Soil pH and phosphorus drive the canonical nitrifiers and comammox Nitrospira communities in citrus orchards with different cultivation ages

Highlights

● Comammox Nitrospira clade A and B showed contrasting responses to citrus planting.

● 54d9-like AOA and Nitrobacter -NOB dominated in the 5Y and 10Y soils.

● Nitrososphaera -like AOA and Nitrospira -like NOB dominated in the 20Y and 30Y soils.

● Soil pH and P content were the major factors shaping nitrifying communities.

Abstract

Ammonia oxidizing bacteria (AOB), archaea (AOA), nitrite oxidizing bacteria (NOB) and complete ammonia oxidizers (comammox Nitrospira) are major players in nitrification. However, the distribution and community composition of these nitrifiers in intensively managed orchard soils are still unclear. Here, we chose soil samples from citrus orchards that had been planted for 5 years (5Y), 10 years (10Y), 20 years (20Y) and 30 years (30Y), and adjacent woodland (NF), to study the response of nitrifiers to long-term citrus plantation using quantitative PCR and MiSeq sequencing. Our results revealed that the ammonia and nitrite oxidation potentials in the 5Y soil were the highest, and decreased with increasing plantation age. The AOB abundance was higher in 5Y and 10Y soils than that in 20Y and 30Y soils. The abundance of comammox Nitrospira clade A increased with increasing plantation age, but comammox Nitrospira clade B showed the opposite tendency. MiSeq sequencing results indicated 54d9-like AOA and Nitrobacter-NOB were the dominant populations in 5Y and 10Y soils whereas Nitrososphaera-like AOA and Nitrospira-like NOB dominated in 20Y and 30Y soils. The conversion of woodland to orchard resulted in a significant shift of AOB population from Nitrosospira cluster 3a.1 to cluster 3a.2. In addition, soil pH and phosphorus (P) content were the major factors shaping nitrifying communities. This work suggested citrus plantation altered the distribution of community composition of nitrifiers by affecting soil chemical and physical conditions, and comammox Nitrospira could potentially play an important role in nitrification in intensive managed orchard soils.

Graphical abstract

Keywords

AOB / AOA / comammox Nitrospira / NOB / soil pH / phosphorus content

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Acknowledgments

This work was supported by the National Key Research and Development Program of China (2021YFD1700900), the National Natural Science Foundation of China (42007033), the Scientific and Technological Key Projects of Henan Province (232102320117) and the Natural Science Foundation of Henan Province (222300420464).

Conflicts of interest

The authors do not have any personal, financial, or other conflicts of interest with other people or organizations that could inappropriately influence, or be perceived to influence, the submitted manuscript.

Author contributions

WFT designed the study; HYL wrote the manuscript; HYL, ZKT, WX and YYQ collected and analyzed the data; ZJN and HEL edited the manuscript. All authors contributed substantially to the discussion and the manuscript writing.

Electronic supplementary material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s42832-023-0199-x and is accessible for authorized users.

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