MICROBIOLOGY EBIO 3400
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Photosynthetic Bacteria phylogenetically widespread LECTURE 1 3 THE BACTERIA cont Photosynthetic Bacteria gt Green Sulfur chlorobi gt Green Sulfur gt Green Nonsulfur chloroflexi gt Green Nonsulfur Anoxygenic gt Purple Sulfur Photosynthesls gt Purple Sulfur Proteobacteria gt Purple Nonsulfur gt Purple Nonsulfur gt Cyanobacteria Oxygenic Photosynthesis New terms with relation to the cyanobacteria 1 Trichome 2 Akinetes speci zed dormant cells that row of bacteriaI can in a are very resistant to desiccation Ilament Os cilla toria 3 Heterocysts special cells where nitrogen xation takes place Photosystem I s ll makes ATP but get rid of PS ll so no 02 is made The 0 would poison the enzyme that fixes the nitrogen nitrogenase The heterocyst gets nutrients from nearby vegetative cells and gives them the fixed nitrogen that it makes Other tidbits about cyanobacteria gt Many disperse via ng mot ty gt Common in almost all waters and soils gt They are the algae half of most lichens and many others are symbiotic with other organisms Hormogomum T D Erack Helerucyst Vegetative ceHs b Vegetative ceHs The thamydiae and Planctomyces fl A c i Tns39wvmga Emmy uemacmumvems Sprinrnastes Beuemrde es The Chlamydiae 0 obligate intracellular parasites r can39tmake n i eiernATPl small in size 7 and no peptldoglycan thus not sensitive in penicillin 0 genus Chlamydia many human pathogens nd genetical chlamydia inrecuons are caused by dirrereni sirains of c rachomans Elemenmy bodies 7 infectiom spores e culale bodies 7 growing cells imide vacuoles of host cells Planctomyces 7 large group of aquatic bacteria related to Chlamydia but none cause disease Must have never been grown inthe la 7 No peptidoglycan 7 cell walls are protein Selayer e Reproduce by buddi 11 7 Have stalks made of protein no cytoplasm inside 7 have internal compartments eg see nucleoid of Gemmata or anammoxosome of Bracadia The Spirochaetes Fig 1127 gt have exible helical shape gt Also distinguished by motility s can move through viscous solutions gt Use unique structure called the axial filament Fig 2510 C trachoma tis attaching to fallopian tube mucosal cells Fig 1130 Numbers indicate development of infectious elementary bodies The Splrochaetes i Aqiimcae i T m i o ot c i v marinaraii rnrmiis Sacvalclnctcs Spirochaetes live in diverse habitats Usually anaerobic facultative or obligate Group contains some important pathogens but rnosi are harmless muck dwellers or eg beiween your ieein gtTrepanema pallidum s Syphilis gtBarreh39a burgdarferi s Lyme Disease gtLepmspi39rai i39ri terrogans e an aerobic spirochaete leptospirosis kidney infeEUDn BacteroidesFlexibacterCytophaga CFB group L Deiviui uccusri Mammy Cytaphaga and Sparacymphaga obligate aerobes 7 most important aerobic bacterial degmdets of cellulose in the bicsphere Extmcellular cellulmes 7 see overheads W muuwm mu mm mm Bacterai39d es anaerobic 7 hard to culture some canbe Opportunistic pathogens important in rumens and colons 7 Bacteraides dominant genus in the colon 7 10 billion per gmm of human feces own polymeric substrates eg cellulose es 7 break d using extracellular enzym 0 use gliding motility LECTURE 14 GRAM POSITIVE BACTERIA GC content is useful for classifying Bacteria 7 especially Gram ltKIGC GCGCATX100 percentage of guanine G and cytosine C in the DNA of the organism Quick method to group organisms but two or 39sms can have similar GC but completely different DNA sequences It is only useful in conjunction with other tests and for groups that differ by gt 10 or so in GC Mycnpiamm Hahnbacillus Spummuxa WWW Clashidiqu nhzoha let an m Smyvmuycu Mycubactemmi mumhac lus sueyvacaccus Lu HL subdh isnn High um subdh isun The Mycoglasmas I lack cell walls pleomorphic very exible because no cell walls I have smallest bacterial genomes NSOOOOO BPs about 18 the size of E 301139 I most are parasites or commensals Fig 1128 Colonies of Mycoplasma pneumoniae Clostridi um can ferment amino acids remember the Stickland reaction One amino another acid is is the oxidized electron acceptor to restore NADt mm 5 Anv l Vi mm Low Gc Gram Positives o The Mycoplasmas Clostridia Bacilli Lactic Acid Bacteria The Clostridia Clostridium ohligately anaerobic I K 19quot endospore producers is u k E Some pathogens 00 tetani causative agent of tetanus spoil food even canned foods food borne pathogens C botuinurn and C perfringens Boiling 100 C won t kill them autoclaves or pressure cookers needed to kill endospores 121 C for 20 min The Clostridia Heliohacteria photosynthetic hacteriochlorophyll g some will form endospores Fig 1116 a Bacillus The genus Bacillus anthracis spores form in middle of cells b Clostridium tetani spores at the end of cells endospore formers chemoheterotrophs usually motile usually rapid growers diverse group likely to be split into at least 5 groups Sheep were placed in pens and bombs filled with anthrax spores were dropped on the island The sheep started dying 3 days later The island had to be quarantined for 48 years In 1981 they soaked the island with 280 tons of formaldehyde in 2800 tons of seawater then removed the topsoil the island was declared safe in 1990 but there are still few visitors B EllssoMng n1 cugsuls and c Toxins bjnd lolecepxovs activation a owns m 9m Ewthelwm 5 Eplihen m andolaxm r pmmm t Perroxanon of gut mamhvana F D Spores I germlnamand bzcteliz prememe Fig 1 Mechanism m DXlCliy an El Important Bacillus species B an thracis causitive agent of anthrax Organisms studied by Koch important agricultural pathogen Mail tainted with anthrax spores found recently WWII Brits experimented with B anthracjs on Gruinard island off Scotland Bacillus thuringiensis Bt B sphaericus Both species form a parasporal body a solid protein crystal next to their spores These species of bacteria kill insects B thuringiensis moth larvae caterpillars beetle larvae B sphaericus mosquito larvae Genes from Bt have been integrated into several plant genomes to give plants permanent resistance to pests v Mum m 1 mm 0 levliel A mum H mm mm mm 3 Bacillus thuringiensis Bt B sphaericus LECTURE 1 4 Both species form a parasporal body a solid protein crystal next to their spores GRAM POSITIVE These species of bacteria kill insects BACTERIA cont B thuringiensis moth larvae caterpillars beetle larvae B sphaericus mosquito larvae Genes from Bt have been integrated into several a crust Enwssoluingulclgslalsznd c Toxvnsbjndtolecemors plant genomes to give plants permanent activalinn ml to in am Ewth hum 7 resistance to pests r E Sendutnmn WWWquot r Recw I Performquot Acnualsd mm Toxvn 0 Eu membvan 1 a I 0 4 M AWJ J H39 Or D Sppws germlnzleand backsquot moweran Hg 1 Mechanism m taxmny at El Bt is a popular organic insecticide The Giant Bacterium Epulopiscium These bacteria are closely related to Clostridia and Bacillus First isolated from a surgeonfish S P tquot 11 14 ee erspec Ive pg J mum cellrlormlnn Assumed to be protozoa because of their size up to 600 uM ennmpuemmm DNA sequencing showed however that EpuIOpiscium is a bacteria not a protozoan man is 51st 551112 head of a uu y sawm m staphquot mammary ammuc mnmm ml am form lrmllllar emum F15 22 1 The shnas acamplex landscape in edee mu 1 searsanlsms ymdunefany Ends 25 ympmmcamd by fermennns adsfmm the sehmeaus 51m Aha glam mumquotk Thlw39mo tm mm mm mm mm m ms an a loam and mm a an olmmn annular Fanonm mm hatth 9 hm I am a much a 9m mmquot call mum Mn 2 vacuole mum wm quotmm mm 11 1 Menu ammm mums a a amedm dry cmdmrms Inble 221 PFiquwa l Mi e t e Noy al Skin Flnn mm ChandevisI 5 wwwm Aral Amwn Mymw WWW MN m mmmm 1m mmmm amen WWW m MMwmmuwu mm mm MIMIc quotmm mmm mamm mm mm mum m um MmummhilMmem r M cur uvmn Table 231 The Nose andupper resyiram tract Staphylococcus aureus are the predomina See Table 231 2 0 much borer snore husFl umans carry S aureus athogen and s epidermidis nt bacteria in the nose miwozkers of an opportunistic P Fig 22 3 Boil or pimple formation mused by coagulaserposiuve Smphylococchu ohm Table 32 i Cummun genera Streptommus Enterococcus Lactococcus and Laczobamlus norm produce spores Lactic Acid Bacteria R 511 Fzzmaumnns pruduce lactic acid as fermentaxiun prnduct gtHomolactic fermentation 7 only lactic acid 2 per sugar fermented gtHeterolactic fermentation 7 other things too usually 1 lactic acid and 1 acetaldehyde or oioohoi mic mid bumm are mamxiv bacteriathat can mleraIe 02 but can t use 02 in their metabulism aemmlerant Live in rich envimnments hie your rhroer or milk and have last the ability rhroogh evoiooonory r o synthesize many aminu acids and vitamins Such Drganisms are referred ro as midis streptococci strep e cr furtwisted some are Impa am pathogens eg S pneumoniae and s morom very oo o inhabitants thhe human body and funds wuic memck o m minui l Homolactic fermentation FIDde 2 ionic and fur every glut se used in feri39i39EnmnDn Fig ii 3 Streptowlwxspp Streptococcal Diseases varmus srrepramcus species We Will renrenrrare en reern decay denral canes Dday read pgs 5027504 new i l mum tilts mimenueenreeeeme vzx 575579 Sucrose and 5 mulmu are needed because 5 mulrmr can39t cause canes mLhOut sucrose and 5 mulansrfree animals don39t get mines even in the presence of sucrose Lacmbaclllus used 0 make many foods 7 yogurt sauerkraut beer Wine cheese sour dough bread Usually rnds see Fig 114 can live ar luwer pHs rnan srrepromcus spp rnus is lmpnnant in larer stages or fund termenrariens eg in yegurr sauerkraut Home Dr hetemlacuc fermenmrs Fig1 Lauobau uxsp in mgurt Namdenamredpmiems milled milk meters is eepnmeryeeise afdental tees wees Heenmdzdenzyme dzxtrulsucng wbmh eeelyees use fallmmng 11 sucrose e damn n fructose Dexuen is esuekypelymer alyharl 5 linkages af glunase malecules me am i WWW mdnve mined Remember 5 Minaix else bnmafermntanve sa itelsa camem every rruemse fmm elmve m z leeuc acids 11 sucrose e damn 2n lactic acid ceries ee caused by this and eating away at the enamel Fig 243 Dental Plaque Many types ofBacIeria in apolysaocharide marix Fig 244 Increase in acidity a er sugar addition to dental plaque Table 32 l meessrdh m mremhral edmmuhmes