Pursuit: life-history patterns, systematics, and biogeography of widespread but cryptic patescibacteria

Federal Grant Award Summary

The National Science Foundation's Division of Ocean Sciences awarded a $350,000 Project Grant (CFDA 47.050, Geosciences Program) to Bigelow Laboratory for Ocean Sciences effective September 1, 2025, through August 31, 2028. The award supports fundamental research investigating the life-history patterns, systematics, and biogeography of Patescibacteria and Chloroflexota—abundant yet understudied bacterial lineages residing in marine sediments. The primary deliverables include thousands of high-quality single-cell genomes (single-amplified genomes and metagenome-assembled genomes) representing these cryptic microorganisms and other "microbial dark matter" lineages, which will be contributed to the broader scientific community to advance understanding of microbial physiology, evolution, and function in global chemical cycling.

The research leverages advanced single-cell and metagenomic technologies to address why these widespread bacterial lineages have resisted laboratory cultivation and to elucidate their true evolutionary positions within the tree of life. Secondary deliverables include workforce development through mentored research and field work opportunities that will train student researchers in omics, systematics, and biogeochemistry techniques, thereby enhancing microbiology expertise while advancing fundamental discovery in marine microbiology and ocean ecosystem science.

Abstract

An astounding revolution in our understanding of life on earth has taken place since the turn of the 21ST century, shaking the tree of life and our view of evolution. IT involves adding new branches to the tree of life through the discovery of previously unknown groups of archaea and bacteria ? Life?s smallest yet most abundant cells. This project advances fundamental knowledge about the evolutionary patterns and functional roles of two abundant yet largely unstudied lineages of bacteria: patescibacteria and chloroflexota. These cryptic microbes thrive in marine sediments, one of the largest and least understood microbial habitats, where chemical cycling occurs that affects the global ocean. This project aims to disentangle why these lineages are so prevalent, their true place in the evolutionary history of life on earth, and how they function. The research will also shed light on why some of these lineages have resisted cultivation, which is necessary to realize their biotechnology potential. These studies will contribute thousands of high-quality single-cell genomes representing not only patescibacteria and chloroflexota, but also other 'microbial dark matter' lineages to the broader scientific community. Through mentored research and field work opportunities, student researchers will be trained in -omics, systematics, and biogeochemistry research techniques, leading to enhanced microbiology expertise while advancing discovery. This project leverages new single-cell and metagenomic technologies for studying microbial cells that prevail in nature but resist laboratory cultivation. Single-amplified genomes and metagenome-assembled genomes of patescibacteria and chloroflexota will significantly expand our understanding of their physiology and the evolutionary forces driving their delineation. These lineages share a last common ancestor, are distributed globally, and often CO-occur in the same anoxic regions of marine sediments; however, their metabolisms and physiologies contrast starkly. As patescibacteria appear to lack the capacity for cellular respiration, we hypothesize they primarily generate energy through fermentation. Meanwhile, chloroflexota have flexible metabolisms and can harness a range of redox reactions involving reduced sulfur compounds and, potentially, more exotic halogenated compounds. Employing comparative phylogenomics, the true evolutionary history of patescibacteria and chloroflexota will be uncovered. The analysis of physiological and metabolic traits of individual, uncultured cells will ground-truth genome-based findings and explain the distribution and CO-existence of these widespread yet enigmatic organisms within anoxic marine sediments. This project uses innovative technologies to isolate single microbial cells and characterize their metabolic traits, linking physiologies with evolutionary patterns and biogeochemical processes. This project is CO-funded by the systematics & biodiversity science and biological oceanography programs. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the foundation's intellectual merit and broader impacts review criteria.- subawards are not planned for this award.