Salinity changes the nitrification activity and community composition of comammox
Nitrospira
in intertidal sediments of Yangtze River estuary
Authors: Jiang Ran , Qin Wen-Jing , Zhang Ru-Yi , Zhang Kai , Huang Xing , Li Yong , Zhou Chen-Hao , Zhu Ting , Zhang Yan , Zou Bin , Nie Ming , Rhee Sung-Keun , Quan Zhe-Xue 
Published: June 2023

The newly discovered complete ammonia-oxidizing (comammox)
Nitrospira
has been identified in different environments, including coastal environments, where salinity is one of the most important factors for the abundance and activity of nitrifiers. Here, we demonstrate the effect of salinity on comammox
Nitrospira
, canonical ammonia-oxidizing bacteria (AOB), and ammonia-oxidizing archaea (AOA) in the intertidal sediments of the Yangtze River estuary based on microcosm experiments, DNA stable-isotope probing (DNA-SIP), and potential ammonium-oxidation rate (PAR) tests for different groups of ammonia oxidizers with selective inhibitors. During microcosm incubations, the abundance of comammox
Nitrospira
was more sensitive to increased salinity than that of other ammonia oxidizers. The results obtained with DNA-SIP heavy fractions showed that the dominant phylotype in clade A.2 (containing genes involved in the adaptation to haloalkaline environments) had high proportions in comammox
Nitrospira
community under both freshwater (0.06% salinity) and highly saline water (3% salinity) conditions. In contrast, another phylotype of clade A.2 (which lacks these genes) was dominant only under freshwater conditions. The PARs confirmed that comammox
Nitrospira
presented greater contributions to nitrification under freshwater conditions with a PAR of 4.37 ± 0.53 mg N·day
–1
·kg soil
–1
(54%) than under saline water conditions with a PAR of 0.60 ± 0.94 mg N·day
–1
·kg soil
–1
(18%). Moreover, AOA were specific to saline water conditions, whereas AOB were common under both freshwater and saline water conditions (44% and 52%, respectively). The present study provided evidence that salinity markedly affects the activity of comammox
Nitrospira,
and that the salt sensitivity of different phylotypes varies.

IMPORTANCE

Complete ammonia oxidation (comammox) is a newly discovered type of nitrification through which ammonia is oxidized to nitrate in an organism. Comammox
Nitrospira
were abundantly found in coastal ecosystems and demonstrated high community diversity. Changes in salinity are considered one of the most important factors to comammox
Nitrospira
in coastal ecosystems; however, reports on the correlation between them remain inconsistent. Therefore, it is critical to experimentally determine the influence of salinity on comammox
Nitrospira
in the coastal ecosystem. This study demonstrated a clear effect of salinity on the abundance, activity, and relative contribution of different ammonia oxidizers, especially for comammox
Nitrospira
. To the best of our knowledge, this is the first study demonstrating comammox
Nitrospira
activity at seawater salinities, implying the existence of a salt-tolerant type comammox
Nitrospira
, despite its activity being much lower than in freshwater conditions. The indicated correlation between the activity of specific comammox
Nitrospira
and salinity is anticipated to provide insights into the distribution of comammox
Nitrospira
and their potential contributions in estuaries and coastal ecosystems.