This is a list of mycologists, or scientists with a specialisation in mycology, with their author abbreviations.

7 Erik Acharius (17571 1!" # Ach. $ichel A%anson (17&71 '(" # Adans. )eo**rey +lough Ainsworth (1!'5 1!! " # Ainsw. )eorge ,rancis Atkinson (1 5-1!1 " # G.F.Atk. A%am A*.elius (175'1 /7" # Afzel. +arl A%olph Agar%h (17 51 5!" # C.Agardh 0acob )eorg Agar%h (1 1/1!'1" # J.Agardh +onstantine 0ohn Ale1opolous (1!'7 1! (" # Alexop. 2avi% Arora (1!5/" # D.Arora +hurchill 3abington (1 &11 !" # C.Bab. +harles 2avi% 3a%ham (1 '51 57" # Badham )iuseppe )abriel 3alsamo4+rivelli (1 ''1 7-" # Bals. Cri!. Anton %e 3ary (1 /11 Bary " # de

0akob Emanuel 7ange # J.#.$ange +harles %e l89cluse (15&(1('!" # Cl"s. )ustav 7in%au (1 ((1!&/" # $inda" 0ohann 6einrich ,rie%rich 7ink (17(7 1 5'" # $ink +arolus 7innaeus (17'7177 " # $. :u%olph Arnol% $aas )eesteranus (1!11&''/" # %aas Geest. +harles $c;lvaine (1 -'1!'!" # %c&l!. :en< +harles 0oseph Ernest $aire (1 7 1!-!" # %aire )eorge =. $artin (1 G.'.%artin (1!71" #

)eorge E%war% $assee (1 5'1!17" # %assee 0ohn $acoun (1 /11!&'" # %aco"n >estor 7<on $archan% (1 //1!11" # %archand +arl ,rie%rich ?hilipp von $artius (17!-1 ( " # %art. Tom $ay # (.'.%ay 5onstantin $ereschkowski (1 551!&1" # %ereschk. )eorg ,rie%rich =ilhelm $eyer (17 & 1 5(" # G.%ey 5ingo $iyabe (1 ('1!51" # %iyabe ?ierre $arie Arthur $orelet (1 '! 1 !&" # $einhar% $oser %.%.%oser (1!&-&''&" #

August 0ohann )eorg 5arl 3atsch (17(11 '&" # Batsch )aspar% 3auhin C.Ba"hin 0ohann 3auhin J.Ba"hin (15('1(&-" (15-11(1/" # #

6enry +urtis 3ear%slee (1 (51!- " # Beardslee $aurice 3eeli (1 7!1!57" # Beeli $iles 0oseph 3erkeley (1 '/1 !"
1

# Berk.

+hristine $arie 1!/&" # Berkh.

3erkhout

(1 !/

,er%inan% von $ueller (1 &51 !(" # F.%"ell. =illiam $urrill (1 (!1!57" # %"rrill 5arl =ilhelm von >Bgeli (1 171 !1" # *+geli +hristian )ott*rie% 2aniel >ees von Esenbeck (177(1 5 " # *ees ,rank >ewhook $achiel >oor%eloos *oordel. (1!-! " #

6owar% E. 3igelow (1!&/1! 7" #> ).#.Bigelow +arl 7u%wig 3lume (17 !1 (&" # Bl"me 0ames 3olton (175 17!!" # Bolton $arcel 3on (1!&5 " # Bon 0ean 7ouis 9mile 3ou%ier (1 & 1!&'" # Bo"d. 6ubert 3our%ot Bo"rdot (1 (11!/7" #

?. 2. Crton (1!1(&''5" # ,.D.-rton ,re%erick ?arker4:ho%es (1!1-41! 7" # ,ark. .hodes A.A. ?earson (1 7-1!5-" # A.,earson +harles 6orton ?eck (1 //1!17" # ,eck +hristiaan 6en%rik ?ersoon (17(11 /(" # ,ers. Thomas ?etch (1 7'1!- " # ,etch E%uar% ,rie%rich ?oeppig (17!11 ( " # ,oepp. ;llty% 3uller ?ole4Evans (1 7!1!( " # ,ole #!ans ?atricio ?once %e 7eDn (1!1!&'1'" # ,.,once de $e/n 5arel ?resl (17!-1 5&" # C.,resl. >athanael ?ringsheim (1 &/1 !-" # ,ringsh. 7ucien Eu<let (1 /&1 !!" # 0"1l. +onstantine Aamuel :a*inesFue (17 / 1 -'" # .af.