e apdreaudhs ID dddspddage ahdehhareemem meessrdh m Duds rs amen related d H changes due rd lean and haehena san umh and spmlage see gure an 4 szml sueeessrorral processes ear be mzmpulzted to enhance avor and preserve food Brample of yogurt and cheeses Avd wnzmmumwzmmwl cheese Curd edagulahed denatured mdk prduems surmundmg at am caused by lame an tachenaand rermin ah aerd protme from calf stomachs or uhgd aerd proreases Curds are then npened e 3 mar ways to hpeh cheese 1 Onglml bachenamths Cheese e5 hmgu mam Emma XMSS 2 Mmmbes neeuedmsrde the cheese h uraraamr m a mm mm 3 Mmmbes that gm Dnthe ChBESE r unusrmmumumn mm and prarrrarmrm Mast s 50 4 WW I Warm WWW rm WW f iV V v r uj a 7 r 3 Therm xmmmsmmmumamuny emm her mum r Manama ranrmahaawaarwam bums mama hummus 3 Incubilzubs39 vpmmtxs wand 5 memwmhuzmwx and dreamer hen icvd cdvmdnmky mmrar may saw ywamm ha aamarram mar sankdam mua bmuadu yr a Lic aic h are more and wknnuhmsmvmcocu Thereme he ibwukv enhance mmn minI vreeerr Mar man a andw yarn humanle andbpmhu mammary srsaamarrmsrmm ee hammer m m coYumxethe human hem have derive we armored mm dvinhei em Fig 323 w 55 Table 323 Table 32 2 min a m m ummm Let39s look at Soy Sauce Shoyu m a llt e rnote delall r a suecesslon of rnlcrobes based on release of dl erent orgnlc conshtuents over urne Alcahallc rermemauan 2 step process m m Used to make hreadwme and beer The dlfference between whlte and red wlnes h s a a e m D ll en whlte and red wrnes yeast Sacchammyce ceremslae are usually added D the wrne D perfurm the ethanu ferm t But many red wrne grapes are plcked befureth su are ferm 130 and hactena eg Lactobaclulus spp car But a fermentauun that canverts mall and D 18 and and cog The Villa1min Mmtnion lntl Because mall ls a dlcarbnxlllc and and lactic ls a mnnncarbnxlllc and thls reactl n can Cut the acidity thhe wlne byup D halfr mmgfmamaxeme wwme COOH HCOH cog CH3 COOH Mall and Law and Thls step ls absnlutely essentlal furthe pdeuEan Bf hlgh quallt red wrnes especlelly m mummy Ind soldam where the gmwmg seasnn ls shun Vinegar production from wine by Acetobacter aceli an aerobic alpha Proteobacterium and related bacteria that oxidize ethanol to acetic acid Colonies ofAcetobacter aceti an alpha Proteobacterium on calcium carbonate agar Zone ofclearing indicates acetic acid production Exhaust H Recirculation lube Pump Beechwood WC d t s avings o gralng Oxldation alr lnlakes Collectlng 7 removal V2 02 VHQO Cylochrome o Proton motive force ATP 2 H UQ CHSCHQOH 3 CH3000H Al 0th Aldehyde Ethanol GemMash Acetaldehyde dehymgemse Acetic acid One lat microbial food Edible cmobuwria Spimlimz platensi is used directly as food in parts ofAfrica and now in Europe Spimlimz platensi is harvested fromseasonally dry ponds near Lake c a The mats of bacteria are cut into cakes called Dihe Very high protein content 65 and Very high yield of protein per acre in France 10 tons protein per Mm as compared to 002 for beefaud 02 tons per acre for wheat LECTURE 10 MICROBIAL EVOLUTION amp Classification HgJOJ4 SUmmnd a Fossilized photosynthetic microbial mats The earliest organisms probably did not have any DNA They consisted of RNA and just a few if any proteins When selfreplicating RNA molecules became enclosed in membranes they became the rst cellular life forms Soon proteins become main cellular enzymes Using DNA as the genome likely resulted from the need to store genetic information in a more stable form What is the origin of eukaryotes Many theories eg 1 Archaealike cells evolved a nucleus endomemhranes and cytosketeton 2 Endosymhiotic theory Archaea like cell engulfed a Gram bacterium mitochondrion or a cyanohacterium chloroplast See next slide and read Perspective 31 on page 16 The Earth is about 45 billion years old Microorganisms have been around for about 4 billion years The early Earth was anoxic and much hotter The evidence suggests that biologically important molecules could be formed when gaseous mixtures like the primitive Earth are irradiated or shocked Evolution of Life a Time Scale mihle Mammal2i mm a WEImans Plummnln DEED mllhm ms Igul a m m WWW The Evolution of Endosymhiosis Planls Anin als 936 arranell es Eslablishmanlola Modem 1 siahlomlalionshlp eukaryole wiih a nmpmmmpmc Mcfm kmquot 95 cell prlmlllve 1 mm d mitochondria l m C 7 quota Endusymhiusls mg n 39 Establishmsnlol a sxabla mm lrelalionshlpw a anmw phylume m a h c u eukaryote I prlmlllval chloroplasl l l Classifying Microorganisms The grouping of organisms according to distinguishing characteristics that they share History of attempts to classify microbes A little after the time of Leeuwenhoek 190 2 Linnaeus tried to classify all living things 1759 named all known organisms using the binomial system Genus species divided the world into Animal Vegetable and Mineral Not much was known about microbes at that time so Linnaeus gave up in frustration and put all microscopic life into one genus Chaos Planing Ammlha Aims poise Pmlv39sm N at mnnnphylelic sineru i mum Archaea39n Why is taxonomy and systematics important 1 Allows a on to be organized so it can be easily accessed by all inthe scienu c community 2 By known properties and characteristics we can make predictions about related oranlsms model organisms 3 Allows to a common language En orces met rules 4 Essential to amter idendIy organisms Whittaker 1969 and others kingdom system39 Plants Animals Fungi Protists and Bacteria 3 main modes of nutrition photosynthesis adsorption and ingestion show foot tree next slide This tree of life has been widely accepted but it is not phylogenetically correct What is mnnnphyly Mnnnphylelic group Not a mnnnphylelic group An Esme on zaxunumm mnks and the bmumxal Kg 101 The 37Dom2in system usedin sxem H I n o 10 v Table 101 Iaxonomlz Ranks of the Baclevium Esdlen39znia wli Hmml Rink EXA m um Wm Pmmbamm m cmmmmm 011m mmmgm mm s m a 671m mm spm The Binomial syn systematics Th um ofchnmn39xin m1 orgakin llV39 ll W39 v MPEINIY in I WM n Enc lu mMmciI may wlyuii wolu mnn ly mamaI V gt m upquot 1013 a 5mm 7 m Genus species na es should be 39 alias or underlined E cali or 0 N 39amvm m m m chars ea 01 Exampk Df H M m Informailon used 0 mm ovum h 0 Eng m 2 g Wham mmquot Nudes mam quotIdaho c gymquot branch pom or molecular gymquot pum of m L 5mm immuwmu Table 195 Sums Murphulogical Features Used In Classl callon and ldenu cation mm 0 mm AH quotmurme 05 M AH nmiurgmup Mound mmmmmg AH mamng Lhm mcmm chm39nclmvlm AH ma or group Simumg huhavmr Hammm mm Fungi mu uml mm AH majurgrmm M lmmkmm mnhhly nmiugmmu qnmdvclc mmer lwv m ucumu WNW 10 1mm span mmphnl 7 and nmmm umma algm I39ungw cHuIav mumswns H may grow Mm AH nmym gmum n m wmymm Mmmum m mm m m w Mam Molecular Systematics Less ambiguous esp for microbes E c c u N w u c 43 5 Li L x 90 100390 Thhlt 194 Some Physiological and Membolic amch nc 39scd m Clussi uuvjun and ldcnn mtion mmemmmn mum mam mnrmnnnl w vuumum And mm 6mm murmur nmwwm V mmn M pH upmmvm mm mm muge GC content of DNA 7 useful for groupng Bacteria G C content may seem like a crude measum but it s prawn to be quite valuable fur microbial taxonomy But it still doesn t tell you anything about the sequence ofthe otganisms DNA Fig 1017 DNADNA hybriization Molecular characters II DNADNA WymtrmWmiwww hybridization mam m Brumm MM m Lil J mum mmmmm 1 W hoelslmallemnalu MNquot in mm WWW m rlwblguvanus l mum Wm n m i mmwm Iy yHyyyHf w s w m W emits my WW I mm W Wquot i m mmm m WNW v mmmnm MM mm w W W Wm in mm m mnumr nu wmkmmmmmm u mvuumw unuum w h WWW 7 equot 39 CW WWW 7 Fig 1n11 my uuyicvdmvmauly AWLWL39O mm WWW mum Table 196 Comparison of Neisseria Species by D Modern systematics is based on 39rect NA Hybridization Experiments d1 examination of the blue prints of life ie DNA and RNA sequences MembraneAllaclied Dl Percenl Homologyquot Ajuimrua mermgmdtr 100 The most useful sequences for classifying 2 l mmquot all forms of life are ribosomal 39N mm 35 RNA because they are 1foundinallfonns oflife 2 change slowly over evoh nnary lime A nwmwgmdisDNAhunmlinmrenmdih mm X W Figure 109 nomiwmUDNA 39 mciisumu Th mun mummy mm m gitm mt imnmlngy mmquot um m iCnL cV quot Amunui Mu AU mum mum Molecular characters SSU Rihosomal RNA Nucleic Acid Sequencing WW Hm m M WWW mu 5 H mm mm mm Eirei mum Emamneb slime mm with mu wwmm Fig 101 Mumm rnmmm Mm M00420 W n hamwa s Mumwuu Bacteria Archaea Eukaryote W km mums LECTURE 7 PHOTOSYNTHESIS amp CARBON FIXATION From lec 2 I uyver and van Niel proposed that all photosynthetic reactions could be summarized with CO2 2 HZA gt CHZO cell material HZO 2 A CO2 is being reduced HZA is being oxidized Table 69 Five main groups of Bacteria are photosynthetic Purple bacteria sulfur and nonsulfur Green sulfur bacteria Green nonsulfur bacteria Heliobacteria Cyanobacteria 2 parts to photosynthesis light reactions light energy is trapped by molecules and converted to chemical energy ATP NADPH dark reactions this chemical energy is used to reduce 602 Photosynthesis is the conversion of light energy to chemical energy usually using only 602 as a carbon source Photosynthesis exists in all 3 domains of life although eukaryotes are photosynthetic only Via the presence of symbiotic organelles Phototrophy is wide spread in bacteria and appears to be a very ancient trait fossil stromatolites in rock over 3 billion years old show photosynthetic prokaryotes Fig 1014 Modem day smmzmliles in Au 392 Photosynthesis is perhaps the most important biological process on the planet Produces most organic carbon on Earth These organisms completely transformed the planet The earliest photosynthesis was anoxygenic did not produce 02 gas Oxygenic photosynthesis created our atmosphere including the ozone layer which allowed life to evolve onto land Need molecule that is capable of absorbing light CHLOROPHYLLS Similar in structure to cytochromes from the ETC but instead of iron in their center they have a magnesium atom WWW 0 Photosynthetic 9 39 also chlorophylls cu v a though there is u a m ch greater Hc r I k diversity in the N V c types of me 0 w molecules Me s NJ H NCo w c m a ror example k Furc fN Chlamle purple bacteria was we have acterio 0 o chlorophyll a oica In