Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios

doi:10.1016/S1002-0160(19)60803-9

Pedosphere

Volume 30, Issue 1, February 2020, Pages 87-97

https://doi.org/10.1016/S1002-0160(19)60803-9 Get rights and content

Abstract

Long-term nitrogen (N) fertilization imposes strong selection on nitrifying communities in agricultural soil, but how a progressively changing niche affects potentially active nitrifiers in the field remains poorly understood. Using a 44-year grassland fertilization experiment, we investigated community shifts of active nitrifiers by DNA-based stable isotope probing (SIP) of field soils that received no fertilization (CK), high levels of organic cattle manure (HC), and chemical N fertilization (CF). Incubation of DNA-SIP microcosms showed significant nitrification activities in CF and HC soils, whereas no activity occurred in CK soils. The 44 years of inorganic N fertilization selected only ¹³C-ammonia-oxidizing bacteria (AOB), whereas cattle slurry applications created a niche in which both ammonia-oxidizing archaea (AOA) and AOB could be actively ¹³C-labeled. Phylogenetic analysis indicated that Nitrosospira sp. 62-like AOB dominated inorganically fertilized CF soils, while Nitrosospira sp. 41-like AOB were abundant in organically fertilized HC soils. The ¹³C-AOA in HC soils were affiliated with the 29i4 lineage. The ¹³C-nitrite-oxidizing bacteria (NOB) were dominated by both Nitrospira- and Nitrobacter-like communities in CF soils, and the latter was overwhelmingly abundant in HC soils. The ¹³C-labeled nitrifying communities in SIP microcosms of CF and HC soils were largely similar to those predominant under field conditions. These results provide direct evidence for a strong selection of distinctly active nitrifiers after 44 years of different fertilization regimes in the field. Our findings imply that niche differentiation of nitrifying communities could be assessed as a net result of microbial adaption over 44 years to inorganic and organic N fertilization in the field, where distinct nitrifiers have been shaped by intensified anthropogenic N input.

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Evidence for niche differentiation of nitrifying communities in grassland soils after 44 years of different field fertilization scenarios

Abstract

Soil Biol Biochem

Trends Microbiol

J Microbiol Methods

Appl Soil Ecol

Soil Biol Biochem

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes

Nat Commun

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

ISME J

Shifts between Nitrospira-and Nitrobacter-like nitrite oxidizers underlie the response of soil potential nitrite oxidation to changes in tillage practices

Environ Microbiol

Evaluating rRNA as an indicator of microbial activity in environmental communities: Limitations and uses

ISME J

Growth and death of bacteria and fungi underlie rainfall-induced carbon dioxide pulses from seasonally dried soil

Ecology

Oxidation of inorganic nitrogen compounds as an energy source

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

Proc Natl Acad Sci USA

Long term effects of slurry on grassland

Search and clustering orders of magnitude faster than BLAST

Bioinformatics

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea

FEMS Microbiol Rev

The global nitrogen cycle in the twenty-first century

Philos Trans Roy Soc B: Biol Sci

Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean

Proc Natl Acad Sci USA

Influence of inorganic nitrogen management regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils

Appl Environ Microbiol

Niche specialization of terrestrial archaeal ammonia oxidizers

Proc Natl Acad Sci USA

Diversity, physiology, and niche differentiation of ammonia-oxidizing archaea

Appl Environ Microbiol

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices

Environ Microbiol

Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil

Environ Microbiol