Dynamics of viable nitrifier community, N-mineralization and nitrification in seasonally dry tropical forests and savanna

The study was conducted in Vindhyan region, to assess the N-mineralization, nitrification and size of viable community of ammonium- and nitrite-oxidizing bacteria as affected by different sites and seasons. Six different ecosystems (four forests and two savannas), which differ in terms of topography, vegetation and moisture status, were selected for the present study. The soils of the study sites differ significantly in its physico-chemical properties. The savanna site had significantly higher pH (7.2), bulk density (1.37 g cm(-3)) and silt content (67.80%) but lower water holding capacity (1.37%), total-C (16,356 microg g(-1) dry soil), N (1090 microg g(-1) dry soil) and P (213 microg g(-1) dry soil) than forest sites. The soil moisture content, N-mineralization, nitrification rates and numbers of ammonium- and nitrite-oxidizing bacteria were highest in the wet season and lowest in dry season, while the size of mineral-N (NH4(+)-N and NO3(-)-N) showed a reverse trend at the sites. The N-mineralization, nitrification and nitrifier population size differ significantly across the site and season. The numbers of free-living cells of ammonium- and nitrite-oxidizing bacteria were significantly related to each other and to N-mineralization, nitrification, soil moisture and mineral-N components. The N-mineralization, nitrification and the viable number of nitrifying cells were consistently higher for forest soils compared to savanna sites. It was concluded that soil microbial process (N-mineralization and nitrification) and nitrifier population size were dependent on site topography, vegetation cover and soil moisture status.     

Surface attachment of nitrifying bacteria and their inhibition by potassium ethyl xanthate

Ion exchange resins and glass microscope slides were used to investigate factors affecting attachment of nitrifying bacteria to solid surfaces and the effect of attachment on inhibition ofNitrobacter by potassium ethyl xanthate. The ammonium oxidizerNitrosomonas attached preferentially to cation exchange resins while the nitrite oxidizerNitrobacter colonized anion exchange resins more extensively. Colonization was always associated with growth, and the site of substrate (NH₄ ⁺ or NO₂ ^–) adsorption was the major factor in attachment and colonization. The specific growth rate of cells colonizing either ion exchange resin beads or glass surfaces was greater than that of freely suspended cells, butNitrobacter populations colonizing glass surfaces were more sensitive to the inhibitor potassium ethyl xanthate. The findings indicate that surface growth alone does not protect soil nitrifying bacteria from inhibition by potassium ethyl xanthate and explain different patterns of inhibition for ammonium and nitrite oxidizers in the soil.     

Fluxes of nitrous oxide from boreal peatlands as affected by peatland type,water table level and nitrification capacity

Peat soils with high nitrogen content are potential sources of nitrous oxide (N₂O). Fluxes of nitrous oxide were measuredin situ on nine virgin and ten drained peatlands of different hydrology and nutrient status. Numbers of nitrifying bacteria were estimated in different layers of the peat profiles with a most-probable-number technique. Nitrification potentials were determined in soil slurries of pH 4 and 6 from the profiles of six peat soils. Many virgin peatlands showed low N₂O uptake. Lowering of the water table generally increased the average fluxes of N₂O from the soils, although more in minerotrophic (nutrient rich) than in ombrotrophic (nutrient poor) sites. Ammonium oxidizing bacteria were found on only two sites but nitrite oxidizers were detected in almost all peat profiles. More nitrite oxidizers were found in drained than in virgin peat profiles. Nitrification was enhanced after lowering of the water table in minerotrophic peat but not in ombrotrophic peat. The N₂O fluxes correlated positively with the numbers of nitrite oxidizers, nitrification potential, N, P and Ca content and pH of the soil and negatively with the level of water table (expressed as negative values) and K content of the soil.     

