Recently, Professor Yang Liu's team from the Institute for Advanced Study, Shenzhen University, in collaboration with the Institute of Microbiology, Chinese Academy of Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Xiamen University, and other institutions, published a research article entitled "A deep-sea rare bacterium exhibits extraordinary metabolic versatility" in Cell Reports. The study reports the first successful isolation and cultivation of a rare bacterial lineage that had previously been known only from metagenomic datasets. By establishing its taxonomic status and combining genomic analyses with physiological characterization, the researchers revealed its extraordinary metabolic versatility, providing important experimental evidence for understanding the ecological functions and evolutionary strategies of rare microorganisms. Professor Yang Liu from Shenzhen University is one of the corresponding authors, while Zhimeng Li, Baihui Chi, and Chujin Ruan contributed equally as co-first authors. Shenzhen University is one of the contributing institutions to this work.
A large proportion of microorganisms persist at extremely low abundance in natural microbial communities and are collectively referred to as the rare biosphere. Although numerically scarce, increasing evidence suggests that these rare microorganisms play important roles in maintaining ecosystem stability and driving global biogeochemical cycling of carbon, nitrogen, and sulfur. However, because the vast majority of rare microorganisms have not been obtained in pure culture, their physiological characteristics, metabolic capabilities, and ecological functions have largely been inferred from metagenomic data rather than validated experimentally.
In this study, the researchers collected deep-sea seawater samples from a depth of 4,213 meters in the Northwest Indian Ocean. Using fluorescence-activated cell sorting combined with high-throughput single-cell cultivation, they successfully isolated a novel deep-sea bacterium, designated strain D14T, which exhibits extremely slow growth. Phylogenetic analyses showed that strain D14T belongs to the candidate lineage NORP267, which had previously been identified only through metagenome-assembled genomes (MAGs) and lacked any cultured representative. Based on comprehensive taxonomic, genomic, and physiological evidence, the researchers established a new bacterial family, Metabolovariaceae, and proposed Metabolovarius oceani as its type species. This represents the first cultured representative of this lineage worldwide and provides an important foundation for investigating this previously unexplored group of microorganisms.
Genome analysis demonstrated that strain D14T possesses remarkable metabolic versatility. Its genome encodes complete pathways for carbon dioxide fixation via the Calvin–Benson–Bassham cycle, denitrification, thiosulfate oxidation, and polyhydroxyalkanoate (PHA) biosynthesis, while also enabling the utilization of a wide range of organic carbon substrates. These metabolic capabilities were further validated through stable isotope labeling, transmission electron microscopy, and physiological experiments. The results showed that strain D14T is capable of thiosulfate-dependent carbon dioxide fixation under aerobic conditions, supporting autotrophic growth, and can also couple nitrate reduction with thiosulfate oxidation during anaerobic autotrophic growth, demonstrating thiosulfate-dependent autotrophic denitrification. In addition, under carbon-rich conditions, intracellular polyhydroxyalkanoate granules were observed, indicating its ability to store and regulate internal carbon reserves. This combination of autotrophic and heterotrophic lifestyles, together with the ability to function under both aerobic and anaerobic conditions, reflects a highly flexible metabolic strategy and makes strain D14T one of the most metabolically versatile rare bacteria described to date.
The researchers further investigated the global distribution of the family Metabolovariaceae. Analysis of publicly available metagenomic datasets showed that members of this family are widely distributed across diverse environments, including marine and freshwater ecosystems, soils, groundwater, biofilms, and wastewater treatment systems, spanning regions from the polar oceans to tropical environments. Nevertheless, their relative abundance remained below 0.1% in approximately 80% of the samples analyzed, consistent with the defining characteristics of the rare biosphere. Only a small number of activated sludge and biofilm samples exhibited relatively higher abundances. These findings indicate that although members of Metabolovariaceae are globally distributed, they consistently persist at low abundance, representing a typical globally distributed rare bacterial lineage.
Article: https://doi.org/10.1016/j.celrep.2026.117671