prnkaryntes the chlnrnphylls are intergrated intn intemal e rane systems in different places in different bacteria purple bacteria the membrane he bacteria the membrane itself nvaginatinn nf green bacteria bath the membrane and in membraneenclnsed structures called chlnrnsnmes cyannbacteria thylaknid membranes Chlorophylls and accessory plgments are arranged in arrays called antennas fig 626 Fig 626 light energy being used to excite an electron Purple bacteria chlnrnphylls a and 1 Green sulfur bacteria chlnrnphylls c d and 9 Green nunsulfur bacteria chlnrnphyll ts Helinbacteria chlnrnphyll g In additinn tn chlnrnphylls nrganisms may have nther plgments such as carntennids and p nteins phycnb These accessnry pigments absnrb light in nther areas nf the spectrum and can transfer the trapped energy tn chlnrnphyll Remember that as electrons ow down an electrochemical gradient energy is released A similar prncess nccurs in phntnsynthetic nrganisms e they use membranebnun prnteins tn pass electrnns dnwn a gradient generating a prntnn mntive fnrce This is called phntnphnsphnrylatinn Because electrons are being driven out of W chlorophyll using light energy they must be replaced Eukaryotes cyanobacteria and some other bacteria 0 oxygenic photosynthesis the source is water 02 is produced as a by product Use water as an electron source and produce oxygen as a final product 0 Anoxygenic photosynthesis the source is reduced sulfur compounds organic compounds hydrogen gas or Fell Oygenic photosynthesis involves 2 distinct but The products ofthese Ilght reactIons then are Interconnected reactIons 0 Photosystem I chlorophyll Pm and 0 ATP noncyclic photophosphorylation absorbs light at long wavelengths far red 0 NADH Where the electrons end up 0 Photosystem ll chlorophyll P680 and 3902 from Splitting OfWater absorbs light at shorter wavelengths near red Fig 627 The path of electron ow looks like a Z turned on its side so it is alien called he Z schemequot The process we just talked about was oxygenic photosynthesis and was used by cyanobacteria and eukaryotes Green Sulfur Bacteria Other bacteria use anoggenic photosynthesis ie harvest light energy to synthesize ATP without Use H25 or water as an electron source no 02 is produced 5203239 as In these organisms light energy also excites a ele m pigment molecule 3223 thus no often do cycli c Electrons also cascade down a series of photophosphorylation to drive 39 to generate ATP If enough carbon is present cyclic electron flow cyclic photophosphorylation Table 6 9 um i s Lamaan Mml nm lu lerKhmlml um ry mayrllhuillm 39 le mast ccmmch way that crgahlsms llx carbch ls vla the calvm cycle 1hls ls used by cyahcpacterla purple pacterla algae am scme Archaea Seehg 523 At the end at che turn at the calvm cycle we have eg ed cur lhccrpcratea 1 c 2 need a carpch lar plcsyhthesls 39 ms we ca sum up the eguatlch Icrthe lcnhatlch cl gluccse as Icllcws 5 cu r 12 rumpquot r 1EAYP gt 126quotan r 12 runw r 1 a ADP 39 lose were all llght reactlchs 39 le hen steps called the dark reactlchs lhvclve the leatlch cl lhcrgahlc car h usmg the up am mum geheratea quotI the llght reactlchs lh cmer tc laml Martian sugars such as gluccse cr ctcsethe calvmcycle must turn 5 tlmes Yhe lhccrpcratl h at m2 mtc ah crgahlc ccmpcuha regulres 2 up am 2 Hunt Yherelare the lcrmatlch c1 gluccse regulres 1 Green sullur hacteha ac hct usethe calvmcycle 39 ley just run the nu cycle backwards called reauctwe mA LECTURE 12 w Wummm mm mmng mm H THE BACTERIA 4 Agnix Ind I39mmm ermatayn m a aheahl like nhgn ldest branches of he Bacteria mummy hypermennophues nAquzfexspp re H2 umdxzers and m cog by mm m m Eyck backyards cm 0mg 3 only hyperzhennuphm aembes 7 Use Dsz by 50 many beeply bmnchmg themuphxles Suggests H2 W very cummnn on the early earrh m alwes nearsubmarme hydrothermal mus have a prumm 5mm mga Anaerobic ferm nzurs him Themquot Deinomugt1hemlua 2 mm groups meniaan mund a 1 5mm Mayer rhus 1 mm Gm Has Sevemlcupxesufc mm sumepercelland 5 very effluent a DNA reps l ALPHAPROTEOBAGTERIA K baclena emeapamei a nmmonomnm Caml canlnhacteraceae amp Hyplmmicrnhiaceae These 2 groups of bacteria have some sort of appendage extension of the cell that is wer than the mature cell gt Reproduction by budding see Iec 5 gt A prnsllleca an narm reproduction via a small protrusion llal enlarges In farm a new cell The Proteohacteria 0 largest cultured group ofbacten39ar 380 genera amp at least 1500 species 0 5 major groups classes gtAlplaprnlenhacleria gtBelapmlenhacleria gtGammaprnlenhacleria gtDellaprnlenhacleria gtEpsilnnprnlenhacleria ALPHAPROTEOEACTEHA caml Ricke ttsia I many important pathogens eg cause Rocky Mountain spotted fever Typhus 0 genome sequencing shows that they are very similar to m1 hondria 7 probably ancestor of Rickettsia was involved in endosymbiotic event me Hyplmmicmbium species a melllylnlrnplls can use melllane or other 1 n compounds as energy and carbon snurces Fig 1124 Budding u Hyphamicrabliun Fig 1123 Caulabacter life cycle nunnarmmcmm my Rhiznbium synlzioMS willin rool nodules a plans an lix nilmgen Mmbactarium does no samulm rooi nodIIe lomalion or x nilrogen Insiqu Ihese huhli imde plant Iissues an cause mums Wm gil 39 ease Aunnanmnnnm a Rinzobmmxs the most mtalswely studied symbxoult1mutuahsult1 bactenum Very impomnl agncultumlly mmk soy bean bean clover Kzotherlegumes etc Plant exudes homonerhke avonoxd compounds to 21mm Rimmme Nmsomnnas all llets e in her yours of Ike wohohaehlia nm e Nmsl ur noun use moxygenlc uoinsynlhesis In can someli mes be chemheluoim s Fig 1120 Acrown gallr planttumur Induced chemically by Agmbacrenum F15 an ampF15HZI EEYAPROYEOEACYERIA quot Pmam 9mm GAMMAPROTEOBACTERIA Neisseriales Neisseria gonorrhea some meningitis I largest group of Proteobacteria Bordetella whooping cough I many familiar genera Escherichia Salmonella Other members of this order PSE UdOI OHaS Burkholderiales have a sheath I incredibly diverse Colorless sulfur bacteria Thiobacillus GAMMAPROTEOBACTERIA com GAMMAPROTEOEACTERIA com Pumle Sulfur Bacteria Pseudomonas I motile polar flagella usually anaemhes 1 Involved in mineralization taking organic compounds back to inorganic hotos nthet c ano en 1 P y I xyg I substances oxidize H25 to S and sometimes S to 504239 2 Useful model organisms eg Pseudomonas aeruginosa 5 also an opportunistic pathogen esp in CF patients and burn victims see next slide GAMMAPROTEOBACTERIA com Vihrios I some are important pathogens eg Vibrlo cholerae Fig 267 I some Vibrlo and Photobacterlum species are capable of bioluminescence These bacteria can live symbiotically with squid or fish Fig 1126 Preudomona aeruginom 7 plate shows diffusing green uorescent pigment a siderophore Bottom shows polar monotrichous flagellum Very top is too gross to show in class same as in fire ies 7 green discolored skin on a burn patient Enzyme luciferase is involved GAMMAPROTEOBACTERIA com Enterobacteria grouped together because they are found intestines look similar metabolic properties are useful in classification flow charts contains many common bacteria E coli Salmonella etc DELTAPROTEOBACTERIA Conn M obacteria soil bacteria complex life cycle Fig 1118 most are micropredators or scavengers secrete digestive enzymes that lyse cells of yeast and other bacteria many produce antibiotics DELTAPROTEOBACTERIA com Sulfate and Sulfurreducing Bacteria use these sulfur compounds as electron acceptors anaerobic respiration Desulfovibrio Desulfuromonas Important in sulfur cycle in nature Fig 3012 DELTAPROTEOBACTERIA Two main groups 1 Predatory bacteria bdellovibrios and myxobacteria 2 Sulfate and sulfur reducing bacteria The Life Cycle of Bdellovibrio Fig 1125 DELTAPROTEOBACTERIA COHL Myxospores are dessication resistant may survive up to 10 yeals Communal living may allow them to digest prey more ef ciently wolf pack as opposed to lone predator like BdeIIOVibrio EPSILONPROTEOBACTERIA I Smallest of S proteobacteria groups I 2 important genera gt Campylobacter gt Helicobacter I Helicobacter pylori cause ulcers will discuss more later Campylobacter some are pathogens Flagella stains for the light microscope Basically staining flagella is a two step process 1 Coat the flagella with something that sticks to proteins eg tannic acid 2 Stain the whole organisms with a general stain eg pararosaniline or basic fuchsin LECTURE 4 cont GROWTH One microbial cell can39t make a difference takes millions of cells per ml or cc to cause any sort of effect One cell of the most virulent microbe on the planet cannot hurt you Growth of singlecelled prokaryotes growth and reproduction Bacteria basically clone themselves when they reproduce Binary fission Fig 43 Fig 74 Budding off of smaller cells yeast or Hyphomicrobium Fig 1124 1214 Filamentous bacteria and fungi grow via extension of the hyphal tip Fig 1215 In fungi growth is supplied by vesicles Fungi and actinomycetes also reproduce via spores hyphal growth followed by fragmentation in Actinomyce es While we re on staining someone asked about the role of iodine in the Gram stain I said it is a mordant a chemical that helps fix dye on or in a cell which is true the iodine reacts with the crystal violet making a larger compound that cannot escape through the pores in the peptidoglycan layer of Gram Bacteria Also the decolorization step is thought to shrink the pores in the peptidoglycan layerthus further preventing the escape of the dye in Gram Bacteria Fig 12 14 Budding yeast 1 Cell wall bulges out 2 amp 3 Nucleus divides by mitosis 4 One nucleus migrates to bud 5 Bud cell wall forms and bud breaks off MICROBIAL Ponulation GROWTH Microbial populations grow exponentially when supplied with enough nutrients The time it takes to divide is called the generation time g Exponential growth of bacten39a um quotmen mil l EQUATION FOR EXPONENTIAL GROWTH BBux2n where BB is the initial cell number BI is the nal cell number and n is the number of generations Taking the log of both sides and solving for n we get nlnBlrlnBD ln2 mum a mm mm lm4 In mu anldalinn l ime Number 2 L x2quot 1 0 l 2quot l 1 41v 2 4 an 3 as 30 4 lb mu 5 3 my 6 54 w unmmmwmmm M w Mummyquot m Example unmadequot