Genome-resolved metagenomics of tropical peatland ammonia-oxidising archaea

Nitrogen cycling, a critical biogeochemical process in ecosystems, involves a complex microorganism network. In nitrification, ammonia oxidation is mainly governed by ammonia-oxidizing archaea (AOA) in acidic soil. Limited information exists about these taxa in tropical peatlands. This genome-centric metagenomic study aimed to identify key taxa and their functional potential driving nitrification in tropical peatlands. After cleaning Illumina reads, draft bins were created, refined, reassembled, and decontaminated through various strategies, involving both semi-supervised and unsupervised binners, including deep-learning-based approaches. This process resulted in 271 medium to high-quality archaeal metagenome-assembled genomes (MAGs). Five near-complete high-quality AOA MAGs were constructed. Phylogenomic analyses placed the AOA MAGs in the Nitrosotalea genus within the Nitrosopumilaceae family. Comparisons to reference genomes using average amino acid identity (AAI) and average nucleotide identity (ANI) suggested these MAGs might represent separate Nitrosotalea species. Besides core ammonia monooxygenase (amoCAB), these Nitrosotalea MAGs also encoded for nitrite reductase (nirK), ferredoxin-nitrite reductase (nirA) and nitric oxide reductase (norQ) that could also lead to the production of nitrous oxide (N₂O), a potent greenhouse gas. These tropical peatland autotrophic Nitrosotalea MAGs fixed carbon with the hydroxypropionate/hydroxybutyrate pathway and survive in low pH environments through flagellar motility, various transport proteins, substrate acquisition and pH regulation systems for oxidising ammonia. Genomic analyses of candidate taxa can provide a thorough understanding of important biogeochemical functions as critical baseline information to assess microorganism resilience and response to anthropogenic-induced land use change.