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Phylogenetic Tree of Bacteria

Phylogenetic Tree of Bacteria. Phylum Deinococcus-Thermus represent radioactive resistant bacteria of the Deinococcaceae and Trueperaceae family and slightly thermophilic / thermophilic bacteria of Thermaceae family

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Phylogenetic Tree of Bacteria

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  1. Phylogenetic Tree of Bacteria

  2. Phylum Deinococcus-Thermus represent radioactive resistant bacteria of the Deinococcaceaeand Trueperaceaefamilyand slightly thermophilic/thermophilic bacteria of Thermaceaefamily have been recognized solely on the basis of their branching patterns in 16S rRNA, no biochemical or physiological characteristic is currently known that is unique to this phylum. all members have outer membrane and stain gram-negative while others have outer membrane and also thick peptidoglycan layer that cause them stain gram-positive widely distributed proteins in this phylum include 8 proteins : seryl-tRNAsynthetase, threonyltRNAsynthetase, RNA polymerase β′ subunit, signal recognition particle protein Ffh/SR54, major sigma factor 70, ribosomal protein L1 and UvrA.

  3. Taxonomy So far there are 49 species and subsp.

  4. Phylogenetic Tree based on 16S rRNA analysis

  5. Genus Deinobacter (Dei. no. bac’ter. Gr. adj. deinosstrange or unusual; M.L. n. buctermasculine equivalent of Gr. neut. n. bacterium a rod; M.L. masc. n. Deinobacterunusual rod Genus Deinococcus Deinococcusunusual cocci Famous species : Deinococcusradiodurans

  6. potential for sewage treatment on long space flights, there is also speculation that we can use this bacteria in environmental engineering of Martian surface. • producing synthetic organism Mycoplasmalaboratorium by Craig Venter Institute (2006) because the DNA repair system of D.radiodurans is capable of joining fragments of DNA. • Information storage that survive nuclear catastrophe. Information is translated into DNA sequences and inserted into the bacteria (2003).

  7. Deinococcusradiodurans • listed in Guinness Book of World Records as the world’s toughest bacterium • can survive drought, lack of nutrients and a thousand times more radiation than a person can stand. • radiodurans means ‘withstands radiation’ • is the most radiation resistant organism known. • have a DNA repair system known as RecA system that is highly effective in repairing damaged DNA

  8. Application of Deinococcusradiodurans • in Environmental cleanup – for sites contaminated with heavy metal, such as mercury, toxic chemicals and radioactive wastes. • simulation to predict where to search life on Mars – because this bacteria was found in Antarctic dry valleys which closely resemble Mars

  9. Genus Truepera • Named in honor of the German microbiologist Hans G. Truper • from a hot spring within a geothermal area located along an almost vertical wall and dry bed of a stream

  10. Characteristics • Gram indeterminate • Colonies are orange/red pigmented • Endospores are not formed • Alkaliphilic • Slightly thermophilic • Slightly halophilic • mole G + C of the DNA of the type species is 67–68%.

  11. Trueperaradiovictrix ra.di.o.victrix. L. n. radius, beam, N. L. prefix radio- pertaining to radiation, L. fem. n. victrix, female winner, N. L. fem. n. radiovictrix, the vanquisher of radiation • forms spherical shaped cells 1.25–2.0 lm in diameter • The cells stain Gram-indeterminate • Not motile • Colonies are orange/red pigmented • Extremely ionizing radiation resistant • Facultativelyhalophilic • mole G + C ratio of the DNA is 67.6–67.8%

  12. Genus Vulcanithermus • Vul.ca.ni.ther9mus. L. n. Vulcanus the Roman god of fire; Gr. adj. thermos hot; N.L. masc. n. Vulcanithermus heat-loving organism, living in the vicinity of volcanic areas • from the Rainbow deep-sea hydrothermal vent field

  13. Characteristics • non-motile • Gram-negative rods • Moderately thermophilic • Neutrophilic • Adapted to the salinity of sea water • Microaerophilic • Capable of aerobic growth • Able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols • Capable of anaerobic growth with nitrate, which is reduced to nitrite

  14. Vulcanithermusmediatlanticus me.di.at.lanti.cus. L. adj. medius middle; L. masc. adj. atlanticus Atlantic; N.L. adj. mediatlanticus from the middle of the Atlantic • Optimal growth temperature is 70 C • The optimal pH is around 6,7. • The optimum salinity is 3% NaCl. • The G+C content of the DNA of the type species is 68,4 mol%.

