Taxonomy of Bacteria, Bergey's Manual of Systematic Bacteriology and Gram negative Bacteria

According to latest edition of Systematic Bacteriology (2nd edition)

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3. TAXONOMY OF BACTERIA, BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY -GRAM NEGATIVE BACTERIA Srikanth H N PGS16AGR7189 Plant Pathology

4. 4 TAXONOMY OF BACTERIA

5. 1923 - Bergey's Manual of Determinative Bacteriology initiated It originated in the Society of American Bacteriologists (SAB) 1936 - Bergey's Manual Trust 1930 - of an International Association of Microbiological Societies ( lAMS ) 1984 - first edition of BMSB 1994 - ninth edition of BMDB 2011 second edition of BMSB 2015 - digital edition of BMSAB 5 History in brief

6. 6 David Henricks Bergey (1860-1937)

7. TAXONOMY Taxonomy is the science of classification of organisms. (Greek. ‘Taxis’ – arrangement; ‘ nomos ’ – law Bacterial taxonomy consists of three separate, but interrelated areas : Classification, Nomenclature and Identification . 7

8. Classification is the arrangement of organisms into groups ( taxa ) on the basis of similarities or relationships. Nomenclature is the assignment of names to the taxonomic groups according to international rules International Code of Nomenclature of Bacteria The rules are maintained by ICSP Identification is the practical use of a classification scheme to determine the identity of an isolate as a member of an established taxon or as a member of a previously unidentified species. 8

9. Etymology Etymology means "origin and historical development of a word, "Etymology" is derived from Greek etymon means "the truth" and thus aims at the true. In principle the language of biological nomenclatural names is Latin. In nomenclature, words of Greek origin as well as those of any other origin are " latinized “ before their use 9

10. latinisation Is the proctice of rendering a non latin name (or word) in a latin style Latinisation is common proctice for scientific names The main purpose of latinisation may be to produce a name which is internationally consistent Ex . Escherichia : named after Theodor Escherich , who iso lated the type species of the genus. 10

11. TAXONOMIC RANKS Formal rank - Example Domain - Bacteria Phylum - Proteobacteria Class - Alphaproteobacteria Order - Xanthomonadales Family - Xanthomonadaceae Genus - Xanthomonas Species - axanopodis Pathovar - punicae Xanthomonas axanopodis sub sp punicae 11

12. BERGEY’S MANUAL 12

13. Compilation of known bacteria  In lab , you will use the most recent edition of  Bergey's Manual of Determinative Bacteriology , published in 1994 and reprinted in 2000 , to help you identify your isolates 13

14. Bergey’s Manual of Systematic Bacteriology The volumes are organized according to molecular classification systems including 16s rRNA sequences rather than by phenotypic characteristics Basis for classification the 'gold standard' for determining phylogenetic relationships is DNA:DNA homology by hybridization or genomic sequencing. 14

15. HOW IT IS ARRANGED DIVISIONS EXAMPLE Edition First, second. Volumes 1, 2, 3, 4, 5. First edn have 4 volumes Sec edn have 5 volumes Parts A, B, C, etc Vol. 2 have three parts (2A ,2B and 2C) Vol. 5 have two parts(5A and 5B) Vol.1, 3, 4, have no parts chapters Volume two, part A contain 24 chapters 15

16. Bergey’s Manual of Systematic Bacteriology EDITION EDITOR-IN-CHIEF No. Of VOLUMS YEAR PUBLISHER FIRST John G. Holt et al., 4 1984 - 1989 Williams & wilkins in USA SECOND George M.Garrity et al., 5 2001 - 2012 Springer new York 16

17. FIRST EDITION volumes content Vol ume 1 (1984) G –ve bacteria of general, medical or industrial importance. Vol ume 2 (1986) G +ve bacteria other then AM Vol ume 3 (1989) Archaeobacteria,cynobacteria Vol ume 4 (1989) Actinomycets 17

18. SECOND EDITION volumes content Vol ume 1 (2001) The Archaea and deeply branching and phototrophic bactera . Vol ume 2 (2005) The Protobacteia (gram negative bacteria) Vol ume 3 (2009) The Fermicutes (most of the gram positive bacteria). Vol ume 4 (2011) The Bacteroidetes , Planctomycetes , Chlamydiae , spirochaetes , Fiberobacteres , Fusobacteria , Verrucomicrobia , Dictyoglomi , acidobacteria and Gemmatimonadetes . Vol ume5 (2012) The Actinobacteria (gram positive bacteria with high G+C content); 18

