Examination of an acid forest soil for ammonia- and nitrite-oxidizing autotrophic bacteria

1984 ◽  
Vol 30 (9) ◽  
pp. 1125-1132 ◽  
Author(s):  
T. R. Hankinson ◽  
E. L. Schmidt
Keyword(s):  
Forest Soil ◽  
Ammonia Oxidation ◽  
Acid Soil ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizers ◽  
Nitrite Oxidation ◽  
Probable Number ◽  
Acid Forest Soil ◽  
Nitrite Oxidizers

An acid forest soil (pH 3.9 – 4.4) from an undisturbed mixed oak stand in southern Indiana was examined for the occurrence of ammonia- and nitrite- oxidizing chemoautotrophs. Populations of both nitrifiers were detected in pH 7 most-probable-number (MPN) autotrophic media, and a Nitrosospira was isolated from highest dilution ammonia oxidizer MPN tubes. Populations of nitrite oxidizers were 10 to 1000 times higher than those of ammonia oxidizers. In pH 4.0 MPN media, ammonia oxidation was slight and unsustainable on 10% transfer to fresh medium, whereas nitrite oxidation was vigorous and sustainable. In pure culture the Nitrosospira isolate (Np IO1a) was completely inhibited by nitrapyrin at 5 μg mL−1, tolerant of 1.0 and 10.0 mM chlorate, and capable of growth only at pH 6.2 and above. Fluorescent antibodies raised against Np IO1a were used to confirm the predominance of Np IO1a in all MPN series examined. These results suggest that autotrophic ammonia oxidizers may be restricted to circumneutral microsites in this acid soil, whereas autotrophic nitrite oxidizers may not be limited to such sites.

Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment

1991 ◽  
Vol 37 (11) ◽  
pp. 828-833 ◽  
Author(s):  
W. T. Smorczewski ◽  
E. L. Schmidt
Keyword(s):  
Lake Sediment ◽  
Environmental Changes ◽  
Ammonia Oxidation ◽  
Eutrophic Lake ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Probable Number ◽  
Nitrite Oxidizers

The microbiological and chemical potential for ammonia oxidation in a freshwater, eutrophic lake sediment was examined in relation to environmental changes caused by seasonal, dimictic circulation. Poulations of both ammonia and nitrite oxidizers as estimated by most probable number (MPN) were sustained throughout extended anaerobic summer intervals, with nitrite oxidizers outnumbering ammonia oxidizers by a factor ranging from 3.0 to 8.1. Ammonia oxidation potential on a per cell basis was affected by seasonal changes and was seen to decrease as oxygen was removed from the sediments. Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira. These strains did not react with known ammonia-oxidizer serotypes and, therefore, extend the serological diversity of this group of bacteria. An immunofluorescence analysis of MPN tubes from sediment collected during a period of lake stratification revealed progressive changes in the diversity of the ammonia-oxidizer population. The genera Nitrosomonas, Nitrosolobus, and Nitrosospira, including the novel serotype of Nitrosospira isolated from the sediment a year earlier, were found to coexist in well-oxygenated sediment. This diversity was seen to disappear, with Nistrosomonas surviving, as anaerobic conditions persisted. Key words: ammonia oxidizers, lake sediments, nitrifiers, nitrification.

scholarly journals Effects of Agronomic Treatments on Structure and Function of Ammonia-Oxidizing Communities

2000 ◽  
Vol 66 (12) ◽  
pp. 5410-5418 ◽  
Author(s):  
Carol J. Phillips ◽  
Dave Harris ◽  
Sherry L. Dollhopf ◽  
Katherine L. Gross ◽  
James I. Prosser ◽  
...  
Keyword(s):  
Denaturing Gradient Gel Electrophoresis ◽  
Deciduous Forest ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizer ◽  
Most Probable Number ◽  
Ammonia Oxidizers ◽  
Probable Number ◽  
Gradient Gel Electrophoresis ◽  
And Function

