Questions-Lecture 18:What are the three fundamental groups (Domains) of life-forms?What is polyphasic taxonomy and what criteria are used in this approach?What features are common to all cells? What features are shared by bacterial and archaeal organisms that differ from those in eukaryal cells?What is a prokaryote?What bacterial organism challenges this definition?What features of the16 r!"# make this the preferred molecule for constructing phylogeneticrelationships?What are the steps in a polymerase chain reaction? What are the roles of the primers and D"# polymerase?$ow can the se%uence of the16 r!"# from an unclassified organism be used to predict itstaxonomic classification?When is the term &andidatus used?What are the se'en phyla (or groups of phyla) that were discussed? What are their general characteristics? Which fall under the groupings of gram positi'e and gram negati'e?What cellular feature is shared between #%uifex and archaea? $ow are these organisms classified with respect to their optimal growth temperature?What commonly used en(yme was first isolated from )hermus a%uaticus?What physiological adaptation is characteristic of Deinococcus radiodurans?What photosystem is found in the &hloroflexus species and where is this complex located within the cell?What photosystem is found in the cyanobacteria? What gas is produced during phototrophic grow? What subcellular structures are often found in these organisms and what are their functions? What relationship do cyanobacteria ha'e to modern eukaryal organelles?What type of spores are released from #nabaena under stressful conditions?What general features are shared by *irmicutes and #ctinobacteria? $ow do they differ in their genomic +& content?What type of spore is form by ,acillus species? $ow does the formation of spores in ,acillus differ from that occurring in treptomyces species?What catabolic processes in &lostridium ha'e made these organisms useful for industrial processes?What are examples of pathogens from this genus? What popular cosmetic product has been obtained from these organisms?What characteristic of -pulopiscium fishelsoni distinguishes this bacteria from nearly all other bacteria? What are the three fundamental groups (Domains) of life-forms ?What is polyphasic taxonomy and what criteria are used in this approach?What features are common to all cells? What features are shared by bacterial and archaeal organisms that differ from those in eukaryal cells?What is a prokaryote? What bacterial organism challenges this definition?What features of the 16 r!"# make this the preferred molecule for constructing phylogenetic relationships?What are the steps in a polymerase chain reaction? What are the roles of the primers and D"# polymerase?$ow can the se%uence of the16 r!"# from an unclassified organism be used to predict its taxonomic classification?When is the term &andidatus used?What are the se'en phyla (or groups of phyla) that were discussed? What are their general characteristics? Which fall under the groupings of gram positi'e and gram negati'e?What cellular feature is shared between #%uifex and archaea? $ow are these organisms classified with respect to their optimal growth temperature?What commonly used en(yme was first isolated from )hermus a%uaticus?What physiological adaptation is characteristic of Deinococcus radiodurans?What photosystem is found in the &hloroflexus species and where is this complex located within the cell?What photosystem is found in the cyanobacteria? What gas is produced during phototrophic grow? What subcellular structures are often found in these organisms and what are their functions? What relationship do cyanobacteria ha'e to modern eukaryal organelles?What type of spores are released from #nabaena under stressful conditions?What general features are shared by *irmicutes and #ctinobacteria? $ow do they differ in their genomic +& content?What type of spore is form by ,acillus species? $ow does the formation of spores in ,acillus differ from that occurring in treptomyces species?What are the stages of endospore formation by ,acillus? What features of the endospore contribute to its 'iability under harsh conditions?$ow do endospores return to 'egetati'e growth?What catabolic processes in &lostridium ha'e made these organisms useful for industrial processes?What are examples of pathogens from this genus? What popular cosmetic product has been obtained from these organisms? What characteristic of -pulopiscium fishelsoni distinguishes this bacteria from nearly all other bacteria?What are examples of non-spore forming *irmicutes?$ow does the enteric pathogen .isteria monocytogenes mo'e within host cells? What other non-firmicute bacteria uses a similar mechanism?$ow does the cell structure of the /ycoplasma differ from other firmicutes?What morphological characteristic is used to describe the two main groups of #ctinomycetes?What molecule or structure in the #ctinomycetes is the basis for their positi'e acid fast staining?What morphological state (or from) of treptomyces coelicolor produces arthrospores? What important biomedical molecules are produced by these organisms and what key en(yme system participates in their formation? What is the structure of D"# in these cells?