Salinity changes the nitrification activity and community composition of comammox Nitrospira in intertidal sediments of Yangtze River estuary

Abstract

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.

Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications

“…Sediment microbial community structure also varied between sinkholes and only the sulfate‐reducing bacteria (SRB) belonging to the genus Desulfatiglans (Suzuki et al, 2014 ) was abundant in both sinkholes. The 16S rRNA genes recovered from the PolAc54M metagenome and the taxonomic annotation of metagenomic reads suggest there is a high abundance of families associated with sulfate reduction (Desulfobulbaceae, Desulfobacteraceae, Desulfatiglandaceae, Desulfosarcinaceae, Desulfobaccaceae, Desulfococcaceae) (Suárez‐Moo et al, 2022 ; Zhang et al, 2022 ), and genera associated with ammonia oxidation ( Nitrospira ) (Jiang et al, 2023 ) and denitrification ( Pseudomonas and Bacillus ) (Arat et al, 2015 ; Yang et al, 2020 ). Though the investigation of microbial communities and their role in biogeochemical cycles were not the goals of this study, it is interesting to highlight that the presence of these microorganisms in sinkhole environments suggests they hold important roles in sulfate reduction, ammonia oxidation, and denitrification (Suárez‐Moo et al, 2022 ).…”

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers

“…24 Although occasionally detected, complete ammonia oxidizers (comammox) are generally less active and abundant than AOA and AOB in intertidal zones. 25 ally, AOA typically dominate archaeal communities in estuarine sediments 26,27 and exhibit higher diversity than AOB. 28 However, due to cultivation challenges and lack of genomic information, the full phylogenetic diversity, novelty, and functional features of AOA remain largely unexplored in intertidal aquifers under periodic oxic-anoxic conditions.…”