From rags to enriched: metagenomic insights into ammonia‐oxidizing archaea following ammonia enrichment of a denuded oligotrophic soil ecosystem

Abstract

Summary Stored topsoil acts as a microbial inoculant for ecological restoration of land after disturbance, but the altered circumstances frequently create unfavourable conditions for microbial survival. Nitrogen cycling is a critical indicator for ecological success and this study aimed to investigate the cornerstone taxa driving the process. Previous in silico studies investigating stored topsoil discovered persistent archaeal taxa with the potential for re‐establishing ecological activity. Ammonia oxidization is the limiting step in nitrification and as such, ammonia‐oxidizing archaea (AOA) can be considered one of the gatekeepers for the re‐establishment of the nitrogen cycle in disturbed soils. Semi‐arid soil samples were enriched with ammonium sulfate to promote the selective enrichment of ammonia oxidizers for targeted genomic recovery, and to investigate the microbial response of the microcosm to nitrogen input. Ammonia addition produced an increase in AOA population, particularly within the genus Candidatus Nitrosotalea, from which metagenome‐assembled genomes (MAGs) were successfully recovered. The Ca. Nitrosotalea archaeon candidates' ability to survive in extreme conditions and rapidly respond to ammonia input makes it a potential bioprospecting target for application in ecological restoration of semi‐arid soils and the recovered MAGs provide a metabolic blueprint for developing potential strategies towards isolation of these acclimated candidates.

Comparative genomics reveals the adaptation of ammonia‐oxidising Thaumarchaeota to arid soils

“…Besides, the grouping of both genomes from arid soils into clade 473 also failed, in which one was indeed grouped into this clade (GCA_023252395.1), whereas another one (GCA_023252335.1) was closer to those from freshwater (Figure S6). This might be caused by the high phylogenetic and metabolic diversities shaped by hydrological selection at different soil depths (about 0–40 cm) (Vuong et al, 2022). A similar scenario was also detected for the genomes from semi‐arid floodplain sediments (a 234 cm depth gradient of hydrological variables) (Reji et al, 2022).…”

Chameleon-like Anammox Bacteria for Surface Color Change after Suffering Starvation

“…Growth conditions, such as nutrients and temperature, can change the metabolism of microorganisms and enable them to respond to stress. Microorganisms undergo physiological responses to ensure survival. , In various oligotrophic ecosystems (e.g., oceans and sediments) , and sludge storage, where microorganisms typically experience long-term starvation, these bacteria may have evolved a complex regulatory network integrating a series of enzymatic and molecular mechanisms that enable them to survive during substrate depletion . During the initial starvation, bacteria often activate regulators such as cAMP, PHO, and (p)­ppGpp to enhance tolerance.…”