n lnBlr lnBD ln2 BD 2 x 107 cells per ml after 2 bolus Bl 32 x 10E cells per ml 11 196 7 168 0593 4 genera on What is the generation mne n VS By rearrangement g 1n2t 1n BI 7 1n BB g 0693 2 1967168 05 how Converting g to a growth rate We can relate Gm gmwth rate u via 1 1u2 3 where u 15 he slnpe Bf a semrlug gmwth curve Table 61 An Example of Exprmenlinl Growth Faclnrs affecting Micrnhial Grnwtll One E 501139 cell g 035 hr or 20 minutes would grow to be a mass 2000 x that of earth if it could grow unchecked for 48 hours So why don39t bacteria take over the world mu Emilanmmal rum that tum Miaumal meth mm Wu nhivmr mm w my u uut t u thmie t39mmkm temperature pH nxygen cancentralinn pressure mare In nature competition for nutrients ma space predation and 9mmquot umtt the exponential growth of rnicrob es Fig 44 HVW hmmnthias Thermopmles Mesophiiei Psychmtmpha Growth rate Psychropmles 4n n m 20 an no 90 100 Uizo 40 so an 70 Temperaluve gtc amtMm Fig 417 vmumxunmmmmm enmume mnn tmwnmw mm mm m uwutwmwwutumutmttuWt u Wt Imam mum mt muttthmmtmu End of Log phase is brought about by Exhaustion of limiting nutrient uutawumm AMt m 0 quotf if quot Build up oftoxins e 3 alcohol in yeast cultures mmuumumnuu ttutuWmutuuutatmtu umuwtut uuwuutuuttu mnmmwmtt uu mmm1umnmnnmwg mu 39 cum wwmlh hnhwimiwm tmmmu tut um nuuuuuumtum mm Primary Metabolism relates to the growth phase Fig 418 Secondary Metabolism metabolic pathways that are not involved in growth of cells take place when cells have stopped growing eg production of antibiotics by bacteria and fungi Figure 418 primary and secondary metabolic products metabolites e g Production of Bacitracin by Bacillus Iichenifonnis prior to endospore formation Chemostat Fresh medium Conlml valve Receptacle How do you keep a culture going Exponemlai lag phase Lag numhe of viable cells 4 rlme 4 Continuous culture techniques Table 63 Microbial Responses to Environmental Factors DEcnmiw Term D ileun milalumnu ill umulkimblu Sam M wmr Aclivil Osmanl m comm3quot Hallmlnle uhnul ngt MJ w hnpnmlllvlhnwvll Hlmnni mm m lt 3mm x l mm ammum hemmll m as mm l I 5 l ST or mu J c imlt m spam ht39eleall m m l c mum muu 35 c mum mm 104 sayHillary v w ma pml lnu Dbl Mlcmamupmlc rpmm Emma wxlummw WWW Wuses and Pnuns Outline of Lemma vm hams andmmresungfams Three mmqu nth hast nuns Discmsmn quesunnwcan wruses be benenmm ues 151mm anyhme mm 13 I WIIII I I Vlrlu l 1 Wmses m ol gate imne oleellar ransiles 1 The vims gemme4ilherof mm or am 4 mm genome Hinds he prodmien of ew wins ranides Fig 132 A Nahdvmls a Envelnpedvmls Many 31 Vaccinia Virus EdwamJermev Fwswaccme Different Interactions with Host Fig 134 modi ed In uenza Herpes HPV In uenza u virus is a ss RNA enveloped virus Fig 2321 that infects cells of the respiratory tract he Nemmimdase N protein on the viral surface hydrolyzes the host mucous coating allowing the Hemaggiutinin H to bind to protein receptors on mucosal ce s The virus is taken up and H fuses with the membrane causing the viral RNA to be released into the cytoplasm quotantigenic drill39 year to year minor variations mutations in the viral membrane proteins quotantigenic shiftquot major changes in these proteins Major change was cause of deadly pandemics eg 1918 and 1957 Possible genetic rearrangement among duck swine and human u viruses probably in pigs Influenza 159586588 gt Highly mutable virus changes antigens very quickly gt Many animal reservoirs Continually evolving New strains every year Variants via mutations and genetic rearrangement of last year s virus H changes slightly H becomes new antigen not recognized by last year s antibodies New shot every year In uenZaWHumariity evolution arms race Major rearrangements antigenic shin more than one strain of u infect a single cell at the same time Thus during assembly ofthe viruses eight different segments of the viral genome rmixed and matched into new viruses rmajor new antigenic presentation See Fig 2322 gt Influenza caused worst world pandemic in 19181919 killing over 20 million people about 80 of the American casualties during WWI gt Viruses are inhaled or ingested Spread Via sneezing and coughing gtResults in fever chills headache aches gtMost of the symptoms are caused by Virus lysis bursting cells of the respiratory tract gtleads to secondary infections by bacteria and other Viruses gt Death occurs due to secondary infections gt 1000040000 deaths due to flu every year Genital Warts probably most common sexually transmitted disease pp 654655 Cause human papillomavirus HPV naked Viruses resistant to drying At least 50 different HPVs cause tumors malignant andor benign Warts are benign tumors Cancer causing PapillomaViruses code for proteins that inhibit antioncogenes Worrisome pandemic of genital warts gt Cancer causing forms just as easily transmitted as wartcausing Both often both found in women with cervical cancer Herpes See Fig 1413 HPV of genital warts are related to HPVs that cause cancer HPV16 gt cervical cancer in the USA 7 of all cancers in females 5000 deaths annually PAP test detecm early HPVs are ds DNA Viruses incorporated into host chromosome or becomes plasmid cause infected cell to multiply more rapidly than normal gt tumor HPV Preventior Treatment No sex With people With waits duh Condoms Avoid sex With people With multiple partners PAP tests regularly Wart removal DOES NOT cure cancer causing infection The T011 of AIDS HIV More than 33 million people Infected pp 739 749 worldwide 16 million have died gtFirst described in 198183 gtEpidemiologists predicted a bloodborne virus gt1984 Gallo linked a retrovirus to immunodeficiency syndrome AIDS Fourth leading cause of death in the world Fig 291 Human lmmunodeficieny Viruses AIDS pandemic Retrovirus 55 RNA as of 2001 infect mononuclear phagocytes Fig 299 Percentage of AIDS cases in women in HIV targets cells with CD4 receptors A the US See Fig 293 Life Cycle of HIV Fig 296 The Three Phases of HIV Disease HIV infectionmost infected cells show no lysis bursting no latency integrated genome no virus produced accumulating and releasing viral products integrated genome Fig 298 Blood levels of HIV virus red circulating HIV RNA green CD4 cellsblue Epidemiology of HIV V acc1ne Transmitted via No vaccine for HIV yet sexual intercourse HIV constantly changing its proteins blood and blood products evolution mother to infant Sloppy reverse transcriptasegthigh mutation ratesgthigh evolution rate Treatment Antiviral cocktails Drug toxicity and inconvenience H H E HAART highly active antiretrOVIral therapy Xpense Viral Drug Resistance MIXture Of Inhlbltors Residual Virus Replication HIV continues to replicate reverse transcriptase eg AZT 321553fr ztspenetrate a PLUS LongLived Reservoirs of Virus Infection protease Combined therapy especially effective Why Pnons Result of prion diseases holes in brain tissue infectious protein particles spongelike appearance thus quotspongiform encephalitisquot cause diseases in animals and humans Prionsthe only infectious agents that do NOT All caused by exposure to bmlns contain any nucleic acids Kuru was gured out by Gajdusek Cause brain diseases in spread Via burial ceremomes sheep scrapie I people smeared brains of dead relatives on cows mad cow disease their bodies BSE ans Kuru and CreutzfeldJakob disease elk deer Chronic Wasting Diswe see Table 1412 Mad Cow Disease bovine spongiform encephalopathy BSE British added ground up sheep amp cows to cattle feed cattle then ground up and fed to humans burgers Prions are not destroyed by cooking incidence of CreutzfeldJakob disease in humans recently increased in Britain Clin Lab Med 2002 Dec 224849862 Variant CreutzfeldtJakob disease and bovine spongiform encephalopathy Belay ED and LB Schonberger Abstract Strong epidemiologic and laboratory evidence indicate that a novel variant form of creutzfeldt Jakob disease vCJD first reported in the United Kingdom in 1996 is causally linked w39th bov39ne spongiform encephalopathy BSE BSE was first identified in the early 1980s in the United Kingdom and has since spread to other European countries and recently to Japan and Israel Although the United Kingdom SE epizootic is on the ec39ne wi espread exposure of humans to infected cattle products ma ave already occurred raising concerns about the ultimate magnitude of the vCJD outbreak which as of Odober 2002 has already affected 138 patients worldwide including 128 patients in the United Kingdom Figure Chronic wasting disease among freeranging deer and elk by county United States rom ED Belay R A Maddox ES Williams M W Miller P Gambetti and LB Schonberger 2004 Chronic Wasting Disease and Potential Transmi ion to Humans Emerging Infectin Diseases 106 June 2004 BSE latent period up to 15 years long time before full impact on people in Britain is known detected recently 2003 in a cow in the USA Emerging Infectious Diseases Vol 10 Number 6 June 2004 chronic Wasting Disease and Potential Transmission to Humans E D Belay R A Maddox E S Wllllam M W Mlller P can em and LB smonberger Chronic wasting disease CWD of deer and elk is endemic in a tricorner area of Colorado Wyomin and Nebraska and new foci of CWD have been detected in other parts of the United States Although detection in some areas may be related to increased surveillance introdudion of CWD due to translocation or natural migration of animals ma account for some new foci of increasing human exposure to the CWD agent The foodborne transmission of L 39 quot 39 39 species barrier may not completely protect humans from animal prion diseases Conversion of human prion protein by cWD associat d prions h mited as been demonstrated in an invi o cellfree experiment but i investigations have not identified strong evidence for CWD transmission to huma 39 39 39 Iauulmuly 39 d d quot the possibility of such transmissions How do prions cause disease and replicate without nucleic actds First ideainducers or repressors of gene ression The latest theoxyrecruit proteins similar to themselves in the membranes of brain cells Proposed mechanism for prion replication prions line up next to similar proteins that line brain cells cause a shift in their tertiary