Niche specialization of comammox <i>Nitrospira</i> in terrestrial ecosystems: Oligotrophic or copiotrophic?

Li, Chaoyu; He, Zhou; Hu, Hang‐Wei; He, Ji‐Zheng

doi:10.1080/10643389.2022.2049578

Cited by 41 publications

(16 citation statements)

References 73 publications

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“…3). The relatively high abundance of comammox Nitrospira in fertile irrigated dairy land suggests that comammox Nitrospira found in terrestrial ecosystems may be copiotrophic (Li et al, 2022).…”

Section: Discussionmentioning

confidence: 99%

Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Chisholm

Di²,

Cameron³

et al. 2023

Science of The Total Environment

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Section: Discussionmentioning

confidence: 99%

Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Chisholm

Di²,

Cameron³

et al. 2023

Science of The Total Environment

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“…With the discovery and prevailing occurrence of comammox Nitrospira in engineered, coastal and terrestrial environments ( Li et al, 2022 ; Zhu et al, 2022 ), our previous knowledge about the niche differentiation of different nitrifiers and their relative contribution to nitrification in agricultural ecosystems need to be reconsidered. Distinct fertilization effects on canonical nitrifier abundance and community structure have been reported in many previous studies ( He et al, 2007 ; Wang et al, 2019 ; Lin et al, 2020 ; Cai et al, 2021 ), and our study further confirmed this information.…”

Section: Discussionmentioning

confidence: 99%

“…The theoretical ammonia concentration in the soil aqueous solution based on the ionization equilibrium ranged from 400 to 14,270 nM ( Supplementary Table S4 ), which facilitated the growth of both AOA and AOB with optimal survival ammonia concentrations ranging from 0.007 to 1,220 nM and 6,730 to 323,000 nM, respectively ( He et al, 2012 ; Hu et al, 2014 ). Obviously, AOB are better adapted to soils with relatively high ammonia concentrations due to their higher maximum activity and half-saturation constant value for ammonia than AOA ( Hu et al, 2014 ; Li et al, 2022 ). ABT analysis demonstrated that AOB abundance was positively correlated with the soil TN and NH 4 + -N contents, while AOA abundance was significantly and negatively correlated with the NH 4 + -N content ( Supplementary Figure S1 ).…”

Section: Discussionmentioning

confidence: 99%

Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China

Wang

Zeng

et al. 2023

Front. Microbiol.

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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 NH4+-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, NH4+-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.

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“…In addition, the recent discovery of complete ammonia oxidizers, comammox Nitrospira which perform both steps of nitrification, has significantly changed our perspective on the nitrification. The complete genomes of comammox organisms possess the full set of genes encoding ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase for ammonia oxidation, and genes encoding nitrite oxidoreductase for nitrite oxidation, indicating their genetic potential to utilize both ammonia and nitrite as energy sources (Daims et al, 2015; Li et al, 2022; van Kessel et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…The complete genomes of comammox organisms possess the full set of genes encoding ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase for ammonia oxidation, and genes encoding nitrite oxidoreductase for nitrite oxidation, indicating their genetic potential to utilize both ammonia and nitrite as energy sources (Daims et al, 2015;Li et al, 2022;van Kessel et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments

et al. 2022

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1. A better understanding of how nitrogen (N) cycling genes are involved in ecological processes is one of the crucial areas of microbial ecology. Currently, most molecular biological techniques investigating N cycling genes in the environment heavily rely on the accuracy of the polymerase chain reaction (PCR) primers; however, their specificity and coverage have not been comprehensively evaluated.Here, we collected a sequence database, NcycFunGen, aimed for primer evaluation and redesign.2. NcycFunGen was based on hidden Markov model profiles for 22 marker genes involved in N cycling, which included 607,359 paired nucleotide and protein sequences with their taxonomic information. Then, a total of 608 published primers were fully evaluated through NcycFunGen, as well as against full-length sequences collected from KEGG. The new primers were designed by DegePrime.In the experiment, the updated ureC gene primer pair ureC607F/ureC898R and nifH gene primer pair nifH107F64/nifH379R64 was applied to a urea amendment site using droplet digital PCR and high-throughput amplicon sequencing.3. The results showed that the majority of primer pairs cover less than 30% sequences of target genes and that 22.55% were inappropriate for quantitative PCR and amplicon sequencing (<100 bp or >550 bp). In general, this in-silico evaluation demonstrated that although many primers have been adopted in published studies, some of them should be validated and updated as needed according to the updated gene database. Therefore, new degenerate primer pairs for ureC | 1977Methods in Ecology and Evoluঞon WANG et al.

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Niche specialization of comammox Nitrospira in terrestrial ecosystems: Oligotrophic or copiotrophic?

Cited by 41 publications

References 73 publications

Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Soil moisture is a primary driver of comammox Nitrospira abundance in New Zealand soils

Differential responses of canonical nitrifiers and comammox Nitrospira to long-term fertilization in an Alfisol of Northeast China

Evaluation and redesign of the primers for detecting nitrogen cycling genes in environments

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