)iacomo 3resa%ola (1 -71!&!" # Bres. >athaniel 7or% 3ritton (1 5!1!/-" # Britton $a1 3rit.elmayr (1 /!1!'!" # Britzelm. +hristopher E%mun% 3roome (1 1& 1 (" # Broome Arthur 6enry :eginal% 3uller (1 7- 1!--" # B"ller 0ean 3aptiste ,ran@ois ?ierre 3ulliar% (17-&17!/" # B"ll. )ertru%e Aimmons (1 7&1!5&" # B"rl. 3urlingham

E%win 0ohn 3utler (1 7-1!-/" # #.J.B"tler

A. ?. %e +an%olle (177 1 -1" # DC. )eorge =ashington +arver (1 (-E 1!-/" # Car!er ;gnacio +hapela # Chapela 0ohn 3urton +lelan% (1 7 1!71" #
2

Cleland

0Grg 6. :aithelhuber # .aithelh. 0ohn :amsbottom .amsb. (1 51!7-" #

$elville Thurston +ook (1 (!1!5&" # %.(.Cook Crator ,uller +ook (1 (71!-!" # -.F.Cook $or%ecai +ubitt +ooke (1 &51!1-" # Cooke =illiam 3ri%ge +ooke (1!' 1!!1" # '.B.Cooke August +arl 0oseph +or%a (1 '! 1 -!" # Corda E%re% 0ohn 6enry +orner (1!'( 1!!(" # Corner +arl ,ran. 0oseph Erich +orrens (1 (-1!//" # Correns A.2. +otton (1 7!1!(&" # Cotton

+arleton :ea (1 (11!-(" # .ea 6einrich :ehm (1 & 1!1(" # .ehm 7u%wig :eichenbach (17!/1 7!" # .chb. 2erek :ei% (1!&7&''(" # D.A..eid 6enry >icholas :i%ley (1 551!5(" # .idl. 6enri :omagnesi .omagn. (1!1&1!!!" #

Emil :ostrup (1 /11!'7" # .ostr. )eorg Eberhar% :umphius (1(& 17'&" # ."mph. ?ier An%rea Aaccar%o (1 -51!&'" # 2acc. Augustin Aaint46ilaire (17!!1 5/" # A.2t. )il. 0acob +hristian AchB**er (171 17!'" # 2chaeff. 2ie%erich ,ran. 7eonhar% von Achlechten%al (17!-1 ((" # 2chltdl. ,ran. ?aula von Achrank (17-71 /5" # 2chrank. 0oseph AchrGter J.2chr3t. (1 /71 !-" #

+harles +rosslan% (1 --1!1(" #A Crossl. )or%on 6erriott +unningham (1 !& 1!(&" # G.C"nn. =illiam +urtis (17-(17!!" # C"rtis :.=.). 2ennis (1!1'&''/" # Dennis )uiseppe 2e >otaris (1 '51 77" # De *ot. :en< 7ouiche 2es*ontaines (175' 1 //" # Desf. >icaise Auguste 2esvau1 1 5(" # Des!. (17 -

0ames 2ickson (17/ 1 &&" # Dicks. 0ohann 0acob 2illenius (1( 717-7" # Dill. 0oan 2ingley # Dingley Ethel $ary 2oi%ge (1 Doidge 71!(5" #

7ewis 2avi% von Achweinit. (17 ' 1 /-" # 2chwein. )iovanni Antonio Acopoli (17&/17 # 2cop. ,re% 0ay Aeaver (1 771!7'" # 2ea!er 7ouis Aecretan (175 1 /!" # 2ecr. 0ohn Aibthorp (175 17!(" # 2ibth. "

