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Microbial Diversity and the Biosphere

by: Mrs. Willis Mante

Microbial Diversity and the Biosphere MCDB 4350

Mrs. Willis Mante

GPA 3.6


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This 33 page Class Notes was uploaded by Mrs. Willis Mante on Thursday October 29, 2015. The Class Notes belongs to MCDB 4350 at University of Colorado at Boulder taught by Staff in Fall. Since its upload, it has received 40 views. For similar materials see /class/231843/mcdb-4350-university-of-colorado-at-boulder in Molecular, Cellular And Developmental Biology at University of Colorado at Boulder.

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Date Created: 10/29/15
Lecture 5 What is the species E coli Conventional and Molecular Taxonomy Text pp 368 395 300 328 in 11th Identification in the clinical setting Text pp 900 929 779 815 in 11th History Text pp 10 24 9 20 in 11th Proteobacteria Text peruse pp 398 441 331 373 in 11th Look at mostly excellent photos Note spectacular metabolic diversity of Proteobacteria They are the kinds of microbes about which we know the most by far 1 The best studied microbial organism is Escherichia coll usually what is thought 0f in the context of typical Gram negativequot bacterium Yet Eco is neither abundant nor environmentally significant How did it get so popular A Note abbreviation Eco for E gli This is used for enzyme names and jargonistic text eg Eco R1 restriction enzyme Others eg are Hin d aem0philis Lnfluenzae strain d Sau taphylococcus wreus Taq lhermus Muaticus etc B The popularity of E coli and our perception of the microbial world is rooted of course in the history of the field A Bit of History 2 There is no history of natural historyquot in microbial biology There was no recognition of microbial life before 3 Late 1600s A Antoni van Leeuwenhoek improved early microscopes invented by Robert Hooke and described quotanimaculesquot in saliva pond water infusions semen lots other places gt500 letters on the matter to various societies For my money Leeuwenhoek is the Father of Microbial Biology B Microscope remained a parlor curiosity for next 150 years 4 lVlid lSOOs A Louis Pasteur experimentally dispelled spontaneous generationquot as the origin of life B Invented vaccines B Much focus on microbes as causative agents of disease field of quotbacteriologyquot is articulated C Robert Koch 1870 90s y Pure culture techniques introduction of agar as a solidifying agent Frau Fannie Hesse wife of a postdoc Text p 17 15 in 11th 2 Koch Postulatesquot In order to ascribe a disease to a microbe one must a Observe the organism in all instances of the disease b Culture the organism from the disease c Cause the disease by inoculation with the pure culture d Re isolate the microbe from the disease Medical microbiology remains stuck in this culture based paradigm to the detriment of our understanding of many human microbe interactions 4 Showed that TB is caused by Mycobacterium tuberculosis TB remains the major cause of death by infectious disease D Ferdinand Cohn 1850s 90s 1 Developed quotasepticquot techniques note you can39t transfer cultures sterilelyquot 2 Considered father of bacterial classification 5 Sergei Winogradsky 1900 one of the founders of microbial natural historyquot 1 Discovered lots of chemolithotrophic microbes eg Beggiatoa an H28 oxidizer 2 Articulated the concepts of quotlithotrophyquot and the involvement of microbes in quotprimary productivityquot making biomass from C02 3 Isolated first N quotfixerquot NZ gt biological N Clostridium pasteurianum B Martinus Beijerinck 1 Invented technique of quotenrichment culturequot If you provide a nutrient source something will grow be selected for 2 Isolated lots of critters eg N fixers including root nodule microbes Rhizobium 3 Founder of the quotDelft Schoolquot of microbiology strongly in uenced the development of microbial physiology Others Kluyver quotDie Einheit in der Biochimie late 1930s Donker Van Niel Stanier 6 The period 1900 1950 has been called the quotGolden Agequot of bacteriology microbiology because lots of organisms were described and lots of disease processes were explained Ie biology became aware of the microbial world NP thinks of it as early Middle Ages we haven39t gotten to the Golden Age