$ow does the presence of mycolic acids and phenolic glycolipids in /ycobacterium affect its growth?What are examples of pathogens in this group?What are the key features the gram negati'e cell en'elope? $ow does it differ from the gram positi'e structures?What are the fi'e ma0or classes of the 1roteobacteria?What aspects of metabolism 'ary among members of the 1roteobacteria that account for the metabolic di'ersity obser'ed in this group?$ow do the general growth properties of alphaproteobacterial organisms !hodobacter sphaeroides and &aulobacter crescentus differ? What cellular structure is produced by &aulobacter crescentus that allows it to adhere to surfaces? What important metabolic process is pro'ided by !hi(obium and inorhi(obium when these cells are associated with plants? $ow does the plant help to protect nitrogenase in these cells?What relationship do !ickettsias ha'e to modern eukaryal organelles? $ow are these organisms similar to .isteria with respect to their mo'ement within their host?What is the electron donor in the lithotrophic betaproteobacteria "itrosomonas nitrite is produced? What speciali(ed components are present in its respiratory electron transport chain?What molecule is produced during respiration by )hiobacillus when $2 is the electron donor?What is the en'ironmental impact of producing this compound? Why are a portion of the electrons used is in re'erse electron flow during respiration?What do the gamma proteobacterial organisms &hromatium and ,eggiatoa produce when cells use $2 as the electron donor?What important facultati'e anaerobe is a member of the -nterobacteriaceae family?What benefit to humans are pro'ided by -3 coli strains in the gut?What are the oxygen re%uirements for 1seudomonas aeruginosa and 13 fluorescens? What role do these organisms paly in the en'ironment? What pathogenic process is associated with 13 aeruginosa?What unusual product is produced by +eobacter metallireducens when cell use *e45 as the electron donor?What steps occur during the de'elopmental program of /yxococcus xanthus when cells are star'ed for nutrients?$ow does ,3 dello'ibrio propagate using proteobacterial cells as a host?$ow does $elicobacter pylori alter the chemical en'ironment of the stomach to facilitate itsgrowth? 6s this organism an obligate acidophile?What are the growth characteristics of "itrospira? What form of nitrogen does it remo'e from the en'ironment?Where are ,acteroidetes found in humans? What benefits do they pro'ide to the host?What is the function of the chlorosome in &hlorobium species? What other organism possess this structure?What is the characteristic cell morphology of pirochetes? What is unusual about the location of their flagella and how do they swim7mo'e? What diseases are associated with this group?What are the two de'elopment stages of &hlamydia and how do they function in the lifecycle ofthis organism?$ow does the morphology of a 1lanctomycetes cell differ from most bacteria and archaealcells?What eukaryal-like protein is found in 8errucomicrobia?Why are 1lanctomycetes and 8errucomicrobia described as ha'ing compartmentali(ed cell plans?What are the two archaeal phyla? What features constitute 9archaeal signatures:?$ow do archaeal lipids differ from those found in bacteria and eukarya?What 'ariations in the -D and -/1 pathways are found in some archaea? $ow do these differences affect the yield of #)1 when glucose is con'erted to pyru'ate?$ow is the archaeal transcription system related to the eukaryal en(ymes? Lecture 19:,ased on recent estimates; what is the approximate number of microbes on the plant?What is an ecosystem and how is this related to a niche?What are assimilatory and dissimilatory processes?What is a tropic le'el and how would a cyanobacterial species be classified in an ocean foodweb?$ow are mutualism and synergism related? $ow do they differ?Who are the microbial partners in the termite gut example described in the notes and what biological acti'ities do they pro'ide? $ow would you classify these interactions?What are the 'arious subdi'isions of a marine water column and what in what di'isions are photorophs found?$ow are planktonic communities defined? 6n what group (or class) would you most likely find 1rochlorococcus ?What methods are commonly used to detect organisms in an en'ironment? What methods ha'e been used to predict microbial acti'ity?What is marine snow? Where does it form and what is its role in the marine food web?What are examples of common microbes (growth classification) found in ocean benthic communities?