User:Ku Itoi/sandbox

Practice writing.

Modify the following text by using A

'Week 4 assignment 'Evaluate Wikipedia - How to edit: Wikicode vs Visual Editor^[1]'

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Bullets - we can also create numbered list by clicking the bullets option and choose numbered list.
Insert - it allows us to add media, images, or tables.
Special characters - §äǢῇֲֲֳֳֳֳֳֳ–ᕓᛶ°—≤

Possible references

Brine pool microbial community 'Proteobacteria' and 'Archaea' based on DNA sequence^[2]

Bacterial community in Atlantis II Deep and Discovery Deep^[3]

Microbial Composition[edit]

Metagenomics Analysis[edit]

Metagenomics is a powerful genomic analysis to identify the microbiome communities in variety of environments. One problem of previous gene analysis, which requires culturing microorganisms, is that most of the microorganisms precent in nature is not culturable^[4]. Unlike the old gene analysis, metagenomics allows researchers to directly sample and analyze the microbe community from desired environment^[5]. Despite the harsh environment for living organisms, metagenomics has revealed presence of previously unknown microbiome communities in multiple Brine pools^[6]. Common procedures of marine microbe metagenomics include: sampling, filtration and extraction, DNA sequencing, and database analysis. Shotgun sequencing and 454 pyrosequencing are typically used to sequence genes and 16S rRNA are used for identification of species^[7].

Main clades and Species ^[8][edit]

Bacteria
- Firmicutes
- Em19
- Cyanobacteria
- Planctomycetes
  - Candidatus Scalindua
  - Candidatus Brocadiales
- Candidatus division od1
- Actinobacteria
- Proteobacteria
  - Gammaproteobacteria
    - Alteromonadales
    - Oceanospirillales
  - Deltaproteobacteria
  - Betaproteobacteria
  - Alphaproteobacteria
    - SAR11(Pelagibacterales)
- Planctomycetaceae
- Deferribacteres
- Chloroflexi
- - SAR406 clade(Marinimicrobia)

- Sar202_clade
Anaerolineae

Bacteroidetes

Flavobacteria

Actinobacteria

Actinobaacteria
Acidobacteria

Archaea[edit]

Euryarchaeota

Thermoplasmata
Methanomicrobia
Halobacteria
Archaeoglobi

Crenarchaeota

Psl12
Misc crenarchaeotic group
Marine group i
Marine benthic group b
Marine benthic group a
Group c3

details of archaea group ^[9][edit]

Proteobacteria

Archaea

Brine pool microbial community 'Proteobacteria' and 'Archaea' based on DNA sequence^[2] Bacterial community in Atlantis II Deep and Discovery Deep^[3] ^[10]

reconstruction of phylogeny ^[11]

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To find the right sandbox for your assignment, visit your Dashboard course page and follow the Sandbox Draft link for your assigned article in the My Articles section.

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Reference[edit]

^ "VisualEditor", Wikipedia, 2022-02-10, retrieved 2022-02-11
^ ^a ^b Esau, Luke; Zhang, Guishan; Sagar, Sunil; Stingl, Ulrich; Bajic, Vladimir B.; Kaur, Mandeep (2019-06-20). "Mining the deep Red-Sea brine pool microbial community for anticancer therapeutics". BMC Complementary and Alternative Medicine. 19 (1): 142. doi:10.1186/s12906-019-2554-0. ISSN 1472-6882. PMC 6587256. PMID 31221160.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
^ ^a ^b Bougouffa, S.; Yang, J. K.; Lee, O. O.; Wang, Y.; Batang, Z.; Al-Suwailem, A.; Qian, P. Y. (2013-06-01). "Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns". Applied and Environmental Microbiology. doi:10.1128/AEM.00254-13. PMC 3648036. PMID 23542623.{{cite journal}}: CS1 maint: PMC format (link)
^ Hugenholtz, Philip; Goebel, Brett M.; Pace, Norman R. (1998-09). "Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity". Journal of Bacteriology. 180 (18): 4765–4774. ISSN 0021-9193. PMID 9733676. {{cite journal}}: Check date values in: |date= (help)
^ Simon, Carola; Daniel, Rolf (2011-02-15). "Metagenomic Analyses: Past and Future Trends". Applied and Environmental Microbiology. 77 (4): 1153–1161. doi:10.1128/aem.02345-10. ISSN 0099-2240. PMC 3067235. PMID 21169428.{{cite journal}}: CS1 maint: PMC format (link)
^ Behzad, Hayedeh; Ibarra, Martin Augusto; Mineta, Katsuhiko; Gojobori, Takashi (2016-02-01). "Metagenomic studies of the Red Sea". Gene. Marine Genomics. 576 (2, Part 1): 717–723. doi:10.1016/j.gene.2015.10.034. ISSN 0378-1119.
^ Kennedy, Jonathan; Flemer, Burkhardt; Jackson, Stephen A.; Lejon, David P. H.; Morrissey, John P.; O’Gara, Fergal; Dobson, Alan D. W. (2010-03-15). "Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism". Marine Drugs. 8 (3): 608–628. doi:10.3390/md8030608. ISSN 1660-3397. PMC 2857354. PMID 20411118.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Wang, Yong; Yang, Jiangke; Lee, On On; Dash, Swagatika; Lau, Stanley C K; Al-Suwailem, Abdulaziz; Wong, Tim Y H; Danchin, Antoine; Qian, Pei-Yuan (2011-10). "Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea". The ISME Journal. 5 (10): 1652–1659. doi:10.1038/ismej.2011.42. ISSN 1751-7362. PMC 3176515. PMID 21525946. {{cite journal}}: Check date values in: |date= (help)
^ Lauer, Antje; Sørensen, Ketil Bernt; Teske, Andreas (2016-09-06). "Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225)". Microorganisms. 4 (3): E32. doi:10.3390/microorganisms4030032. ISSN 2076-2607. PMC 5039592. PMID 27681926.{{cite journal}}: CS1 maint: unflagged free DOI (link)
^ Wang, Yong; Cao, Huiluo; Zhang, Guishan; Bougouffa, Salim; Lee, On On; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan (2013-04-29). "Autotrophic Microbe Metagenomes and Metabolic Pathways Differentiate Adjacent Red Sea Brine Pools". Scientific Reports. 3: 1748. doi:10.1038/srep01748. ISSN 2045-2322. PMC 3638166. PMID 23624511.
^ Coleman, Gareth A.; Davín, Adrián A.; Mahendrarajah, Tara A.; Szánthó, Lénárd L.; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.; Williams, Tom A. (2021-05-07). "A rooted phylogeny resolves early bacterial evolution". Science. 372 (6542). doi:10.1126/science.abe0511. ISSN 0036-8075.