yet A Microbial physiology industry driven expanded in 1950s and developed into quotmolecular biologyquot in the 1960s 7 Remarkably all this progress was attained without any real sense of quotwhat is a bacteriumquot in the context of the rest of life Clearly the underlying biochemistries of bacteria and other large organisms were similar quotIf it is good for E call it is good for elephantsquot But the fundamental description of a bacterium was and usually remains quotnot a eucaryotequot aka quotprocaryotequot Is lack of a property a relatable property Logically this does not follow 8 1977 First Woese paper outlining the Big Treequot This sequence based perspective allows a formal description of the organism in the context of all other organisms in the context of quotgenetic lines of descen quot quotcladesquot relatedness groups If it has that particular rDNA sequence it must be that quotkindquot of organism at least in the generality 9 1950s quotModelquot organisms emerge including Escherichia coli A Discovered 1895 Migula as common inhabitant of gut B Public health use since 40s to track human fecal contamination Note that in fact Eco is not particularly abundant in the human gut Unlike most gut microbes which tend to be strictly anaerobic Eco can survive in waterways and be grown easily in the presence of 02 C Late 40s Sex genetics first well established with E coli Lederberg Note Eco ML strains MLquotmerde Lwoffquot D Molecular biology built on the back of E coli phages biochemistry genetics 10 What is this E coli How to describe a bacterium 11 The phylogenetic perspective has enormous importance for microbial taxonomy but unfortunately the ground rules for classification are not phylogenetic but rooted in physiology the properties of the organism that interact with the environment Which often are the most volatile evolutionarily A Traditional taxonomy does not necessarily correlate well with phylogenetic results with eg rRNA 1 Note there are exceptions traits that have phylogenetic signific ancequot eg the quotOrderquot quotSpirochaetalesquot is defined morphologically by a helical structure with an axial filament and is quotphylogenetically coherentquot see BBM 12th figs Pp 477479 causative agents of syphilis Lyme39s Disease Leptospirosis other charmers eg endosporequot formation indicates members of Low GC Gram positivequot phylogenetic group one of about 40 phylogenetic divisions of bacteria currently known 2 Thus if organisms have these properties you know they belong to these groups If they don39t have them it does not mean that they are not those organisms 3 what if an organism of one of these types happens not to have retained the single distinctive character or does not manifest it in culture How to identify eg Mycoplasmas wall lessquot bacteria long mysterious often deemed ancientquot turned out to be a degenerate offshoot group of Low GC Gram Positivequotaka quotfirmicutesquot group of bacteria the quotclostridiaquot defined classically as quotGram positive anaerobic endospore formers 12 For lack of distinguishing properties microbes have been classified traditionally by most unsystematic properties Cell shape Staining reaction eg Gram stain Position of flagella polar vs peritrichous tufts vs single Nutritional properties use of different sugars use of NO3 as election acceptorquot etc A By accumulating a lot of such properties taxonomic grades have been derived These are collected in Bergey39s Manual of Systematic Bacteriologyquot 4 vols so far with the following hierarchy Formal Rank Kingdom Division Class Order Family Genus Species 2g Procaryotae Gracilicutes 4 procaryote divisions Scotobacteria Spirochaetales ales suffix Leptospimceae eae suffix Leptospim Leptospim interrogcms Names below species are sometimes used eg Biovar Biotype Serovar serotype Pathovar pathotype Phagovar phagotype special biochemical property antigenic properties pathogenic properties eg host bacteriophage susceptibility Morphovar morphotype special morphological properties C Note some conventions Organism names always Latin no k Genus name capitalized eg Escherichia Species name lower case eg E coli In text use the genus name the first time you mention the organism then abbreviate thereafter C Currently Bergey39s Manual collects organisms into quotsectionsquot