Nitrosophilus labii HRV44^T is a thermophilic chemolithoautotroph isolated from a deep-sea hydrothermal vent in the Okinawa Trough, Japan. It grows using hydrogen as an electron donor and N₂O as an electron acceptor. Credit: Muneyuki Fukushi/ Hokkaido University.

Scientists have unearthed a clue to the molecular mechanisms involved in nitrous oxide reduction by deep-sea hydrothermal vent bacteria.

Nitrous oxide (N₂O) is the third most potent greenhouse gas after carbon dioxide and methane.

It can also be oxidised by physical processes to form ozone-depleting substances.

Atmospheric concentrations of N₂O have increased since the preindustrial era, making N₂O reduction a global challenge.

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

Corresponding author Sayaka Mino, assistant professor at the Faculty of Fisheries Sciences, Hokkaido University, said: “Time series transcriptomic analysis of HRV44^T in response to N₂O was more challenging than expected.

“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.”

Strain HRV44^T rapidly respires N₂O, forming bubbles at the gas-liquid interface. Credit: Jiro Tsuchiya/  Hokkaido University.

Efficient energy metabolisms

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.

Robert M Morris, associate professor at the University of Washington, said: “We hypothesise that this feature may contribute to efficient energy metabolisms in deep-sea hydrothermal environments where alternative electron acceptors are occasionally depleted.”

First author Jiro Tsuchiya, a JSPS research fellow DC2 at Hokkaido University, and colleagues, conducted a statistical analysis of time series data.

Tsuchiya said: “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.”

Deep-sea hydrothermal environments have steep chemical and physical gradients, making them hotspots for bioresources.

This study demonstrates the potential for micro-organisms in these environments to contribute to N₂O mitigations that may help combat climate change.

Search for microbial resources with high greenhouse gas reduction efficiency, optimisation of their abilities, and elucidation of molecular mechanisms specific to these micro-organisms will contribute to developing technologies for environmental remediation by micro-organisms.

The researched is published iScience.