific sequences not clustering with any deposited nirK sequences were found, indicating that silver induces enrichment of novel nirK denitrifiers.

In situ ground water denitrification in stratified, permeable soils underlying riparian wetlands

The ground water denitrification capacity of riparian zones in deep soils, where substantial ground water can flow through low-gradient stratified sediments, may affect watershed nitrogen export. We hypothesized that the vertical pattern of ground water denitrification in riparian hydric soils varies with geomorphic setting and follows expected subsurface carbon distribution (i.e., abrupt decline with depth in glacial outwash vs. negligible decline with depth in alluvium). We measured in situ ground water denitrification rates at three depths (65, 150, and 300 cm) within hydric soils at four riparian sites (two per setting) using a 15N-enriched nitrate "push-pull" method. No significant difference was found in the pattern and magnitude of denitrification when grouping sites by setting. At three sites there was no significant difference in denitrification among depths. Correlations of site characteristics with denitrification varied with depth. At 65 cm, ground water denitrification correlated with variables associated with the surface ecosystem (temperature, dissolved organic carbon). At deeper depths, rates were significantly higher closer to the stream where the subsoil often contains organically enriched deposits that indicate fluvial geomorphic processes. Mean rates ranged from 30 to 120 microg N kg(-1) d(-1) within 10 m versus <1 to 40 microg N kg(-1) d(-1) at >30 m from the stream. High denitrification rates observed in hydric soils, down to 3 m within 10 m of the stream in both alluvial and glacial outwash settings, argue for the importance of both settings in evaluating the significance of riparian wetlands in catchment-scale N dynamics.

Immunological method for direct assessment of the functionality of a denitrifying strain of Pseudomonas fluorescens in soil

This work describes an immunological method for detection and quantification in complex environments of the dissimilative nitrate reductase (NRA) responsible for the reduction of nitrate to nitrite, which plays an important role in ecosystem functioning. The alpha-catalytic subunit of the enzyme was purified from the denitrifying strain Pseudomonas fluorescens YT101 and used for the production of polyclonal antibodies. These antibodies were used to detect and quantify the NRA by a chemifluorescence technique on Western blots after separation of total proteins from pure cultures and soil samples. The specificity, detection threshold and reproducibility of the proposed method were evaluated. A soil experiment showed that our method can be applied to complex environmental samples.

Nitrification and denitrification rates of Everglades wetland soils along a phosphorus-impacted gradient

Little information is available on the effect of phosphorus (P) enrichment on nitrogen (N) biogeochemical cycling in wetland soil. Of particular importance are the coupled nitrification-denitrification reactions that regulate the microbially mediated loss of N from wetland systems. Soils from the northern Florida Everglades have been affected by P loading from surface waters over the past 40 years. Elevated P levels have been show to have an effect on the size and activity of the microbial pool and a decrease in the N to P ratio of the microbial biomass. The objective of the study was to determine if P enrichment in soils affected microbial activities related to nitrification and denitrification in these flooded, peat soils. Potential nitrification rates of soil and detritus were determined using constantly stirred reactors under aerobic conditions while denitrification rates were determined from anaerobic incubations of slurry. Nitrification rates showed two distinct linear phases, a slower initial rate, signifying activity of nitrifiers present, followed by a sharp increase in the NH4+ conversion rate indicative of maximum potential rates. Initial rates of nitrification were highest in the surficial detrital layer decreasing with soil depth and did not correlate to soil total P. The potential rates of nitrification were 13 times greater than the initial rates. Potential denitrification rates were highest in the detritus and 0- to 10-cm soil interval with significantly lower values in the 10- to 30-cm soil interval, significantly correlated to total P of the soil. A significant (P < 0.01) relationship was seen between potential denitrification rates and soil total P suggesting an increased rate of N removal from P-enriched regions of the northern Everglades.