in essence chapters in the Manual with no relationships implied 1 See BBM Appendix 2 pp A5 A12 for the current effort at grafting phylogenetic classification onto traditional taxonomy 2 Note lots of inconsistencies eg Pseudomonas a proteobacterium used to be classified in same group as Halobacterium an archaeon because they are both quotGram negative polarly flagellatedquot cells the old definition of p seudomonasquot a Be really suspicious when you bear the term typical PseudomonadquotGram polarly flagellated b Use of terms such as typical Gram negative organismquot indicates a profound lack of understanding or acknowledgement of microbial diversity When you hear the term the speaker usually means a representative of the bacterial phylogenetic division Proteobacteria D In summary the classical phenotypic methods consist in essence of anecdotes regarding the particular organism If you have enough anecdotes you can do pretty well Hence medical diagnostics of overt pathogens have been very successful relatively few organisms to classify ie disease related Only 7 of the 100 bacterial phylogenetic divisions known contain pathogens and even there pathogens are rare Note Why no archaeal pathogens Many diagnostic tests can be leveled Limited number of physiologies to worry about with medically relevant organisms all are chemoheterotrophs ie eat meat us 13 What is E coli The classical phenotypic descriptions aren39t very incisive are collections of anecdotal information The quotofficialquot Bergey39s Manual 1984 Linnaean description is Text Appendix 2 Kingdom Procaryotae Division phylum Note Is not the same as phylogenetic division Gracilicutes one of four divisions thinner cell walls implying a Gram negative type of cell wallquot quotSectionquot next page about 40 defined no formal Class or Order currently Facultatively anaerobic Gram negative rodsquot E coli along with eg Thermoplasma acidophilus an archaeon Family Enterobacteriaceae broken taxonomically by biochemical anecdotes next 2 pp 14 But the Linnaean system of genusspecies to identify organisms soon crashed described organisms turned out to be populations of closely similar but distinct organisms 10 SECTION 5 Facultatiye ly An erobic GramNegative Rods Table 51 Some differential characteristics of the families of Section 5quot Entero Vibrio baczerlhceae m Pastel Characteristics p 406 p 516 laceae p 550 Cell diameter um 03 15 0313 0243 Straight rods D Curved rods D Motility D 5 Flagellar arrangement liquid media Polar Lateral Oxidase test w 5 Na required or stimulatory for D grth Contain enterobacterial com man antigen Cells contain menaquinones D D Parasitic on mammals and D J birds Heme andor nicotinamide ade D nine dinuclcolide required for growth Plant pathogenicity D Organic nitrogen sources re quot J quired 39 Symbols see standard de nitions A few exceptions may occur Except Tatumella which may have polar subpolar or lateral agella Erwirw chrysanthemi does not contain the antigen Pleisomoms shigellaides contains the antigen quot Pasteurellaceae do contain demethylmenaquinones but not menaqui nones ubiquinones may or may not be produced Enterobacterioceae and Vibrionaceae may contain menaqui39nones demethylmenaquinones and ubiquinones FAMlLY39I ENTE OBAC l ERlACl ZAE HAHN 1937 Nom fam cons Opin 15 Jud Comm 1958 73 Ewmg Farmer and Brenner 1980 674 Judicial Commission 1981 104 Don J BRENNER Ehterobacteria39oeae ML n enlerabacten um an intestinal bacterium aceae ending to denote a family ML fem pl n Enterobacteriaceae the lamin of the enterobaclena Rahn39s original derivation is not certain It may have come from his genus Enterob39aclar or may have come from the root enterobaclen um Gramnegative cmiight rods 0310 x 10 60 urn motile by peritri chops agella except for Tatumlla or nonmotil e Do not form endo spores or microcysts not acidfast Grow in the presence and absence of oxygen Grow well on peptone meat extract and usually Mac Conkey39s media Some grow on Dglucose as the sole source of carbon others require vitamins andor amino acids Chemoorganotrophic res pituitary and l39ermentative metabolism Not halophilic Acid and ofte visible gas is produced during fermentation of Dglucose other curly hydrates and polyhydroxyl alcohols Catalasepositive except for Sh gella dysenterioe 0 group 1 and Xenorhabdus