Microbial dark matter: Difference between revisions
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{{short description|Microbiological non-culture dependent methods}} |
{{short description|Microbiological non-culture dependent methods}} |
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'''Microbial dark matter'''<ref name="FileeTetart2005">{{cite journal|last1=Filee|first1=J.|last2=Tetart|first2=F.|last3=Suttle|first3=C. A.|last4=Krisch|first4=H. M.|title=Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere|journal=Proceedings of the National Academy of Sciences|volume=102|issue=35|year=2005|pages=12471–12476|issn=0027-8424|doi=10.1073/pnas.0503404102|pmid=16116082|pmc=1194919|bibcode=2005PNAS..10212471F|doi-access=free}}</ref><ref name="EA-20180925">{{cite press release |author=University of Tennessee at Knoxville |title=Study: Microbial dark matter dominates Earth's environments |url=https://www.eurekalert.org/pub_releases/2018-09/uota-smd092518.php |date=25 September 2018 |website=[[Eurekalert!]] |access-date=26 September 2018 |author-link=University of Tennessee at Knoxville }}</ref> comprises the vast majority of [[microbial organism]]s (usually [[bacteria]] and [[archaea]]) that [[microbiologists]] are unable to [[microbiological culture|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]]<ref>{{Cite book| publisher = Springer New York| isbn = 978-1-4939-8728-3| pages = 99–111 |editor=Robert G. Beiko |editor2=Will Hsiao |editor3=John Parkinson | last = Rinke| first = Christian| title = Microbiome Analysis: Methods and Protocols| chapter = Single-Cell Genomics of Microbial Dark Matter| location = New York | series = Methods in Molecular Biology | date = 2018| volume = 1849| doi = 10.1007/978-1-4939-8728-3_7| pmid = 30298250}}</ref> and [[metagenomics]].<ref>{{Cite journal| doi = 10.1093/nsr/nwaa280| issn = 2095-5138| volume = 8| issue = 3| pages = –280| last1 = Jiao| first1 = Jian-Yu| last2 = Liu| first2 = Lan| last3 = Hua| first3 = Zheng-Shuang| last4 = Fang| first4 = Bao-Zhu| last5 = Zhou| first5 = En-Min| last6 = Salam| first6 = Nimaichand| last7 = Hedlund| first7 = Brian P| last8 = Li| first8 = Wen-Jun| title = Microbial dark matter coming to light: challenges and opportunities| journal = National Science Review| date = 2021-03-01| pmid = 34691599| pmc = 8288357}}</ref> These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes,<ref name="HedlundDodsworth2014">{{cite journal|last1=Hedlund|first1=Brian P.|last2=Dodsworth|first2=Jeremy A.|last3=Murugapiran|first3=Senthil K.|last4=Rinke|first4=Christian|last5=Woyke|first5=Tanja|title=Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter"|journal=Extremophiles|volume=18|issue=5|year=2014|pages=865–875|issn=1431-0651|doi=10.1007/s00792-014-0664-7|pmid=25113821|s2cid=16888890}}</ref><ref>{{cite journal |last1=Rinke |first1=Christian |last2=et|first2=al.|title=Insights into the phylogeny and coding potential of microbial dark matter |journal=Nature |year=2013 |volume=499 |issue=7459 |pages=431–437 |doi=10.1038/nature12352 |doi-access=free |pmid=23851394 |bibcode=2013Natur.499..431R |s2cid=4394530}}</ref> providing valuable knowledge required for the cultivation of microbial dark matter lineages. |
'''Microbial dark matter'''<ref name="FileeTetart2005">{{cite journal|last1=Filee|first1=J.|last2=Tetart|first2=F.|last3=Suttle|first3=C. A.|last4=Krisch|first4=H. M.|title=Marine T4-type bacteriophages, a ubiquitous component of the dark matter of the biosphere|journal=Proceedings of the National Academy of Sciences|volume=102|issue=35|year=2005|pages=12471–12476|issn=0027-8424|doi=10.1073/pnas.0503404102|pmid=16116082|pmc=1194919|bibcode=2005PNAS..10212471F|doi-access=free}}</ref><ref name="EA-20180925">{{cite press release |author=University of Tennessee at Knoxville |title=Study: Microbial dark matter dominates Earth's environments |url=https://www.eurekalert.org/pub_releases/2018-09/uota-smd092518.php |date=25 September 2018 |website=[[Eurekalert!]] |access-date=26 September 2018 |author-link=University of Tennessee at Knoxville }}</ref> comprises the vast majority of [[microbial organism]]s (usually [[bacteria]] and [[archaea]]) that [[microbiologists]] are unable to [[microbiological culture|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]]<ref>{{Cite book| publisher = Springer New York| isbn = 978-1-4939-8728-3| pages = 99–111 |editor=Robert G. Beiko |editor2=Will Hsiao |editor3=John Parkinson | last = Rinke| first = Christian| title = Microbiome Analysis: Methods and Protocols| chapter = Single-Cell Genomics of Microbial Dark Matter| location = New York | series = Methods in Molecular Biology | date = 2018| volume = 1849| doi = 10.1007/978-1-4939-8728-3_7| pmid = 30298250}}</ref> and [[metagenomics]].