structure to the prion form causes the outer lining of brain cells to become rigid and cavity forming Fig 1422 Discussion Question Are Viruses always harmful Are they ever beneficial Ideas 0 Protection against disease 7 Vaccinia 0 Ecological 7 Australian rabbits and Viral eco7control 0 Host modification 7 Turn on anti7oncogenes 7 Manipulate gene expression 0 As vectors 7 Transfer useful genes to other hosts 7 Gene therapy 0 Target Viruses to kill tumor cells Beneficial Microbes Cyanobacteria atm0spheric O2 Rhizobium7N fixation soil fertility Rumen ora digest cellulose in horses Eicoli and 0thers pr0tective intestinal ora Mitochondrion ATP Etc Brainstorm ideas Small groups 393 to 5 people per group 395 minutes to meet Compile group s ideas spokesperson QUESTION in What ways could Viruses be beneficial ms are almost gmded so far the mean is higher than last time 76 7 should be done tomorrow Microbial Life in Barren Soils And review for the final a Glacier forefronts in the Andes 5000 m N and C cycling Microbial succession b Talus soils in Colorado 3800 m C and N cycling Novel Eukaryotic kingdoms Sampled soils at 0 10 100 and 1000 meters out from receding glaciers this represents a chronosequence of time since the soils were uncovered BetaProteobacten39a dominated soils from 0 meters and under the glaciers Glacier forefronts in the Andes 5000 m N and C cycling Microbial succession BETAPROTEOBACTERIA wProlaobaclena 7 y m an acnema Proteobame a Beta Proteobacteria Order NeisseIiales Neirseria Chromobacterium Order Nitrosomonadales Nitrosomonas Spirillum Gallionella Order Burkholderiales Families 1 Alcaligenaceae Bordetella 2 Oxalobacteriaceae Janthmobacterium 3 Burkholderiaceae 4 Comamonadaceae Acidovomx Variovorax Polaronwnas Xenophilus Rhodoferwc Most of clones from under glaciers Betaproteobacteria cont Chromobacterium violaceum common in soil and sometimes as an opportunistic pathogen of wounds Some strains are very cold tolerant and can be isolated by incubation of rice grains in soils near 0 C Purple pigment Violacein is produced in the presence of the amino acid tryptophan Soluble in organic solvents acts as a weak antibiotic Review for final BetaProtehacteria we have already discussed Neisseria gonorrhea some meningitis Bordetella whooping cough Chromobacterium lecture 12 Nitrosomonas From Lecture 9 Nitrification in Nitrosomonas NH3 02 gt N027 H20 NiTrifying bacteria are chemoau ro rrophs Thai use reduced N compounds as Their e donors The Comamonadaceae B eta Proteobacteria dominate the under glacier environment in the Andes Nemergut et al unpublished What are these bacteria doing there Only known relatives of under glacier clones Polaromonas found in sea ice Antarctic sediments cold lakes Heterotrophic degrades complex organic molecules eg naphthalene dichloroethene Rhodoferax found in sea ice coldlakes Heterotrophic and photosynthetic degrades complex organic molecules eg herbicides Can use Mn Fe and nitrate as e7 acceptors anaerobic respiration Variovorax found in vadose zone and hydrothermal vents Can respire arsenic and H2 has novel P cleaving enzyme The other major group found under the glaciers was the CytophagaBacteriodes group Conclusions about What is going on Cyanobacteria dominate soils that had been uncoverd for 5 10 years and longer in Peru and measured N fixation rates were highest at 100 meters out from the glacier Show data from Sasha Reed Nitrogen fixation is highest at 100 meters distance from receding glaciers This corresponds with development of a high diversity of cyanobacteria in the soil clone libraries Data are from March 2005 Sasha Reed et al Unpublished N xers are mostly in Nostocaceae and Oscillawriaceae Ba c teroid es anaerobic hard to culture some can be opportunistic pathogens important in rumens and colons dominant genus in the colon 10 billion per gram of human feces break down polymeric substrates eg cellulose using extracellular enzymes use gliding motility Cytophaga and Sporocytophaga Obli gate aerobes most important aerobic bacterial degraders of cellulose in the biosphere Extracellular cellulases a see Lecture 4 Heterocysts special cells where nitrogen fixation takes place Photosystem I still makes ATP but get rid of PS ll so no 02 is made The 02 would poison the enzyme that fixes the nitrogen nitrogenase The heterocyst gets carbon from nearby vegetative cells and gives them the fixed nitrogen that it makes C02 uptake by barren soils M Pescador et al unpublished Carbon inputs ng39lyr to barren talus soils in Colorado Photosynthesis 20 Pescadoretalunpublished Heterocyst Dust 02 Leyetal2004 Vegetative cells Vegetative cells 13 Utah Microbial Biomass in barren soils at elevations of 3600 r 5200 meters 12500 r 17000 ft in Colome and Peru n 134 Meyer et a1 2004 unpublished Bolivia March 2005 Rosa and Preston digging for Polylepis roots 2Microbial biormss given as ugCg39l Biomass levels are much higher than expected Eucaryal library of barren talus soils More novel Eucs in banen soils than in tundm soils Meyeretal unpublished Table 122 Impnninl aamrinp g Exam 2 Mean 72 after adding 7 points to all tests Q 19 answers were messed up real answer is c so part of the 7 points was for that question Spend a little time going over the test Transductionquot Transfer of host DNA Via bacteriophage 2 types Specialized 8 Generalized Transduction Generalized results from the lytic cycle of certain phage see Fig 816 Specialized results from lysogeny followed by the lytic cycle Fig 1311 Table 132 Note the variety of shapes nucleic acid content and life cycle Bauzunpnage Host snip 5mm 5mmquot ml 7 udd maN mm mm W Mm u r m lll mnlnns a m m r n39msm 1074 mu 111 mm m mm m w laxwormlr m at handquot g Hm 1111 nm in mmm mm Mrwnr m mm m max w mmmuu m kmutlmlnn 1 WWW See Fig 131c Bacterial Genetics we will only discuss mechanisms of genetic exchange gene transfer in bacteria Read pages 3237334 and 2037215 Three modes of genetic exchange 1 Transduction figs 816 and 1311 2 Transformation persp 81 pg 205 3 Conjugation Figs 818 822 In order to understand transduction we need to knowViruses of Bacten39a bacteriophage or phage Always are naked Viruses no membrane why7 Huge variety One species of bacteria can have many different phage Table 132 Important for 1 Genetic transfer transduction 2 Control of Bacteria in Natureread Pemp 131 pg 330 e can cause bacteria to become pathogens eg diphtheria A see Table 133 Host ranges of phage Phage are usually very specific to the species they infect they attach to specific receptors on the outer layers of the bacterium eg some phage of E 301139 attach specifically to the proteins of the flagellum see Figures 1312 and 817 Phage for a particular bacterium also have DNA methylation patterns like their host and thus avoid having their DNA cleaved by restriction enzymes when the DNA enters the cell See Figure 1313 Bacteriophage attached to pilus of Flg 13 12 E coli Phage tail fibers entwined aroun agellum Phage T4 attached to speci c receptors cell wall proteins of E coli VI rioii Infection Hosl ceii Fig 134 Geneiic alteration i host ceii Disease DI host celi LATENT STATE Nucleic acid cl Virus bcumes partoi host ceii DNA FRODUCTIVE iNFECTION More virus pm use Lte 3 nt state Lysis of Cal Release ui viriuns Lysogenic mm re ease o noniysis of cells Husl cell dies Husi cell is onen modified and caniinues m muiiipiy Summary of lytic and lysogenic cycles Lyiic cycle Phage 3 DNA Eactc a iimn rial my Virus interactions with host cells or Replication Cycles of phage See Figs 134 137 Fig 135 Example of the lytic cycle T4 of E co Fig 136 Phage Lambda can undergo a lytic or the lysogenic cycle Fig 137 Insertion of Lambda into a specific spot the bacterial chromosome Consequences of the lysogenic cycle Cells are immune to further infection by that phage Can lead to specialized transduction later Can cause lysogenic conversionquot Viral genes that change the phenotype of the host cell eg some phage have genes for toxin production and can convert a nonpathogenic bacterium to a pathogenic one See Table 133 for examples Table 13 3 Lysogemc oonvemon of mama confa nng pathogem propemes Buck to Buttlnll Games Transducuun Transfer Bf hast DNA ma bactenuphage 2 lypES Spenehzed amp Generehzed Transducuun quot39quotquot quot Generahzed tesu1ts mm the 1yt1c cyc1e Df t h F 815 Pmphage the 1yscgemc phage mcctpcteted 9 am p age see g mm he bac er a hmmDSDmQquotu Spenahzed tesu1ts mm lyngeny fullDwed by the 1yt1c cycleF1g1311 Emu11 Genetics Gene hzed uansducnan esuhs vm the lync cycle chmmsame ts dxgesmd mm smallpi ces 7 same 17f wheh end up 239 T summon uptake and W3 imaged SPEM ES mEDrpDraan mtD the chrDmDste Bf naked DNA mm the envlmnment F1g 13 11 Speaahzed tmmdueuon byatempemte Bpressmn urthxs new DNA can altetthe phage Results tom the lysogemc cycle Specme phenmype nfrhe urgamsmt e canvemng a p1eces of DNA near msemon s1tesare tmstetted quotDn39Pa hDgen mm a Pa hDgen egS r4pmouxpwwrwma th 19111 Strapnxoaux Wt What ts padmgenm Duly when xtplmiunes mysuhe F1g 13 1 lb Specmhzed mmducuon bya temperate phage M1161 My 11 mm human by mnhndnzs all phim y zs Flg 814 Transfnrmaunn Ufa cell mm nDnr Pasp 81 Pg 205 Expenmemcmedombycnmn teststant am In resistant D strepmmycm Styx showmg that somethmg was tmnsfared fr m dead pathogeme pnehmmae to l1ve nonpamogemc cells 7 txansotming them mto pathong 1t was 1atet 1944 Shawn that the ransfm39mmg lequot vmmn ptmc1p ms DNA that mm mm W ta ta mahth em tthtgtmmmmtm ccm There are many ammlal ways to make bactenal cells competent fortmnsformatlon electropomuon and man chemlml treatments make tempolary holes ln the cell wall and men 6 E that blane Fl 2 25 llttmlw ttwltttuw um tut but t tusut lullststwltltustt Quick review uI thiis r Emachromosomalt circular doublerstmnded DNA m l l o ecu es Plasmlds diylde and coples go to both daughter cells on Many plasmids can be tsausmlned betueeuulusely lelated species butsume ale mtllmlued m ulnse lelatiyes a ans tn 3 tm mans Tbeleture plasmlds are men unstable lu abustbautenum due tn the mcmed metabulluluad Asa tuuud lu Amhaea Fungi and utber eule Transfnrmexmn can take place between even unrelated