The ocean's aphotic zone — the dark, high-pressure region below the surface, where sunlight cannot reach — is home to a vast wealth of microbial life.
Yet scientists know relatively little about the genetic makeup, growth, and function of many of these enigmatic organisms.
To help close that knowledge gap, scientists at Bigelow Laboratory's Single Cell Genomics Center (SCGC) spearheaded Global Ocean Reference Genomes Dark (GORG-Dark), the first global atlas of single-cell microbes living in the aphotic ocean.
The resource contains more than 9,600 genomes from individual microbial cells collected across a broad range of depths and locations, including the Mariana Trench and the Antarctic — the ocean's deepest and coldest regions.
A new publication in Cell demonstrates the resource's power, using its vast genome collection to uncover surprising insights into the distribution and capabilities of these previously understudied deep-sea microbes.
"By turning uncultivated microorganisms from Earth's largest and least understood habitat into a shared, single-cell-resolved genomic catalog, GORG-Dark gives us a powerful resource to explore microbial ecology, evolution, and biotechnology," said Tianyi Chang, first author and former postdoctoral researcher at Bigelow Laboratory.
Along with Chang, the study features a broad array of current and former Bigelow Laboratory postdoctoral researchers, including Alaina Weinheimer, Maria Pachiadaki, and Keir Macartney. Postdoctoral researchers having the opportunity to publish their work in a prestigious journal speaks to the strength of postdoctoral training and opportunities at Bigelow Laboratory, which is a core focus of the institution's education program.
To create GORG-Dark, Bigelow Laboratory's Center for Aquatic Cytometry isolated individual cells from ocean samples, measured their size, and estimated their DNA content. The team then used technologies and data tools developed by SCGC to sequence individual cells' genomes.
"This approach allows us to link a genome to a specific cell," said Gregory Gavelis, a bioinformatician at the SCGC. "This precision enables researchers to study, in detail, some of the rarest things in the world."
The SCGC's growing wealth of genomic data has contributed to several recent publications, including a recent study revealing shifts in microbial communities as Maine's kelp forests decline.
GORG-Dark was the second phase of a larger initiative that began with GORG-Tropics, an effort to sequence genomes from microbes living in the sunlit ocean.
Extending the effort into the deep ocean provides a critical baseline for understanding an environment that could face unprecedented changes as human activities move farther down the water column.
"It is critical to understand what's down there before we change it," Gavelis said.
Using the new database, the researchers identified unexpected functions and capabilities among some of the ocean's most abundant microorganisms.
For example, they found widespread genetic potential for chemoautotrophy, a process like photosynthesis, but instead of sunlight, organisms use inorganic chemicals to fuel their growth. They found this capability even among the deepest sampled regions, highlighting the potential importance of deep-sea microbial communities to global carbon and nutrient cycles.
The researchers also identified genes associated with producing specialized compounds with potential pharmaceutical and blue biotechnology applications. These findings offer new opportunities to investigate the deep ocean as a source of discoveries that could improve human health.
"The fact that we were able to use this vast amount of data from across the deep ocean is really exciting," said Weinheimer, a postdoctoral researcher at Bigelow Laboratory. "It unlocks a lot of research to have individual cellular genomes all the way to the bottom of the sea."
This groundbreaking work and the GORG-Dark database were made possible by a grant to Bigelow Laboratory from the Simons Foundation, leveraging samples of opportunity collected from multiple collaborators across the globe. SCGC's founding director, Dr. Ramunas Stepanauskas, led this study, building from his deep expertise in the genomics of the ocean's microbes since he began working at Bigelow Laboratory in 2005. Now director emeritus of SCGC and an adjunct scientist with Bigelow Laboratory, collaboration on uncovering the diversity and potential of microbial life continues with Stepanauskas in his new role at Aalborg University.