Soil nutrient supply in natural and managed forests

The effect of a laboratory addition of 10, 100 and 500 mg Cd kg_{dry soil} ^-1 on ammonification and nitrification was studied using soil samples of two unpolluted grassland soils. Calcareous and non-calcareous soil were selected for this purpose. Various parameters of nitrifying activity were investigated simulataneously: activity during long-term laboratory incubations in the presence and absence of a substrate, mineralization potentials, and potential activity of both ammonium and nitrite oxidizers during short-term incubations in soil slurries. Cadmium was added as aqueous CdCl₂.Additions of both 100 and 500 mg Cd kg_{dry soil} ^-1 doses significantly lowered the ability of both soils to nitrify 100 g added NH₄ ⁺-N g_{dry soil} ^-1 as a substrate, which was reflected in a decreased rate of nitrate formation (maximum inhibition reached 60% in the calcareous soil and 45% in the non-calcareous soil). Furthermore, these two concentrations of Cd caused an abnormal accumulation of nitrite immediately after incorporation, particularly in the calcareous soil. The addition of 10 mg Cd kg_{dry soil} ^-1 intensified N-mineralization in both soils, probably as a consequence of a higher concentration of readily metabolized substrate originating from killed bacteria or fungi. An excess of nitrate was then formed as a final step. The harmful effect of cadmium was more pronounced in calcareous soil, probably due to the higher sensitivity of nitrite-oxidizers in these soil samples.     

Cultivation impacts soil microbial dynamics in dry tropical forest ecosystem in India

We studied for two years the seasonal changes in plant available nitrate and ammonium nitrogen (N), nitrification, N-mineralization, microbial biomass carbon (MBC), nitrogen (MBN) and phosphorus (MBP) in two forest and three cropland sites, derived from a tropical forest ecosystem of India. Results indicated that seasonal values of nitrate N, ammonium N and phosphate P ranged from 7.33–12.99, 5.1–10.22 and 4.0–7.8 μg g^?1 in forest and 4.13–9.26, 9.35–14.46 and 2.8–5.8 μg g^?1 in cropland ecosystems, respectively, with maximum values in summer and minimum in rainy seasons. Nitrification and N-mineralization values varied from 6–28 and 4–26 μg g^?1 mo^?1 in forest and 3–14 μg g^?1 mo^?1 and 4–17 μg g^?1 mo^?1 in cropland, with maximum values in rainy season and minimum in summer season.MBC, MBN MBP ranged from 393–753, 34–80 and 16–36 μg g^?1 in forests and 186–414, 21–41 and 11–22 μg g^?1 in croplands, being maximum in summer and minimum in rainy seasons. There was gradual increase in the values of inorganic N, nitrification, N-mineralization and MBC, MBN and MBP along the age of cropland. Analysis of variance indicated significant difference in the concentration of inorganic N, nitrification and N-mineralization and MBC, MBN and MBP due to sites and seasons.Cultivation caused decline in the mean annual organic C, N and P by 42%, 29% and 13%. The values of nitrate N were decreased by 23–38%, while ammonium N was increased by 39–74%. Nitrification and N-mineralization values were reduced by 39–63% and 40–60%, respectively. Microbial C, N and P were reduced by 44–54%, 41–50% and 28–44%, respectively. Nonetheless, the contribution of soil microbial biomass reflected in total N was enhanced from 4.76% in forest to 5.03% in cropland ecosystem. Enhancement of plant available ammonium-N and microbial contribution in total N are an indicator of natural conserving mechanism to check the nitrogen loss from the nutrient poor agro-ecosystem.     

