Microbiology

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An agar plate streaked with microorganisms Microbiology (from Greek , mkros, !small!" #$ , bios, !life!" and %&'$(, -logia) is the st*dy of microscopic organisms, either *nicell*lar (single cell), m*lticell*lar (cell colony), or acell*lar (lacking cells)+,-. /icro0iology encompasses n*mero*s s*0%disciplines incl*ding 1irology, mycology, parasitology, and 0acteriology+ 2*karyotic microorganisms possess mem0rane%0o*nd cell organelles and incl*de f*ngi and protists, whereas prokaryotic organisms3which all are microorganisms3are con1entionally classified as lacking mem0rane%0o*nd organelles and incl*de e*0acteria and archae0acteria+ /icro0iologists traditionally relied on c*lt*re, staining, and microscopy+ 4owe1er, less than -5 of the microorganisms present in common en1ironments can 0e c*lt*red in isolation *sing c*rrent means+,6. /icro0iologists often rely on e7traction or detection of n*cleic acid, either 89A or :9A se;*ences+ <ir*ses ha1e 0een 1aria0ly classified as organisms,,=. as they ha1e 0een considered either as 1ery simple microorganisms or 1ery comple7 molec*les+ >rions, ne1er considered microorganisms, ha1e 0een in1estigated 0y 1irologists, howe1er, as the clinical effects traced to them were originally pres*med d*e to chronic 1iral infections, and 1irologists took search3disco1ering !infectio*s proteins!+ As an application of micro0iology, medical micro0iology is often introd*ced with medical principles of imm*nology as microbiology and immunology+ ?therwise, micro0iology, 1irology, and imm*nology as 0asic sciences ha1e greatly e7ceeded the medical 1ariants, applied sciences+
,@.,A.,B.

Contents
- Cranches o -+- >*re micro0iology -+-+- Da7onomic arrangement -+-+6 Entegrati1e arrangement -+-+= ?ther o -+6 Applied micro0iology 6 Cenefits = 4istory

=+- Ancient o =+6 En the medie1al Eslamic world o =+= /odern @ Fee also A :eferences B 27ternal links
o

Branches
Dhe 0ranches of micro0iology can 0e classified into p*re and applied sciences+,G. /icro0iology can 0e also classified 0ased on ta7onomy, in the cases of 0acteriology, mycology, protoHoology, and phycology+ Dhere is considera0le o1erlap 0etween the specific 0ranches of micro0iology with each other and with other disciplines, and certain aspects of these 0ranches can e7tend 0eyond the traditional scope of micro0iology+

Pure microbiology
Taxonomic arrangement CacteriologyI Dhe st*dy of 0acteria+ /ycologyI Dhe st*dy of f*ngi+ >rotoHoologyI Dhe st*dy of protoHoa+ >hycology (or algology)I Dhe st*dy of algae+ >arasitologyI Dhe st*dy of parasites+ Emm*nologyI Dhe st*dy of the imm*ne system+ <irologyI Dhe st*dy of 1ir*ses+ 9ematologyIDhe st*dy of the nematodes /icro0iologyIDhe st*dy of micro0es+ Integrative arrangement /icro0ial cytologyI Dhe st*dy of microscopic and s*0microscopic details of microorganisms+ /icro0ial physiologyI Dhe st*dy of how the micro0ial cell f*nctions 0iochemically+ Encl*des the st*dy of micro0ial growth, micro0ial meta0olism and micro0ial cell str*ct*re+ /icro0ial ecologyI Dhe relationship 0etween microorganisms and their en1ironment+ /icro0ial geneticsI Dhe st*dy of how genes are organiHed and reg*lated in micro0es in relation to their cell*lar f*nctions+ Jlosely related to the field of molec*lar 0iology+ Jell*lar micro0iologyI A discipline 0ridging micro0iology and cell 0iology+ 21ol*tionary micro0iologyI Dhe st*dy of the e1ol*tion of micro0es+ Dhis field can 0e s*0di1ided intoI o /icro0ial ta7onomyI Dhe naming and classification of microorganisms+ o /icro0ial systematicsI Dhe st*dy of the di1ersity and genetic relationship of microorganisms+ Generation micro0iologyI Dhe st*dy of those microorganisms that ha1e the same characters as their parents+ Fystems micro0iologyI A discipline 0ridging systems 0iology and micro0iology+ /olec*lar micro0iologyI Dhe st*dy of the molec*lar principles of the physiological processes in microorganisms+