19. DETERMINATIVE vs SYSTEMATIC BERGEY’S MANUAL OF DETERMINATIVE BACTERIOLOGY BERGEY’S MANUAL OF SYSTEMATIC BACTERIOLOGY Provides identification schemes for identifying bacteria and archaea Provides phylogenetic information on bacteria and archaea Based on Morphology, differential staining, biochemical tests Based on rRNA sequencing Standard reference for laboratory identification of bacteria. Standard reference on bacterial classification 19

20. The organization of  Bergey's Manual of Systematic Bacteriology  makes it impractical for helping place unknown bacteria into major taxa , BUT it contains far more detail on the families, genera, and species and is far more up to date than the  Determinative  manual. 20 DRAWBACKS OF SYSTEMATIC BACTERIOLOGY

21. DYNAMIC TAXONOMY Lot of updates and additions About a hundred new genera and 600+ new species have been described per year for each of the last 5 years. To provide up-to-date description   Bergey's Manual Trust (BMT) thought about an digital edition 21

22. Bergey's Manual of Systematics of Archaea and Bacteria First Edition Publishing Online from April 2015 Editor(s): Prof. William B. Whitman Publisher : John Wiley & Sons, Inc. 22

23. Taxonomic Outline BMSAB JOHN WILCY AND SONS.pdf 23

24. 24 Bacteria are traditionally divided into the two groups: gram-positive  and gram-negative ,

25. GRAM NEGATIVE BACTERIA 25

26. 26 Reviewe is conducted in association with the journal Molecular Plant Pathology according to scientific/ ecoomic importance Volume 13, Issue 6 August 2012   Pages 614–629 Rank Bacterial pathogen  1 Pseudomonas syringae pathovars  2 Ralstonia solanacearum  3 Agrobacterium tumefaciens  4 Xanthomonas oryzae   pv .  oryzae  5 Xanthomonas campestris   pathovars  6 Xanthomonas axonopodis   pv . manihotis  7 Erwinia amylovora  8 Xylella fastidiosa  9 Dickeya  ( dadantii  and  solani ) 10 Pectobacterium carotovorum   ( and P.  atrosepticum )

27. As of January 2016, there are 30 phyla in the domain "Bacteria" accepted by  LPSN . (List of Prokaryotic Names with Standing in Nomenclature ) There are no fixed rules to the nomenclature of bacterial phyla. Generally the name of the phylum is the plural of the type genus , ( ex. Fusobacteria from Fusobacterium ) With the exception of the  Firmicutes , Tenericutes , Crenarchaeota , and   Proteobacteria , whose names do not stem from a genus name 27

28. Domain bacteria is divided into 30 phyla Acidobacteria Actinobacteria Aquificae Bacteroidetes Chlamydiae Chlorobi Chloroflexi Chrysiogenetes Crenarchaeota Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Euryarchaeota Fibrobacteres Firmicutes Fusobacteria Gemmatimonadetes Lentisphaerae Nitrospirae Planctomycetes Proteobacteria Spirochaetes Synergistetes Tenericutes Thaumarchaeota Thermodesulfobacteria Thermomicrobia Thermotogae Verrucomicrobia 28

29. Volume 2 of the Manual covers the Proteobacteria (most gram negative bacteria) in three parts. This volume is subdivided into three parts. Part A - The Introductory Essays, Part B - The Gammaproteobacteria and Part C - The Alpha-, Beta-, Delta- and Epsilonproteobacteria . The majority of gram negatives will be found in part B. Look in part C if a description of your species is not in volume B. PLACE FOR GRAM NEGATIVE BACTERIA IN BERGEYS MANUAL 29

30. PROTEOBACTERIA In 1988, Stackebrandt et al . named the Proteobacteria after the Greek god Proteus, who could assume many different shapes, to reflect the enormous diversity of morphologies and physiologies observed within this bacterial phylum. 30

31. PROTEOBACTERIA The largest prokaryotic phylum Phenotypically most diverse phylogenetic lineage. It encompasses 74 families and includes descriptions of 425 genera and over 1875 named species . (Out of 425, I am going to mention 47 important genera) account for more than 40% of all validly published prokaryotic genera 31

32. PROTEOBACTERIA 5 classes Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Deltaproteobacteria & Epsilonproteobacteria . 32