<ref>{{Cite journal| doi = 10.1093/nsr/nwaa280| issn = 2095-5138| volume = 8| issue = 3| pages = –280| last1 = Jiao| first1 = Jian-Yu| last2 = Liu| first2 = Lan| last3 = Hua| first3 = Zheng-Shuang| last4 = Fang| first4 = Bao-Zhu| last5 = Zhou| first5 = En-Min| last6 = Salam| first6 = Nimaichand| last7 = Hedlund| first7 = Brian P| last8 = Li| first8 = Wen-Jun| title = Microbial dark matter coming to light: challenges and opportunities| journal = National Science Review| date = 2021-03-01| pmid = 34691599| pmc = 8288357}}</ref> These studies have enabled insights into the evolutionary history and the metabolism of the sequenced genomes,<ref name="HedlundDodsworth2014">{{cite journal|last1=Hedlund|first1=Brian P.|last2=Dodsworth|first2=Jeremy A.|last3=Murugapiran|first3=Senthil K.|last4=Rinke|first4=Christian|last5=Woyke|first5=Tanja|title=Impact of single-cell genomics and metagenomics on the emerging view of extremophile "microbial dark matter"|journal=Extremophiles|volume=18|issue=5|year=2014|pages=865–875|issn=1431-0651|doi=10.1007/s00792-014-0664-7|pmid=25113821|s2cid=16888890}}</ref><ref>{{cite journal |last1=Rinke |first1=Christian |last2=et|first2=al.|title=Insights into the phylogeny and coding potential of microbial dark matter |journal=Nature |year=2013 |volume=499 |issue=7459 |pages=431–437 |doi=10.1038/nature12352 |doi-access=free |pmid=23851394 |bibcode=2013Natur.499..431R |s2cid=4394530}}</ref> providing valuable knowledge required for the cultivation of microbial dark matter lineages. |
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==Microbes with highly unusual DNA== |
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It has been suggested certain microbial dark matter genetic material could belong to a new (i.e., fourth) domain of life,<ref name="PLOS One">{{cite journal | vauthors = Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA | title = Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees | journal = PLOS ONE | volume = 6 | issue = 3 | pages = e18011 | date = March 2011 | pmid = 21437252 | pmc = 3060911 | doi = 10.1371/journal.pone.0018011 | bibcode = 2011PLoSO...618011W | doi-access = free }} |
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*{{cite magazine |author=Colin Barras |date=18 March 2011 |title=Biology's 'dark matter' hints at fourth domain of life |magazine=New Scientist |url=https://www.newscientist.com/article/dn20265-biologys-dark-matter-hints-at-fourth-domain-of-life/ |url-access=registration}}</ref><ref name="Biology Direct">{{cite journal | vauthors = Lopez P, Halary S, Bapteste E | title = Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life | journal = Biology Direct | volume = 10 | pages = 64 | date = October 2015 | pmid = 26502935 | pmc = 4624368 | doi = 10.1186/s13062-015-0092-3}} |
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*{{cite magazine |author=Colin Barras |date=11 November 2015 |title=Mystery microbes in our gut could be a whole new form of life |magazine=New Scientist |url=https://www.newscientist.com/article/mg22830474-800-mystery-microbes-in-our-gut-could-be-a-whole-new-form-of-life/ |url-access=registration}}</ref> although other explanations (e.g., viral origin) are also possible. |
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==See also== |
==See also== |
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Revision as of 17:30, 17 August 2023
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.
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.
See also
References
- ^ 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. Bibcode:2005PNAS..10212471F. doi:10.1073/pnas.0503404102. ISSN 0027-8424. PMC 1194919. PMID 16116082.
- ^ University of Tennessee at Knoxville (25 September 2018). "Study: Microbial dark matter dominates Earth's environments". Eurekalert! (Press release). Retrieved 26 September 2018.
- ^ 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. ISBN 978-1-4939-8728-3. PMID 30298250.
- ^ 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. PMC 8288357. PMID 34691599.
- ^ 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. S2CID 16888890.
- ^ Rinke, Christian; et, al. (2013). "Insights into the phylogeny and coding potential of microbial dark matter". Nature. 499 (7459): 431–437. Bibcode:2013Natur.499..431R. doi:10.1038/nature12352. PMID 23851394. S2CID 4394530.
- ^ 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.
- Colin Barras (18 March 2011). "Biology's 'dark matter' hints at fourth domain of life". New Scientist.
- ^ 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.
{{cite journal}}: CS1 maint: unflagged free DOI (link)- Colin Barras (11 November 2015). "Mystery microbes in our gut could be a whole new form of life". New Scientist.