Other 9ano micro0iologyI Dhe st*dy of those microorganisms on nano le1el+ 27o micro0iology (or Astro micro0iology)I Dhe st*dy of microorganisms in o*ter space (seeI Kist of microorganisms tested in o*ter space) Ciological agentI Dhe st*dy of those microorganisms which are 0eing *sed in weapon ind*stries+

Applied microbiology

/edical micro0iologyI Dhe st*dy of the pathogenic micro0es and the role of micro0es in h*man illness+ Encl*des the st*dy of micro0ial pathogenesis and epidemiology and is related to the st*dy of disease pathology and imm*nology+ >harmace*tical micro0iologyI Dhe st*dy of microorganisms that are related to the prod*ction of anti0iotics, enHymes, 1itamins,1accines, and other pharmace*tical prod*cts and that ca*se pharmace*tical contamination and spoil+ End*strial micro0iologyI Dhe e7ploitation of micro0es for *se in ind*strial processes+ 27amples incl*de ind*strial fermentation and wastewater treatment+ Jlosely linked to the 0iotechnology ind*stry+ Dhis field also incl*des 0rewing, an important application of micro0iology+ /icro0ial 0iotechnologyI Dhe manip*lation of microorganisms at the genetic and molec*lar le1el to generate *sef*l prod*cts+ Food micro0iology and 8airy micro0iologyI Dhe st*dy of microorganisms ca*sing food spoilage and food0orne illness+ Lsing microorganisms to prod*ce foods, for e7ample 0y fermentation+ Agric*lt*ral micro0iologyI Dhe st*dy of agric*lt*rally rele1ant microorganisms+ Dhis field can 0e f*rther classified into the followingI o >lant micro0iology and >lant pathologyI Dhe st*dy of the interactions 0etween microorganisms and plants and plant pathogens+ o Foil micro0iologyI Dhe st*dy of those microorganisms that are fo*nd in soil+ <eterinary micro0iologyI Dhe st*dy of the role of micro0es in 1eterinary medicine or animal ta7onomy+ 2n1ironmental micro0iologyI Dhe st*dy of the f*nction and di1ersity of micro0es in their nat*ral en1ironments+ Dhis in1ol1es the characteriHation of key 0acterial ha0itats s*ch as the rhiHosphere and phyllosphere, soil and gro*ndwater ecosystems, open oceans or e7treme en1ironments (e7tremophiles)+ Dhis field incl*des other 0ranches of micro0iology s*ch asI o /icro0ial ecology o /icro0ially mediated n*trient cycling o Geomicro0iology o /icro0ial di1ersity o Cioremediation Water micro0iology (or A;*atic micro0iology)I Dhe st*dy of those microorganisms that are fo*nd in water+ Aeromicro0iology (or Air micro0iology)I Dhe st*dy of air0orne microorganisms+