ABSTRACT The aim of this study was to determine the effects of different agricultural treatments and plant communities on the diversity of ammonia oxidizer populations in soil. Denaturing gradient gel electrophoresis (DGGE), coupled with specific oligonucleotide probing, was used to analyze 16S rRNA genes of ammonia oxidizers belonging to the β subgroup of the division Proteobacteria by use of DNA extracted from cultivated, successional, and native deciduous forest soils. Community profiles of the different soil types were compared with nitrification rates and most-probable-number (MPN) counts. Despite significant variation in measured nitrification rates among communities, there were no differences in the DGGE banding profiles of DNAs extracted from these soils. DGGE profiles of DNA extracted from samples of MPN incubations, cultivated at a range of ammonia concentrations, showed the presence of bands not amplified from directly extracted DNA. Nitrosomonas-like bands were seen in the MPN DNA but were not detected in the DNA extracted directly from soils. These bands were detected in some samples taken from MPN incubations carried out with medium containing 1,000 μg of NH4 +-N ml−1, to the exclusion of bands detected in the native DNA. Cell concentrations of ammonia oxidizers determined by MPN counts were between 10- and 100-fold lower than those determined by competitive PCR (cPCR). Although no differences were seen in ammonia oxidizer MPN counts from the different soil treatments, cPCR revealed higher numbers in fertilized soils. The use of a combination of traditional and molecular methods to investigate the activities and compositions of ammonia oxidizers in soil demonstrates differences in fine-scale compositions among treatments that may be associated with changes in population size and function.

Microbiological aspects of ammonia oxidation of swine waste

1991 ◽  
Vol 37 (12) ◽  
pp. 918-923 ◽  
Author(s):  
S. St-Arnaud ◽  
J. -G. Bisaillon ◽  
R. Beaudet
Keyword(s):  
Ammonia Oxidation ◽  
Most Probable Number ◽  
Ammonia Oxidizing Bacteria ◽  
Swine Waste ◽  
Anaerobic Conditions ◽  
Rotating Biological Contactor ◽  
Probable Number ◽  
Inorganic Medium ◽  
Number Of Cells ◽  
Microbiological Aspects

Ammonia-oxidizing bacteria were present at 102 MPN/mL (most probable number per millilitre) in swine waste, and they were outnumbered by a factor of 105 by the heterotrophs of the indigenous flora. To study these ammonia-oxidizing bacteria we attempted to isolate them in pure culture. We succeeded in increasing the concentration of these bacteria by successive transfers to an inorganic medium, but the heterotrophs were always dominant. To overcome this problem Nitrosomonas europaea ATCC 19718 was adapted to grow in stabilized swine waste. With this adapted strain it was shown that the number of cells inoculated into swine waste rapidly decreased both under the aerobic conditions used to oxidize the organic matter of swine waste and under the anaerobic conditions found in stored swine waste. Ammonia oxidation was delayed when adapted N. europaea was inoculated into a partially stabilized swine waste as compared with results in a completely stabilized waste. A biofilm of 107 MPN/cm2 of N. europaea was developed after 114 days of incubation at 29 °C on polyvinyl chloride discs covered with geotextile in a rotating biological contactor using an inorganic medium. This biofilm was gradually adapted to stabilized swine waste and the rate of disappearance of ammonia reached 270 mg∙L−1∙day−1 in the compartment of the reactor containing 2.5 L of waste. Key words: amonia-oxidizing bacteria, swine waste, ammonia oxidation, biofilm, most probable number.

scholarly journals Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment

2010 ◽  
Vol 76 (22) ◽  
pp. 7626-7634 ◽  
Author(s):  
Nejc Stopnišek ◽  
Cécile Gubry-Rangin ◽  
Špela Höfferle ◽  
Graeme W. Nicol ◽  
Ines Mandič-Mulec ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Inorganic Nitrogen ◽  
Peat Soil ◽  
Selective Advantage ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Rrna Gene ◽  
Ammonia Oxidizers ◽  
Ammonia Release