Wastewater nitrification kinetics using reciprocating jet bioreactor

Kinetic investigations on growth parameters of nitrifying and COD oxidizing bacteria were carried out with recourse to a three stage reciprocating jet bioreactor system using real life wastewater. The system employed in this investigation essentially consisted of separate aerobic oxidation stage along with nitrification stage and anaerobic denitrification stage with facility for biomass recirculation whenever necessary. Steady-state COD oxidation reactor performance was assessed for various values of residence time. Yield coefficient and decay coefficient of COD oxidizing biomass were obtained as 0.3329 kg BM/kg COD and 0.0032 (1/h) respectively.It was observed that COD oxidizing bacteria co-existed with nitrifying bacteria during nitrification process due to the nature of wastewater used. Steady-state nitrification reactor performance was also assessed for various residence time values. Exact concentration of nitrifying and COD oxidizing biomass in the nitrification reactor was then estimated with the help of kinetic growth parameters of COD oxidizing biomass and extent of COD oxidation achieved in nitrification reactor. This further enabled evaluation of corrected kinetic growth parameters estimated as 0.4272 kg BM/kg NH ₄ ⁺ -N and 0.00626 (1/h) for nitrifier biomass yield coefficient and decay coefficient respectively.     

Molecular analysis of the diversity of nitrifying bacteria in the soils of the forest and steppe zones of European Russia

Nitrifying bacteria play a key role in the global nitrogen cycle due to their ability to convert reduced nitrogen compounds (ammonium) to oxidized ones (nitrite and nitrate). Recent investigations based on the methods of molecular ecology revealed that bacteria are responsible for nitrification in natural ecosystems. At the same time, data on the species composition of the nitrifiers in soil microbial communities are scarce. Soil samples collected in the forest and steppe areas of European Russia and the enrichment cultures of nitrifying bacteria isolated from these samples were used for molecular studies of the diversity of the amoA gene encoding the synthesis of the key enzyme of autotrophic ammonium oxidation. The nitrifying bacteria of the genera Nitrosospira and Nitrosovibrio were found in all the studied soils from natural biocenoses and agrocenoses.     

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.     

Patterns of restoration of soil physciochemical properties and microbial biomass in different landslide sites in the sal forest ecosystem of Nepal Himalaya

The pattern of natural restoration in soil components and processes was documented in five landslide-damaged (1–58-year-old) sites in the moist tropical sal (Shorea robusta) forest ecosystem of Nepal Himalaya. Comparisons were made with an undisturbed forest site in the same region. Concentrations of soil organic C, total N, total P and extractable nutrients (Ca, Mg and K) increased with the age of sites. The 58-year-old site showed concentrations of soil organic C, total N and total P that were 75–89% of concentrations in the undisturbed sal forest. The soil microbial biomass, the active fraction of soil organic matter, showed similar seasonal variations at all sites. The amount of mean microbial biomass (expressed as C, N and P contents) increased 4–5 times at the 58-year-old site relative to the 1-year-old site, and the bulk increase occurred within the initial 15 year. The increase in the C/N ratio of soil microbial biomass with age (9.4–11.6 years) reflected change in its composition. Although the net N-mineralization rate increased consistently until 58 years of age, the proportion of nitrification rate relative to ammonification rate distinctly decreased beyond 40 years. On the other hand, the soil available-N (both NO₃⁻ and NH₄⁺) concentrations increased from 1 to 40 year and then declined; with age the proportion of NH₄⁺ increased, however. Rates of restoration in soil properties were faster in the early successional stages (1–15 year) than late stages. Among different soil properties the restoration of soil microbial biomass (C and N) was faster than soil organic C and total N. Best fit power function models showed that the estimated times for the 58-year-old site to reach the level of the undisturbed, mature sal forest would be about 30–35 year for microbial biomass (C and N) and about 100–150 year for organic C and total N. Higher accumulation of soil microbial biomass and high N-mineralization rate at late successional stages indicated the re-establishment of enriched soil and restitution of nutrient cycling during the course of ecosystem restoration.     