$arinus Anton 2onk (1!' 41!7&" # Donk 3arth<lemy +harles 0oseph 2umortier (17!71 7 " # D"mort. ,ranklin Aumner Earle (1 5(1!&!" # #arle ,inn4Egil Eckbla% (1!&/&'''" # #ckblad +hristian )ott*rie% Ehrenberg (17!5 1 7(" # #hrenb. 0akob ,rie%rich Ehrhart (17-&17!5" # #hrh. 0ob 3icknell Ellis (1 &!1!'5" # #llis Atephan 7a%islaus En%licher (1 '- 1 -!" # #ndl. )eorge Engelmann (1 '!1 #ngelm. -" #

:ol* Ainger (1!'(1!!-" # 2inger Ale1an%er 6anchett Amith (1!'-1! (" # A.).2m. 0ames E%war% Amith (175!1 & " # 2m. =orthington ). Amith (1 /51!17" # '.G.2m. $iroslav Amotlacha (1!&'&''7" # 2motl. =alter 6enry Anell (1 2nell !1! '" #

Clav 0ohan Aopp 1 ('1!/1" # 2opp 0ames Aowerby 2owerby (17571 &&" #

+arlos 7uigi Apega..ini (1 5 1!&(" # 2peg. 5urt Aprengel (17((1 //" # 2preng. >icolay 5onstantinovich (1 -/ 1!' " 2red. Elvin +. Atakman (1 2takman. Are%insky 51!7!" #

+onstantin von Ettingshausen (1 &( 1 !7" # #ttingsh. :ev. =.7.=. Eyre (1 -11!1-" # #yre +harles E. ,airman (1 5(1!/-" # Fairm. =illiam )ilson ,arlow (1 --1!1!" # Farl. Hictor ,ayo% (1 ('1!''" # Fayod 0ohn ,incham (1!&(&''5" # 2avi% =. ,ischer (1!5!" # )eorg ,orster G.Forst. (175-17!-" #T

?aul Atamets (1!55" # 2tamets )reta Atevenson G.2te!. 2aniel E. Atunt. D.#.2t"ntz. (1!111!!'" (1!'!1! /" # #

:ichar% +. Aummerbell (1!5(" # 2"mmerb. 6ans Ay%ow (1 7!1!-(" # 2yd. ,i%el Tapia ?hilippe 9%ouar% 7<on Han Tieghem (1 /!1!1-" # (iegh. :olan% Tha1ter (1 5 1!/&" # (haxt. 6arry 2. Thiers (1!1!&'''" # (hiers

Elias $agnus ,ries (17!-1 7 " # Fr. 3ruce A. ,uhrer # F"hrer

0oseph )aertner (17/&17!1" Gaertn. :ichar% H. )aines

+arl ?eter Thunberg (17-/1 & " # (h"nb. ?hillippe 9%ouar% 7<on van Tieghem (1 /!1!1-" # (iegh. 0ohn Torrey (17!(1 7/" # (orr. # (orr. 0oseph ?itton %e Tourne*ort (1(5(17' " # (o"rn. E%war% Tuckerman (1 171 ("ck. +harles Tulasne (1 1(1 (" #

+harles )au%ichau%43eaupr< (17 ! 1 5-" # Ga"dich. 7<on )aston )enevier (1 /'1 # Gene!. Ewal% )erhar%t # #w.Gerhardt 0ohann ,rie%rich )melin (17- 1 '-" # J.F.Gmel. Aamuel ,re%erick )ray (17((1 & " # Gray 2avi% )rimal%i # Grimaldi 0ohan Ernst )unnerus (171 177/" # G"nner"s L '"

-" # C.("l. 5" #

7ouis :en< Tulasne (1 151 ("l.

7ucien $arcus Ln%erwoo% (1 5/1!'7" # 5nderw. $artin Hahl (17-!1 '-" # 4ahl. A<bastien Haillant (1((!17&&" # 4aill. 0ose* HelenovskM 4elen. (1 5 1!-!" #

)astDn )u.mIn # (1!/& " # H G"zman 6elen )wynne4Haughan (1 7!1!(7" # Gwynne 4a"ghan Emil +hristian 6ansen (1 -&1!'!" # #.C. )ansen 5anesuke 6ara (1 51!(&" # )ara 6. =. 6arkness (1 &11!'1" # )arkn. 2avi% 7eslie 6awksworth (1!-( " # D. )awksw. ?aul +hristoph 6ennings (1 -11!' " # )enn. 7e1emuel :ay 6esler (1 )esler 1!77" # =