bacteria but lt ls rarer than between related because most fnrelgn DNA ls degraded berure lt can be methylated 7 see gure 826 here are also genetic platfurms imamans Wlthln bacterial chmmnsnmes that can mublllze large pieces ufDNA and lntegrate ar e pieces or fnrelgn DNA behlnd a hat they are easll pmmuter so t y transcribed Bantuill Gmetics n a n E E E a a Fl 2 l7 Canluganan between F and and Fr 5 oh All sorts thralts can be transferred Vla conjulniv Ilsmids e the most relevant tralts rurus are anubmut resistance genes But Ether lmpurtant genes are also fuund an Antibiotic res39ianoe e usually by coding or an en e that renders the anublouc nonrfunctlonal Eemrlammase inactivates Eemrlactams 15 one example Penelllln ls a Betarlactam Spedal mazbolic properties e some plasmlds allow bacteria to take adlmntage of sltuauons that mlglt be othenltlse harmful Breakdown ofcomplex otgamc molecules ls often plasmld encoded Izhlz 34 Same Fla mi39Heded Is Inll own15m 1n thn Yriil 1s round em 0111 t amt r vutmnnm mm mm awarequot 1t tune QVoDmmum nmeaner Mm Mm taunts Munchr1 at unearthquot new we ms t t 1 H5400 ehws ht mm synmuxls 241M mynwmsh 111mm anesrnttsu racer Anlmollzsymhrsh 5m mmmSD lumen nut re WIN1M entmlttn vxlnl m mm mm men The rea1searyth1ng about plasmlds 1s that man of them have the above trarts AND are Jugauve as We Conjugauon 1s brought about Vla mformauon stored on rertrhty plasmlds Conjugauve plasmldswh1ch contarn genes for F s oblllze the plasmld Tram erhcwrx 3 An orlgm of repheatron See gure 322 mam term r MLM Flg 8 22 The regrens Mmmnhrnzn Virulence Plasmids there are a number er my that a plasmld ean cunfervlmleme m a haetenum 1 The preuuenen Ufune er mere texrns that ean be dlrechedmmxd the hester temrus ether haetena baeteneerns 2 The ahrhty te terma eapsule The reeent anthraxseare 15 an exam 5 fur ve nnary waclnauunlacks the eapsule funnlng p e1 Other virulence factors on plasmids The pmuuetten er siderophores that enable the haetenum te seavenge 1mnmthe hee1y e g 5 during sans pmterns er glyeepmterns that are usuallya eempenent chapsules er nmhnae that alleuthe haetenum te aehere te speeme ee11s Fig 818 emtgaammmmr emu nuamrmerm rsmrmmangeespuc Fig 319 Hfrfmmaunn vta mtegranen nfthe Frplasmldlmu the hestehremeseme atspeeme msernen sequenees 1 55 F1 20 Cernugatten 1nve1v1ng aanmell Basreauy the whele ehremeseme 1s new a grantF p135de hutthe whele thmg 1s rarely transferred Flg 8 21 An F39 plasmruresults 1fsum2 ehremesemal DNA 1s exerseu when the plasmld peps haek eut Plasmlds and a type of Conjugauon are also mvulved m the transrer ngeneuc mrarmanan from battens to some Eucarymes Remember Agrooaetenum Umefaclens s cm alphapmzeubaczenum related ta Rarzearum Flg 112 has a T1 plasmld tumor mducmg plasmld that codes ran 1 A p11us 2 Transfer factors 3 Transferred DNA TVDNA that codes for plant hormone producuon and the producuon of opmes 4 Metabollc genes that allows A Umefaclens to eat opmes Farsp 82 pg 211 Mavement or DNA wlthln eells eg ranspDSDns m 323 Mwem n urs usnspusun through abatzensl eummunuy m 524 aJnseman SEQuelee b Campame nunspnsnn canmmmg m annmaut lessunee Sam Table 83 Transposition lnvolves small segmean of DNA Lransposons jumping genes am an move around chromosomes or plamlds e g Frpla nlds have msemon sequences mm to the o que as are very slmple and ty call ooneun only the lnformauon needed for msemon see gure 8 24 semen mumsle mm sneuncme ransposors omnmunnslen names mare more complex and may ooneun a number of genes mm confer e g anlelOLlc Eslstance andor Loxm producuon Anew2 huu39 W s m Mmch more l on em lulssmssm m LECTURE 23 2 topics 1 Immunology 2 Emerging Pathogens Probiotics inoculation with normal ora to prevent infection or to recover from antibiotic therapy e g Yogurt intestinal ora Bene ts of the Normal Flora 1 Protect us from colonization by other bacteria and fungi competitive exclusion 2 Many synthesize vitamins eg E coli make Vitamin K and some B vitamins 3 They can stimulate the development of certain tissues 4 Nitrogen xation in intestines of vegetarians Review other barriers to infection See Figure 153 and read pages 372376 Many baby animals are now treated with normal ora to prevent colonization by pathogens chickens are treated to prevent colonization by antibioticresistant Salmonella Fig 153 Barriers to infection Other defenses The In ammatory Response removes invaders H N DJ from an injured area via one or more of the following dilation of capillaries allows more phagocytes to get to the invaders release of chemotactic factors attracts phagocytes to the area increased permeability of capillary walls allows phagocytes to get into damaged tissues clot formation blocks further invasion in large wounds See figure 1510 The Immune Response just enough immunology so that we can understand the basics of how the immune system responds to microbes and viruses some concepts and terminology Antigens molecules to which the immune system responds Common antigens are found on the outside of cells or viruses eg polysaccharide portion of the LPS of gram bacteria Other antigens include pili agella porin proteins and exotoxins Outer proteins of viruses are also good antigens Almost an protein greater than 1000 daltons in size can be an antigen but most 10000 daltons Antigens from body g erator substances that elicit an immune response Epitopes or antigenic determinants specific molecular sites that antibodies bind to on antigens Fig 163 Antibodies belong to the immunoglobulin superfamily of molecules Table 161 shows the main types of immunoglobulins These molecules function as the feelers that detect and bind to antigens Don39t memorize all the different types of immunoglobulins Fig 163 Fig 164 Basic antibodies Fig 165 Model of an antibody Figure 166 Protective outcomes of Antibody Antigen binding 1 Neutralization 2 Opsonization 3 Prevent Adherence 4 Activate complement 5 Agglutination 6 Activate killer cells Antibodies Immunoglobins Made in response to an antigen and can recognize and bind to it Humans can make as many as 100 million different antibodies Charadzrislirs of he ilarinus Classa a Human Jammy Table 15 0mm Pena m T able 161 Moltmllv Might delims mm Pruumizs main iz Wm mmm WW minimum WWWquot mm m mam 111 mum 1 m mu 2 mmmmmnmmm m m mm mumquot mam 111m i iuw39rm 5043 mvuzumnmw Autumn mmmmmn mmn nu mw Wadi 41111 auval an immune rem mum in mm m 1 1w mum mumr Emma mm slim m it numb qumn w Wm mum by is m and aim mm mm mm mummy mumi m mm 1 51 mm amtm mum mummlyl irmuv in send u m iiiwiml ml Idtwlumnmuulmi a m ummmw mm mynavnmxmL m m hmndn y zsmlml mm 41 m Mums n m a 3 m mwvmis 1mm n mm mm mm A 21an mutant lnE m m minim mm m mrc min in um um mm a mm m parwit mm mm Emerging Diseases New reemerging or drugresistant infections whose incidence in humans has increased within the past two decades or whose incidence threatens to increase in the near future Fig 2010 Some emerging infectious diseases Most are old diseases that are re emerging Some reasons for emerging diseases increased international travel changes in food handling human encroachment on wilderness climate change over use of antibiotics GAMMAPROTEOBACTERIA I largest group of Proteobacteria I many familiar genera Escherichia Salmonella Pseudomonas I incredibly diverse Cholera cont Emerging evolution of a new strain with a capsule antigen see Fig 1115 Figure 2413 Mode of action of cholera toxin Table 245 Features of Cholera Cholera I Caused by Vibrio cholerae I Exotoxin I Severe diarrhea GAMMAPROTEOBACTERIA COHL Vihrios I some are important pathogens eg Vibrio cholerae I some Vibrio and Photobacterlum species are capable of bioluminescence Some live symbiotically with squid or fish Figure 2412 Scanning electron micrograph of Vibrio choerae Viral Encephalitis pgs 675677 Epidemics usually caused by arboviruses arthropodborne viruses Mosquitos are vectors and often reservoirs main reservoirs are wild birds and mammals see Figure 613 eg West Nile Virus an emerging disease Middle East to New York in 1999 and has now spread all the way to California fall 2003 2947 cases and 63 deaths in Colorado in 2003 reported to CDC most of any state Table 141 West Nile Virus is in the Flavivirus family Flaviviridae ssRN M ny mosquitovectored viruses in this group including Dengue and Yellow Fever vimses West Nile Virus casea39eported to CDC in 2003 in his human disezsa 2525 Note that the number of cases dropped off in Colorado in 1004 compared to 2003 This is because the birds reservoirs either died from the disease or became immune s the reservoir of the disease greatly decreased this is why the disease spreads in a wavelike fashion across the world l Aviananimaloumusquiminfecuuns Slide from CDC April 2004 Horses and humans are incidental or terminal hosts not reservoirs Yellow Fever another emerging disease that is spread Yellow fever by mosquitoes causedby arbovuuses Not a present problem in the USA but the specific type of 39 ZOOHOUC mosquito that spreads it has recently reappeared in the Affects the heart and blood vessels SE USA Vaccine available Important historicallyI prevented along with Malaria the French attempt to build the Panama Canal Only a er Walter Reed and colleagues showed that Yellow Fever was spread by mosquitoes were mosquito control measures put in place and work on the canal could I Figure 2810 Distribution onellowfeverrcun39entlypossiblysprezding proceed read perspective 282Y pg 731 39 SA north into Cenh39zl America and the SE U Features of Yellow Fever Table 237 Ebola An example of an emerging Hemorrhagic Fever caused by a Filovirus Filoviridae many such diseases exist in wild TABLE 287 Yellow Fever SVmDKCMS o tl l only hsa zche am leve SEVEN EASE f ig f izzifjquotl d WWW vertebrate populations and are potentially transferable to humans eg Marburg outbreak among Germans who li lLUDilmli veiiod Usially 3 to 5 day handled monkey meat Causalive agent Vulluw revc39 ll39JS a1 enveloped s nglcrsliandad RNA vim 0 re llavlvims lamily Magma Vinn m up in inmlly m m of ma Minn by M mimn mmqu in m in s r and ilimughoiir thelmdybyihz niuonsmam Vimmmysimms gt Ebola rst Struck humans in causing iaurdlcc