Assessment of Three Methods for Detection and Quantification of Nitrite-Oxidizing Bacteria and Nitrobacter in Freshwater Sediments (MPN-PCR, MPN-Griess, Immunofluorescence)

Abstract Nitrification in freshwater, a key process in the nitrogen cycle, is now well known to take place predominantly on suspended particles and in sediment. Nitrobacter is the most commonly isolated nitrite oxidizing bacteria from water environments. Three methods for counting nitrite oxidizing communities (especially Nitrobacter) in sediment were investigated: MPN-Griess, fluorescent antibodies (immunofluorescence), and a more recent molecular method coupling specific DNA amplification by PCR and statistical MPN quantification. After preliminary adjustments of the MPN-PCR technique, the detection level and the yield of each method were determined by inoculating a sediment with a pure Nitrobacter culture. The best recovery yield was obtained with the immunofluorescence technique (21.3%) and the lowest detection level was reached with the MPN-Griess method (10³ Nitrobacter/g dry weight sediment). The MPN-PCR method resulted in the lowest recovery yields and needs further adaptation to become a reliable and precise tool for investigations of nitrifying bacteria in sediment. Received: 6 July 1998; Accepted: 17 December 1998     

Heterotrophic nitrification in add forest soils

Ninety cultures of heterotrophic organisms were isolated from soils of four acid Norwegian forest sites, which were active in nitrifying. The isolates were tested for ability to form nitrite in a glucose-ammonium-inorganic salts medium. Eleven cultures were found capable of oxidizing ammonium to nitrite. The nitrifying organisms consist of 4 bacteria and 7 fungi.     

Measurement of potential activity of fixed nitrifying bacteria in biological filters used in drinking water production

Nitrification during biological filtration is being used more and more in drinking water production to remove ammonia, which can be the source of several water quality problems during distribution. In this process, ammonia is converted into nitrite and then into nitrate by fixed autotrophic nitrifying bacteria. The purpose of this work was to develop a technique to estimate fixed nitrifying biomass (sum of ammonia- and nitrite-oxidizing populations). The quantification of autotrophic nitrifying biomass was determined by potential nitrifying activity measurement. The production of oxidized forms of inorganic nitrogen (nitrates and nitrites) was measured after an incubation of 2 cm³ of colonized solid support in the presence of a 5-ml nitrifier medium containing 10 mg N-NH₄ L⁻¹ for 30 min at 32°C. The production rate of oxidized nitrogen in optimal conditions was measured and converted into nitrifying biomass by using the maximum specific oxidizing activity. This technique was shown to be appropriate for conditions encountered in the biological filters used in drinking water production and sufficiently simple to be used for routine measurements. Journal of Industrial Microbiology & Biotechnology (2000) 24, 161–166. Received 28 July 1999/ Accepted in revised form 11 November 1999     

Characterization and performance of constructed nitrifying biofilms during nitrogen bioremediation of a wastewater effluent

Constructed ammonium oxidizing biofilms (CAOB) and constructed nitrite oxidizing biofilms (CNOB) were characterized during the bioremediation of a wastewater effluent. The maximum ammonium removal rate and removal efficiency in CAOB was 322 mg N-NH₄⁺ m⁻³ d⁻¹ and 96%, respectively, while in CNOB a maximum removal rate of 255 mg N-NH₄⁺ m⁻³ d⁻¹ and a removal efficiency of 76% was achieved. Both constructed biofilms on low-density polyester Dacron support achieved removal efficiencies higher than that of the concentrations normally present in reactors without constructed biofilms (P < 0.05). Nitrifying bacteria from the constructed biofilms cultures were typed by sequencing 16S rRNA genes that had been amplified by PCR from genomic DNA. Analysis of enrichment biofilms has therefore provided evidence of high removal of ammonium and the presence of Nitrosomonas eutropha, N. halophila and N. europaea in CAOB, while in CNOB Nitrobacter hamburgensis, N. winogradskyi and N. alkalicus were identified according to 16S rRNA gene sequences comparison. The biofilm reactors were nitrifying over the whole experimental period (15 days), showing a definite advantage of constructed biofilms for enhancing a high biomass concentration as evidenced by environmental electron microscopic analysis (ESEM). Our research demonstrates that low-density polyester Dacron can be effectively used for the construction of nitrifying biofilms obtaining high removal efficiencies of nitrogen in a relatively short time from municipal effluents from wastewater treatment plants. CAOB and CNOB are potentially promissory for the treatment of industrial wastewaters that otherwise requires very large and expensive reactors for efficient bioremediation of effluents.     

