Nitrification and Autotrophic Nitrifying Bacteria in a Hydrocarbon-Polluted Soil

ABSTRACT In vitro ammonia-oxidizing bacteria are capable of oxidizing hydrocarbons incompletely. This transformation is accompanied by competitive inhibition of ammonia monooxygenase, the first key enzyme in nitrification. The effect of hydrocarbon pollution on soil nitrification was examined in situ. In a microcosm study, adding diesel fuel hydrocarbon to an uncontaminated soil (agricultural unfertilized soil) treated with ammonium sulfate dramatically reduced the amount of KCl-extractable nitrate but stimulated ammonium consumption. In a soil with long history of pollution that was treated with ammonium sulfate, 90% of the ammonium was transformed into nitrate after 3 weeks of incubation. Nitrate production was twofold higher in the contaminated soil than in the agricultural soil to which hydrocarbon was not added. To assess if ammonia-oxidizing bacteria acquired resistance to inhibition by hydrocarbon, the contaminated soil was reexposed to diesel fuel. Ammonium consumption was not affected, but nitrate production was 30% lower than nitrate production in the absence of hydrocarbon. The apparent reduction in nitrification resulted from immobilization of ammonium by hydrocarbon-stimulated microbial activity. These results indicated that the hydrocarbon inhibited nitrification in the noncontaminated soil (agricultural soil) and that ammonia-oxidizing bacteria in the polluted soil acquired resistance to inhibition by the hydrocarbon, possibly by increasing the affinity of nitrifying bacteria for ammonium in the soil.

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Ammonia-oxidizing archaea are integral to nitrogen cycling in a highly fertile agricultural soil

ISME Communications ◽

10.1038/s43705-021-00020-4 ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Laibin Huang ◽

Seemanti Chakrabarti ◽

Jennifer Cooper ◽

Ana Perez ◽

Sophia M. John ◽

...

Keyword(s):

Nitrogen Cycle ◽

Agricultural Soil ◽

Agricultural Soils ◽

Ammonia Oxidizing Bacteria ◽

Central Process ◽

Soil Nitrification ◽

Plant Nitrogen ◽

Ammonia Oxidizing Archaea ◽

Activity Measurements ◽

Nitrite Oxidizing Bacteria

AbstractNitrification is a central process in the global nitrogen cycle, carried out by a complex network of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Nitrification is responsible for significant nitrogen leaching and N2O emissions and thought to impede plant nitrogen use efficiency in agricultural systems. However, the actual contribution of each nitrifier group to net rates and N2O emissions remain poorly understood. We hypothesized that highly fertile agricultural soils with high organic matter mineralization rates could allow a detailed characterization of N cycling in these soils. Using a combination of molecular and activity measurements, we show that in a mixed AOA, AOB, and comammox community, AOA outnumbered low diversity assemblages of AOB and comammox 50- to 430-fold, and strongly dominated net nitrification activities with low N2O yields between 0.18 and 0.41 ng N2O–N per µg NOx–N in cropped, fallow, as well as native soil. Nitrification rates were not significantly different in plant-covered and fallow plots. Mass balance calculations indicated that plants relied heavily on nitrate, and not ammonium as primary nitrogen source in these soils. Together, these results imply AOA as integral part of the nitrogen cycle in a highly fertile agricultural soil.

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Nitrification exhibits Haldane kinetics in an agricultural soil treated with ammonium sulfate or dairy-waste compost

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2010.00960.x ◽

2010 ◽

Vol 74 (2) ◽

pp. 316-322 ◽

Cited By ~ 47

Author(s):

Teresa E. Koper ◽

John M. Stark ◽

Mussie Y. Habteselassie ◽

Jeanette M. Norton

Keyword(s):

Ammonium Sulfate ◽

Agricultural Soil ◽

Dairy Waste

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Operational modifications for the development of nitrifying bacteria in a large-scale biological aerated filter and its impact on wastewater treatment

Water Science & Technology ◽

10.2166/wst.2018.447 ◽

2018 ◽

Vol 78 (8) ◽

pp. 1704-1714 ◽

Cited By ~ 1

Author(s):

François-René Bourgeois ◽

Frédéric Monette ◽

Daniel G. Cyr

Keyword(s):

Large Scale ◽

Oxygen Demand ◽

Bacterial Biofilm ◽

Nitrifying Bacteria ◽

Nitrification Rate ◽

Total Biomass ◽

Ammonia Oxidizing Bacteria ◽

Operational Conditions ◽

Nitrite Oxidizing Bacteria ◽

Aerated Filter

Abstract To develop a better understanding for fixed biomass processes, the development of a nitrifying bacterial biofilm, as well as the performance of treatment during modifications to operational conditions of a full-scale submerged biological filter were examined. The development of the nitrifying biofilm was investigated at four depth levels (1, 2, 4 and 5 feet). The result of bacterial subpopulations analyzed by qPCR relative to the physico-chemical parameters of the wastewater during the various tests (sustained aeration, modified backwash parameters and inflow restriction) revealed an increase of the relative presence of nitrifying microorganisms throughout the biofilm (especially for nitrite oxidizing bacteria (NOB)), but this was not necessarily accompanied by a better nitrification rate. The highest observed nitrification rate was 49% of removal in the test cell during backwashing conditions, whereas the relative ammonia oxidizing bacteria (AOB) population was 0.032% and NOB was 0.008% of the total biomass collected. The highest percentage of nitrifying bacteria observed (0.034% AOB and 0.18% NOB) resulted in a nitrification rate of 21%. The treatment of organic matter determined by measuring the chemical and biochemical oxygen demand (COD, CBOD5) was improved.