  15. Genus Oceanithermus • O.ce.a.ni.thermus. L. n. oceanus the ocean; Gr. fem. n. therme heat; N.L. masc. n. Oceanithermus warmth-loving organism living in the ocean • isolated from a deep-sea hydrothermal vent

  16. Characteristics • non-motile • Gram-negative rods • Moderate thermophile • Neutrophile • Adapted to the salinity of sea water • Microaerophile • Flagella and spores are not observed

  17. Oceanithermusprofundus (pro.fundus. L. gen. n. profundus of the abyss, the depths of the ocean • The optimal growth temperature is 60 C. • The optimal pH is 7,5 • The optimum salinity is 30 g/L • The G+C content of the DNA of the type strain is 62,9 mol%

  18. Meiothermus

  19. Banyak ditemukan pada teresterial hotspring dengan pH netral atau basa. Berasal dari bahasa Yunani meion (sedikit) dan thermus (panas)

  20. Karakterisasi : • diameter 0.5-0.8 um. • Berfilamen, gram negatif, non-motil • berwarna merah atau kuning • respirasi aerobik, namun ada juga yang menggunakan nitrat sebagai akseptor elektron • suhu optimum = 500C - 650C • pH optimum = 8 • menghidrolisis protein dan peptida • hanya beberapa spesies yang menghidrolisis pati • Membutuhkan yeast extract dan kofaktor untuk tumbuh • %GC = 59-70 mol % Meiothermus slime (www.biocenter.helsinki.fi)

  21. Contoh Spesies : • Meiothermus ruber • Koloni berwarna merah • Temperatur pertumbuhan optimum pada 60-650C. Tidak tumbuh pada 700C • Tidak menghidrolisis pati dan tidak mereduksi nitrat • % GC = 61-63% Meiothermus ruber (www.jgi.doe.gov/education/adoptagenome/index.html

  22. Meiothermus silvanus • membentuk koloni merah • pertumbuhan optimum pada 550C. Tidak tumbuh pada 650C • menghidrolisis pati dan mereduksi nitrat • menggunakan xylose dan ribitol untuk pertumbuhan • % GC = 63.6 mol% • kegunaan : Biofouler (bakteri yang dapat mendegradasi berbagai macam bahan, seperti kertas, baja, dsb) Meiothermus silvanus (www.jgi.doe.gov/education/adoptagenome/index.html)

  23. Marinithermus

  24. Banyak ditemukan pada deep-sea hydrothermal vent chimney • Berasal dari kata marine (laut) dan thermus (panas)

  25. Karakterisasi : • berbentuk batang, gram negatif, heterotrof aerobik • thermophilic • pertumbuhan cocok pada pH dan salinitas air laut • kondisi optimum : • Suhu = 55-700C • pH = 6.2 - 7.7 • Salinitas = 1- 4.5% NaCl • dapat menggunakan substrat organik, asam amino, asam karboksilat, dan gula • % GC = 68 mol %

  26. Contoh Spesies : • Marinithermus hydrothermalis • gram negatif, non-motil, batang • Ukuran : 7.5-9.4 x 0.9-1 um • koloni putih dengan diameter 2.5-3 mm • serobic, thermophilic, neutrophilic heterotrof • kondisi optimum : suhu : 67.50C pH : 7 salinitas : 3% NaCl • % GC = 68.6 mol% Marinithermus hydrothermalis (Sako, 2003)

  27. THERMUS

  28. Ditemukan pada habitat thermal seperti thermal spring, hot tap water, dsb • nama Thermus berasal dari bahasa Yunani, thermos, yang berarti panas

  29. KARAKTERISASI : • batang dan filamen, diameter 0.8-0.8 um • gram negatif. Tidak memiliki endospora dan flagella • koloni kuning padat • tidak butuh faktor untuk pertumbuhan • kondisi optimum : • Suhu : 70-720C • pH : 7.5 – 7.8 • sensitif terhadap streptomycin, penicillin, novobyocin, actinomycin D, chloramphenicol • % GC = 65.4-67.4 mol % Thermus aquaticus (Brock, 1969)