nematophilus oxides 408 11 414 SECTION 5 FACULTATIVELY ANAEROBIC BEAMNEGATIVE RODS Table 53 Biochemical identification ofEnterobacteriageae E a e 3 E 3 3 he a 3 3 2 w 2 quot 39 u 7 3 39 c 2 3 3 s e 3 5 e is 2 e g at 3 3 a 3 A N s 393 g g g 2 2 2 3 9 a 5 a g E 8 EgaEE eeee 5 3 g E 2 3 3 5 E 2 2 2 S 3 g g cmmm Indoleproduction 1 1 1 1 Methylred d 9 d d d 1 d VogesProskauer 1 d d Citrate Simmons 1 1 d d Hydrogen sul de on TSI 1 a UreaseChristensen s 1 d 1 d d d Phenylalanine deaminase 1 d Lysine decarboxylase 1 d Argininedihydrolase d i d d d 1 Omithine decarboxylase 1 d d 1 Motility 1 1 1 Gelatin liquefaction at 22 C d KCNgr0wthin d d 1 Malonate utilization 1 1 d 1 1 d c1 DGlucose acid production DGlucose gas production 1 d d d 11 l Lactose d d d d d d 1 1 Sucrose 11 1 d 1 d d l DMannitol Dulcitol d d 1 1 d d d Salicin d d d 1 d 1 DAdonitol 1 myoInositol 3 l 1 D Sorbitol w d 1 LArabinose 1 1 Raf nose d d d 1 m LRhamnose 1 4 1 d Maltose 1 1 DXylose d Trehalose 1 Cellobiose d d 1 aMethylDglucoside d 1 d Esculin hydrolysis d d d d d Melibiose 1 d d d 1 d DArabitol d ucate d 1 m d d d Lipasecom oil 1 Deoxyribonuclease at 2539C NOa39 gtNO 1 OxidaseKovacs ONPG galactosidnse 1 d d Yellow pigmen 1 DMannose Symbols I 9010093 of strains are positive 1 76 89 positive d 26 75 positive 1 1125 positive 0 10 positive Data are calculated for a 48h incubation period unless otherwise indicated geiatin liquefaction and deoxyribonuclease The incubation temperature was 36 1 l39C for all species except Yersinia ruckeri and Xenorhabdus species which were incubated at 25 1 C 12 A Because of often bewildering variation in otherwise quotdefinedquot species subspecies designations have been used more anecdotes strain serotype pathotype etc Dd These qualities intrinsically are not descriptions of organisms but ways to distinguish what is basically the same organism except for particular traits This is ok for medical applications but not for general descriptions of microbes C Note E coli 0157H7 an emergent pathogenquot is quotstandardquot Eco but makes shiga like cytotoxin has plasmids l that direct production of adhesin to gut wall and intimin gooses uptake of bound cells by intestinal microvilli and 30 of its genome that Eco doesn39t have 15 Thousands of E coli and Eco like organisms have been isolated over the century since Migula with much literature confusion The first quotclarityquot in the relationships among the enterics came from DNA homologyquot tests in the 1970s C DNA homologyquot tests measure bulk DNA sequence similarities in a DNA DNA hybridization analysis more below pp 387 388 in 12th 13 FAMILY L ENTEROBACTERIACEAE Shigella 4050 30 60 3040 l l j 40 50 Enterobacter Klebsiella IC39 I Salmone a 2050 2530 20 10 15 1015 Providencia Proteus Figure 52 DNA relatedness among Enterobacteriaceae The numbers represent the approximate percentage of relatedness Morganella Edwardsiella A Note some important genera besides Eco Shigella common waterborne dysentery worldwide S dysenteriae Salmonella common food pathogen S typhimurium Erwinia common plant pathogen 14 Klebsiella model for molecular biology of Nfixation how general Yersinia causes Black Plague Proteus common environmental isolate P vulgaris 16 Although llDNA homology tests give local phylogenetic relationships the results do not re ect on the relationships of the enterics to the rest of biology From the perspective of the rRNA overview Eco is seen to be a representative of the llGamma subgroup of the divisionlevel clade Proteobacteria aka llPurple photosynthetic bacteria and relatives in Woese nomenclature largescale rRNA tree of Proteobacteria Rh mlopseudonl anus Magnetospi rill um Ricketm39u Sari Group Mitochondria Alpha proteobacteria Escherichia L39oli Salmonella P gem0771mm spy BegginUa Shewanella Gamma proteobacterla Chmmmium Riiia symbiqu smdomonm rpp N ilmmmomis Aztiuetabavter Neisseriz Beta proteobacteria Desulfovibriu Swztmph almer BrPllovibrio Mumbu ctz39r Delta proteobacteria Helicaburfer Cnmpylvbacrer Ali inellz Arrabuclcr Thiovul um Epsilon proteobacteria 15 17 In order to provide a ground reference collection of Ecos the ECOR Collectionquot of 72 reference cloned strains has been established and is used for population studies A Lots of restriction studies show substantial mixing between the ECOR