UH Mānoa Team Catalogs Largest Microbe Genome to Date

A rosette sampler captures water at specified depths at Station ALOHA. Credit: Tara Clemente, UH Mānoa.

A University of Hawai‘i at Mānoa Oceanography Professor and his team have compiled the largest single-site microbiome gene catalog to date.

Using this information, Professor Ed DeLong and his team discovered that nutrient limitation is a key factor in the evolution of ocean microbe genomes. The study was published in the journal Nature Microbiology.

Microbes are the dominant lifeform on the planet, especially in the ocean, and form the foundations of the entire marine food web. Marine microbes come in a variety of forms with myriad metabolic abilities which are encoded in their genes. Some have gene codes that allow them to extract energy from sunlight to turn carbon dioxide into organic matter. Others reverse this process, using organic matter as a carbon and energy source to create carbon dioxide as an end-product of respiration.

“But how do we characterize all these diverse traits and functions in virtually invisible organisms, whose numbers approach a million cells per teaspoon of seawater?” asked DeLong. “This newly constructed, comprehensive gene catalog of microbes inhabiting the ocean waters north of the Hawaiian Islands addresses this challenge.”

DeLong and his team collected water samples over two years and cataloged the most abundant microbes found in the upper 3,000 feet of water at the Hawai‘i Ocean Time-series (HOT) Program’s open ocean field site, Station ALOHA. The microbe genes and genomes were then decoded using modern genome sequencing technologies. As a result, the researchers discovered that just below the sunlit layer of ocean water—roughly 250 to 650 feet beneath the surface—microbial communities shift dramatically in their genomes and protein makeup.

“In surface waters, microbial genomes are much smaller, and their proteins contain less nitrogen—a logical adaptation in this nitrogen-starved environment,” said Daniel Mende, a post-doctoral researcher at UH Mānoaʻs School of Ocean and Earth Science and Technology (SOEST) and lead author on the paper. “In deeper waters, between 400 to 650 feet, microbial genomes become much larger, and their proteins contain more nitrogen, in tandem with increasing nitrogen availability with depth.”

“These results suggest that the availability of nutrients in the environment may actually shape how microbial genomes and proteins evolve in the wild,” said DeLong. “Another surprising finding of the study is that the microbial ‘genomic transition zone’ observed occurs over a very narrow depth range, just beneath the sunlit layer. Below about 650 feet deep, the fundamental properties of microbial genomes and proteins are relatively constant, all the way down to the seafloor.”

The new microbiome database is now available to scientists worldwide. The information is being made available through collaboration with a University of Arizona computer science group led by Professor Bonnie Hurwitz.

“These new data will provide an important tool for understanding the nature and function of the ocean’s microbiome today, as well as help predict its trajectory into the future,” said DeLong.