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

2016 ◽  
Vol 96 ◽  
pp. 4-15 ◽  
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

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

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.

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

2011 ◽  
Vol 77 (24) ◽  
pp. 8635-8647 ◽  
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.”

Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil

2008 ◽  
Vol 40 (1) ◽  
pp. 13-18 ◽  
Author(s):  
T.R. Cavagnaro ◽  
L.E. Jackson ◽  
K. Hristova ◽  
K.M. Scow
Keyword(s):  
Population Dynamics ◽  
Agricultural Soil ◽  
Ammonia Oxidizing Bacteria ◽  
Short Term

Analysis of Nitrification in Agricultural Soil and Improvement of Nitrogen Circulation with Autotrophic Ammonia-Oxidizing Bacteria

2012 ◽  
Vol 169 (3) ◽  
pp. 795-809 ◽  
Author(s):  
Toshihide Matsuno ◽  
Sachie Horii ◽  
Takanobu Sato ◽  
Yoshiki Matsumiya ◽  
Motoki Kubo
Keyword(s):  
Agricultural Soil ◽  
Ammonia Oxidizing Bacteria

Multidimensional Reveal of Nitrogen Regulation on Comammox

2020 ◽  
Author(s):  
Yuxiang Zhao ◽  
Jiajie Hu ◽  
Weiling Yang ◽  
Jiaqi Wang ◽  
Zhongjun Jia ◽  
...  
Keyword(s):  
Nitrogen Source ◽  
Nitrate Reduction ◽  
Ammonia Oxidation ◽  
Enrichment Culture ◽  
Ammonia Oxidizer ◽  
Nitrification Rate ◽  
Ammonia Oxidizing Bacteria ◽  
Metagenomic Sequencing ◽  
Sole Nitrogen Source ◽  
Total Bacteria

Abstract Background The discovery of complete ammonia oxidizer (comammox) was groundbreaking. Comammox can use ammonia as the sole nitrogen source and turn it to nitrate. Moreover, genomic data indicated that comammox contained genes which can metabolize urea and nitrite. However, the feasibility of enriching comammox with urea and nitrite in long term has not been proved. This study enriched comammox’s culture by using nitrite in reactor SA and urea in reactor SB. Results The nitrification rate of reactor SB (1.29 mg N·g -1 biofilm · d -1 ) was higher than that in reactor SA (0.6 mg N · g -1 biofilm · d -1 ) at the 390 th day. Comammox outnumbered ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in both reactor SA (9.04 × 10 9 copies / g biofilm) and reactor SB (5.34×10 10 copies/ g biofilm). In reactor SA, comammox’s amoA accounted for 92% of the total amoA, which was higher than that in reactor SB (85%). However, the percentage of comammox (4%) in total bacteria was much lower than reactor SB (14%). The results of metagenomic sequencing showed that all the pathways of nitrogen cycle including nitrification, nitrogen fixation, denitrification, assimilation nitrate reduction, and dissimilation nitrate reduction can be detected in both reactor SA and reactor SB except the anammox pathway. The genes related to nitrite oxidation and nitrate reduction in reactor SA (TPM = 5099; TPM = 3329) was higher than that of in reactor SB (TPM = 4071; TPM = 2984), presumably due to the demand of turning nitrite to nitrate and turning nitrate to ammonia. While genes related to ammonia oxidation and urea metabolism in reactor SB (TPM = 3915; TPM = 3638) was higher than that in reactor SA (TPM = 2708; TPM = 3002). Conclusion Nitrite and urea can regulate the enrichment culture of comammox by converting its metabolic pathway. Using nitrite as sole nitrogen source can improve the proportion comammox’s amoA in total amoA while using urea as the sole nitrogen source may increase comammox’s proportion in total bacteria. These results can accelerate the enrichment of comammox and facilitate the promotion of comammox’s engineering operation.

Ammonia‐oxidizing bacteria are the primary N 2 O producers in an ammonia‐oxidizing archaea dominated alkaline agricultural soil

2018 ◽  
Vol 20 (6) ◽  
pp. 2195-2206 ◽  
Author(s):  
Kelley A. Meinhardt ◽  
Nejc Stopnisek ◽  
Manmeet W. Pannu ◽  
Stuart E. Strand ◽  
Steven C. Fransen ◽  
...  
Keyword(s):  
Agricultural Soil ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea

scholarly journals Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil

2011 ◽  
Vol 77 (18) ◽  
pp. 6551-6558 ◽  
Author(s):  
John J. Kelly ◽  
Katherine Policht ◽  
Tanya Grancharova ◽  
Lakhwinder S. Hundal
Keyword(s):  
Agricultural Soil ◽  
Terrestrial Ecosystems ◽  
Gene Copy ◽  
Ecological Niches ◽  
Corn Yield ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Synthetic Fertilizer ◽  
Gene Copy Numbers

ABSTRACTThe recently discovered ammonia-oxidizing archaea (AOA) have been suggested as contributors to the first step of nitrification in terrestrial ecosystems, a role that was previously assigned exclusively to ammonia-oxidizing bacteria (AOB). The current study assessed the effects of agricultural management, specifically amendment of soil with biosolids or synthetic fertilizer, on nitrification rates and copy numbers of archaeal and bacterial ammonia monooxygenase (amoA) genes. Anaerobically digested biosolids or synthetic fertilizer was applied annually for three consecutive years to field plots used for corn production. Biosolids were applied at two loading rates, a typical agronomic rate (27 Mg hectare−1year−1) and double the agronomic rate (54 Mg hectare−1year−1), while synthetic fertilizer was applied at an agronomic rate typical for the region (291 kg N hectare−1year−1). Both biosolids amendments and synthetic fertilizer increased soil N and corn yield, but only the biosolids amendments resulted in significant increases in nitrification rates and increases in the copy numbers of archaeal and bacterialamoAgenes. In addition, only archaealamoAgene copy numbers increased in response to biosolids applied at the typical agronomic rate and showed a significant correlation with nitrification rates. Finally, copy numbers of archaealamoAgenes were significantly higher than copy numbers of bacterialamoAgenes for all treatments. These results implicate AOA as being primarily responsible for the increased nitrification observed in an agricultural soil amended with biosolids. These results also support the hypothesis that physiological differences between AOA and AOB may enable them to occupy distinct ecological niches.

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