Deep-sea hydrothermal vent bacteria hold key to understanding nitrous oxide reduction

The only known biological sink of N₂O in the biosphere is microbial denitrification. Denitrification is a series of reduction reactions starting with nitrate and ending with the reduction of N₂O to nitrogen gas, with no greenhouse effect. This reaction is unique to microorganisms possessing N₂O reductase (N₂OR; NosZ), highlighting the importance of identifying the molecular mechanisms mediating high N₂O reduction activity.

Researchers at Hokkaido University, in collaboration with colleagues at the Institute of Physical and Chemical Research (RIKEN) and the University of Washington, investigated the molecular mechanisms underlying N₂O reduction of a microbial species, Nitrosophilus labii HRV44^T, which had been discovered by Hokkaido University researchers in 2020, from a deep-sea hydrothermal vent. The team recently published their results in the journal iScience.

The research team developed a method that enabled them to analyze time-series gene expression at a genome-wide level, called the transcriptome, using RNA extracted from very few cells.

"Time series transcriptomic analysis of HRV44^T in response to N₂O was more challenging than expected," said corresponding author Sayaka Mino, Assistant Professor at the Faculty of Fisheries Sciences, Hokkaido University. "We have performed transcriptomic analysis using methods often used in microbial studies, but we failed to capture the gene expression dynamics over short time scales because we could not get enough RNA from just a few cells. The method demonstrated in the current study requires only 1 ng of messenger RNA (mRNA), making it useful for analysis at low cell densities, from which RNA extraction is difficult."

The time series transcriptomic profiling of HRV44^T demonstrated that N₂O is not a critical inducer of denitrification gene expression, including nos genes, which are expressed under anaerobic conditions even in the absence of nitrogen oxides as electron acceptors.

"We hypothesize that this feature may contribute to efficient energy metabolisms in deep-sea hydrothermal environments where alternative electron acceptors are occasionally depleted," said Robert M. Morris, Associate Professor at the University of Washington.

Jiro Tsuchiya, the first author and a JSPS research fellow DC2 at Hokkaido University, and colleagues conducted a statistical analysis of time series data. "Our findings suggest that the denitrification gene nosZ is negatively regulated by transcriptional regulators that typically function as transcriptional activators in response to environmental changes. Although we still need to investigate this result, our study extends the understanding of the regulatory mechanisms controlling gene expression in N₂O-reducers and may help increase their ability to respire N₂O," said Tsuchiya.

Deep-sea hydrothermal environments have steep chemical and physical gradients, making them hotspots for bioresources. This study demonstrates the potential for microorganisms in these environments to contribute to N₂O mitigations that may help combat climate change. Search for microbial resources with high greenhouse gas reduction efficiency, optimization of their abilities, and elucidation of molecular mechanisms specific to these microorganisms will contribute to developing technologies for environmental remediation by microorganisms.