33. CLASS I ALPHA PROTOBACTERIA 6 ORDERS ( 18 families ) PROTEOBACTERIA (G – ve bacteria) Caulobacterales Rhodospirillales Rhodobacterales Rickettsiales Rhizobiales Spingomonodales 33

34. Italicized name bearing following colours Green – Benificial Red – Phytopathogenic Blue – Animal and human pathogenic Pink – Beneficial + harmful Black – other useful organisms 34

35. order Family Genera Caulobacterales (1) Caulobacteraceae Caulobacter Rhizobiales (10) Beijerinckiaceae Bradyrhizobiaceae Hyphomicrobiaceae Rhizobiaceae Beijerinckia Bradyrhizobium Nitrobacter Azorhizobium Rhizobium Agrobacterium Rhodobacterales (1) Rhodobactereacea Rhodobacter Rhodospirillales (2) Acetobacteraceae Rhodospirillaceae Acetobacter Gluconobacter Azospirillum Rickettsiales (3) Rickettsiaceae Anaplasmataceae Ricke ttsia Anaplasma Sphingomonadales (1) Sphingomonadaceae Sphingomonas 35

36. CLASS II Betaproteobacteria 6 ORDERS ( 11 Families ) XII PROTEOBACTERIA G –ve bacteria Burkholderiales (4) Hydrogenophilales (1) Methylophilales (1) Rhodocyclales (1) Nitrosomonadales (3) Neisseriales (1) 36

37. order Family Genera Burkholderiales (4) Burkholderiaceae Ralstoniaceae Comamonadaceae Oxalobacteriaceae Burkholderia Ralstonia Acidovorax Xylophilus Herbaspirillum Janthinobacterium Hydrogenophilales (1) Hydrogenophilaceae Hydrogenophilus Thiobacillus Methylophilales (1) Methylophilaceae Methylophilus Neisseriales (1) Neisseriaceae Neisseria Nitrosomonadales (3) Nitrosomonadaceae Spirillaceae Nitrosomonas Spirilum Rhodocyclales (1) Rhodocyclaceae Rhodocyclus 37

38. Gammaproteobacteria Contain 14 orders and 26 families Acidithiobacillales (2) Aeromonadales (2) Alteromonadales (1) Cardiobacteriales (1) Chromatiales (3) Enterobacteriales (1) Legionellales (2) Methylococcales (1) Oceanospirillales (4) Pasteurellales (1) Pseudomonadales (3) Thiotrichales (3) Vibrionales (1) Xanthomonadales (1) Enterobacteriales (1) Methylococcales (1) Pasteurellales (1) Pseudomonadales (3) Vibrionales (1) Xanthomonadales (1) 38

39. CLASS III Gammaproteobacteria 6/14 ORDERS XII PROTEOBACTERIA G –ve bacteria Enterobacteriales (1) Methylococcales (1) Pasteurellales (1) Xanthomonadales (1) Vibrionales (1) Pseudomonadales (3) Enterobacteriales (1) Methylococcales (1) Pasteurellales (1) Vibrionales (1) Pseudomonadales (3) 39

40. order Family Genera Enterobacteriales (1) Enterobacteriaceae Erwinia Pectobacterium Brenneria Serratia Tatumella Pantoea Enterobacter Ewingella Salmonella Methylococcales (1) Methylococcaeae Methylococcus Pasteurellales (1) Pasteurellaceae Pasteurella Pseudomonadales (3) Pseudomonadaceae Pseudomonas Azotobacter Rhizobacter Vibrionales (1) Vibrionaceae Vibrio Xanthomonadales (1) Xanthomonadaceae Xanthomonas Xylella 40

41. CLASS 4 DELTAPROTEOBACTERIA Contain 8 orders and 17 families Bdellovibrionales (1) Desulfarcales (1) Desulfobacterales (3) Desulfovibrionales (4) Desulfurellales (1) Desulfuromonales (2) Myxococcales (5) Syntrophobacterales (2) 41

42. Bdellovibrio Parasitize other Gram-negative bacteria, forms a structure called a  bdelloplast order Family Genera Bdellovibrionales (8) Bdellovibrionaceae Bdellovibrio 42

43. CLASS 5 EPSILONPROTEOBACTERIA order Family Genera Campylobacterales Campylobacteraceae Helicobacteraceae Campuylobacter Helicobacter Contain 1 order and 2 families 43

