Microbial dark matter can be found ubiquitously and abundantly across multiple ecosystems, but remains difficult to study due to difficulties in detecting and culturing these species, posing challenges to research efforts.
[5] These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes,[6][7] providing valuable knowledge required for the cultivation of microbial dark matter lineages.
Single-cell techniques have also successfully identified numerous new branches on the tree of life, providing insight into the gaps of current phylogenetic understanding and metabolic potential of these organisms.
In recent years, research on artificial intelligence and machine learning has produced new ways to increase our ability to predict the behavior of microbial species using their genetic data.
It has been suggested certain microbial dark matter genetic material could belong to a new (i.e., fourth) domain of life,[14][15] although other explanations (e.g., viral origin) are also possible, which has ties with the issue of a hypothetical shadow biosphere.