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Biological dark matter

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Biological dark matter is an informal term for unclassified or poorly understood genetic material. This genetic material may refer to genetic material produced by unclassified microorganisms. By extension, biological dark matter may also refer to the un-isolated microorganisms whose existence can only be inferred from the genetic material that they produce. Some of the genetic material may not fall under the three existing domains of life: Bacteria, Archaea and Eukaryota; thus, it has been suggested that a possible fourth domain of life may yet be discovered,[1][2] although other explanations are also probable. Alternatively, the genetic material may refer to non-coding DNA (so-called "junk DNA")[3][4][5] and non-coding RNA produced by known organisms.[6][7][8]

Genomic dark matter

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Main article: Junk DNA

Much of the genomic dark matter is thought to originate from ancient transposable elements and from other low-complexity repetitive elements.[9][10] Uncategorized genetic material is found in humans and many other species.[1][11] Their phylogenetic novelty could indicate the cellular organisms or viruses from which they evolved.[12]

Unclassified microorganisms

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Up to 99% of all living microorganisms cannot be cultured,[13][14][15][16][17] so few functional insights exist about the metabolic potential of these organisms.

Sequences that are believed to be derived from unknown microbes are referred to as the microbial dark matter,[18] the dark virome,[19] or dark matter fungi.[20] Such sequences are not rare. It has been estimated that in material from humans, between 40 and 90% of viral sequences are from dark matter.[21][22][23] Human blood contains over three thousand different DNA sequences which cannot yet be identified.[24] A mycological study from 2023 found that dark matter fungi seem to dominate the fungal kingdom. [25]

Algorithms have been developed that examine sequences for similarities to bacterial 16S RNA sequences,[26] K-mer similarities to known viruses,[27] specific features of codon usage,[28] or for inferring the existence of proteins.[29] These approaches have suggested, for example, the existence of a novel bacteriophage of the microviridae family,[29] and a novel bacterioidales-like phage.[30] Other studies have suggested the existence of 264 new viral genera, discovered in publicly available databases,[31] and a study of human blood suggested that 42% of people have at least one previously unknown virus each, adding up to 19 different new genera.[32] A comprehensive study of DNA sequences from multiple human samples inferred the existence of 4,930 species of microbes of which 77% were previously unreported.[33] Health-related findings include a prophage that might be associated with cirrhosis of the liver,[27] and seven novel sequences from children with type-1 diabetes that have characteristics of viruses.[34] Although they might exist, no organisms that clearly cause human disease have been discovered in the dark matter.

In February 2023, scientists reported the findings of unusual DNA strands from the microorganisms in the "dark microbiome" in the driest non-polar desert on Earth.[35][36]

See also

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References

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  1. ^ a b Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA (March 2011). "Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees". PLOS ONE. 6 (3): e18011. Bibcode:2011PLoSO...618011W. doi:10.1371/journal.pone.0018011. PMC 3060911. PMID 21437252.
  2. ^ Lopez P, Halary S, Bapteste E (October 2015). "Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life". Biology Direct. 10: 64. doi:10.1186/s13062-015-0092-3. PMC 4624368. PMID 26502935.
  3. ^ Carey N (2015). Junk DNA: A Journey Through the Dark Matter of the Genome. Columbia University Press. ISBN 9780231170840.
  4. ^ Kolata G (5 September 2012). "Bits of Mystery DNA, Far From 'Junk', Play Crucial Role". The New York Times. Retrieved 2015-09-09.
  5. ^ Boyle R (6 September 2012). "Inside the Mysterious Dark Matter of the Human Genome". Popular Science. Retrieved 2015-09-09.
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  8. ^ van Bakel H, Nislow C, Blencowe BJ, Hughes TR (May 2010). Eddy SR (ed.). "Most "dark matter" transcripts are associated with known genes". PLOS Biology. 8 (5): e1000371. doi:10.1371/journal.pbio.1000371. PMC 2872640. PMID 20502517.
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  25. ^ Nilsson RH, Ryberg M, Wurzbacher C, Tedersoo L, Anslan S, Põlme S, Spirin V, Mikryukov V, Svantesson S, Hartmann M, Lennartsdotter C, Belford P, Khomich M, Retter A, Corcoll N, Gómez Martinez D, Jansson T, Ghobad-Nejhad M, Vu D, Sanchez-Garcia M, Kristiansson E, Abarenkov K (2023). "How, not if, is the question mycologists should be asking about DNA-based typification". MycoKeys. 30 (96): 143–157. doi:10.3897/mycokeys.96.102669. hdl:10138/357843. PMC 10194844. PMID 37214179.
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  31. ^ Roux S, Hallam SJ, Woyke T, Sullivan MB (July 2015). "Viral dark matter and virus-host interactions resolved from publicly available microbial genomes". eLife. 4. doi:10.7554/eLife.08490. PMC 4533152. PMID 26200428.
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