and increased pmdudlon oi bloudr domng minim Hemorrhage and decreased srang1h El the liar resin in cirulamry l2 lira and kdney ai we Epiremialngy Vim miifs in ma Winnie an ill masquiim mm m m lhcm in Am and grin and mm Amara himari ecidmiks mm when on virus mm hmsehol mnsquiioes llial few an humans 1976 in northern Zaire Prwrninri and men l a highly fferiiw live mmumm mi VPmmrm vnr irw m pram minim th ll y H mm ere quotI39ec e l 33 e l quotIcl dl39l gt spread vla alr or contaminated bleed many hospital workers gtSrml semnern Lane In 1935 but was gt Incubatlan perlad 11a days qulcldy camamed gt 22 days later nausea vomiting blood hemarmagmg gt rasn men death 59 days later was outbreak ln Heston Vlrglnla 4 people acqulred Ebola lrern Inlected rnenke s y Ebela ls a Illewrus because underthe EM n quot399 mm Wquot 57 5quot a werrn leeu llke must caused by r nuvlruses panuf plcumavlrus famlly mg 14h Ebolavlns quotFlca39 lmall rna ans wanenvelupeu Table 14 l Ebola and Marburg are Fllovmdae hk2 sllgmly cuulel upllmum tempelaluves 33 auapleu lu me nuse Reservull ls humans unly aslal aswe knuw 5 avcalds are caused hv Aham rn 11a Camrlavlmses seas lsalm caused lava Camnawus Table 1 Cold are caused mosuyby Rec 4 1 maVlmeS and Coronavlmses mm 23 nn mm mm quotl 11 m mmm Mum lmmwmv mm ml sum n nlmasm Mn blzxssrldwlulmah quotMu mime e rm 4m Emu mama mmuum quotquot mu m 42quot mixlienquot n m um um m m WWW mm sewage treatment Environmental microbiology Why do we treat sewage 0 Sewage treatment 0 Avoid drinking water contamination Bioremediation 0 Avoid food contamination 0 Avoid ecological damage via 0 Microbes and climate change eutrophication Drinking water contamination sewaget39ea me Cholera Food contamination o Caused by librio choleae o l choleae is gram rod salt tolerant acid sensitive 39 Meat daerr ShellfISh become reserVOlrS for o Virulence determined by bacteriaphage pathogens and account for 90 Of US 0 Produces exotogtltin that interferes with intestinal water f00d borne dlsease Bacillus Cereus CIOSITI39dI39UIquot ShI39gela balance Staphylococcus Listeria Yersi39ni39a Aerumonas o Togtltin is destroyed by heating Histo of Cholera Sewage contaminated waterfertilizer sprayed 4quot Jo n Snow on vegetable crops get have caused food 18131858 HospitaDoctpr magazine39s greatest doctor of all time poisoning outbreaks E coli 0157H7 Cycluspora Toxoplasma Cryptosporidi39um Campylobacter Salmondla Sewage trmlment Sewage trmlment Eutroghication How do we treat sewage Goal reduce the BOD Biochemical Oxygen Demand L A A A lhe WaLci I 5 m Basically an index of contamination Sewage treatment plants in US use a series of two processes as mandated by the Clean Water Act of 1972 0 Primary Treatment a physical process 0 econdag treatment a microbial process Sewage trmlment Primal y treatment Treatment via GRAVITY Raw sewage is passed through series of screens The sewage is allowed to settle in the sedimentation tank yielding sludge This process typically removes 50 of the solids and 25 of the BOD Sewage trmlment Other secondary treatment processes Lagoons Sewage is channeled into shallow ponds Algae and cyanobacteria provide 02 for the aerobic organisms in the pond to degrade the sewage Artificial Wetlands Similar to lagoons except they provide a habitat for birds and other wildlife Figure 313 Sewage trmlment Tertia treatment of Effluent o Nitrates removed by denitrification 2N0339 5H2 2Hb N2 GHZO Energy NiTmTe Dini trogen Gas 0 Phosphates removed either chemically or microbially but both result in precipitation of phosphates out of solution 5 t tm t ewage ma aquot Secondary treatment Treatment via MICROBIAL ACTIVITY Naturally occurring and inoculated microbes oxidize organic material into CO2 Aerobic conditions must be maintained via mixing in an aerator Oxidation is greatly enhanced by formation of bio lms Bio lmsFlocsMicroorganisms living in communities suspended in liquidish environments attached to surfacs sometims gravel This process can remove as much as 95 of the BOD Sewage trmlment eftovers Effluvent liquid from 2 treatment ig in nitrates and phosphorus Sterilized by UV ozone or chlorine By now pathogens have usually been entirely removed by competition by sewage adapted organisms Sludge solids from 1 amp 2 treatment Warning may contain hmvy metals amp pollutants Processed by digestion Sewage trmlment Digestion of sludge reactions in digestion organic compounds gtorganic acids CO2 H2 organic acids gtacetate C02 H2 acetate CO2 H2gtCH4 note ANAEROBICH The result is a nutrient rich product called stabilized sludge It can be burned disposed of in landfills or used as a fertilizer Sewage treatment overv ew molecular form nutrient availability empemmre mois re 02 concentrations microbial communityecology other chemicals ImQrtant term 2 cometabolism game pullutarits are ga d by acnde by miernne erlg tn deqadescmettnlnn ese Miannes Dnmte enzymes t lade sutsvates in side tn SLWWE ittlne mzyme is Qmaal mum it wlll degrade mha dame as wel Ths is cur meandism it ycu Dmvlde mae nfthe sutlsvate tine micth is attenntnn tn degrade yuu Carl acceaate tine beakmwn et mendlutart Bl oremedlau on Overview Bloremedanol39l the use ofllvll39vg drgansm sudn as bacteria and rung m degrade or demxlfy pdlumrte Wren plane are used it is called plnytdremedaton aiaremeaaiim i maxi oRen attempieam lznrflllx ulx sauna Mlhrdx snail le Important term 1 Xenobiotis syrithenc compounds matare mtally dtrerertt from any that ecu iri natue Tlney can be lnarder to get rid of because there arel lt organisms that ye evolved to degrade them Enter genenc erigneeririgll Two main bioremediation strategies 1 Einstmuatm mhamrlu the 9m at alleadwulzem mltmtz by uuyidirn then ylnat they are limied by e n nammts mean 2 Elnaug munm adan aganisms that were ridt already great Exzmde mam ulwll aimaism aimaism Example TCE breakdown Magic bullet right Well went nmununds an be mm dawn m stmething Worse TCE mmlume wlma is a may Dullutant imm elemmi mmpunems fume vans vs ND known micvnbes use mg as a pvimaiv subsvate L A 1 mm desiveo mi Dbial n leavgescalesucczs biuaugmenutinn m Dulqu newsSvstans ecumbinant minutes 3 Damn saw tduene mm Wuva n msmetabnlize TCE om dung Environmental microbiology Sources of our major and global climate change greenhouse gases lb abandiaxdersail yemmsn mi hel mm mums mining Nmausm rsewsze treatment mm fevhlizevs summamieemug Mahme 7 we mdi livesmtk memimmn stage 395 detmvasitiam ulhnqrmml at nauvd gs Flumtahans w ygnqaams oimmsnge amusing G al carbon dioxide concentration is on the rise Radla VE iman campuund m Wm WM WWWsz mm mm Climate mange Climate mange Carbon dioxide sources amp So what haggens to soil resgiratio Sinks nder global warming The onlyl iacural system Models predict greatest warming at the poles We 0th Wl lbrlum The arctic contains 40 of the world s soil le can affect cabon balance 5 me carbon frozen as perm ost terestriai ecosystem when mmperamres increase permafrost Recent iargescaie 5 and membolic rates increase slightly SW65 NW 13 90 increasing soil respiration i asing co2 in respiration is rmch me a m I more rrutabl e an t osphere increasing warming ether photosynthesis or plant respiration 0 means a flux out of the arm Amherst means a flux into the atmasvheve Climate mange Climate than Methane sources W ensquot Denitri cation is a twossmp process N20 is r a released whenever the second step is blocked or slow N20 is also produced during biomass burning and by soils after a burn oN20 conoentrations in an E the atmoqahere has I aim Increased by more than Minnalmemanc 15 since 1750 WW n n Climate mange Climate marl Microbes and global change i Sources of nitrous OXIde Microbes are a major natural and stimulamd source of most greenhouse gases careful measuremenE of microbial gas emissions are vital for predicting global climate Microbial emission rates increase with the effects of human landsuse change livestock modern agriculture practice waste production and 39 rning All are secondary effecE of human overpopulation LECTURE 3 PROKARYO39I39IG CELL STRUGTU RE We39ll nme one lamrla mom about Aquot a a nkarye Later Cell grouping a g a m quot3399 E 3 I o a a 37 39 o immune 7 Figure 322 Fig 1118 Very complex mul cellular aeroseopie fruiu39ng o ies of yxobaelena The Shape o1 39rhings Morphology TWo main shapes 039 bacteri Figure 320 Spheres cocci ingular coccus Rods ba singular baclllus mher shapes Comma shaped vibrio Spiral sp la spirochete Varying shapes pleomorphic Unusual 12 shapes Figure 321 Fig 112 Methanosarcina sp all Archaea a note the packets of 4 or more 05115 Some Bacteria have even more elaborate morphologies Fig 117 Complex mulucellular morphology In mrlous cyanobactena 21 Spiral mehome of plruzum b Oscillalorm 9 Filamentous hyphae of an Acunohactenum N Fig 11 1 lreplomym Sp OLE muluoellular hyphae and sphenml spores comma Back to a single Bacterial cell Fig 323 The Plasma Membrane Every ce whether prokaryotic or eukaryotic has a plasma membrane Very thin about 5 nm thick Separates the i side olthe cell quotam the environment mu mu ch asmsmmnmnmss r 125 cenemion of Enemv nvton Motive rm r 12 Ilier Movement of Molecules 321 ACTICE numsron g quot a venue y lulrier wevelIs leakJ of ac manequot quotno and out of 0 eumnelh wow mnsloenion rig 330 My do laden Ive eel m squot umor mssm us about 2 nmosphms or about the same mssm s in a canine c I mus hell winsum these pressms and Ewe the cells shape The gmmposuive can waH Peptldoglycan Plasma membrane Can waH Gram pnslllve Gel Wa Is The gramnsgalws csquot waH Cell wan 4 Omar membrane Pepuduglycan Magma membrane Lr Penpiasmic space Inuuo mmllle recounillon of lame Fig 333 Hnw dues the Gram stain wnrk39 The best hypnllle ick pepadogyean pores close preven v no esc zing The Structure nf Peptidnglycan g 332 Gram negatlve 0e Wa Is Lipnpnlysaccharide LPS mm or immune Fig 335 Ecnlnglcal slgnlflcance nf Gram and wal s W Icll wnuld reslsl drying better Components External to the Cell Wall Glycocalyx Capsule a la er of well organized ma erial not easily washed off May help resist phagocytosis Filamentous protein appendages Flagella Pili Fimhriae pili used to attach to surfaces