clones groups 1 By comparing the different genome maps it can be seen that the rate of intragenic recombination is several fold higher than the neutral mutation rate 2 Ca 6 8 of Eco genes have aberrant GC contents perhaps implying xenologs 3 Lots of insertion sequences recombinational hotspots quotfootprintsquot of sequences that jumped into the genome and out again temperate phage weird things Whoa Where did that come from etc 18From the current view there probably isn39t anything like a microbial speciesquot Each isolate may well be unique in the last analysis the definition of the organism is embodied in the genome an historical junkyard under the very heavy hammer of evolution A That is really problematic for formal taxonomy because a lot of the E coli genome isn39t even E 001139 And it39s probably changing continuously 16 An E coli genome Position base pairs Fig 2 Base composition is not randomly distributed in the genome GC skew G CG C is plotted as a 10kb window average for one strand of the entire E coli genome Skew plots for the three codon positions are presented separately leftward genes rightward genes and non protein coding regions are shown in lines 5 6 and 7 The two horizontal lines below the skew plots show the distribution of two highly skewed octamer sequences GCTGGTGG Chi and GCAGGGCG 8mer Tick marks indi cate the position of each copy oi a sequence in the complete genome and are vertically offset to indicate the strand containing the sequence The 1456 next 18 horizontal lines correspond to distinct classes of repetitive elements The penultimate iine contains a histogram showing the simi larity the product of the percent of each protein in the pairwise alignment and the percent amino acid identity across the aligned region of known phage proteins to the proteins encoded by the complete E coli genome The last line indicates the position and orientation of the EcoK restrictionv modification site AACNNNNNNGTGC N any nucleotide Two vertical lines through the plots show the location of the origin and terminus of replication SCIBQCE VOL 27 s 5 SEPTEMBER X997 0 www5clencemagorg A Are such events elements responsible for the generation of gene families Some are quite large eg 37 paralogous ABC Transporter proteins ABC ATPbinding cassette B Bottom lines Genome structures are volatile 17 amsms mat lunk the same by same cntena may defer pmfuundly by uthers The classical dEscnpths grades Dfmlatedness Campanng 17 Em gEnumEs 14 ylnazm x rm vm m 39llllllll HIHII llquotquotquot I yanssaqssmxunwaryluv vz 5 s v n a 1DH1ZII 1 5VEY IW um I m Emnmai a mmmbes am anecdutes nut 19Microbiologists at least some have long recognized the problems with the traditional descriptions and have striven for more specific relevant criteria However if you can39t even define what is a bacterium you have a problem 20 If you know what you are looking for a specific organism there are a number of techniques for identifying the presence of the organism eg using fluorescent antibodies A Culture organism a shoot into bunny which will develop antibodies 9 bleed out bunny a You now have anti organism antibody B You can detect the organism microscopically in two ways quotdirectquot or quotindirectquot staining 1 Direct Isolate antibody column chromatography covalently conjugate with uorescent chemical eg fluorescine rhodamine add to suspension containing organism and view in UV light Ab binds to organism and it glows 2 Indirect Treat suspension with serum then with anti immunoglobulin coupled to fluor The first Ab binds to the organism the second fluorescent Ab binds to the first making organism glow C We39ll discuss more general ways of using hybridization probes to visualize individual organisms 19 21 Some speclallzed tests are morerorrless useful one commonly encountered ls FAME Fatty Acld Methyl Ester quotpro lesquot text pp 386 FAs are components of membranes esterlfled to eg glycerldes unsaturated at varlous posltlons clstrans In varlous Ways but umform In partlcular Organlsm grown In partlcular Condltlons Cell mass ca 40mg treat with NaOH to saponify esters a HCl CH30H amethyl esters Shoot gemlsch through gas chromatography sum emu m mwmm s Immllumnnn lmlnnnt resn Compare results to a database of previously determined FAME profiles there are companies who do this the results