44. List of plant diseases caused by gram negative bacteria Sl. No Bacterial pathogen Disease 1 Pseudomonas syringae pv syringae Leaf blight of barley Holcus spot of maize 2 Pseudomonas syringae pv coronafaciens Haloblight of oat 3 Ralstonia solanacearum Wilt of solanaceous crops Moko disease of banana 4 Agrobacterium tumefaciens Crown gall of apple 5 Xanthomonas oryzae   pv .  oryzae BLB of rice 6 Xanthomonas campestris   pv citrumelo Citrus leaf spot 7 Xanthomonas axonopodis   pv .  citri   and  Xanthomonas axonopodis   pv .  Aurantifolii Citrus canker 8 Xanthomonas axonopodis   pv . punicae Bacteial blight of pomegranate 9 Xanthomonas axonopodis   pv . manihotis bacterial blight of cassava 44

45. Sl. No Bacterial pathogen Disease 10 Dickeya  ( dadantii  and  solani ) black leg disease of potato 11 Pectobacterium chrysanthemi Soft rot of chrysanthemum   12 Erwinia amylovora Soft rot of potato   13 Xylella fastidiosa Grape (Pierce's disease), Citrus (citrus variegated chlorosis or CVC), Almond (leaf scorch disease) and Olives (quick decline syndrome) 14 Brenneria goodwinii   acute oak decline (AOD) 15 Brenneria nigrifluens , Shallow Bark Canker of Walnut 16 Brenneria salicis watermark disease in willow 17 Serratia marcescens  Cucurbit Yellow Vine Disease 45

46. Sl. No Bacterial pathogen Disease 18 Acetobacter aceti Pink disease of pineapple  19 Acidovorax konjaci Bacterial Black Spot Disease in Cucumber 20 Acidovorax avenae Red stripe disease of oat 21 Burkhoderia gladioli  rot of gladiolus corms 22 Gluconobacter Discolouration in apple 23 Herbaspirillum rubrisubalbicans Mottled Stripe Disease on Sugarcane 24 Tatumella  Pink disease of pineapple  25 Xylophillus Bacterial necrosis and canker of grape 26 Rhodococcus fasciens Fasciation in sweet pea 27 Pantoea stewarti Stewart’s wilt of corn 28 Enterobacter cloacae Internal Decay of Onions

47. Bacterial Plant PathogenWebsites of Interest Bacterial Nomenclature Bacterial Nomenclature Up-to-date http://www.dsmz.de/bactnom/bactname.htm List of Bacterial Names with Standing in Nomenclature http://www.bacterio.cict.fr/ Bergey's Manual of Systematic Bacteriology 2nd Edition – Taxonomic Outline of the Procaryotes http://dx.doi.org/10.1007/bergeysoutline200210 Microbiology Cells Alive http://cellsalive.com/ Microbe World http://www.microbeworld.org/ Bacteria Museum http://www.bacteriamuseum.org The Microbiology Information Portal http://www.microbes.info/ Plant Pathology Plant Path Internet Guide Book http://www.pk.uni-bonn.de/ppibg/ppigb.htm Plant Disease Control Picture Index http://plant-disease.ippc.orst.edu/image_index.cfm

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49. BIBLIOGRAPHY Bergeys manual of systematic bacteriology 2 nd edition Bergey's Manual of Systematics of Archaea and Bacteria taxonomic outline, wiley Bergeys manual trust home Plant bacteriology by Kalyan Mondal https://www.google.co.in/#q=bergey's+manual+trust&* The British Society for Plant Pathology http://www.bspp.org.uk/news/article.php?id NCBI https://www.ncbi.nlm.nih.gov/pubmed/22672649 APS.net http://www.apsnet.org/edcenter/intropp/PathogenGroups/Pages/Bacteria.aspx Using Bergey's Manuals http://www.ruf.rice.edu/~bioslabs/BIOC318/bergeys.asp http://classes.midlandstech.edu/carterp/Courses/bio225/chap10/Bergeys%20Manual.htm  Bacterial phyla  https://www.revolvy.com/main/index.php?s=Bacterial%20phyla&itemtype=topic wikipedia https://en.wikipedia.org/wiki/Gram-negative_bacteria https://en.wikipedia.org/wiki/Bacterial_phyla LPSN. Bacterionet http://www.bacterio.net/index.html 49

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51. My questions.... Trust responsible for publishing bacterial classification....?, when it is started...? What is the title of digital edition of Begey’s manual....? How many phyla are there in domain Bacteria...? Prominent phylum of the domain Bacteria...? Classification of bacteria in determinative bacteriology is based on......? Classification of bacteria in systematic bacteriology is based on......? 51