Unexpected novel clade III type nitrous oxide-reducing bacteria from incubated lake sediments
Source: PubMed Central Open Access, NCBI / U.S. National Library of Medicine
Abstract Nitrous oxide-reducing bacteria (NORB) play a pivotal role in regulating NO emissions in aquatic ecosystems, with clade I and clade II-harboring microorganisms representing well-recognized contributors to microbial NO consumption. Beyond conventional NORB, the recently identified clade IIIfrom soil may represent a previously overlooked potential NO sink, yet the distribution and characterization remain largely unexplored in aquatic ecosystems. Here we established microcosm systems using sediments from five lakes and subjected them to warming temperature gradients to investigate the diversity and genomic characteristics of NORB. Hidden Markov model (HMM)-based analyses identified a total of 45 nonredundantsequences, including 12 affiliated with clade III. Clade IIIaccounted for 10.2%–40.6% of totalgenes, indicating that clade III-harboring NORB is widespread and non-negligible. Reconstruction of metagenome-assembled genomes (MAGs) identified four phylogenetically novel clade III-harboring NORB, with these MAGs showing low average amino acid identity to their closest known reference genomes. These MAGs showed different denitrification gene inventories, with MAG33 lacking identifiable genes for upstream NO-producing steps, suggesting a potential non-denitrifying NO reducer. They also encoded oxygen-related stress-response genes, suggesting a potential ability to perform NO respiration in the presence of oxygen. Unlike canonical clade I/IIclusters, clade III-harboring MA
Abstract
Abstract Nitrous oxide-reducing bacteria (NORB) play a pivotal role in regulating NO emissions in aquatic ecosystems, with clade I and clade II-harboring microorganisms representing well-recognized contributors to microbial NO consumption. Beyond conventional NORB, the recently identified clade IIIfrom soil may represent a previously overlooked potential NO sink, yet the distribution and characterization remain largely unexplored in aquatic ecosystems. Here we established microcosm systems using sediments from five lakes and subjected them to warming temperature gradients to investigate the diversity and genomic characteristics of NORB. Hidden Markov model (HMM)-based analyses identified a total of 45 nonredundantsequences, including 12 affiliated with clade III. Clade IIIaccounted for 10.2%–40.6% of totalgenes, indicating that clade III-harboring NORB is widespread and non-negligible. Reconstruction of metagenome-assembled genomes (MAGs) identified four phylogenetically novel clade III-harboring NORB, with these MAGs showing low average amino acid identity to their closest known reference genomes. These MAGs showed different denitrification gene inventories, with MAG33 lacking identifiable genes for upstream NO-producing steps, suggesting a potential non-denitrifying NO reducer. They also encoded oxygen-related stress-response genes, suggesting a potential ability to perform NO respiration in the presence of oxygen. Unlike canonical clade I/IIclusters, clade III-harboring MAGs lacked typical accessory genes and instead exhibited distinct neighboring transporter- and cytochrome-related genes. Together, our results provide evidence for the occurrence of clade III-harboring NORB in non-soil ecosystems and expand current understanding of their genomic traits.