can be quite precise if you are looking for something very specific But if your critter hasn39t been examined previously you won39t get a specific answer What happens if you do this with an archaeon Although FAME analyses do not provide specific genetic relatedness results commonly are presented as quotdendrogramsquot since some types of FAs are common others less so still others rare eg of an analysis These two organisms happen to be really close relatives quotspeciesquot level SSE MJS39 SUB fII E Pseu39o a mamas S em39gflrBSS Ssfmmmfs gapm I Came TESfGS39fBIE f Ll n k0 wn W 21DNA quothomologyquot tests can be useful but are cumbersome and not generally applicable the data cannot be used with a database Nonetheless there is a large literature and a lot of people do it for taxonomic purposes see BBM pp 387 388 342 343 in 11th DNA Homologyquot or DNA hybridizationquot analysis gives a somewhat subjective view of bulk DNA similarity 21 A O VLMiJw AMA Mmle 0 quotha 15 mm mmquot quot6 max 3 1 El f a i a Mm MA MN waJK h MLLVM 30 hmwwl MA luv3V HIV Vi anhwrL DixA M13 Jre Fri 11 ME I rum mgm39ww Mk MMW K inlc lJv 39 f 39l39l l MWLM Nla whirl JurlH w gt217 5 lutle alumni1 KW 4W la in mm um All JAN half LAM JANla Sl d uk my wkwd MA UM WMIMVViv j PM M04 val 94 eg polymer is precipitated by acid 5 trichloracetic acid TCA digested nucleotides are acid soluble Measure label in polymer before and after digestion CPM countsminafter CPM before x 100 homology note poor use of homology better is textuse of hybridization By comparing lots of organisms the ruleof thumb has emerged 100 genomic hybridization same organism 75 quotspecies levelquot relatedness corresponds to ca 97 rRNA sequence identity 25 quotgenus levelquot 95 rRNA sequence identity lt20 no information The typical inter phylogenetic divisionphylum level of conservation in rRNA sequence identity is 75 much more conservative than bulk genome B A lot of this has been done over the years and you will encounter if you read on bacterial taxonomy but is not generally applicable as a characterization tool for a number of reasons Have to compare each new organism with many other DNAs experimentally You get no information unless closely related The data don39t store can39t put in database and transfer from lab to lab The methods are not precisely reproducible the results are method dependent and idiosyncratic 23 B Hybridization data give whole genome similarities do not confuse with molecular sequence comparisons Eg Stackebrandt and Goebel HSB 448461994 MK Mr 9 lulu41 IGSrRNAWVy we a 3 2 a Shrkdam a bond wum I g inwa H Ramada 45 3 0 In summary Classical physiological descriptions of microbes constitute a taxonomy but do not provide relationships except as might be inferred subjectively Methods such as FAME or DNA DNA reassociation establish relationships but only if close le they are not sufficiently general to be broadly applicable All these methods require pure cultivation of organisms for characterization but we can t cultivate much of what is out there What kinds of organisms are out there in the environment anyway Introduction to the Lectures Fall 2008 These Lectures consist ofthe overhead notes used for the oral lectures in the 2007 version of MCDB 43505350 Microbial Diversity and the Biosphere Each Lecture is not a single lecture but a series to address a general topic The notes can be downloaded from the class Web site In some cases the class notes will contain material added at the last moment and may not be reflected in the Web available text In general the Lectures will be provided as PDFs If you have questionssuggestions on how to better provide the information please bring them up Lecture 1 Introduction to Microbial Diversity 0 Please tell us who you are On paper slips list Name Email address Year Major Professional intent Note Schedule is a projected outline unlikely to be the real thing since presentation times and discussions are hard to judge Examination times are fixed unless by class consensus Read Text Chapter 1 for background pp 2633 on visualizing microbes and the consequences of small really small size Note that the resolution what means of the light microscope is 02 microns Note in passing for future reference historical roots remarkably recent in history Koch s Postulates what if you can