Nitrapyrin affects the abundance of ammonia oxidizers rather than community structure in a yellow clay paddy soil

ABSTRACT The effect of ammonium addition (6.5, 58, and 395 μg of NH4 +-N g [dry weight] of soil−1) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N2O release rates and a shift toward a higher contribution of nitrification to N2O release occurred after incubation for 5 days at 4°C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the small subunit of ammonia monooxygenase. The DGGE fingerprints were invariably the same whether the soil was untreated or incubated with low, medium, or high ammonium concentrations. Phylogenetic analysis of cloned PCR products from excised DGGE bands detected amoA sequences which probably belonged to Nitrosospira 16S rRNA clusters 3 and 4. Additional clones clustered with Nitrosospira sp. strains Ka3 and Ka4 and within an amoA cluster from unknown species. A Nitrosomonas-like amoA gene was detected in only one clone. In agreement with the amoA results, community profiles of total bacteria analyzed by terminal restriction fragment length polymorphism (T-RFLP) showed only minor differences. However, a community shift occurred for denitrifier populations based on T-RFLP analysis of nirK genes encoding copper-containing nitrite reductase with incubation at medium and high ammonia concentrations. Major terminal restriction fragments observed in environmental samples were further described by correspondence to cloned nirK genes from the same soil. Phylogenetic analysis grouped these clones into clusters of soil nirK genes. However, some clones were also closely related to genes from known denitrifiers. The shift in the denitrifier community was probably the consequence of the increased supply of oxidized nitrogen through nitrification. Nitrification activity increased upon addition of ammonium, but the community structure of ammonium oxidizers did not change.

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Diversity and community structure of ammonia oxidizers in a marsh wetland of the northeast China

Applied Microbiology and Biotechnology ◽

10.1007/s00253-018-9225-9 ◽

2018 ◽

Vol 102 (19) ◽

pp. 8561-8571 ◽

Cited By ~ 3

Author(s):

Dawen Gao ◽

Fengqin Liu ◽

Lu Li ◽

Chuhong Chen ◽

Hong Liang

Keyword(s):

Community Structure ◽

Northeast China ◽

Ammonia Oxidizers ◽

Marsh Wetland

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Variations of Abundance and Community Structure of Ammonia Oxidizers and Nitrification Activity in Two Paddy Soils Polluted by Heavy Metals

Geomicrobiology Journal ◽

10.1080/01490451.2018.1471108 ◽

2018 ◽

Vol 36 (1) ◽

pp. 1-10

Author(s):

Yuan Liu ◽

Chen Xue ◽

Shirui Yu ◽

Feng Li

Keyword(s):

Heavy Metals ◽

Community Structure ◽

Paddy Soils ◽

Ammonia Oxidizers ◽

Nitrification Activity

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Spatio-temporal variability of microbial abundance and community structure in the puddled layer of a paddy soil cultivated with wetland rice (Oryza sativa L.)

Applied Soil Ecology ◽

10.1016/j.apsoil.2013.06.002 ◽

2013 ◽

Vol 72 ◽

pp. 93-102 ◽

Cited By ~ 24

Author(s):

Hannes Schmidt ◽

Thilo Eickhorst

Keyword(s):

Oryza Sativa ◽

Community Structure ◽

Paddy Soil ◽

Temporal Variability ◽

Oryza Sativa L ◽

Wetland Rice ◽

Microbial Abundance ◽

Spatio Temporal

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Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions

10.1101/2020.07.21.205765 ◽

2020 ◽

Author(s):

Ruth Schmidt ◽

Xiao-Bo Wang ◽

Paolina Garbeva ◽

Étienne Yergeau

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Communities ◽

Microbial Community Structure ◽

Fungal Community ◽

Soil Microbial Community ◽

Ammonia Oxidizers ◽

Soil Microbial Community Structure ◽

Soil Microbial ◽

Fungal Community Structure

AbstractNitrapyrin is one of the most common nitrification inhibitors that are used to retain N in the ammonia form in soil to improve crop yields and quality. Whereas the inhibitory effect of nitrapyrin is supposedly specific to ammonia oxidizers, in view of the keystone role of this group in soils, nitrapyrin could have far-reaching impacts. Here, we tested the hypothesis that nitrapyrin leads to large shifts in soil microbial community structure, composition, diversity and functions, beyond its effect on ammonia-oxidizers. To test this hypothesis, we set-up a field experiment where wheat (Triticum aestivum cv. AC Walton) was fertilized with ammonium nitrate (NH4NO3) and supplemented or not with nitrapyrin. Rhizosphere and bulk soils were sampled twice, DNA was extracted, the 16S rRNA gene and ITS region were amplified and sequenced to follow shifts in archaeal, bacterial and fungal community structure, composition and diversity. To assess microbial functions, several genes involved in the nitrogen cycle were quantified by real-time qPCR and volatile organic compounds (VOCs) were trapped in the rhizosphere at the moment of sampling. As expected, sampling date and plant compartment had overwhelming effects on the microbial communities. However, within these strong effects, we found statistically significant effects of nitrapyrin on the relative abundance of Thaumarchaeota, Proteobacteria, Nitrospirae and Basidiomycota, and on several genera. Nitrapyrin also significantly affected bacterial and fungal community structure, and the abundance of all the N-cycle gene tested, but always in interaction with sampling date. In contrast, nitrapyrin had no significant effect on the emission of VOCs, where only sampling date significantly influenced the profiles observed. Our results point out far-reaching effects of nitrapyrin on soil and plant associated microbial communities, well beyond its predicted direct effect on ammonia-oxidizers. In the longer term, these shifts might counteract the positive effect of nitrapyrin on crop nutrition and greenhouse gas emissions.

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