2025/04/29 by Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee +2 · 1 voice
Environmental Science · #Microbial Community Ecology and Physiology #Microbial Fuel Cells and Bioremediation #Wastewater Treatment and Nitrogen Removal
paper · doi:10.71150/jm.2502002
openalex publication_date 2025/04/29 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31
Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FFbin01 and FFbin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FFbin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FFbin01 and FFbin02 are identified as novel species within the genera "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively, while FFbin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FFbin01 and FFbin02 harbor a gene encoding manganese catalase and FFbin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.