t culture Gram stain method lots of medical importance 1 Microbial diversity reflects the different ways in which microbial organisms Obtain energy and nutrients Respond to the environment and other organisms Regulate genes and metabolism Prof Norman Pace MCDB 4350 Lecture 1 Grow and divide and just tickover Sunive adverse conditions resting states Differ evolutionarily and relate to one another A Microbial organisms have the same needs as large organisms mAcrobes Indeed most of biological diversity is mlcrobial in nature historical focus aside most eucaryotes are microbial as well B Note the differing biological strategies manifest by macrobial and microbial phenotypes 1 Large creatures are comprised of different celltypes differentiated from a common genome that collectively and interdependently form the functioning community the macroorganism e you get the same organism again and again I The constituents of communities of microbial organisms are selected upon by the local chemistry and physical properties and collectively and interdependently form the functioning community eg a quotbiofilmquot In the mAcro case the organism carries the information for the required celltypes in the micro case the environment selects from the global metacommunity for the suite of required celltypes Hence the composition of a microbial community has a very large stochastic component and all differ at least subtly Prof Norman Pace MCDB 4350 Lecture 1 2 2 Traditional largeorganism biology has focused on organism shape and isolated cells general biology texts usually paint procaryotes Bad Word as simple cells rods bacilli s bacillus note contrast with Bacillus a genus name cocci s coccus spirals misnomer really helices vibrios partial helices 2 But many otherforms occur eg Slides Long filaments gt 100 pm 01 mm common eg Beggiatoa Thiopoca Branched filaments eg Streptomyces Starshaped Stela Amorphousshaped eg Sufoobus Flatlooking eg Haoarcua 3 General texts often emphasize individual cells but aggregates are the common theme in nature as in the large creature world ours most biomass is stuck to a surface of some sort Chains strepto eg streptococci Tetrads 88 and higher regular clusters Rosettes o o K o o eg Planctomyces Commonly embedded in biofilms goop Prof Norman Pace MCDB 4350 Lecture 1 Be sure that you can sketch the conspicuous cell types 4 Seldom do organisms in nature occur in isolation freeliving celltypes Microbes form complex communities ensembles of different organisms in contrast to a population which refers to a collection of the same type of organism 5 Most microbes in nature are attached to surfaces and associated with communities biofilms and mats containing interdependent quotsyntrophicquot suites of organisms syntrophs that often cannot be grown in pure culture Just like it is hardimpossible to culture most human differentiated cell lines Note differentiated states vary in environmentdependent ways eg Saccharomyces cerevisiae when starved for N becomes filamentous rather than yeast in form 6 Highly variable in size commonly 110pm in diameter but some are visible to the naked eye eg Epuopiscium gets to 100nm X 700pml Pic on p 69 Others ca 50 of what you see in the environment by microscope are only 01 03pm in diameter note that volume scales with r3 are they starved normal cells or truly small How to find out A Communities of microbes are commonly large eg metersize blobs and strata in sediments diffuse colonies in soils are little documented but potentially very large In general the structures of microbial communities Prof Norman Pace MCDB 4350 Lecture 1 are little characterized but expected to be dictated by local chemical and physical conditions rather than geography and they are always blowing around with winds waters and geological action B Stromatolites are fossil manifestations of ancient microbial communities 7 Sizeterminology funky nonstandard a nannobacteria sic really small b Planktonic terminology microplankton 20200 microns dia nanoplankton 220 microns picoplankton 022 microns etc c I ll use the term ultrasmall No definition but you know it when you see it eg hydrothermal vent community slides 8 Structural diversity A Many types of cell walls some terms you should know Gram negative Doublemembrane thin peptidoglycan wall periplasm Prof