:ytas Hilgalys (1!5 " # 4ilgalys Thomas Holk # (.J.4olk +harles Hon 6olstein (17 -1 51" )Gran =ahlenberg (17 '1 51" # 'ahlenb. Elsie $au% =ake*iel% (1 (1!7&" # 'akef. >athaniel =allich (17 (1 5-" # 'all. Eugenius =arming (1 -11!&-" # 'arm. :oy =atling (1!/ " # 'atling +hristian Ehren*rie% =eigel (17- 1 /1" # 'eigel ,rie%rich =elwitsch (1 '(1 7&" #

2avi% A. 6ibbett # )ibbett ,ran. Javer :u%ol* von 6Ghnel (1 5&1!&'" # )3hn. Theo%or 6olmskKol% (17/117!/" #

)olmsk.

'elw.

0oseph 2alton 6ooker (1 171!11" # )ook.f. 0ohn =. 6otson (1 7' N" # )otson Anna $aria 6ussey (ca. 1 &' 1 77" # )"ssey Emil 0. ;mbach (1 !71!7'" # &mbach

+arl 7u%wig =ill%enow (17(51 1&" # 'illd. =illiam 'ith. =ithering (17-117!!" #

Alec =oo% (1!// " # A.#.'ood 0ohn $e%ley =oo% (1 &71!15" # J.%.'ood ,ran. Javier von =ul*en (17& 1 '5" # '"lfen Anthony $. Roung # A.%.9o"ng =an%a OabSocka (1!''1!7 " #

>ikolaus 0oseph von 0acFuin (17&7 R 1 17" # Jac6. Abraham O. 0o**e (1!'!&'''" # Joffe O

5Iroly 5alchbrenner (1 '71 (" # 7alchbr. )ustav 5arl =ilhelm 6ermann 5arsten (1 171!' " # ).7arst. ?etter A%ol* 5arsten (1 /-1!17" # ,.7arst +alvin 6enry 5au**man (1 (!1!/1" # 7a"ffman 3ryce 5en%rick '.B.7endr. (1!//" #

,rantiPek 5otlaba (1!&7 " # 7otl. 0ulius Hincen. von 5rombhol. (17 & 1 -/" # 0ulius )otthel* 5Qhn (1 &51!1'" # J.G.78hn :obert 5Qhner 78hner ?aul 5ummer ,.7"mm. (1!'/1!!(" (1 /-1!1&" # #

The *ollowing is a list o* Kournals an% maga.ines in the *iel% o* mycologyT

Title Acta Mycologia Acta Mycologia Sinica Location/Publisher Polish Botanical Society; Cracow Years 1965

The Institute of Microbiology The 19%& Chinese !ca"e#y of Sciences; Bei$ing 1996'1( 199+ &,,1

African Journal of Mycology and Cairo )gy*t Biotechnology Agarica L'Amateur de Champignons Anais da Associao Micolgica "A A!"#$$A" Annales Mycologici Berlin 3er#any -orges So**. og nytte/e0stforbun" Paris 1rance

19,% 19&2 &,,1 19,+ 1922'&( 196, 1966

Atas do %nstituto de Micologia& 4ecife Bra5il 'ni(ersidade do $ecife Australasian Mycologist Beihefte )ur My+ologie Belarra "he Bi,liography Mycology "he Bryologist Bolet-n Micolgico Bolet-n de la Sociedad Me.icana de Micolog-a of Systematic *eitschrift fur

The !ustralasian Mycological Society; 1996 7tago -ew 8ealan" 3er#an Mycological Society Socie"a" Micologica Bara0al"o C!BI.Bioscience 9:;< Broo0lyn =aboratorio "e Micolog>a 9=aboratory of Mycology< :ni/ersity of ?al*ara>so 196% 19%6'+( 1%9% 1965

Bulletin de la Soci/t/ Mycologi0ue 3ene/a de 1ene(e Bulletin of the British Mycological British Mycological Society Society Bulletin "rimestriel de la Soci/t/ Paris Mycologi0ue de 2rance 3es+a My+ologie 9C)ech Mycology< Coolia Cryptogamie'5( 4.perimental Mycology 2ield Mycology 2riesia "he 2orayer 2ungal Biology 2ungal Biology $e(ie5s 2ungal 6i(ersity 2ungal 4cology 2ungal genetics and ,iology 2ungal Science 2ungi 2ungus 1re(illea 7er)ogia Gageningen =on"on ?a"u5

