Cargando…
Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China
The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox N...
Autores principales: | , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9929954/ https://www.ncbi.nlm.nih.gov/pubmed/36819044 http://dx.doi.org/10.3389/fmicb.2023.1095937 |
_version_ | 1784888961097793536 |
---|---|
author | Wang, Yanan Zeng, Xibai Ma, Qiang Zhang, Yang Yu, Wantai Zheng, Zhong Zhang, Nan Xu, Liyang |
author_facet | Wang, Yanan Zeng, Xibai Ma, Qiang Zhang, Yang Yu, Wantai Zheng, Zhong Zhang, Nan Xu, Liyang |
author_sort | Wang, Yanan |
collection | PubMed |
description | The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0–20 cm, topsoil; 20–40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH(4)(+)-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH(4)(+)-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems. |
format | Online Article Text |
id | pubmed-9929954 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-99299542023-02-16 Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China Wang, Yanan Zeng, Xibai Ma, Qiang Zhang, Yang Yu, Wantai Zheng, Zhong Zhang, Nan Xu, Liyang Front Microbiol Microbiology The newly identified complete ammonia oxidizer (comammox) that converts ammonia directly into nitrate has redefined the long-held paradigm of two-step nitrification mediated by two distinct groups of nitrifiers. However, exploration of the niche differentiation of canonical nitrifiers and comammox Nitrospira and their ecological importance in agroecosystems is still limited. Here, we adopted quantitative PCR (qPCR) and Illumina MiSeq sequencing to investigate the effects of five long-term fertilization regimes in the variations of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), nitrite-oxidizing bacteria (NOB), and comammox Nitrospira abundances and comammox community composition in two soil layers (0–20 cm, topsoil; 20–40 cm, subsoil) in an Alfisol in Northeast China. The fertilization treatments included no fertilizer (CK); chemical nitrogen (N) fertilizer; chemical N; phosphorus (P) and potassium (K) fertilizers (NPK); recycled organic manure (M) and chemical N, P, K plus recycled manure (MNPK). Compared with CK, manure and/or chemical fertilizer significantly increased the AOB amoA gene abundance. Long-term recycled manure increased soil organic matter (SOM) contents and maintained the soil pH, but decreased the NH(4)(+)-N concentrations, which markedly promoted the nxrA and nxrB gene abundances of NOB and the amoA gene abundances of comammox Nitrospira clade A and AOA. Although the comammox Nitrospira clade B abundance tended to decrease after fertilization, the structural equation modeling analysis showed that comammox clade B had direct positive impacts on soil potential ammonia oxidation (PAO; λ = 0.59, p < 0.001). The long-term fertilization regime altered the community composition of comammox Nitrospira. Additionally, comammox Nitrospira clades A and B had individual response patterns to the soil layer. The relative abundance of clade A was predominant in the topsoil in the N (86.5%) and MNPK (76.4%) treatments, while clade B appeared to be dominant in the subsoil (from 78.7 to 88.1%) with lower ammonium contents, implying niche separation between these clades. Soil pH, NH(4)(+)-N and SOM content were crucial factors shaping the soil nitrifying microbial abundances and the comammox Nitrospira community. Together, these findings expand the current understanding of the niche specialization and the important role of comammox Nitrospira in terrestrial ecosystems. Frontiers Media S.A. 2023-02-01 /pmc/articles/PMC9929954/ /pubmed/36819044 http://dx.doi.org/10.3389/fmicb.2023.1095937 Text en Copyright © 2023 Wang, Zeng, Ma, Zhang, Yu, Zheng, Zhang and Xu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Wang, Yanan Zeng, Xibai Ma, Qiang Zhang, Yang Yu, Wantai Zheng, Zhong Zhang, Nan Xu, Liyang Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title | Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title_full | Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title_fullStr | Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title_full_unstemmed | Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title_short | Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China |
title_sort | differential responses of canonical nitrifiers and comammox nitrospira to long-term fertilization in an alfisol of northeast china |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9929954/ https://www.ncbi.nlm.nih.gov/pubmed/36819044 http://dx.doi.org/10.3389/fmicb.2023.1095937 |
work_keys_str_mv | AT wangyanan differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT zengxibai differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT maqiang differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT zhangyang differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT yuwantai differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT zhengzhong differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT zhangnan differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina AT xuliyang differentialresponsesofcanonicalnitrifiersandcomammoxnitrospiratolongtermfertilizationinanalfisolofnortheastchina |