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Cited by 10Soil Carbon and Nitrogen DynamicsWastewater Treatment and Nitrogen RemovalMicrobial Community Ecology and Physiology

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Investigating microbial and environmental drivers of nitrification in alkaline forest soil

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Poghosyan, Lianna, Lehtovirta-Morley, Laura E·2024·ISME Communications
DOI 10.1093/ismeco/ycae093PMC PMC11310595
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Abstract

Ammonia oxidation is a key step in the biogeochemical cycling of nitrogen, and soils are important ecosystems for nitrogen flux globally. Approximately 25% of the world’s soils are alkaline. While nitrification has been studied more extensively in agricultural alkaline soils, less is known about natural, unfertilized alkaline soils. In this study, microorganisms responsible for ammonia oxidation and several environmental factors (season, temperature, ammonia concentration, and moisture content) known to affect nitrification were studied in an alkaline forest soil with a pH ranging from 8.36 to 8.77. Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea, and comammox were present, and AOB belonging to genera Nitrosospira and Nitrosomonas, originally comprising <0.01% of the total bacterial community, responded rapidly to ammonia addition to the soil. No significant difference was observed in nitrification rates between seasons, but there was a significant difference between in situ field nitrification rates and rates in laboratory microcosms. Surprisingly, nitrification took place under many of the tested conditions, but there was no detectable increase in the abundance of any recognizable group of ammonia oxidizers. This study raises questions about the role of low-abundance microorganisms in microbial processes and of situations where zero or very low microbial growth coincides with metabolic activity. In addition, this study provides insights into nitrification in unfertilized alkaline soil and supports previous studies, which found that AOB play an important role in alkaline soils supplemented with ammonia, including agricultural ecosystems.

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Figure 1 The NOx− production (A–C) and nitrification rates (D–F) in soil microcosms following application of different treatments (temperature (A, D), moisture (B, E), ammonia concentration (C, F)), and comparing nitrification rates between seasons. Laboratory microcosms testing the effect of moisture and ammonia concentration (panels B, C, E, and F) were carried out using soil sampled in spring. The gravimetric water content in the ammonia-amended microcosms (C, F) was 16%. Additional data indicating the times at which ammonium was added to the microcosms are shown in the Supplementary Material. Data were presented as mean values with standard errors of the mean (n = 3). Nitrification in situ and in unamended microcosms depends on the production of ammonium from mineralization. As the soil is not water logged, and presumed to be aerobic, it is expected that little or no denitrification takes place under the tested conditions. Nitrification occurred throughout the incubations at approximately the same rate.
Figure 1 The NOx− production (A–C) and nitrification rates (D–F) in soil microcosms following application of different treatments (temperature (A, D), moisture (B, E), ammonia concentration (C, F)), and comparing nitrification rates between seasons. Laboratory microcosms testing the effect of moisture and ammonia concentration (panels B, C, E, and F) were carried out using soil sampled in spring. The gravimetric water content in the ammonia-amended microcosms (C, F) was 16%. Additional data indicating the times at which ammonium was added to the microcosms are shown in the Supplementary Material. Data were presented as mean values with standard errors of the mean (n = 3). Nitrification in situ and in unamended microcosms depends on the production of ammonium from mineralization. As the soil is not water logged, and presumed to be aerobic, it is expected that little or no denitrification takes place under the tested conditions. Nitrification occurred throughout the incubations at approximately the same rate.CC BY · PubMed Central
Figure 2 Abundance of AOA 16S rRNA, AOB, and comammox amoA genes in the alkaline forest soil microcosms in winter (January (Jan)) and spring (April (Apr)). Timepoints for the sampling are 0, 10, 20, and 30 days for all groups of nitrifiers. The error bars represent the standard error of the mean (n = 3).
Figure 2 Abundance of AOA 16S rRNA, AOB, and comammox amoA genes in the alkaline forest soil microcosms in winter (January (Jan)) and spring (April (Apr)). Timepoints for the sampling are 0, 10, 20, and 30 days for all groups of nitrifiers. The error bars represent the standard error of the mean (n = 3).CC BY · PubMed Central
Figure 3 Average relative abundance of nitrifying communities of bacteria (A) and archaea (B) in the soil microcosms incubated under different in situ and laboratory conditions including temperature, ammonia concentration, and water content. ASVs with the relative abundance of <0.01% of the total reads are not included in the analysis. ASV numbers correspond to the phylogenies shown in Figs S2–S5.
Figure 3 Average relative abundance of nitrifying communities of bacteria (A) and archaea (B) in the soil microcosms incubated under different in situ and laboratory conditions including temperature, ammonia concentration, and water content. ASVs with the relative abundance of <0.01% of the total reads are not included in the analysis. ASV numbers correspond to the phylogenies shown in Figs S2–S5.CC BY · PubMed Central

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References 85 · Cited by 10

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Metadata

Authors
Poghosyan, L., & Lehtovirta-Morley, L. E.
Affiliations
  • University of East Anglia (GB)
  • School of Biological Sciences, University of East Anglia , Norwich NR4 7TJ, United Kingdom
ORCID
Poghosyan, Lianna
Venue
ISME Communications
Publisher
Oxford University Press (OUP)
Published
2024-01
Volume
4
Issue
1
Pages
ycae093-ycae093
ISSN
2730-6151 (ISSN-L)
DOI
10.1093/ismeco/ycae093
PMC
PMC11310595
OpenAlex
W4400524406
Cited by
10
References
85
Citations by year
2026: 4 · 2025: 4 · 2024: 2
FWCI
1.99
Type
journal article
Language
en
Open access
Licence
Locations
  • ISME Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • UEA Digital Repository (University of East Anglia) (submittedVersion)
Funders
  • Royal Society Dorothy Hodgkin Fellowship (DH150187)
  • ERC Starting Grant (UNITY 852993)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Soil Science › Soil Carbon and Nitrogen Dynamics
  • Physical Sciences › Environmental Science › Pollution › Wastewater Treatment and Nitrogen Removal
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
nitrification, ammonia oxidation, alkaline soils, forest soils, ammonia-oxidizing bacteria, ammonia-oxidizing archaea, comammox, Nitrosospira, Nitrosomonas, nitrogen cycling, seasonal variation, soil moisture, ammonia addition

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Poghosyan, L., & Lehtovirta-Morley, L. E. (2024). Investigating microbial and environmental drivers of nitrification in alkaline forest soil. ISME Communications. https://doi.org/10.1093/ismeco/ycae093