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Bioremediation of Nickel and Lead contaminated soil by Vica faba L. plant and AM fungi Glomus mosseae

Baghdad Science Journal ◽

10.21123/bsj.12.2.260-265 ◽

2015 ◽

Vol 12 (2) ◽

pp. 260-265

Author(s):

Baghdad Science Journal

Keyword(s):

Root System ◽

Soil Pollution ◽

Contaminated Soil ◽

Glomus Mosseae ◽

Arbuscular Mycorrhizae ◽

Am Fungi ◽

Polluted Soil ◽

The South ◽

Shoot System ◽

North And South

This study is conducted to determine the activity of plant Vica faba and two isolated from arbuscular mycorrhizae fungi (A,B) in bioremediation of soil pollution by Nickel and Lead elements in north and south of Baghdad city. The results showed that the average of soil pollution by Nickel and Lead elements in north of Baghdad was less than the average of soil pollution in the south of Baghdad which recorded 29.0,9.0PPm and 42.0, 25.0PPm respectively. The results show that the isolate A from the polluted soil is more active from isolate B which isolate from unpolluted soil for bioremediation. Vica faba recorded more in accumulate the Lead element in shoot system which was 19.65PPm and in root system was 27.2PPm and for Nickel element 24.65, 27.55PPm in shoot and root respectively.

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Ammonia-oxidizing bacteria are more responsive than archaea to nitrogen source in an agricultural soil

Soil Biology and Biochemistry ◽

10.1016/j.soilbio.2016.01.012 ◽

2016 ◽

Vol 96 ◽

pp. 4-15 ◽

Cited By ~ 98

Author(s):

Yang Ouyang ◽

Jeanette M. Norton ◽

John M. Stark ◽

Jennifer R. Reeve ◽

Mussie Y. Habteselassie

Keyword(s):

Nitrogen Source ◽

Agricultural Soil ◽

Ammonia Oxidizing Bacteria

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Enrichment and Characterization of an Autotrophic Ammonia-Oxidizing Archaeon of Mesophilic Crenarchaeal Group I.1a from an Agricultural Soil

Applied and Environmental Microbiology ◽

10.1128/aem.05787-11 ◽

2011 ◽

Vol 77 (24) ◽

pp. 8635-8647 ◽

Cited By ~ 154

Author(s):

Man-Young Jung ◽

Soo-Je Park ◽

Deullae Min ◽

Jin-Seog Kim ◽

W. Irene C. Rijpstra ◽

...

Keyword(s):

16S Rrna ◽

Agricultural Soil ◽

Ammonia Oxidizing Bacteria ◽

Sequence Comparisons ◽

Soil Nitrification ◽

Content Type ◽

Group I ◽

Single Sequence

ABSTRACTSoil nitrification is an important process for agricultural productivity and environmental pollution. Though one cultivated representative of ammonia-oxidizingArchaeafrom soil has been described, additional representatives warrant characterization. We describe an ammonia-oxidizing archaeon (strain MY1) in a highly enriched culture derived from agricultural soil. Fluorescencein situhybridization microscopy showed that, after 2 years of enrichment, the culture was composed of >90% archaeal cells. Clone libraries of both 16S rRNA and archaealamoAgenes featured a single sequence each. No bacterialamoAgenes could be detected by PCR. A [13C]bicarbonate assimilation assay showed stoichiometric incorporation of13C intoArchaea-specific glycerol dialkyl glycerol tetraethers. Strain MY1 falls phylogenetically within crenarchaeal group I.1a; sequence comparisons to “CandidatusNitrosopumilus maritimus” revealed 96.9% 16S rRNA and 89.2%amoAgene similarities. Completed growth assays showed strain MY1 to be chemoautotrophic, mesophilic (optimum at 25°C), neutrophilic (optimum at pH 6.5 to 7.0), and nonhalophilic (optimum at 0.2 to 0.4% salinity). Kinetic respirometry assays showed that strain MY1's affinities for ammonia and oxygen were much higher than those of ammonia-oxidizing bacteria (AOB). The yield of the greenhouse gas N2O in the strain MY1 culture was lower but comparable to that of soil AOB. We propose that this new soil ammonia-oxidizing archaeon be designated “CandidatusNitrosoarchaeum koreensis.”