ABSTRACT Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen.

scholarly journals Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

2020 ◽  
Vol 117 (9) ◽  
pp. 4823-4830 ◽  
Author(s):  
Yao Zhang ◽  
Wei Qin ◽  
Lei Hou ◽  
Emily J. Zakem ◽  
Xianhui Wan ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Inorganic Nitrogen ◽  
Maximum Growth ◽  
Ecosystem Model ◽  
Ammonia Oxidizers ◽  
Oxidation Rates ◽  
Deep Waters ◽  
Theoretical Predictions ◽  
Two Populations ◽  
Nitrite Oxidizers

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013to ∼2 × 1013mol of C per year globally through the flux of ∼1 × 1014to ∼2 × 1014mol of N per year of the two steps of oxidation throughout the dark ocean.

Nitrite oxidation inhibition by hydroxylamine: experimental and model evaluation

2004 ◽  
Vol 50 (6) ◽  
pp. 295-304 ◽  
Author(s):  
P. (Lek) Noophan ◽  
L.A. Figueroa ◽  
J. Munakata-Marr
Keyword(s):  
Oxidation Rate ◽  
Biological Nitrogen Removal ◽  
Ammonia Oxidizers ◽  
Batch Experiments ◽  
Nitrite Oxidation ◽  
Ph Values ◽  
Initial Ph ◽  
Nitrogen Concentrations ◽  
Biological Nitrogen ◽  
Nitrite Oxidizers

A proposed approach for biological nitrogen removal significantly reduces cost by reducing biomass production and carbon requirements via inhibition of nitrite oxidation (NO2− to NO3−). Batch experiments were conducted to examine the effect of hydroxylamine (HM) on nitrite oxidizers, ammonia oxidizers, and nitrite reducers. Hydroxylamine effect experiments were done at initial pH values of 7.4-8.4, nitrogen concentrations of 100 mg N/L, biomass concentrations of 100-400 mg VSS/L and HM dosages up to 43 mg/L. Nitrite oxidizer activity was completely inhibited by HM at dosages of 7.0 and 8.9 mg/L for pH values of 8.4 and 7.6, respectively. Relatively low HM concentrations (0.35-5.5 mg/L) can be used to completely inhibit nitrite oxidation, but do not significantly affect ammonia oxidizers and nitrite reducers. A model developed to describe the effect of pH on nitrite oxidation rate fits the data well (R2 = 0.89) with values for Vmax of 0.372 (mg N/mg VSS-hr), pH* of 7.72, and the inhibition constant Kh of 0.154. Incorporation of HM inhibition into the model provided a good fit to relative nitrite oxidation rate as a function of undissociated HM concentration (R2 = 0.80, Vmax = 0.028 mg N/mg VSS-hr, pH* = 7.89, Kh * 0.302, a * 0.195, and Ki = 0.277 mg/L).

scholarly journals Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

2021 ◽  
Author(s):  
Man-Young Jung ◽  
Christopher J. Sedlacek ◽  
K. Dimitri Kits ◽  
Anna J. Mueller ◽  
Sung-Keun Rhee ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Oxidation Kinetic ◽  
Ammonia Oxidizer ◽  
Substrate Affinity ◽  
Kinetic Properties ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Kinetic Measurements ◽  
Ammonia Oxidizing Archaea ◽  
Wide Range

AbstractNitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co- occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest substrate affinity of any characterized AOA, which are similar to previously determined affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values strongly supports the hypothesis that – like for AOB – ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.

scholarly journals Microbial community analysis of biofilters reveals a dominance of either comammox Nitrospira or archaea as ammonia oxidizers in freshwater aquaria