Flagella amp Moti Y Flagella sing flagellum are used for locomotion Flagella may be distributed in specific patterns rrrmonotrichous jampllitrichous f Inpllotrichous Perilrichnns Components External to the Cell Wall Slime layer unorganized material that is removed easily Slayer a regularly structured layer composed of protein or glycoprotein May perform many functions 0 protect against ionic fluctuations 0 protect against predation 0 attach to surfaces and other cells Pili fimbriae Pili sing pilus larger genetically determined by sex factors and used for mating Figure 817 Figure 342 Fig 318 Flagella Visualized with a stain that coats them with a thick layer of stain so that they can be seen with the light microscope Fig 33 39Ilichous agella de visu e seaming electron microscope 5 EM The directinn at the rntatinn determines hnw the cell n es m g 4 V W IE Bacteria rntate their flagella very rapidly as much as 10 rpsl Althnugh bacteria nnly mnve 000011 kmlhr this equates tn 5060 cell lengthssec In cnntrast a cheetah can nnly run at a rate at 25 bndy lengthssec Flagella are cnmpnsed at 3 parts the filament the basal bndy the hunk Fig 339 chemntaxis In a cnnstant envirnnment bacteria will mnve ran nmly They can hnwever exhiblt directed mnvement tnward an attractant eg fond nr away frnm a repellant eg waste This is chemntaxis See Fig 340 The c nnlasmic Matrix Unlike eukaryntes bacteria dn nnt have membranebnund nrganelles The cytnplasmic matrix is the material between the plasma membrane and the nIIcleni What s in there Ribnsnmes cytnskeletnnlike system at prnteins n pooolnca RNA BMein si1c of plo1cin aynulcai Granules 05 llm Slorzga gmnu Figme 45 PDMbeIkMimyb lyma lmsmuoel la The Nuclco Baderin nanally navc 1 chmmmmal in an incgnlarly anapco lcgion1nc nucleoid nunmmle Wmi l uimhnhm s1oragc grannlca a type of nclnaion body solnc alc membranebound lnoa1 alcn1 used iora1oragc Photosynlhd c baderin navc gaa vacuole 1na1 icy can fill in na r This givca 1ncnl pooyancy an icy can 1ay ncar 1nc anilacc of 1nc wa1crano clooc 1o annlign1 They can lcgnlau 1ncir pooyancy py collapsing vacuole and cona1nlc1ing ncw How pig alc haduinl gcnoincal 1 million 10 million paac pair lra1lc1cnco ou 1nc coligcnolnc would pcapon1 1 mm in lcng1n p11 1nc pactcr 39 If i only 23 um longl npelcoilco 1o The DNA in 1nc nnclco packagc 1 compacuy The Endospore Gram very resistant dormant structure Cannot be killed by boiling must he autoclaved Many bacteria also contain plasmids These are also circular Plasmids are typically Makes them dangerous pathogens but most endospore formers are not pathogens passed on to all daughter cells They are generally not essential for survival but very often contain genes that provide a selective advantage such as antibiotic resistance The structure of an endospore is complex mmym Endospore formation CW core wall ex cortex SC spore coat EX exosporium CR core N nucleoid Flgure 347 Fig 2612 Fig 1116 middle ol cells clasfridium emani spores It ends ol cells Clostridium botulinum Spores at ends of cells LECTURE 16 EUKARYOTIC MIC ROBIAL DIVERSITY Fig 121 Phylogeny of the Eucarya Note the distribution of Algae Fungi and Protozoa Algae encompass many diverse groups I II III ltlt2 Green algae Chlorophyta Euglenoids Euglenophyta GoldenBrown Diatoms Stramenophiles Brown Algae Phaeophyta Red Algae Rhodophyta Dino agellates Pyrrophyta Classi cation based on many properties inc u mg I chlorophyll molecules I agella I reproductive structures I life histories I and others ALGAE Phycology is the study of algae Algae have chlorophyll a and use oxygenic photosynthesis Fig 123 Note that algae are not monophyletic and are mixed in with the Protozoa there may have been several jumps of chloroplasts cyanos into 1 Green Algae Chlorophyta I have chlorophylls a and b I wide variety of forms I closely related to land plants I both sexual and asexual reproduction R d r 39 cm d V elm Iquot Iquot quotI amy email II Euglen01ds photosynthetic protozoa 0 have chlorophyll a and b Complex life eyde sexual and asexual Diversity of Dialnms III GoldenBrown and Diatoms Chrysophyta 0 diatoms have a 2piece cell wall of silica called a frustule VLDino agellates Pyrrhophyta PROTOZOA E 126 g 0 alveolate algae 7 related to Ciliates Protozoa Protozoolo is the stud of rotozoa 0 some are bioluminescent gy y p may cause red udes Not a monophyletic group 7 defined as a 0 some are symbionts in other marine organisms moulex eukaryotlc unlceuular ce 1 especially corals 7 called Zooxanthellae Most are chemoheterotrophic gtingest solid nutrients via Ehagocyto is gtingest soluble nutrients and small solids via Binoc osis muQ39u39phyleuu group Also can take up small nutrients Via 39 siorl See Figure 350 Flgure 12 9 PolyImrphlc Some can encyst n foun restlng stage or cyst Mamie oh 1 help protist survive harsh periods 0102031 Nueglmu 2 allow or transler ol parasites A Amebold stage m ammal Llssue or between host so B Flagellared Stagem water Feeding or vegetative stage is called a hozoite trop c CysLunderdrymg Condmons Protisb move via Reproduction in protists is Via 1 pseudopodia false leel39 r cy oplasmic ssion extensions Fig 1210 Valiations on asexual 2 agella rqiroduction in protozoa l cilia 2 sexual reproduction r eg conjugation common among Paramecium any disease causing pronsts have a sexual cycle Many grnllps we ll cancenlrate an 3 39 Phylum sarc mas ig l39h ra Sarcnmaslignplmra agella subphylum Mastigophora Apicnmplexa pseudopodia subphylum Sarcodina Rlbasomes Masllgnphnra cnmams Impnnanl grunts Undulannu Fold l WW9 membran mm agellMM v gt Giardia Fig 2422 Gianh39a lamblia Irophozoites in hurmn intem39nes Endo lasmlc ellcu um gt Triclmmanas gtlrypannsnmes Nucleus Mimchundvion Free agellum KWWN Table 2413 rd asivswu W39faml39a lg ilg39 Sarcndina amnehnid prnlisls Symmums Mild illness lndlgestlon amlema nausea severe gt same have 95 shew pmvides vumllmgdlanhea abdominal ramp weight loss prnle lnwballon penod 5020 days gt quota quotan marine amnehae Causatwe agent Narnia lambis a flagellated pezrrshaped pmwzoan with nmale 9515 Wquot M m gt Many are symhinlic Palhogenesls Ingesled cysts sunIve stnmach passage lmpholulles emer elmm he SE in lhe small lnleslinE where some math to eyllnelium and others move freely mumsal fundlnn ls lmpalred by adhevenl wotozoa and host lmmune response Epideminlogy Ingestlon n1 fatally ontaminated walen pawnto pmon m daytare centers Prevenllan and Balllnq or dislnfedlnq drmking waler mmion M mlmem mmmuni waler su plies ealmenl39 qumam ne nydmmlonde AlabnnE nr memnidmlz Flagyl Pseudapodi n V Ni leils39 39 quotM Endoplasm II Apicnlnplexa have a sparefarming stage in their life cycle at some paint generally lack Incnlnntnry organelles all are parasites includes some of most important parasi e gt P lasmadium Inalaria gt Taxaplasma gt cryptaspan39dium Phagocytic Contraeule Ecloplasm vacuole vacuole 111 Ciliates Phylum Ciliophora The Fungi 0 move with cilia Fungus eukaryntic sparehearing organisms with absorptive nutrition nn clllnrnpll I an that reproduce hntll sexually and asexually rMajor predators of bacteria in natural systems Have 2 nuclei Ilt Mycnlngy the science of studying fungi rTransVerse binary ssion figure 1210 Fig 18 Fig 1211 sequence Some general fungal terms based phylogeny of the fungi Mycelium many hyphae Chitin the glycoprotein that makes up a fungal cell wall polymer of N7 acetylglucosamine Where else do you nd ch1un77 Saprophytes nutrients come from dead material decomposers ehemoheterotrophs Many fungi are mutualists with plants mycoxrhlzae and cyanobacteria or algae lichens Mold filamentous long branched filaments or hyphae Together hyphae form a mycelium I coenocytic continuous no cross walls I septate cross walls with pores Figure 1213 Yeast unicellular fungus Fungal reproduction Asexual or sexual Asexual 1 Divide into 2 equal cells binary fission 2 Budding Fig 1214 Asexual reproduction budding in a yeast 3 Form asexual spores conidia 4 Fig 1215 Asexual reproduction in a filamentous fungus Dlplom stage 2N stage NN mama Haplald stage 1N Dimorphic fungi alternate between yeast form and mold forms the YM shift Common in pathogenic fungi but with opposite patterns in animal vs plant hosts Animals yeast in host mold in environment Plants mold in host yeast in environment Fungal reproduction Sexual the union of compatible nuclei haploid gametes gameteproducing bodies hyphae Major Fungal Divisions based on DNA sequencing I Zygomycota II Ascomycota Ill Basidomycota IV Chytridomycota x Zysumymu Sammy mm mm buxu ar rnytunhuie phi are mm m a w mwm Ema x pxudutum Fianna ZYEDXPUXEX mum a Mwummy mmhnmmm 4 n 4 m quotswungm squot mmyumn many y usllyli mums gharaghn w mum runun vrygm Ismanyhrm a MW n gnwn mill 3 mmuaxge W gmquot sung 93 and Inbryhylnm 1m oi ampamwna mm momma a um s in mmquot m 9mm ENDOM COKKHIZAE r m m n 11 5mm gamma afEmiwmycs s a mam xsmmmwa c WWW m amywmnzal mns mm 11 n mmm afaWCdEmiwmycme me mm sun mum mm INNark msmmmm u S Sexual life cycle of 2 Basidiomyce39te tuse to farm 555mm maintains is 139 u ul Ff llf ed Dlplold nucleus 0 ql cover News mm to m mm 0e Mmkarym myD lm Basldlaswm y Basldlaswre a myoelmm V chytridnmycnta the chytrids asexual stages are mntile znnspnres have important in that they have been implicated in the devastation of frog pnpulatinns worldwide Fig 121 Phylogeny of the Eucarya Note the distribution of Slime Mo 5 and Dam cates ruo lou get co usidered to be fun i E CTOMYCO KKH IZAE 1 Ec lomycorrhizae are mostly Basidiomyce les many of The large mushrooms in forests are The sexual stage of ec lomycorrhizal fungi SLIME MOLDS resemble fungi in their appearance and lifestyle phylugenetically distinct from fungi Eukzryou39c microbes and food Bread Produ n Along with cheese bread is one ofthe most ancient foods Here yeasts grow more aerobically Saccharomyces an ascomycete is a facultative anaerobe which makes more CO2 and less alcohol evaporated trimming cooking The alcohol that lsluvmed l5 Bakers will add enough yeast to allow the dough to rise in 2 hours or less T make snurdnugh breads bath a yeast and Lactabacillus bacteria are used to give them their acidity and flavor