  30. Contoh Spesies : • Thermus aquaticus • nama Thermus aquaticus berasal dari bahasa latin, aqua, yang berarti air. • terinhibisi oleh tryptone dan yeast extrast dengan konsentrasi 1% • membentuk microbial mat • koloni kuning, gram negatif, non-motil, berbentuk batang • sensitif pada actinomycin D • utilitas : sumber enzim DNA Taq poltmerase, Taq I restriction enzyme, RNA polymerase, aldolase Thermus aquaticus (Brock, 1969)

  31. References Brock TD, Freeze H. 1969. Thermusaquaticus gen. n. and sp. n., a NonsporulatingExtreme Thermophile. J Bacteriol98 : 289-297. Griffith E, Gupta RS. 2007. Identification of signature proteins that are distinctive of the Deinococcus-Thermusphylum. IntMicrobiol10:201-208. Hobel, CFV. 2004. Access to Biodiversity and New Genes from Thermophiles by Special Enrichment Methods. [Dissertation]. Iceland : University of Iceland. Luciana A, Catarina S, Fernanda N, Nicole MP, John RB, Manuel TS, Fred AR, Milton SC. 2005. Trueperaradiovictrix gen. nov., sp. nov., a new radiation resistant species and the proposal of Trueperaceae fam. nov. FEMS Microbiol247 : 161–169 Madigan MT, et. al. 2009. Brock’s Biology of Microorganisms. 12th edition. San Fransisco : Benjamin Cummings. Miroshnichenko ML, et. al.2003. Vulcanithermusmediatlanticusgen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J SystEvolMicrobiol53 : 1143– 1148. MiroshnichenkoML, et. al. 2003. Oceanithermusprofundusgen. nov., sp. nov.,athermophilic,microaerophilic, facultativelychemolithoheterotrophicbacterium from a deep-sea hydrothermal vent. Int J SystEvolMicrobiol53 : 747–752 Nobre MF, Truper HG, Costa MS. 1996. Transfer of ThermusruberThemussilvanus, and Themuschliarophilusto Meiothemzusgen. nov. as Meiothermusrubercomb.nov., Meiothermussilvanuscomb. nov., and Meiothermuschliarophiluscomb.nov., and Emendation of the Genus Thermus. Int J SystEvolMicrobiol46 : 604-606.

  32. Oyaizu H, et. al. 1987. A Radiation Resistant Rod-Shaped Bacterium, Deinobactergrandisgen.nov., sp. nov., with Peptidoglycan Containing Ornithine. Int J SystBacteriol 37:62-67 Rainey FA, et. al. 1997. Phylogenetic Diversity of the Deinococci as Determined by 16S Ribosomal DNA Sequence Comparison. Int J SystBacteriol 47 (2) : 510-514. SakoY, Nakagawa S, Takai K, Horikoshi K. 2003. Marinithermushydrothermalis gen. nov., sp. nov.,a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int J SystEvolMicrobiol53 : 59-65. Salkiloja-Salonen M, Peltolla M, Kuosmanen T. 2006. Biofouling Bacteria. [online] www.biocenter.helsinki.fi/.../page4.htm. [13 October 2009]. Anonim1. 2009. What is The Adopt A Genome Program? [online]. www.jgi.doe.gov/education/adoptagenome/index.html. [13 October 2009]. Anonim2. 2006. Detection and quantitation of colored deposit-forming Meiothermus spp. in paper industry processes and end products. Electr J Microbiol Biotech 34 (3). 211p. [online]. http://www.springerlink.com/content/b5162m28018q5332/. Issued March 2007 [13 October 2009] Anonim3. 2009.Texas Geothermal Energy. http://www.seco.cpa.state.tx.us/Images/re_geo-hotspring.jpg. Tanggalakses : 13 Oktober 2009 Anonim4. 2009. Hydrothermal Vent. http://i.treehugger.com/images/2007/10/24/deep-ea%20hydrothermal%2 0vent-jj-001.jpg. Tanggalakses : 13 Oktober 2009

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