Physicochemical and biological factors affecting atmospheric methane oxidation in gray forest soils

The decline of methane oxidizing activities in gray forest soil upon its conversion into arable land was shown to be caused by major changes in biotic and physicochemical properties of soil. Using the method of immune serums, methane-oxidizing bacteria were detected in both forest and agricultural soils, but their populations differed significantly in both abundance and composition. In the forest soil, the number of methanotrophs was an order of magnitude higher than in arable soil, amounting to 3.5 × 10⁸ and 0.24 × 10⁸ cells/g soil, respectively. All methane-oxidizing bacteria identified in the forest soil belonged to the genus Methylocystis, and 94% of these were represented by a single species, M. parvus. The arable soil was dominated by type I methanotrophs (Methylobacter and Methylomonas, 67.6%), occurring along with bacteria of the genus Methylocystis. In addition, arable soil is characterized by a low content of microbial biomass, lower porosity and water resistance of soil aggregates, and the predominance of nitrogen mineralization processes over those of nitrogen immobilization. These factors can also contribute to lower rates of methane oxidation in arable soil as compared to forest soil.__________Translated from Mikrobiologiya, Vol. 74, No. 2, 2005, pp. 255–260.Original Russian Text Copyright © 2005 by Kravchenko, Semenov, Kuznetsova, Bykova, Dulov, Pardini, Gispert, Boeckx, Cleemput, Galchenko.     

Lithotrophic and Heterotrophic Bacteria in Deep Subsurface Sediments and Their Relation to Sediment Properties

Subsurface sediments obtained from three cores drilled to depths of 260 m below the surface in South Carolina were analyzed for heterotrophic bacteria; N₂‐fixing microaerophiles; and nitrifying, sulfur‐oxidizing, and H₂‐oxidizing lithotrophic bacteria. In addition, pore waters were extracted for chemical analysis of inorganic nitrogen species, sulfate, dissolved organic carbon, pH, and Eh. Autotroph populations were generally less than 10³ most probable number (MPN) g^‐1 dry sediment with sulfur‐oxidizing bacteria, detected in 60% of the sediment samples, being the most frequently encountered group. Nitrifying bacteria were detected mainly in sediments from one borehole (P28), and their populations in those sediments were correlated with pore‐water ammonium concentrations. Populations of heterotrophic bacteria in 60% of the sediments were greater than 10⁶ colony forming units (CFU) g^‐1 dry sediment and were typically lower in sediments of high clay content and low pH. Microaerophilic N₂‐fixing bacteria were cultured from >50% and bacteria capable of growth on H₂ were cultured from 35% of the subsurface sediments examined. Sediment texture, which controls porosity, water potential, and hydraulic conductivity, appears to be a major factor influencing microbial populations in coastal plain subsurface sediments.     

Soil conditions and regeneration after clear felling of a Pinus sylvestris L. stand in a nitrogen experiment,Central Sweden

Forest N fertilization is a common practice in areas of Sweden that are not affected by high levels of N deposition. The environmental consequences of high N input to closed forests are fairly well known, but the long-term effects following clear-felling are a lot less well known. Thus, residual effects on soil and planted seedlings of previous N additions at an experimental N gradient 11 years after clear-felling were studied at a naturally nutrient-poor forest site in central Sweden. The experimental N gradient had been established by three repeated applications (in 1967, 1974 and 1981) of six dosages of NH₄NO₃ with increments of 120 kg N ha^–1. Thus, in total, the applied N dose ranged between 0 and 1800 kg N ha^–1. The study examined extractable base cations and P, soil pH, total-N, total-C, net N-mineralization and potential nitrification in four soil horizons (the humus layer, and 0–5, 5–10 and 10–20 cm in the mineral soil). We also measured the survival and growth of planted Pinus sylvestris L. seedlings. The applied N had no effect on the amounts of extractable-P or base cations in the soil. The soil pH decreased with increasing N dose in the deeper soil horizons, while in the humus the pH showed a weak but statistically significant increase due to the N application. Both total-C and total-N increased as a result of the N application, while the C/N ratio decreased. In the humus layer and the uppermost mineral soil layer NH₄ ⁺ was the major inorganic N source, in contrast to the lowest mineral soil horizon where NO₃ ^– dominated. For most of the studied horizons, there was a positive linear relationship between applied N dose and amount of inorganic N. Both net N-mineralization and potential nitrification showed increases with increasing N dose. As for the plants, no difference in survival or growth was found between the different N treatments. For doses generally applied in forest fertilization no significant differences in any of the studied properties were found.     

