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1 2 Balows 1992 bacteria actinomyces cyanobacteria archaeobacteria IUCN, 2 1 Prokaryotic microbe systematics classification nomenclature identification

2 Bull numerical taxonomy molecular systematics chemotaxonomy Goodfellow O Donnel

3 , IS Linne 2 2 (Kingdom/Regnum) Procaryotae Division Diviso Gracilicutes Class Classis Protobacteria Order Ordo Pseudomonadale Family Familia Pseudomonadaceae Genus Genus Pseudomonas Species/Species Pseudomonas aeruginosa International Code of Nomenclature of Bacteria ICSB Species Genus tubercle bacillus (Mycobacterium tuberculosis International Journal of SystematicBacteriology 4 sn nov gen nov comb nov

4 2 2 DNA g ph PH Actinoplanes Streptoverticillium 4cm 20 l Labeda ,120 1 Micromonospora,Microbispora Streptosporangium 45 2 Rhodococcus 50 10,70 30 Micromonospora 2 :, ~30 7~14,

5 CO ~5ìg ml) Streptosporangium Actinomadura 10ìg ml) Micromonospora 25ìg ml 25 Actinomadura 20ìg ml G(10U ml) Rhodococcus 10 15ìg ml Actinoplanetes 100ìg ml Thermoactinomyces 25ìg ml 25ìg ml Glycomyces G 5 10ìg ml 15ìg ml Saccharothrix G 1ìg ml 5ìg ml Actinomycetes 25ìg ml Actinomycetes 25ìg ml Actinomadura Nocardia 20ìg ml 30ìg ml Micromonospora l 10ìg ml 5ìg ml Amycolatopsis anaerobes CO 2 S 2 O 2 microaerophile 3 2 moderately anaerobic strictlyanaerobic 5 biotransformation., /ml,

6 2 5 Acetobacterium malicum Bacteroides pcctinophilus Eubacterium limosum Ruminal CO 2 CO 2 CO H 2 Eubacterium angustum Hyobacter polytrophus HOAc 3- HOAc l 3-3- HOAc HOAc Oxalobacter formigenes Ruminal CO 2 Pelobacter acetylenlcus Selenomonas acidaminophila Syntrophomonas acidaminophila Ruminal H 2 Syntrophomonas wolfei Ruminal O 2 Eh Eh -50 mv Clostridium perfringems,bacteroides fragalis Peptostreptococcus magnus N 2 CO archaeobacteria

7 2-6 Methanothermus sociabilis Solfatara 97 H 2 CO 2 CH 4 Pyrobaculum organotrophum Solfatara 100 H 2 S H 2 S Staphylothermus marinus S H 2 S XO S H 2 S Thermoanaerobium brockii 65 H 2 CO 2 Thermoanaerobium ethanolicus Thermal 70 CO 2 Thermoproteus tenax Solfatara H 2,CO : ;

8 0 1 W V Na 2 P 2 O 7 10H 2 O PH t n n t S sm S sm a + d n (% ) = a d n

9 technique single linkage cluster analysis dendrogram 2 6 MINTS

10 2 3 2 chemotaxonomy Mycobacterium Legionella SIMCA Corynebacterium Nocardia Rhodococcus Streptomyces cyaneus SIMCA Ampcolata Amycolatopsis Pseudonocardia Erwinia,Pseudomonas Xanthomonas Corynebacterium Staphylococcus epidermidis S Haemolyticus Streptococcus pyogenes Corynebacterium Xanthomonas campestris Goodfellow O'Donnell(1994) M N- G N- â-1 4 PePtidoglycan meso DAP 3 4 Corynebacterium Mycobacterium Nocardia

12 Lactobacillus Arthrobacter Propionibacterium Streptococcus Pediococcus Micrococcus Leuconostoc Staphylococcus Bifidobacterium 3 3 LL DAP 3 4 Streptomyces Nocardioides 4 3 L D- 4 D- Lechevalier I L DAP glyclne Streptomyces 11 II meso DAP glyclne Micromonospora 5 III meso DAP Actinomadura 13 IV meso DAP arabinose galactose Nocardia 8 V lysine ornithine Actinomyces israelii 1 VI lysine,(asparic acid,galactose Oerskovia 4 VII DAB glycine Agromyces 1 VIII ornithine Bificobacterium 2 IX meon DAP, Mycoplana 1 * Ala Gln Muramic acid * * 2 9 A Arabinose Galactose Nocardia 10 B Madurose Actinomadura 10 C Thermoactinomyces 5 D Xylose Arabinose Micromonospora Lechevalier M P., LechevalierH.A PE phos phatidyl ethanolamine ; PME phosphatidyl methylethanolamine glycerol containing glucosamine PC phosphatidyl choline PC phosphatidyl Gln Nu Phospholinids of unknown structure