Production and consumption of nitric oxide by three methanotrophic bacteria

We studied nitrogen oxide production and consumption by methanotrophs Methylobacter luteus (group I), Methylosinus trichosporium OB3b (group II), and an isolate from a hardwood swamp soil, here identified by 16S ribosomal DNA sequencing as Methylobacter sp. strain T20 (group I). All could consume nitric oxide (nitrogen monoxide, NO), and produce small amounts of nitrous oxide (N(2)O). Only Methylobacter strain T20 produced large amounts of NO (>250 parts per million by volume [ppmv] in the headspace) at specific activities of up to 2.0 x 10(-17) mol of NO cell(-1) day(-1), mostly after a culture became O(2) limited. Production of NO by strain T20 occurred mostly in nitrate-containing medium under anaerobic or nearly anaerobic conditions, was inhibited by chlorate, tungstate, and O(2), and required CH(4). Denitrification (methanol-supported N(2)O production from nitrate in the presence of acetylene) could not be detected and thus did not appear to be involved in the production of NO. Furthermore, cd(1) and Cu nitrite reductases, NO reductase, and N(2)O reductase could not be detected by PCR amplification of the nirS, nirK, norB, and nosZ genes, respectively. M. luteus and M. trichosporium produced some NO in ammonium-containing medium under aerobic conditions, likely as a result of methanotrophic nitrification and chemical decomposition of nitrite. For Methylobacter strain T20, arginine did not stimulate NO production under aerobiosis, suggesting that NO synthase was not involved. We conclude that strain T20 causes assimilatory reduction of nitrate to nitrite, which then decomposes chemically to NO. The production of NO by methanotrophs such as Methylobacter strain T20 could be of ecological significance in habitats near aerobic-anaerobic interfaces where fluctuating O(2) and nitrate availability occur.

Effects of storage on measurements of potential microbial activities in stream fine benthic organic matter

Sample storage can significantly influence measured microbial activities in stream fine benthic organic matter (FBOM), possibly confounding effects of sample variability and short-term changes in activity. Denitrification potential, acetylene reduction and respiration rates, mineralizable N and extractable ammonium concentrations, and beta-glucosidase and phosphatase enzyme activities of FBOM from first-order mountain streams in the western Oregon Cascade Mountains were assayed at various times after collection to determine potential storage effects. Denitrification potential, phosphatase activity, and extractable ammonium remained stable over a minimum of 11 h of storage at 5 degrees C. Mineralizable N concentrations, respiration rates, and beta-glucosidase activity all decreased within 12 h of collection. Results varied for acetylene reduction. Once assay conditions were established, denitrification potential and respiration rates were linear with incubation time. Based on paired t-tests, measures of acetylene reduction, denitrification potential, respiration rate, beta-glucosidase activity, and phosphatase activity were generally similar at a 1-wk interval within the same stream reaches.

Chloramphenicol inhibition of denitrifying enzyme activity in two agricultural soils

Chloramphenicol, at concentrations greater than 0.1 g/liter (0.3 mM), inhibited the denitrifying enzyme activity (DEA) of slurries of humisol and sandy loam soils by disrupting the activity of existing nitrate reductase enzymes. When the concentration of chloramphenicol was increased from 0.1 to 2.0 g/liter (6.0 mM), the rate of nitrite production from nitrate decreased by 25 to 46%. The rate of NO production from nitrate decreased by 20 to 39%, and the rate of N(2)O production from nitrate, in the presence of acetylene (DEA), decreased by 21 to 61%. The predicted values of DEA at 0 g of chloramphenicol/liter computed from linear regressions of DEA versus chloramphenicol concentration were 18 to 43% lower than DEA measurements made in the absence of chloramphenicol and within a few per cent of DEA rates measured in the presence of 0.1 g of chloramphenicol/liter. We conclude that DEA assays should be carried out with a single (0.1-g/liter) chloramphenicol concentration. Chloramphenicol at concentrations greater than 0.1 g/liter inhibits the activity of existing denitrifying enzymes and should not be used in DEA assays.

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-).

Differential Metabolism of Dimethylsulfoniopropionate and Acrylate in Saline and Brackish Intertidal Sediments

In anoxic Spartina alterniflora-dominated sediments along a naturally occuring salinity gradient (the Cooper River estuary, South Carolina, U.S.A.), dimethylsulfoniopropionate (DMSP) was metabolized to dimethyl sulfide (DMS) and acrylate by sediment microbes. The rate of DMSP degradation and acrylate mineralization by sediment microbes was similar at all sites along this 25-km transect. However, sediments amended with acrylate (or DMSP) showed significantly higher rates of N2 fixation (measured as acetylene reduction activity) (ARA) in the saline sediments downstream than brackish sediments. These results are consistent with the fact that acrylate stimulated the rates of both denitrification and CO2 production in the saline sediments at the mouth of the river more than tenfold over rates in brackish sediments. Enrichment experiments indicate that microbes capable of using DMSP or acrylate were not present in upstream sediments despite the fact that microbial biomass, percent organic matter, and both glucose-stimulated ARA and denitrification were highest upstream. It appears that acrylate utilizing, N2 fixing, and denitrifying populations are insignificant in the lower salinity sediments of the estuary. These results may reflect the availability of DMSP, which averaged 10.3 nmol g wet wt-1 of saline sediments and levels less than our detection limit (1 &mgr;M) in brackish sediments.

