Comammox Nitrospira Clade B is the most abundant complete ammonia oxidizer in a dairy pasture soil and inhibited by dicyandiamide and high ammonium concentrations

Abstract

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94-day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha–1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

“…Soil samples were collected in Autumn 2021 from the Lincoln University Research Dairy Farm (LURDF) (43°38′26″ S, 172°26′37″ E) located on the South Island of New Zealand. This was the same study site used by Hsu et al (2022) . The area was excluded from grazing for at least 6 months before the sample collection.…”

“…Soil microcosms were set up similarly to those described in Hsu et al (2022) . Briefly, 585 g of soil (500 g dry soil equivalent) was placed into polypropylene plastic containers (1 L volume).…”

“…Details of PCR primers and amplification efficiencies observed for all genes are listed in Table 1 (thermal profiles and reaction details are in Supplementary data S2 ). Standards for each gene (plasmid DNA) used in the qPCR analysis were prepared as outlined previously ( Hsu et al, 2022 ). Standard curves for each gene quantification were generated using a series of 1:10 dilutions of amplicon standards over a range of concentrations from 10 1 to 10 7 copies per microlitre.…”

“…Furthermore, comammox Nitrospira can be separated into clade A and clade B based on the phylogeny of the amoA gene, a subunit of AMO. Since their discovery, extensive research has been conducted on the ecology and abundance of comammox Nitrospira in terrestrial ecosystems worldwide ( Shi et al, 2018 ; Zhao et al, 2019 ; Xu et al, 2020 ; Li et al, 2021 ; Sun et al, 2021 ; Wang et al, 2021 ; Hsu et al, 2022 ; Chisholm et al, 2023 ). Some studies suggest that comammox Nitrospira actively contributes to the nitrification process in a nutrient rich environment ( Li et al, 2019 ; Xu et al, 2020 ).…”

“…However, the comammox Nitrospira community in these ecosystems is dominated by clade A, with clade B typically being undetectable. To date, the comammox Nitrospira community found in New Zealand soils consists almost entirely of clade B ( Hsu et al, 2022 ; Chisholm et al, 2023 ).…”