2021 ◽  
Author(s):  
Michelle M McKnight ◽  
Josh D Neufeld
Keyword(s):  
Microbial Communities ◽  
Ammonia Oxidation ◽  
16S Rrna Gene Sequencing ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Ammonia Oxidizer ◽  
Future Research ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers

Nitrification by aquarium biofilters transforms toxic ammonia waste (NH3/NH4+) to less toxic nitrate (NO3-) via nitrite (NO2-). Ammonia oxidation is mediated by ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the recently discovered complete ammonia oxidizing (comammox) Nitrospira. Prior to the discovery of comammox Nitrospira, previous research revealed that AOA dominate among ammonia oxidizers in freshwater biofilters. Here, we characterized the composition of aquarium filter microbial communities and quantified the abundance of all three known groups of ammonia oxidizers. Aquarium biofilter and water samples were collected from representative freshwater and saltwater systems in Southwestern Ontario, Canada. Using extracted DNA, we performed 16S rRNA gene sequencing and quantitative PCR (qPCR) to assess community composition and quantify the abundance of amoA genes, respectively. Our results show that aquarium biofilter microbial communities were consistently represented by putative heterotrophs of the Proteobacteria and Bacteroides phyla, with distinct profiles associated with fresh versus saltwater biofilters. Among nitrifiers, comammox Nitrospira amoA genes were detected in all 38 freshwater aquarium biofilter samples and were the most abundant ammonia oxidizer in 30 of these samples, with the remaining biofilters dominated by AOA, based on amoA gene abundances. In saltwater biofilters, AOA or AOB were differentially abundant, with no comammox Nitrospira detected. These results demonstrate that comammox Nitrospira play an important role in biofilter nitrification that has been previously overlooked and such microcosms are useful for exploring the ecology of nitrification for future research.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

2021 ◽  
Author(s):  
Elizabeth French ◽  
Jessica A. Kozlowski ◽  
Annette Bollmann
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Natural Environments ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Batch Cultures ◽  
Freshwater Systems ◽  
Ammonia Oxidizing Archaea

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group ( Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite – can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

scholarly journals Impact of Blackwater Disposal in Erbil City on Municipal Wastewater and Bounded Soil Characteristics with Potential Solutions

2021 ◽  
Keyword(s):  
Municipal Wastewater ◽  
Ammonia Oxidation ◽  
Oxygen Demand ◽  
Soil Characteristics ◽  
Soil Samples ◽  
Disposal Site ◽  
Most Probable Number ◽  
Oil And Grease ◽  
Probable Number ◽  
The Impact

<p>Direct discharge of black water (BW) without treatment to the natural environment causes problems for the environment. The present research aimed to examine the impact of direct disposal of BW on the municipal wastewater (MWW) and surrounded soil characteristics in the BW disposal site in Erbil City- Kurdistan Region (KR), Iraq. To check the effect of BW on the boarded MWW and the soil; BW, MWW, BW mixed with MWW (BWMWW), polluted soil, and clean soil samples were collected and analyzed. Samples of BW, MWW, and BWMWW were tested for 32 physical-chemical and biological quality parameters such as pH, turbidity, solids, color, dissolved oxygen, five day biochemical oxygen demand (BOD5), chemical oxygen demand (COD), ammonia, oxidation-reduction potential (ORP), sulphate, oil and grease, phosphate, Most probable number (M.P.N.) of coliform, Thermo tolerant, M.P.N. E.Coli …etc. In contrast, soil samples were tested for 37 parameters, for instance pH, ORP, organic matter (OM), sulfite, Titanium, Vanadium, Chromium, Manganese, Iron, Cobalt, Nickel, Copper, Zinc, Gallium, Arsenic, Rubidium, Strontium, Yttrium, Zirconium, Molybdenum, Silver, Cadmium, Mercury, Lead, Thorium and Uranium. Results revealed that the direct disposal of BW without treatment commonly affected on the MWW and the surrounded soil characteristics. Potential treatment processes and solutions for BW disposal were presented.</p>

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