Spatial heterogeneity in the distribution of denitrifying bacteria associated with denitrification activity zones

Denitrifying enzyme activity (DEA) in artificially established denitrification activity zones was, on average, 3.5-fold greater than in bulk soil. Denitrifier biomass was between 1 and 4 orders of magnitude greater in activity zones. Denitrifier specific activity was lower in activity zones and more similar to specific activity values reported for pure cultures of denitrifying bacteria added to soil. Measurements of DEA and biomass carried out on a homogeneous subsample derived from a soil core containing a denitrification activity zone will overestimate the DEA and biomass of the bulk soil and underestimate the DEA and biomass of the activity zone.

Inhibition of existing denitrification enzyme activity by chloramphenicol

Chloramphenicol completely inhibited the activity of existing denitrification enzymes in acetylene-block incubations with (i) sediments from a nitrate-contaminated aquifer and (ii) a continuous culture of denitrifying groundwater bacteria. Control flasks with no antibiotic produced significant amounts of nitrous oxide in the same time period. Amendment with chloramphenicol after nitrous oxide production had begun resulted in a significant decrease in the rate of nitrous oxide production. Chloramphenicol also decreased (greater than 50%) the activity of existing denitrification enzymes in pure cultures of Pseudomonas denitrificans that were harvested during log-phase growth and maintained for 2 weeks in a starvation medium lacking electron donor. Short-term time courses of nitrate consumption and nitrous oxide production in the presence of acetylene with P. denitrificans undergoing carbon starvation were performed under optimal conditions designed to mimic denitrification enzyme activity assays used with soils. Time courses were linear for both chloramphenicol and control flasks, and rate estimates for the two treatments were significantly different at the 95% confidence level. Complete or partial inhibition of existing enzyme activity is not consistent with the current understanding of the mode of action of chloramphenicol or current practice, in which the compound is frequently employed to inhibit de novo protein synthesis during the course of microbial activity assays. The results of this study demonstrate that chloramphenicol amendment can inhibit the activity of existing denitrification enzymes and suggest that caution is needed in the design and interpretation of denitrification activity assays in which chloramphenicol is used to prevent new protein synthesis.

Biodegradation of organic compounds in vadose zone and aquifer sediments

The microbial processes that occur in the subsurface under a typical Midwest agricultural soil were studied. A 26-m bore was installed in November of 1988 at a site of the Purdue University Agronomy Research Center. Aseptic collections of soil materials were made at 17 different depths. Physical analysis indicated that the site contained up to 14 different strata. The site materials were primarily glacial tills with a high carbonate content. The N, P, and organic C contents of sediments tended to decrease with depth. Ambient water content was generally less than the water content, which corresponds to a -0.3-bar equivalent. No pesticides were detected in the samples, and degradation of added 14C-labeled pesticides (atrazine and metolachlor) was not detected in slurry incubations of up to 128 days. The sorption of atrazine and metolachlor was correlated with the clay content of the sediments. Microbial biomass (determined by direct microscopic count, viable count, and phospholipid assay) in the tills was lower than in either the surface materials or the aquifer located at 25 m. The biodegradation of glucose and phenol occurred rapidly and without a lag in samples from the aquifer capillary fringe, saturated zone, and surface soils. In contrast, lag periods and smaller biodegradation rates were found in the till samples. Subsurface sediments are rich in microbial numbers and activity. The most active strata appear to be transmissive layers in the saturated zone. This implies that the availability of water may limit activity in the profile.

Aerobic and anaerobic growth of rifampin-resistant denitrifying bacteria in soil

The growth and survival of several rifampin-resistant isolates of denitrifying bacteria were examined under anaerobic (denitrifying) and aerobic conditions. Two isolates added to nonsterile Bruno soil at densities of between 10(4) and 10(6) CFU g dry soil-1 exhibited an initial period of growth followed by a gradual decline in numbers. After 28 days, both isolates maintained viable populations of between 10(4) and 10(5) CFU g dry soil-1 under both denitrifying and aerobic conditions. One of the isolates consistently grew better under denitrifying conditions, and the other isolate consistently grew better under aerobic conditions. The relative pattern of denitrifying versus aerobic growth for each organism was not affected by the addition of glucose. The growth yields of the two isolates varied with soil type, but the relative pattern of denitrifying versus aerobic growth was consistent in three soils with greatly different properties. Five of nine isolates introduced into Bruno soil at low population densities (approximately 10(5) CFU g dry soil-1) exhibited better growth after 2 days under denitrifying conditions. It was not possible to predict the prevalence of the denitrifying or aerobic mode of growth in nonsterile soil from the growth characteristics of the isolates in pure cultures or sterile soil.