Benefits

Fermenting tanks with yeast 0eing *sed to 0rew 0eer While some fear micro0es d*e to the association of some micro0es with 1ario*s h*man illnesses, many micro0es are also responsi0le for n*mero*s 0eneficial processes s*ch as ind*strial fermentation (e+g+ the prod*ction of alcohol, 1inegar and dairy prod*cts), anti0iotic prod*ction and as 1ehicles for cloning in more comple7 organisms s*ch as plants+ Fcientists ha1e also e7ploited their knowledge of micro0es to prod*ce 0iotechnologically important enHymes s*ch as Da; polymerase, reporter genes for *se in other genetic systems and no1el molec*lar 0iology techni;*es s*ch as the yeast two%hy0rid system+ Cacteria can 0e *sed for the ind*strial prod*ction of amino acids+ Corynebacterium glutamicum is one of the most important 0acterial species with an ann*al prod*ction of more than two million tons of amino acids, mainly K%gl*tamate and K%lysine+,M. A 1ariety of 0iopolymers, s*ch as polysaccharides, polyesters, and polyamides, are prod*ced 0y microorganisms+ /icroorganisms are *sed for the 0iotechnological prod*ction of 0iopolymers with tailored properties s*ita0le for high%1al*e medical application s*ch as tiss*e engineering and dr*g deli1ery+ /icroorganisms are *sed for the 0iosynthesis of 7anthan, alginate, cell*lose, cyanophycin, poly(gamma%gl*tamic acid), le1an, hyal*ronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydro7yalkanoates+,N. /icroorganisms are 0eneficial for micro0ial 0iodegradation or 0ioremediation of domestic, agric*lt*ral and ind*strial wastes and s*0s*rface poll*tion in soils, sediments and marine en1ironments+ Dhe a0ility of each microorganism to degrade to7ic waste depends on the nat*re of each contaminant+ Fince sites typically ha1e m*ltiple poll*tant types, the most effecti1e approach to micro0ial 0iodegradation is to *se a mi7t*re of 0acterial and f*ngal species and strains, each specific to the 0iodegradation of one or more types of contaminants+,-O. Fym0iotic micro0ial comm*nities are known to confer 1ario*s 0enefits to their h*man and animal hostPs health incl*ding aiding digestion, prod*ction of 0eneficial 1itamins and amino acids, and s*ppression of pathogenic micro0es+ Fome 0enefit may 0e conferred 0y cons*ming fermented foods, pro0iotics (0acteria potentially 0eneficial to the digesti1e system) andQor pre0iotics (s*0stances cons*med to promote the growth of pro0iotic microorganisms)+,--.,-6. Dhe ways the micro0iome infl*ences h*man and animal health, as well as methods to infl*ence the micro0iome are acti1e areas of research+,-=. :esearch has s*ggested that microorganisms co*ld 0e *sef*l in the treatment of cancer+ <ario*s strains of non%pathogenic clostridia can infiltrate and replicate within solid t*mors+ Jlostridial 1ectors can 0e safely administered and their potential to deli1er therape*tic proteins has 0een demonstrated in a 1ariety of preclinical models+,-@.

History
Ancient
Dhe e7istence of microorganisms was hypothesiHed for many cent*ries 0efore their act*al disco1ery+ Dhe e7istence of *nseen micro0iological life was post*lated 0y Rainism which is 0ased on /aha1iraSs teachings as early as Bth cent*ry CJ2+,-A. >a*l 8*ndas notes that /aha1ira asserted e7istence of *nseen micro0iological creat*res li1ing in earth, water, air and fire+,-B. Rain script*res also descri0e nigodas which are s*0%microscopic creat*res li1ing in large cl*sters and ha1ing a 1ery short life and are said to per1ade each and e1ery part of the *ni1erse, e1en in tiss*es of plants and flesh of animals+,-G. Dhe :oman /arc*s Derenti*s <arro made references to micro0es when he warned against locating a homestead in the 1icinity of swamps !0eca*se there are 0red certain min*te creat*res which cannot 0e seen 0y the eyes, which float in the air and enter the 0ody thro*gh the mo*th and nose and there 0y ca*se serio*s diseases+!,-M.,citation needed.

In the medieval Islamic orld

A1icenna !i0n Fina! At the golden age of Eslamic ci1iliHation, some scientists had knowledge a0o*t /icroorganisms, s*ch as E0n Fina in his 0ook Dhe Janon of /edicine, E0n T*hr !A1enHoar! who disco1ered Fca0ies Germs, and Al%:aHi who spoke ofparasites in his 0ook !Dhe <irt*o*s Kife! (al%4awi)+ ,-N. En -A@B, Girolamo Fracastoro proposed that epidemic diseases were ca*sed 0y transfera0le seedlike entities that co*ld transmit infection 0y direct or indirect contact, or 1ehicle transmission+,6O. 4owe1er, early claims a0o*t the e7istence of microorganisms were spec*lati1e, and not 0ased on microscopic o0ser1ation+ Act*al o0ser1ation and disco1ery of micro0es had to await the in1ention of the microscope in the -Gth cent*ry+