Control and optimization of nitrifying communities for nitritation from domestic wastewater at room temperatures

To achieve nitritation from complete-nitrification seed sludge at room temperature of 19 ± 1 °C, a lab-scale sequencing batch reactor (SBR) treating domestic wastewater with low C/N ratios was operated to investigate the control and optimization of nitrifying communities. Ammonia oxidizing bacteria (AOB) dominance was enhanced through the combination of low DO concentrations (<1.0 mg/L) and preset short-cycle control of aeration time. Nitritation was successfully established with NO₂^?-N/NO_x^?-N over 95%. To avoid the adverse impact of low DO concentrations on AOB activities, DO concentrations were increased to 1–2 mg/L. At the normal DO levels and temperatures, on-line control strategy of aerobic durations maintained the stability of nitritation with nitrite accumulation rate over 95% and ammonia removal above 97%. Fluorescence in-situ hybridization (FISH) analysis presented that the maximal percentage of AOB in biomass reached 10.9% and nitrite oxidizing bacteria (NOB) were washed out.     

Ammonia oxidation and nitrate reduction marker genes are key indicators of nitrogen losses in temperate forest catchments

Chronic nitrogen inputs can alleviate N limitation and potentially impose N losses in forests, indicated by soil enrichment in ¹⁵N over ¹⁴N. However, the complexity of the nitrogen cycle hinders accurate quantification of N fluxes. Simultaneously, soil ecologists are striving to find meaningful indicators to characterise the “openness” of the nitrogen cycle. We integrate soil δ¹⁵N with constrained ecosystem N losses and the functional gene potential of the soil microbiome in 14 temperate forest catchments. We show that N losses are associated with soil δ¹⁵N and that δ¹⁵N scales with the abundance of soil bacteria. The abundance of the archaeal amoA gene, representing the first step in nitrification (ammonia oxidation to nitrite), followed by the abundance of narG and napA genes, associated with the first step in denitrification (nitrate reduction to nitrite), explains most of the variability in soil δ¹⁵N. These genes are more informative than the denitrification genes nirS and nirK, which are directly linked to N₂O production. Nitrite formation thus appears to be the critical step associated with N losses. Furthermore, we show that the genetic potential for ammonia oxidation and nitrate reduction is representative of forest soil ¹⁵N enrichment and thus indicative of ecosystem N losses.     

Rapid start-up of nitrifying MBBRs at low temperatures: nitrification,biofilm response and microbiome analysis

The moving bed biofilm reactor (MBBR), operated as a post carbon removal system, requires long start-up times in comparison to carbon removal systems due to slow growing autotrophic organisms. This study investigates the use of carriers seeded in a carbon rich treatment system prior to inoculation in a nitrifying MBBR system to promote the rapid development of nitrifying biofilm in an MBBR system at temperatures between 6 and 8 °C. Results show that nitrification was initiated by the carbon removal carriers after 22 h of operation. High throughput 16S-rDNA sequencing indicates that the sloughing period was a result of heterotrophic organism detachment and the recovery and stabilization period included a growth of Nitrosomonas and Nitrospira as the dominant ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) in the biofilm. Peripheral microorganisms such as Myxococcales, a rapid EPS producer, appear to have contributed to the recovery and stabilization of the biofilm.