Rhizobial bacterium helps diatom to bind nitrogen

Scientists from the Max Planck Institute for Marine Microbiology have discovered a new partnership between a marine diatom and a bacterium that can account for a large share of nitrogen fixation in vast regions of the ocean.

The newly discovered bacterial symbiont is closely related to the nitrogen-fixing Rhizobia, which lives in partnership with many crop plants and may open new avenues to engineer nitrogen-fixing plants.

The rhizobial nitrogen fixing symbionts (fluorescently-labeled in orange and green using genetic probes) residing inside diatoms collected from the tropical North Atlantic. The nucleus of the diatom is shown in bright blue. Image credit: MPI f. Marine Microbiology/ Mertcan Esti

Nitrogen is an essential component of all living organisms. It is also the key element controlling the growth of crops on land, as well as the microscopic oceanic plants that produce half the oxygen on our planet. Atmospheric nitrogen gas is the largest pool of nitrogen, but plants cannot transform it into a usable form. Instead, crop plants like soybeans, peas and alfalfa (collectively known as legumes) have acquired Rhizobial bacterial partners that “fix” atmospheric nitrogen into ammonium. This partnership makes legumes one of the most important sources of proteins in food production.

Scientists from the Max Planck Institute for Marine Microbiology in Bremen, Germany, now report that Rhizobia can also form similar partnerships with tiny marine plants called diatoms. This discovery solves a long-standing marine mystery and has potentially far-reaching agricultural applications.

An enigmatic marine nitrogen fixer hiding within a diatom

For many years it was assumed that most nitrogen fixation in the oceans was carried out by photosynthetic organisms called cyanobacteria. However, in vast regions of the ocean there are not enough cyanobacteria to account for measured nitrogen fixation. Thus, a controversy was sparked, with many scientists hypothesizing that non-cyanobacterial microorganisms must be responsible for the “missing” nitrogen fixation.

“For years, we have been finding gene fragments encoding the nitrogen-fixing nitrogenase enzyme, which appeared to belong to one particular non-cyanobacterial nitrogen fixer”, says Marcel Kuypers, lead author on the study. “But, we couldn’t work out precisely who the enigmatic organism was and therefore had no idea whether it was important for nitrogen fixation”.  

In 2020, the scientists travelled from Bremen to the tropical North Atlantic to join an expedition involving two German research vessels. They collected hundreds of liters of seawater from the region, in which a large part of global marine nitrogen fixation takes place, hoping to both identify and quantify the importance of the mysterious nitrogen fixer. It took them the next three years to finally puzzle together its genome.

“It was a long and painstaking piece of detective work”, says Bernhard Tschitschko, first author of the study and an expert in bioinformatics, “but ultimately, the genome solved many mysteries”.

The first was the identity of the organism, “While we knew that the nitrogenase gene originated from a Vibrio-related bacterium, unexpectedly, the organism itself was closely related to the Rhizobia that live in symbiosis with legumes”, explains Tschitschko. Together with its surprisingly small genome, this raised the possibility that the marine Rhizobia might be a symbiont.