13 2 8 a. b c. d e 2 8 fatty acid methyl esters FAMES iso anteiso CH 3 CH CHZ X COOH CH 3 CHZ CH CHZ X COOH CH3 iso CH3 anteiso anteiso iso ANT-ISO 17 4 I anteiso iso ANT ISO II 17 ANT-ISO III 17 ANT ISO IV ANT-ISO 10 Lechevalier M P Lechevalier H A

14 PE PME PC Glu Nu PG P I V PII PIII v v - v PIV v v - - P V V Isoprenoid quinone Jeffrie 1967 Collins Menaquinone V K 2 Ubiquinone Q l MK Gordonaurantiaca Corynebacterium Paurometabolum Micrococcus 2-11 Eubactria scandidus I a MK 7 Thermoactinomyce b MK 9 Gordona aurantiaca Mycobacterium II a MK 8 H 2 Rhodococcus hodochrous 8 9 b MK 8 H 4 Nocardia 2 4 c MK 9 H 4 Mycobacterium Sarcharomonospora III a MK 8 H 4 MK 9 H 4 Saccharomonospora b MK 9 H 4 MK 10 H 4 ActinoPlanes Streptomyces IV a MK 9 H 2 MK 9 H 4 MK 9 H 6 Microtetraspora b MK 9 H 4 MK 9 H 6 MK 9 H 8 StrePtomyces C MK 10 H 4 MK 10 H 6 Nocardiopsis

15 2 3 3 molecular systematics DNA ribotyping RFLP DNA rrna rrna DNA DNA

16 DNA m t C DNA A T G 3 A T G C 4 A T G C G C mol G C mol Saccharompces cerevisiae Bacillus subtilis Homo sapiens G C mol G C mol G C mol DNA 1 DIG DIG Digoxigenin DNA RNA Boehringer Mannheim 1992 DNA DNA TaqDNA DIG 11 UTP RNA SP6 T3 T7RNA DIG 11 UTP 3 DIG 11 UTP -NHS 5 DNA DNA RFLP DNA DNA

17 DNA DNA DNA DNA BamHI 5 GGATCC 3 3 CCTAGG 5 5 G pgatcc 3 3 CCTAGp G 5 DNA S rrna Woese S rrna 16S rrna 16S rrna 16S rrna rrna 30S 50S 30S 16S rrna 21 50S 23S 5S rrna 34 rrna rrna 16S 23S 5S rrna RNA 90 rrna DNA 16S rrna 16S rrna 16S rrna 23S 16S 5S 3 rrna S rrna S rrna S rrna 16S rrna 16S rrna archaeobacteria eubacteria

18 20 60 Uchida 1974 Sanger 16S rrna rrna rrna 16S rrna Aerobacteraerogenes Yersinia Pestis r T 1 G 3 G 6 16S r 1542 T G 20 3n n G

19 S r S r S r 6 16S r S rrna 16S rrna HVE TLC HVE 16S rrna HVE DEAE HVE 16S rrna 2 11 TLC HVE

20 16SrRNA 16S rrna T 1 32 P ATP HVE DEAE 16S r 400 Woese 1987 Woese t t intron t RNA Chloramphenicol Kanamycin Rifomycin S AB S AB 16S rrna Woese S rrna 10 RhodosPirillum Spirochaeta Sulfate reducing bacteria Bacteriodes Cyanobacteria Green sulfurbacteria Flavobacterium Cytophaga Green non sulfurbacteria Deinoccus radiodurans Planctomyces

21 10 10 Phyla

509 (ii) (iii) (iv) (v) 200, , , , C 57

509 (ii) (iii) (iv) (v) 200, , , , C 57 59 (ii) (iii) (iv) (v) 500,000 500,000 59I 18 (ii) (iii) (iv) 200,000 56 509 (ii) (iii) (iv) (v) 200,000 200,000 200,000 500,000 57 43C 57 (ii) 60 90 14 5 50,000 43F 43C (ii) 282 24 40(1B) 24 40(1) 58