Rappe lab graduate student Sarah Tucker sampling in Kāneʻohe Bay. (Credit: Jessica Schaefer)

Move over, cyanobacteria! A large-scale study of the Earth’s surface ocean, co-authored by Michael Rappé, professor at the University of Hawaiʻi at Mānoa School of Ocean and Earth Science and Technology (SOEST), indicates that the microbes responsible for fixing nitrogen there—previously thought to be almost exclusively photosynthetic cyanobacteria—include an abundant and widely distributed suite of non-photosynthetic bacterial populations.

Nitrogen fixation is a critical ecological process in which atmospheric nitrogen is converted to ammonia, making nitrogen “bioavailable” to living organisms to use as a fundamental building block of DNA, RNA and proteins.

“Microbes that can fix nitrogen or carbon are at the center of the ecology of microbial communities in many environments, including the surface ocean,” said lead author Tom O. Delmont of the University of Chicago.

Finding these unique microbes using genetic information

Using anviʻo, a state-of-the-art, open-source bioinformatics platform to analyze metagenomes (the pool of DNA sequences that represent all the microbial organisms found in an environment), the team revealed insights into previously unknown marine microbes with nitrogen fixation capabilities affiliated with Proteobacteria as well as Planctomycetes, a prevalent bacterial phylum that has never before been linked to nitrogen fixation.

These newly described microbial populations occur widely and are particularly abundant in the Pacific Ocean, where they average an estimated 700,000 cells per liter of seawater and up to three million cells per liter. This magnitude is more than previous estimates for non-cyanobacterial nitrogen fixers in the open ocean.

Using data generated from the Tara Oceans expedition from 2009 to 2013, the research team reconstructed about 1,000 microbial genomes from more than 30 billion short metagenomic sequences. Of those 1,000 genomes, nine contained the six genes that are required for nitrogen fixation, and yet lacked the genes needed for photosynthesis. This is the first genomic database of non-photosynthetic microorganisms inhabiting the open ocean and capable of fixing nitrogen.

The research team is led by A. Murat Eren of the University of Chicago and the Marine Biological Laboratory, Woods Hole, and Tom O. Delmont of the University of Chicago.

For the full story, see the SOEST website.

—By Marcie Grabowski