Salt tolerance-based niche differentiation of soil ammonia oxidizers

Abstract

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined 13C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmolc exchangeable Na+ kg−1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of “Candidatus Nitrosococcus sp. Sol14”, a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na+ extrusion/H+ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na+ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

Metagenomic analysis of the soil microbial composition and salt tolerance mechanism in Yuncheng Salt Lake, Shanxi Province

“…Halophilic microorganisms evolved in high salt environments. To understand resistance to the high osmotic pressure present in high salt environments ( Sun X. et al, 2021 ), we investigated mechanisms halophilic bacteria use to adapt to their extreme environment. At present, there are two mechanisms used by halophilic bacteria to cope with high salt: the first is the internal salt mechanism.…”

Facilitating Growth of Maize (Zea mays L.) by Biostimulants: A Perspective from the Interaction between Root Transcriptome and Rhizosphere Microbiome

“…49 Alcanivorax are alkane-degrading bacteria, 50 and their existence in rhizosphere of Calotropis procera was verified to be involved in helping the plant to defend against pathogens. 51 Nitrosococcus are well-documented ammoniaoxidizing bacteria widely found in wastewater, 52 soil, 53 and rhizosphere, 54 which convert ammonia to nitrate so that it can be utilized by plants. 55 The two fungal OTUs, Mortierella and Talaromyces, are well recognized as plant growth-promoting fungi.…”

The ‘microbiome counterattack’: Insights on the soil and root‐associated microbiome in diverse chickpea and lentil genotypes after an erratic rainfall event

“…Elsa lentil root samples were characterized by the Nitrosococcaceae family. These are ammonia oxidizers usually associated with saline aquatic habitats; however, they have also been reported in soils (Pan et al, 2018; Sun et al, 2022). The Eston unique prokaryotic community was the most reduced in terms of the number of prokaryotic families in comparison with the other genotypes (showing just two specific families) and included the Obscuribacteraceae family, phylogenetically related to Cyanobacteria.…”