Modern

Anton 1an Kee*wenhoek, is considered to 0e the one of the first to o0ser1e microorganisms *sing a microscope+ En -BGB, Anton 1an Kee*wenhoek, who li1ed for most of his life in 8elft, 4olland, o0ser1ed 0acteria and other microorganisms *sing a single%lens microscope of his own design+,-. While <an Kee*wenhoek is often cited as the first to o0ser1e micro0es, :o0ert 4ooke made the first recorded microscopic o0ser1ation, of the fr*iting 0odies of molds, in -BBA+,6-. Et has, howe1er, 0een s*ggested that a Res*it priest called Athanasi*s Uircher was the first to o0ser1e micro% organisms+,66. 4e was among the first to design magic lanterns for proVection p*rposes, so he m*st ha1e 0een well ac;*ainted with the properties of lenses+,66. ?ne of his 0ooks contains a chapter in Katin, which reads in translation W XJoncerning the wonderf*l str*ct*re of things in nat*re, in1estigated 0y /icroscope+S 4ere, he wrote Xwho wo*ld 0elie1e that 1inegar and milk a0o*nd with an inn*mera0le m*ltit*de of worms+S 4e also noted that p*trid material is f*ll of inn*mera0le creeping animalc*le+ Dhese o0ser1ations antedate :o0ert 4ookeSs /icrographia 0y nearly 6O years and were p*0lished some 6N years 0efore 1an Kee*wenhoek saw protoHoa and =G years 0efore he descri0ed ha1ing seen 0acteria+,66.

Enno1ati1e la0oratory glassware and e7perimental methods de1eloped 0y Ko*is >aste*r and other 0iologists contri0*ted to the yo*ng field of 0acteriology in the late -Nth cent*ry+

Dhe field of 0acteriology (later a s*0discipline of micro0iology) was fo*nded in the -Nth cent*ry 0y Ferdinand John, a 0otanist whose st*dies on algae and photosynthetic 0acteria led him to descri0e se1eral 0acteria incl*ding Bacillus and Beggiatoa+ John was also the first to form*late a scheme for the ta7onomic classification of 0acteria and disco1er spores+,6=. Ko*is >aste*r and :o0ert Uoch were contemporaries of JohnSs and are often considered to 0e the father of micro0iology,66. and medical micro0iology, respecti1ely+,6@. >aste*r is most famo*s for his series of e7periments designed to dispro1e the then widely held theory of spontaneo*s generation, there0y solidifying micro0iologySs identity as a 0iological science+,6A. >aste*r also designed methods for food preser1ation (paste*riHation) and 1accines against se1eral diseases s*ch as anthra7, fowl cholera and ra0ies+,-. Uoch is 0est known for his contri0*tions to the germ theory of disease, pro1ing that specific diseases were ca*sed 0y specific pathogenic micro%organisms+ 4e de1eloped a series of criteria that ha1e 0ecome known as the UochPs post*lates+ Uoch was one of the first scientists to foc*s on the isolation of 0acteria in p*re c*lt*re res*lting in his description of se1eral no1el 0acteria incl*ding Mycobacterium tuberculosis, the ca*sati1e agent of t*0erc*losis+,-. While >aste*r and Uoch are often considered the fo*nders of micro0iology, their work did not acc*rately reflect the tr*e di1ersity of the micro0ial world 0eca*se of their e7cl*si1e foc*s on micro%organisms ha1ing direct medical rele1ance+ Et was not *ntil the late -Nth cent*ry and the work of /artin*s CeiVerinck and Fergei Winogradsky, the fo*nders of general microbiology (an older term encompassing aspects of micro0ial physiology, di1ersity and ecology), that the tr*e 0readth of micro0iology was re1ealed+,-. CeiVerinck made two maVor contri0*tions to micro0iologyI the disco1ery of 1ir*ses and the de1elopment of enrichment c*lt*re techni;*es+,6B. While his work on the Do0acco /osaic <ir*s esta0lished the 0asic principles of 1irology, it was his de1elopment of enrichment c*lt*ring that had the most immediate impact on micro0iology 0y allowing for the c*lti1ation of a wide range of micro0es with wildly different physiologies+ Winogradsky was the first to de1elop the concept of chemolithotrophy and to there0y re1eal the essential role played 0y micro%organisms in geochemical processes+,6G. 4e was responsi0le for the first isolation and description of 0oth nitrifying and nitrogen%fi7ing 0acteria+,-. French%Janadian micro0iologist Feli7 dP4erelle co%disco1ered 0acteriophages and was one of the earliest applied micro0iologists+,6M.