Microbial dark matter[1][2] comprises the vast majority of
microbial organisms (usually
bacteria and
archaea) that
microbiologists are unable to
culture in the laboratory, due to lack of knowledge or ability to supply the required growth conditions. Microbial dark matter is unrelated to the
dark matter of physics and cosmology, but is so-called for the difficulty in effectively studying it as a result of its inability to be cultured by current methods. It is difficult to estimate its relative magnitude, but the accepted gross estimate is that as little as one percent of microbial species in a given
ecological niche are culturable. In recent years, more effort has been directed towards deciphering microbial dark matter by means of recovering
genomeDNA sequences from environmental samples via culture independent methods such as
single cell genomics[3] and
metagenomics.[4] These studies have enabled insights into the evolutionary history and the
metabolism of the sequenced genomes,[5][6] providing valuable knowledge required for the cultivation of microbial dark matter lineages.
Microbes with highly unusual DNA
It has been suggested certain microbial dark matter genetic material could belong to a new (i.e., fourth) domain of life,[7][8] although other explanations (e.g., viral origin) are also possible, which has ties with the issue of a hypothetical
shadow biosphere.[9]
^Rinke, Christian (2018). "Single-Cell Genomics of Microbial Dark Matter". In Robert G. Beiko; Will Hsiao; John Parkinson (eds.). Microbiome Analysis: Methods and Protocols. Methods in Molecular Biology. Vol. 1849. New York: Springer New York. pp. 99–111.
doi:
10.1007/978-1-4939-8728-3_7.
ISBN978-1-4939-8728-3.
PMID30298250.
^Hedlund, Brian P.; Dodsworth, Jeremy A.; Murugapiran, Senthil K.; Rinke, Christian; Woyke, Tanja (2014). "Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter"". Extremophiles. 18 (5): 865–875.
doi:
10.1007/s00792-014-0664-7.
ISSN1431-0651.
PMID25113821.
S2CID16888890.