Microbial dark matter

Short description: Microbiological non-culture dependent methods

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 genome DNA 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.

## Contents

* 1 Microbes with highly unusual DNA
* 2 See also
* 3 References
* 4 External links

## 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]

## See also

* Microbial ecology

## References

1. ↑ Filee, J.; Tetart, F.; Suttle, C. A.; Krisch, H. M. (2005). "Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere". Proceedings of the National Academy of Sciences 102 (35): 12471–12476. doi:10.1073/pnas.0503404102. ISSN 0027-8424. PMID 16116082. Bibcode: 2005PNAS..10212471F.
2. ↑ University of Tennessee at Knoxville (25 September 2018). "Study: Microbial dark matter dominates Earth's environments". Eurekalert! (Press release). Retrieved 26 September 2018.
3. ↑ Rinke, Christian (2018). "Single-Cell Genomics of Microbial Dark Matter". in Robert G. Beiko. Microbiome Analysis: Methods and Protocols. Methods in Molecular Biology. 1849. New York: Springer New York. pp. 99–111. doi:10.1007/978-1-4939-8728-3_7. ISBN 978-1-4939-8728-3.
4. ↑ Jiao, Jian-Yu; Liu, Lan; Hua, Zheng-Shuang; Fang, Bao-Zhu; Zhou, En-Min; Salam, Nimaichand; Hedlund, Brian P; Li, Wen-Jun (2021-03-01). "Microbial dark matter coming to light: challenges and opportunities". National Science Review 8 (3): –280. doi:10.1093/nsr/nwaa280. ISSN 2095-5138. PMID 34691599.
5. ↑ 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. ISSN 1431-0651. PMID 25113821.
6. ↑ Rinke, Christian; et, al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature 499 (7459): 431–437. doi:10.1038/nature12352. PMID 23851394. Bibcode: 2013Natur.499..431R.
7. ↑ "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. March 2011. doi:10.1371/journal.pone.0018011. PMID 21437252. Bibcode: 2011PLoSO...618011W.
* Colin Barras (18 March 2011). "Biology's 'dark matter' hints at fourth domain of life". New Scientist. https://www.newscientist.com/article/dn20265-biologys-dark-matter-hints-at-fourth-domain-of-life/.
8. ↑ "Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life". Biology Direct 10: 64. October 2015. doi:10.1186/s13062-015-0092-3. PMID 26502935.
* Colin Barras (11 November 2015). "Mystery microbes in our gut could be a whole new form of life". New Scientist. https://www.newscientist.com/article/mg22830474-800-mystery-microbes-in-our-gut-could-be-a-whole-new-form-of-life/.
9. ↑ Schulze-Makuch, Dirk (Feb 28, 2017). "Could Alien Life Be Hidden All Around Us?". Smithsonian Institution. Smithsonian Magazine. https://www.smithsonianmag.com/air-space-magazine/could-alien-life-be-hidden-all-around-us-180962328/.

## External links

* Microbial Dark Matter project site

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