$ow are the different di'isions of the a freshwater lake defined? $ow do the di'ision of the lake change when large concentrations of nutrients are introduced? $ow is the biological community affected by these changes?What are soil hori(ons? Who are the ma0or producers in the soil food web? $ow would you classify the di'ersity of this en'ironment< low di'ersity; some di'ersity but not significantly different from fresh water populations or highly di'erse with many uncharacteri(ed microbes?6n the deep subseafloor biosphere meta study; what were the prominent microbes? What types of tests were used to compare population analyses with biological acti'ity?What distinguishes epiphyte and endophyte plant-microbe interactions?Which microbes are in closer association with plant roots; those in the rhi(osphere or rhi(oplane?What types of microbes are described as /ycorrhi(ae? What distinguishes an endomycorrhi(ae from a ectomycorrhi(ae microbe?What does the carrot fungal symbiont +lomus intraradices pro'ide to the host root? What does the root pro'ide to the fungal cell?What structures and biochemical processes are characteristic of rhi(obia?What are the stages of nodule formation and what initiates this process?What is the function of a bacteriod? What metabolic processes are carried out by the bacteriod and how do they benefit the plant? What plant processes benefit the microbial cell?What disease is caused by the plant pathogen #grobacterium tumefisaciens? $ow is #3 tumefisaciens acti'ated and what is transferred to the plant host? What changes are induced in the plant host and how does the microbe benefit from the interaction?What type of interaction occurs between the #phid (#phis fabae) and ,uchnera aphidicola?What metabolites does ,uchnera aphidicola pro'ide to the aphid and what does the aphidpro'ide to the microbe?What is the first key metabolic intermediate produced from the breakdown of cellulose andstarch in the rumen? What second intermediate is formed that facilitates fermentation processes? What metabolic products are absorbed by the intestinal lining of the animal? What reaction(s) is7are carried out by the methanogens and why might this be an undesirableprocess? Lecture 20:What roles do reser'oirs play in biogeochemical cycling?Which carbon reser'oir has the largest content of carbon and which is the 9fastest: in terms of cycling?Which of the macronutrients has the largest number of oxidation states in the compounds cycled in the en'ironment?What general process occur during minerali(ation? What types of products are formed?What types of methods are used to measure en'ironmental flux of elements? What methods ha'e been used to detect denitrifying acti'ity in the en'ironment?What two elements are closely linked to carbon cycling?Which groups of organisms are most acti'e in assimilating &=2 in aerobic en'ironments?Which organisms con'ert &$2= back to &=2?Which organisms are the primary participants in carbon cycling in anaerobic en'ironments?What role do methanogens play in carbon cycling in anaerobic en'ironments?What is the 9nitrogen triangle: and what metabolic processes are associated with the differentphases?$ow is "2 gas assimilated and what are the re%uirements for this process? $ow is ammonium ion incorporated into carbon skeletons?What intercon'ersions are carried out by "itrosomonas and "itrobacter during nitrification?What intercon'ersions occur during dissimilatory nitrate reduction by 1aracoccus denitrificans?What is the final compound produced?What is the #nammox 1rocess? What organisms carryout the reaction and what special cellular structures are present in these cells?What is the 9sulfur triangle: and what metabolic processes are associated with the differentphases?$ow are adenosine >? phosphosulfate (#1) and phosphoadenosine >?-phosphosulfate (1#1)formed and what role do they play in sulfur assimilation? What amino acid is formed during this assimilatory process and what are the energy re%uirements for this process?6n what form is phosphorous assimilated into cells?What metabolite is most acti'e in assimilating phosphate into cellular materials and how is it formed?What form of iron is most a'ailable to biological systems? What form is incorporated into biomolecules? $ow are *e25 and *e45 used by lithotrophic and heterotrophic organisms as donors or acceptors in their respiratory systems?Lecture 21:What are example of edible microbes? Why are bacteria generally not a good source of single cell protein?What are the purposes or benefits of food fermentation?What types of fermentation processes depend on indigenous flora? What types of processes use highly engineered microbial strains?What is the common starting metabolite used in lactic acid; propionic acid; heterolactic and ethanolic fermentations? What common intermediate do these pathways use?What metabolite is the usual starting material in alkaline fermentations?What are example organisms used in acidic fermentation of dairy products? $ow do these organisms participate in cheese production-what processes do they perform and what do they add to the final product?6n bread making; what process(es) are carried out by accharomyces cere'isiae?What are the starting metabolites in beer and wine production? Why is oxygen excluded in these processes? $ow are desirable fla'ors molecules produced during these processes?What group(s) of organisms are commonly used in the production of fermented foods andbe'erages?What are examples of how microbes render a food product unfit or unpalatable for consumption?