New metagenomic method from the Fuhrman Lab illuminates ocean microbial life in unprecedented detail.
Reporting by Helen Hill for CBIOMES
CBIOMES researchers in the Fuhrman Lab have developed a new metagenomic protocol that enables the precise quantification of microbial populations in the ocean, offering a transformative tool for ecological modeling and biogeochemical research. The study, led by Qicheng Bei was published in ISME Communications and introduces a method for estimating absolute abundances of marine prokaryotes and photosynthetic eukaryotes using genomic internal standards.
Traditional metagenomic approaches have revolutionized our understanding of microbial diversity, but they typically yield only relative abundance data. This limitation has hindered efforts to link microbial community structure to ecosystem function. Bei and colleagues tackled this challenge by incorporating internal genomic standards into high-throughput sequencing workflows, allowing them to convert relative read counts into absolute cell concentrations.
The team applied their method to surface seawater samples collected during the 29th Atlantic Meridional Transect (AMT29), spanning latitudes from 50°N to 40°S. Using the single-copy recA gene as a marker, they estimated bacterial abundances at approximately 1 billion genome equivalents per liter. For eukaryotic phytoplankton, they leveraged the psbO gene—recently shown to be single-copy in most taxa—to derive similar quantitative estimates.
“Our approach bridges the gap between sequencing data and ecological relevance,” said Bei. “By quantifying actual cell numbers, we can better understand microbial contributions to ocean processes like carbon cycling and nutrient flux.”
The metagenomic estimates showed strong agreement with flow cytometry data for cyanobacteria (slope = 1.03, Pearson’s r = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson’s r = 0.84). Notably, the method provided improved taxonomic resolution for nano- and picoeukaryotes compared to flow cytometry, and yielded higher abundance estimates for groups like diatoms, dinoflagellates, and Trichodesmium than traditional microscopy—likely due to undercounting and ploidy variation in microscopy-based methods.
The study’s findings underscore the value of absolute quantification in microbial oceanography. By enabling direct comparisons across taxa and environments, the method opens new avenues for studying microbial biogeography, ecosystem dynamics, and climate feedbacks.
“This is a game-changer for marine microbial ecology,” said project leader Jed Fuhrman. “We now have a scalable, robust framework for measuring the true abundance of key microbial players in the ocean.”
The protocol is designed for use with unfractionated seawater, preserving the natural community structure and avoiding biases introduced by size-based filtering. It also integrates seamlessly with existing sequencing platforms, making it accessible to a wide range of research groups.
Looking ahead, the team envisions applying the method to time-series studies, mesocosm experiments, and global ocean surveys. They also highlight the potential for expanding the approach to include viruses and other microbial groups, further enriching our understanding of ocean life.
Publication
Qicheng Bei, Nathan L. R. Williams, Laura E. Furtado, Daria Di Blasi, Jelani Williams, Vanda Brotas, Glen Tarran, Andrew P. Rees, Chris Bowler, Jed A. Fuhrman (2025), Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes, ISME Communications, doi: 10.1093/ismeco/ycaf131