Norman Pace MCDB 4350 Lecture 1 Gram positive Singlemembrane thick peptidoglycan wall complex mesh probably periplasmlike in many regards SLayers others NOTE For historical reference you need to be familiar with the quotGram reactionquot see BBM 12th pp 2728 5859 in 10 if you are not For all the historical import however it doesn39t have much quotphylogeneticquot significance The commonly used term typical Gram negative organism is an oxymoron more on that in due course People who use that term are usually referring to a representative of the bacterial phylogenetic relatedness divisionphylum Proteobacteria B Many different external structures eg Flagella pili stalks and holdfasts capsules sheaths sometimes with multiple types of organisms etc C Many different internal structures eg Nucleoid bacterial nucleus spores inclusions of energy reserves eg sulfur poly betahydroxybutyrate glycogen etc 10 Metabolic diversity switchhitters common capable of markedly different metabolisms Eg some do photosynthesis when the sun is out and eat organics at night Traditional microbial classification has focused on metabolic traits Terminology Prof Norman Pace MCDB 4350 Lecture 1 6 A Chemoorganotroph aka Chemoheterotroph obtain energy and carbon from reduced organics eg Escherichia Bacillus 03 Chemolithotroph aka Chemoautotroph energy from reduced inorganics eg H28 Beggiatoa Fe2 Galionela carbon by fixing CO2 C Photoorganotroph aka Photoheterotroph carbon from organics energy from light eg Rhodobacter D Photoautotroph carbon from CO2 energy from light cyanobacteria plants the chloroplast is a cyanobacteriuml 11 Ecological diversity Microbial phenotypes can occupy lots of places and conditions that might seem bizarre A Extremes of ionic strength distilled H2O to NaClsaturated brines south SF Bay Dead Sea eg Haoarcua B Extremes of temperature ca 30 C to 120 C C pH pH ltOto11 D All overthe planet from deepsubsurface to clouds in the sky any place there is liquid water and an energy gradient 12 Behavorial diversity Prof Norman Pace MCDB 4350 Lecture 1 7 A Motility and taxis chemotaXis phototaXis magnetotaXis B Developmental processes sporulation Bacillus developmental growth phases Cauobacter metabolic differentiation Anabaena heterocysts for N2 fixation C Communication between like cells Quorumsensing and unlike symbioses antibiotics 13 Evolutionary diversity the basis of it all A For all the differences between different organisms the underlying biochemistries are pretty much the same DNARNA based information transfer ATP NADP chemiosmosis based energy same general pathways for carbonmetabolism and biosynthesis B All life on Earth is related ancestrally Prof Norman Pace MCDB 4350 Lecture 1 Lecture 1 slide captions M4 Nb 50 MMMMMMMM OJVCDUTLWMA WWW M O Prof The common view of microbes Epulopiscium ca 600 microns long and Paramecium 150 microns Epulos on a pinhead Anabaena cyanobacterium Dermocarpa cyano Spirulina cyano Handfullof Oscillatoria Spirulina as food Smoothie Spirulina as food Trail bar Tree Tree as microbial habitat Rhizosphere Green soil Driedup microbial jungle DittoDeath Valley Microbial world at Yosemite Pigmented rock Limestone building Concrete pillar Battleship Promentory Antarctica Cryptoendoliths Flatirons endoliths Open ocean Picoplankton SEM Marine metagenome Columbia River Basalt CRB mafic CRB seep lron Mtn CA community pH ca 1 Red salt Photosynthetic community in salt Walsby s square bacterium Feinduced bloom Galionella Norman Pace MCDB 4350 Lecture 1 CDCDCDC701010101010101UTUTUTUTUTUTLLLLALLALLWWWWWWW WUTAWM OCOOJVCDUTAWM OCOOJVCDUTLWN OCOOJVCDUTLW Feinduced bloom photosynthesis Glenwood hot cave Aditsnottite A biofabric Guerrero Negro microlandscape Guerrero Negro map Guerrero Negro mat GN mat Microcoleus GN mat with chemistry Coring the GN mat Volcano Yellowstone Great Fountain Geyser Octopus Spring Octopus Spring Pink filaments Pink filament community DAPlSEM Obsidian Pool Obsidian Pool contact slide Mid Ocean Ridge Vents collage Alvin and NP Riftia sans tube Riftia trophosome SEM Smoker chimney Vent cap on smoker ca 120 C contact slide SEM Pyrodictium occultum at 112 C HOT Mars Shower curtain soap scum Drinking water concentrated Sampling NYC aerosols The Big Tree The end Guerrero Negro Mat


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