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Biological dark matter

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Biological dark matteris an informal term for unclassified or poorly understoodgenetic material.This genetic material may refer to genetic material produced by unclassifiedmicroorganisms.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,ArchaeaandEukaryota;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 tonon-coding DNA(so-called "junk DNA" )[3][4][5]andnon-coding RNAproduced 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 ancienttransposable elementsand from other low-complexity repetitive elements.[9][10]Uncategorizedgenetic materialis found inhumansand many other species.[1][11]Theirphylogeneticnovelty could indicate the cellularorganismsorvirusesfrom which they evolved.[12]

Unclassified microorganisms

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Up to 99% of all livingmicroorganismscannot becultured,[13][14][15][16][17]so few functional insights exist about themetabolic potentialof these organisms.

Sequences that are believed to be derived from unknown microbes are referred to as the microbial dark matter,[18]the darkvirome,[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 bacterial16S RNAsequences,[26]K-mersimilarities to known viruses,[27]specific features ofcodonusage,[28]or for inferring the existence of proteins.[29]These approaches have suggested, for example, the existence of a novelbacteriophageof themicroviridaefamily,[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 aprophagethat might be associated withcirrhosis of the liver,[27]and seven novel sequences from children withtype-1 diabetesthat 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 thedriest non-polar deserton Earth.[35][36]

See also

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References

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  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.PMC4624368.PMID26502935.
  3. ^Carey N(2015).Junk DNA: A Journey Through the Dark Matter of the Genome.Columbia University Press.ISBN9780231170840.
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  35. ^Achenbach, Joel (21 February 2023)."Strange DNA found in the desert offers lessons in the hunt for Mars life".The Washington Post.Retrieved21 February2023.
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