Other meanings of Dark matter
Biology
Biological dark matter refers to the vast majority of microorganisms—including bacteria, archaea, viruses, and fungi—that are invisible to standard laboratory culture techniques and remain largely uncharacterized. These organisms are detected primarily through environmental DNA sequencing, yet their physiology, ecology, and roles in ecosystems are poorly understood. The term draws an analogy to cosmological dark matter, which is inferred from gravitational effects but not directly observed.
Biological dark matter encompasses all microorganisms that evade detection by conventional cultivation and are known only through molecular signatures, such as DNA sequences recovered directly from environmental samples. This includes not only bacteria and archaea but also viruses, fungi, and protists. The term was popularized in the early 2000s as metagenomics revealed that the vast majority of microbial diversity had never been grown in the laboratory.1
Estimates suggest that less than 1% of microbial species can be cultured using standard techniques, leaving the remaining 99% as biological dark matter. These organisms are found in every environment on Earth, from deep-sea sediments and hydrothermal vents to the human gut and extreme acidic or radioactive sites. Their metabolic capabilities are largely unknown, but they are thought to play crucial roles in nutrient cycling, symbiosis, and even human health.
Metagenomics—the direct sequencing of DNA from environmental samples—has been the primary tool for unveiling biological dark matter. By bypassing the need for culture, researchers can sequence entire microbial communities and assemble genomes from the data, revealing organisms that were previously invisible.2
One landmark project, the Global Ocean Sampling Expedition, sequenced DNA from seawater samples worldwide and uncovered an enormous diversity of new genes and organisms. Similarly, the Human Microbiome Project has cataloged thousands of bacterial species in the human body, many of which are unculturable. These efforts have expanded the tree of life, adding new candidate phyla such as the Candidate Phyla Radiation (CPR), a large group of bacteria with small genomes and symbiotic lifestyles.3
The Candidate Phyla Radiation (CPR) is a major component of biological dark matter, comprising dozens of phyla that are mostly uncultured. CPR bacteria have extremely small genomes (often less than 1 megabase) and are thought to be obligate symbionts or parasites of other microbes. They were discovered through single-cell genomics and metagenomics, and they are abundant in groundwater, sediments, and the human mouth.4
Other notable discoveries include the Asgard archaea, a group of archaea that are the closest known relatives of eukaryotes. Their genomes contain many eukaryotic signature genes, providing insights into the origin of complex cells. These organisms were first identified in deep-sea sediments and have since been found in various environments, though they remain uncultured in pure culture.
Studying biological dark matter is fraught with challenges. Many of these organisms have fastidious growth requirements, slow growth rates, or depend on interactions with other species, making them difficult to isolate. Additionally, their genomes often contain genes with no known function, and their metabolic pathways are poorly understood.5
Advanced techniques such as single-cell genomics, stable isotope probing, and cultivation chips are being developed to overcome these barriers. For example, the iChip (isolation chip) allows in situ cultivation of microorganisms in their natural environment, leading to the discovery of new antibiotics from previously uncultured bacteria. Despite these advances, the vast majority of biological dark matter remains unexplored.
Biological dark matter includes not only prokaryotes but also viruses, which are the most abundant biological entities on Earth. Metagenomic studies of viruses, or viromes, have revealed an immense diversity of phage and eukaryotic viruses, many with genes unrelated to known viruses. These 'viral dark matter' genes may encode novel enzymes and proteins with biotechnological potential.6
Another obscure facet is the role of biological dark matter in extreme environments, such as the deep biosphere, where microorganisms exist in rocks and sediments kilometers below the surface. These organisms have incredibly slow metabolic rates and may be millions of years old. Additionally, some uncultured archaea, such as the DPANN superphylum, have tiny cells and reduced metabolic capabilities, challenging our definitions of life.
Biological dark matter holds immense potential for biotechnology and medicine. Novel genes from uncultured organisms could lead to new antibiotics, enzymes for industrial processes, and insights into disease. For example, the discovery of CRISPR-Cas systems in bacteria, which are now used for genome editing, came from studying microbial dark matter.7
Future research aims to characterize these organisms through improved cultivation methods, synthetic biology, and computational modeling. The ultimate goal is to understand the full diversity of life on Earth and its functional roles, which could transform our understanding of ecology, evolution, and the origins of life.
The term 'biological dark matter' was coined by analogy to cosmological dark matter, reflecting the unseen majority of microbial life.
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