Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

Ian M Clark,Maïder Abadie,Qingling Fu,David J Hughes,Penny R Hirsch

doi:10.1038/s41598-021-95100-9

Ian M Clark, Maïder Abadie + Show 3 more

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https://doi.org/10.1038/s41598-021-95100-9

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Abstract

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes—permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soil from the experimental sites (microcosms amended or not with DCD at concentrations inhibitory to AOB but not AOA), was highest in arable samples and lower in all assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils.

Highlights

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes—permanent bare fallow, grassland, and arable cultivation maintained for more than 50 years
Our previous finding, based on 16S rRNA amplicon sequencing, indicated that ammonia oxidizing archaea (AOA) constitute a higher proportion of the microbial community in tilled soils than undisturbed a reas[18] and that the Nitrospira were more abundant than the AOA, with highest numbers in the arable p lots[36]
The AOA and Ammonia oxidizing bacteria (AOB) were more abundant in the Highfield arable soils compared to grassland and bare fallow, using qPCR, where ~ 5 × 1 06 copies of AOA-amoA and AOB-amoA g-1 dry arable soil with fewer in the other p lots[36]

Summary

Introduction

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted field plots under contrasting management regimes—permanent bare fallow, grassland, and arable (wheat) cultivation maintained for more than 50 years. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome; AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Ammonia oxidizing bacteria (AOB) belong to the betaproteobacterial family Nitrosomonadaceae and the gammaproteobacterial genera Candidatus Nitrosoglobulus terrae and Nitrosococcus[7,8]. They are obligate chemoautotrophs that use type I RuBisCO to fix C O2 via the Calvin cycle and grow very slowly in laboratory culture as a consequence of the low energy yield from oxidation of ammonia[2,7]. Other groups that oxidize ammonia using different mechanisms are the anaerobic ammonia oxidizing (anammox) Planctomycetes in marine environments and wastewater[23] and certain heterotrophic bacteria and fungi in acid soils[24]

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