[1] "VisualEditor", Wikipedia, 2022-02-10, retrieved 2022-02-11

[:0-2] Esau, Luke; Zhang, Guishan; Sagar, Sunil; Stingl, Ulrich; Bajic, Vladimir B.; Kaur, Mandeep (2019-06-20). "Mining the deep Red-Sea brine pool microbial community for anticancer therapeutics". BMC Complementary and Alternative Medicine. 19 (1): 142. doi:10.1186/s12906-019-2554-0. ISSN 1472-6882. PMC 6587256. PMID 31221160.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)

[:1-3] Bougouffa, S.; Yang, J. K.; Lee, O. O.; Wang, Y.; Batang, Z.; Al-Suwailem, A.; Qian, P. Y. (2013-06-01). "Distinctive Microbial Community Structure in Highly Stratified Deep-Sea Brine Water Columns". Applied and Environmental Microbiology. doi:10.1128/AEM.00254-13. PMC 3648036. PMID 23542623.{{cite journal}}: CS1 maint: PMC format (link)

[4] Hugenholtz, Philip; Goebel, Brett M.; Pace, Norman R. (1998-09). "Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity". Journal of Bacteriology. 180 (18): 4765–4774. ISSN 0021-9193. PMID 9733676. {{cite journal}}: Check date values in: |date= (help)

[5] Simon, Carola; Daniel, Rolf (2011-02-15). "Metagenomic Analyses: Past and Future Trends". Applied and Environmental Microbiology. 77 (4): 1153–1161. doi:10.1128/aem.02345-10. ISSN 0099-2240. PMC 3067235. PMID 21169428.{{cite journal}}: CS1 maint: PMC format (link)

[6] Behzad, Hayedeh; Ibarra, Martin Augusto; Mineta, Katsuhiko; Gojobori, Takashi (2016-02-01). "Metagenomic studies of the Red Sea". Gene. Marine Genomics. 576 (2, Part 1): 717–723. doi:10.1016/j.gene.2015.10.034. ISSN 0378-1119.

[7] Kennedy, Jonathan; Flemer, Burkhardt; Jackson, Stephen A.; Lejon, David P. H.; Morrissey, John P.; O’Gara, Fergal; Dobson, Alan D. W. (2010-03-15). "Marine Metagenomics: New Tools for the Study and Exploitation of Marine Microbial Metabolism". Marine Drugs. 8 (3): 608–628. doi:10.3390/md8030608. ISSN 1660-3397. PMC 2857354. PMID 20411118.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[8] Wang, Yong; Yang, Jiangke; Lee, On On; Dash, Swagatika; Lau, Stanley C K; Al-Suwailem, Abdulaziz; Wong, Tim Y H; Danchin, Antoine; Qian, Pei-Yuan (2011-10). "Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea". The ISME Journal. 5 (10): 1652–1659. doi:10.1038/ismej.2011.42. ISSN 1751-7362. PMC 3176515. PMID 21525946. {{cite journal}}: Check date values in: |date= (help)

[9] Lauer, Antje; Sørensen, Ketil Bernt; Teske, Andreas (2016-09-06). "Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225)". Microorganisms. 4 (3): E32. doi:10.3390/microorganisms4030032. ISSN 2076-2607. PMC 5039592. PMID 27681926.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[10] Wang, Yong; Cao, Huiluo; Zhang, Guishan; Bougouffa, Salim; Lee, On On; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan (2013-04-29). "Autotrophic Microbe Metagenomes and Metabolic Pathways Differentiate Adjacent Red Sea Brine Pools". Scientific Reports. 3: 1748. doi:10.1038/srep01748. ISSN 2045-2322. PMC 3638166. PMID 23624511.

[11] Coleman, Gareth A.; Davín, Adrián A.; Mahendrarajah, Tara A.; Szánthó, Lénárd L.; Spang, Anja; Hugenholtz, Philip; Szöllősi, Gergely J.; Williams, Tom A. (2021-05-07). "A rooted phylogeny resolves early bacterial evolution". Science. 372 (6542). doi:10.1126/science.abe0511. ISSN 0036-8075.

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