Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter

Area of Science:

• Environmental microbiology
• Soil science
• Genomics

Background:

• Ammonia-oxidizing archaea (AOA) are crucial for nitrogen cycling in soils.
• Conventional liquid cultures limit the study of surface-adapted soil microorganisms.
• Floating membrane filter cultivation offers a novel approach to simulate solid surfaces and enrich specific microbial communities.

Purpose of the Study:

• To isolate and characterize ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria from agricultural soil using floating membrane filter cultivation.
• To perform metagenomic sequencing to identify novel nitrifier species and analyze their genomic properties.
• To investigate the potential role of conserved genes in microbial adaptation and culturability.

Main Methods:

• Floating membrane filter cultivation was used to enrich surface-adapted soil nitrifier communities.
• Metagenomic sequencing was employed to recover and assemble microbial genomes (bins).
• Phylogenomic, Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses were conducted for taxonomic classification.
• Pan and core genome analyses were performed on retrieved AOA genomes.

Main Results:

• Three novel microbial bins were recovered: FF_bin01 and FF_bin02 (novel species of "Candidatus Nitrosocosmicus" and Nitrososphaera, respectively) and FF_bin03 (novel species of Nitrospira).
• FF_bin01 and FF_bin02 belong to the Nitrososphaeraceae family, while FF_bin03 is affiliated with the Nitrospiraceae family.
• Pan-genome analysis identified 653 core orthologous clusters among 29 AOA genomes and 90 unique orthologous clusters conserved in the Nitrososphaeraceae family.
• Manganese catalase and heme catalase genes were identified in the recovered AOA and nitrite-oxidizing bacterium, respectively, potentially aiding their growth.

Conclusions:

• Floating membrane filter cultivation is a promising method for isolating distinct soil ammonia-oxidizing archaea (AOA) and other nitrifiers.
• The genomic data provides insights into the adaptation mechanisms and evolutionary relationships of soil nitrifiers.
• Further optimization of this technique could enable the cultivation of a wider range of unculturable nitrifying microorganisms from diverse environments.