$ow was the pathogenic strain identified and followed during the 2@@A-2@@B almonella enterica peanut product outbreak? Why weren?t these products identified as unfit immediately after production?What distinguishes food pathogens from their closely related non-pathogenic organisms?What are pathogenicity islands how are they in'ol'ed in 'irulence?What are examples of en'ironmental modifications or chemical treatments that deter the growth of microbes in food? What types of treatments are re%uired to ensure that endospores or an endospore producing microbes was not present in a food?What class of bacterial cells ha'e been used as sources of antibiotics? Which organisms are used as sources of fuels and sol'ents? Which of these processes in'ol'e fermentations? Lecture 22:Csing the strict definition; how does a parasite differ from a pathogen?Why aren?t all infections considered a disease?What distinguishes a primary pathogen from an opportunistic pathogen?What measures are often used to express the 'irulence of lethal and nonlethal pathogens?What is being measured?Does a lower .D>@ indicate more or less 'irulence?What distinguishes a direct transmission from an indirect transmission infection cycle?What are three common routes of indirect transmission?What are example of common roots of entry of pathogens into humans?What types of molecules; or what functions; are classified as 'irulence factors?What are pathogenicity islands and where are they found in the cell? What functions are often associated with these elements?What types of molecules or structures do bacterial cells use to attach to a host cell?$ow do )ype 6 and 68 pili differ in their attachment properties? $ow are these structures assembled?What are the broad categories of exotoxin acti'ities? What type of toxin is .ipid #?What acti'ity is associated with the #, ribosylating toxins? $ow do the #, ribosylating toxins of &orynebacterium diphtheriae and 8ibrio cholerae cause disease?What are the three components of the ,acillis anthracis toxin? What acti'ity is associated with the lethal factor?What are the three ma0or components of the )ype 6 secretory system? What is an example of a toxin secreted by this system?$ow are protein secreted out of the outer membrane by the )ype 66 system? $ow is this system related to the )ype 68 system?What is the fate of proteins secreted by the )ype 666 system? What proteins or cellular structures are related to the )ype 666 system? Where in the genome are the genes for the )ype 666 system often located?What molecules are secreted by the )ype 68 system? $ow do the #grobacterium tumefaciens and ,ordetella pertussis systems differ?Where are the auto-transporters proteins of the )ype 8 system located and what is their fate?What group of organisms ha'e )ype 86 secretion systems?What mechanisms does almonella enterica use to e'ade host killing while in a macrophage?What mechanisms are used by extracellular pathogens to e'ade the host?s immune system? Terms-Lecture 18:,acteria#rchaea-ukarya1olyphasic taxonomy1rokaryote16 r!"#1olymerase chain reaction (1&!)!ibosomal database pro0ect&andidatus1hylumDeep-branching thermophiles&yanobacteria*irmicutes#ctinobacteria1roteobacteria"itrospirae,acteroidetes &hlorobipirochetes&hlamydia8errucomicrobia1lanctomycetes&hlorosomes=xygenic photosynthesis)hylakoid.ipid bodies+as 'esicles&arboxysomes$eterocysts#kinetes-ndospore#rthrospores,otox#ctin propulsion system/ycolic acids8egetati'e7aerial mycelia1olyketides+ram negati'e en'elope=ligotrophy&aulobacter stalk7holdfast.egume nodule7bacteriod.eghemoglobin#mmonia monooxygenase (#/=) hydroxylamine oxidoreductase ($#=)!e'erse electron flow =pportunistic pathogen*e4=D (magnetite)*ruiting bodies/yxosporesCrease&hlorosomes-lementary body!eticulate body&ompartmentali(ed cell plan&renarchaeota-uryarchaeota6soprenoid lipids"on-phosphorylated -Demi-phosphorylated -D!e'erse gyrase#rchaeal histones Lecture 19:-cosystem1opulation"iche#ssimilationDissimilation*ood web)ropic le'el/utualismynergism&ommensalism#mensalism1arasitism"euston-uphotic (one#photic (one,enthos/acroplankton/icroplankton"anoplankton1icoplankton/etagenomicscD"# se%uencing/arine snow-pilimnion)hermocline$ypolimnion,enthic (one=ligotrophic-utrophic-piphytes-ndophytes!hi(osphere!hi(oplane/ycorrhi(ae-ndomycorrhi(ae-ctomycorrhi(ae!hi(obia"od genes,acteriodymbiosome&rown gall disease=pines!umenhort-chain fatty acids Lecture 20:,iogeochemical &ycles,iotic7abiotic!eser'oir/inerali(ation&arbon cycling"itrogen triangle"itrification7denitrification"itrogenase+lutamate dehydrogenase+lutamine synthetase7glutamate synthase"itrosomonas7"itrobacter1aracoccus denitrificans#nammox 1rocess#nammoxosome.adderane lipidDissimilatory7assimilatorysulfate reduction#denosine >? phosphosulfate (#1) phosphoadenosine >?-phosphosulfate (1#1)1olyphosphatesiderophores Lecture 21:)raditional and commercial food fermentation.actic acidpropionic acidheterolacticethanolicalkaline fermentations.actobacillustreptococcusaccharomyces cere'isiae*ood spoilage*ood poisoning1ulse field gel electrophoresis1athogenicity islandsLecture 22:1arasite1athogen-ctoparasites-ndoparasites6nfectionDisease1rimary pathogen=pportunistic pathogen.D>@76D>@6nfection cycleDirect transmission6ndirect transmission$ori(ontal transmission8ertical transmission#ccidental transmission1athogen reser'oir8irulence factors1athogenicity islands#dhesins1ili or fimbrae)ype 6 and 68 pili-xo- and endotoxins#, ribosylating toxins#nthrax toxin)ype 1 through 68 secretory systems#uto-transporters1hagosomes.ysosome