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Bioremediation by Cupriavidus metallidurans Strain MSR33 of Mercury-Polluted Agricultural Soil in a Rotary Drum Bioreactor and Its Effects on Nitrogen Cycle Microorganisms

Microorganisms ◽

10.3390/microorganisms8121952 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1952

Author(s):

Guillermo Bravo ◽

Paulina Vega-Celedón ◽

Juan Carlos Gentina ◽

Michael Seeger

Keyword(s):

Nitrogen Cycle ◽

Agricultural Soil ◽

Agricultural Soils ◽

Mercury Pollution ◽

Nitrifying Bacteria ◽

Innovative Technology ◽

Soil Bioremediation ◽

Nitrogen Fixing ◽

Cupriavidus Metallidurans ◽

Rotary Drum

Nitrogen cycle microorganisms are essential in agricultural soils and may be affected by mercury pollution. The aims of this study are to evaluate the bioremediation of mercury-polluted agricultural soil using Cupriavidus metallidurans MSR33 in a rotary drum bioreactor (RDB) and to characterize the effects of mercury pollution and bioremediation on nitrogen cycle microorganisms. An agricultural soil was contaminated with mercury (II) (20–30 ppm) and subjected to bioremediation using strain MSR33 in a custom-made RDB. The effects of mercury and bioremediation on nitrogen cycle microorganisms were studied by qPCR. Bioremediation in the RDB removed 82% mercury. MSR33 cell concentrations, thioglycolate, and mercury concentrations influence mercury removal. Mercury pollution strongly decreased nitrogen-fixing and nitrifying bacterial communities in agricultural soils. Notably, after soil bioremediation process nitrogen-fixing and nitrifying bacteria significantly increased. Diverse mercury-tolerant strains were isolated from the bioremediated soil. The isolates Glutamicibacter sp. SB1a, Brevundimonas sp. SB3b, and Ochrobactrum sp. SB4b possessed the merG gene associated with the plasmid pTP6, suggesting the horizontal transfer of this plasmid to native gram-positive and gram-negative bacteria. Bioremediation by strain MSR33 in an RDB is an attractive and innovative technology for the clean-up of mercury-polluted agricultural soils and the recovery of nitrogen cycle microbial communities.

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Experimental Study on Stabilization of Chromium Contaminated Soil

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.414.273 ◽

2011 ◽

Vol 414 ◽

pp. 273-279

Author(s):

Ji Da Chen ◽

Li Liu ◽

Li Wei Zhang ◽

Shi Guo Liao ◽

Yong Ting Song ◽

...

Keyword(s):

Experimental Study ◽

Contaminated Soil ◽

Critical Value ◽

Polluted Soil ◽

Pyrrolidine Dithiocarbamate ◽

Stabilization Method ◽

Toxicity Assay ◽

Long Time ◽

Stabilization Effect ◽

Ammonium Pyrrolidine Dithiocarbamate

To develope a practicable stabilization method for remediation chromium contaminated soil, reductant and chelate reagent were investigated for stabilization artificical chromium contaminated soil, and the stabilization effect was tested through extraction toxicity assay after stablized soil was oxidized at pH 12. The experimental results showed that the composition of sodium bisulfite & ammonium pyrrolidine dithiocarbamate was an ideal stabilizer of chromium in soil, and the extraction toxicity was much less than that of classical stabilized chromium polluted soil with only reductant or the maximum critical value in GB16889-2008, which suggested that the composition of reductant & compound of dithiocarbamate might be practically appllied for remediation chromium contaminated soil because it was likely to remain chromium much more stable in soil for a long time and significantly decrease Cr mobility.

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Partial nitrification of non-ammonium-rich wastewater within biofilm filters under ambient temperature

Water Science & Technology ◽

10.2166/wst.2010.424 ◽

2010 ◽

Vol 62 (7) ◽

pp. 1518-1525 ◽

Cited By ~ 1

Author(s):

Hongyu Wang ◽

Jiajie He ◽

Kai Yang

Keyword(s):

Activated Carbon ◽

Room Temperature ◽

Partial Nitrification ◽

Nitrifying Bacteria ◽

Ammonia Oxidizing Bacteria ◽

Filtration Process ◽

Porous Flow ◽

Activated Carbon Filter ◽

Carbon Filter ◽

Filter Layer

This study evaluated the partial nitrification performances of two biofilm filters over a synthetic non-ammonium-rich wastewater at a 20°C room temperature under both limited DO (∼2.0 mg/L) and unlimited DO (∼4.0 mg/L) conditions. The two filters were each of 80 cm long and used different biofilm carriers: activated carbon and ceramic granule. Results showed that partial nitrification was accomplished for both filters under the limited DO condition. However, the effluent NO2-N was higher in the ceramic granule filter than in the activated carbon filter, and was less susceptible to the influent COD/N changes. Further investigation into the water phase COD and NH4-N depth profiles and bacteria population within the two filters showed that by putting upper filter layer (upstream) to confront relatively higher influent COD/N ratios, the filtration process naturally put lower filter layers (downstream) relatively more favorable for nitrifying bacteria (ammonia oxidizing bacteria in this study) to prosper, making the filter depth left for nitrification a crucial factor for the effectiveness of nitrification with a filter. The potentially different porous flow velocities of the two filters might be the reason to cause their different partial nitrification performances, with a lower porous flow velocity (the ceramic granule filter) favoring partial nitrification more. In summation, DO, filter depth, and filtration speed should be played together to successfully operate a biofilm filter for partial nitrification.

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