1912 19+6 1966 19%6'2( 1%%5

Prague 9@es0A /B"ec0A s*oleCnost 1926 *ro #y0ologii< -e"erlan"se Mycologische ?ereniging 9-etherlan"s Mycological Society< Paris -ew Dor0 7rlan"o British Mycological Society Co*enhagen society< 9Eanish 19%, 1966 1995'6( &,,,

#ycological 19+1 19%,'6(

!ssociation of British 1ungus 3rou*s British Mycological Society British Mycological Society Fong ;ong British Mycological Society 7rlan"o Tai*ei Mycological 4e*ublic of China Society of &,1, &,,6 199% &,,% 1995'%( 1995 &,,% 19&9 195% 1%6& 1%92 196% 19%& 199&

%nternational Journal of Mycology Braunschweig and Lichenology

%nternational Journal of Medicinal Mushrooms Journal of Mycology Journal $esearch 8arstenia 8a(a+a 8orean Journal of Mycology "he Lichenologist =on"on 195% 1922 1926 Mycological 196& of Mycopathological Manhattan In"ian Mycological Society; Calcutta Felsin0i Mycological Society of In"ia 195, 1%%5 19,%'9(

Magyar 1om,9s)ati Lapo+& Acta Bu"a*est Mycologica 7ungarica Mc%l(ainea Medical Mycology Micologia %taliana Miscellanea Mycologica -orth !#erican !ssociation Taylor an" 1rancis'1,( :nione Micologica Italiana Cercle "e Mycologie "e Mons

Mitteilungen der :sterreich ?ienna My+ologisches 1esellschaft Mycena Mycologia Mycologia Balcanica Mycological apers Mycological rogress Mycological $esearch Mycologische Central,latt Mycologist Mins0

19+6 19+% &,,1

Mycological Society of !#erica -ew 19,9 Dor0 Bulgarian Mycological Society ;ew 3er#an Mycological Society British Mycological Society Hena British Mycological Society 19%9 &,,9'11( 191& 1915 19%6 &,,6'1&( &,,2 19&5

Mycology an" Phyto*athology Mi+ologiya i 2itopatologiya Mycopathologia Mycorrhi)a Mycoscience Mycoses Mycota.on My+ologia My+ologic+; S,orn-+ !e5 *ealand Journal of Botany !o(a 7ed5igia #hio Mycologial Bulletin

I Publishing Fouse Peterburg 4ussia

J-au0aJ

StK. 19+%'1+(

;luwer !ca"e#ic Publishers S*ringer.?erlag Fei"elberg S*ringer.?erlag To0yo Society of Ha*an< Blac0well Publishing MycotaLon =t"K Prague Prague 4oyal Society of -ew 8ealan" 9Mycological

1962 19&2 19+1 1919 196+ 1959

Colu#bus 7hio

19,+ 19,% 1991

:sterreichische *eitschrift f<r il)+unde 9Austrian Journal of !ustrian Mycological Society Mycology< "he #pen Mycology Journal agine di Micologia ersoonia il)= und 8rauterfreund $e(ista Argentina de Micolog-a $i(ista di Micologia $e(ista Micolog-a %,eroamericana de Ma"ri" Bentha# 7*en !ssocia5ione Micologica Bresa"ola -ational Ferbariu# -etherlan"s Feilbronn of the

1992 1959 1915 19&&'12( 196% 199,'15( 19%6 199,'16(

$e(ista Me.icana de Micolog-a $e(ue de Mycologie

Socie"a" MeLicana "e Micolog>a 19%%'16( 9MeLican Mycological Society< Paris 19+6

10

$e(ue Mycologi0ue $heinland= f>l)isches il)Journal $i(ista di Micologia Sch5ei)erische il)+unde *eitschrift f<r

Toulouse

1%69 19,6 1991

!ssocia5ione Micologica Bresa"ola Bern :trecht Centre CBS 1ungal Bio"i/ersity

1956 19&+ 196&

Studies in Mycology S(ens+ My+ologis+ "ids+rift Sydo5ia "ransactions of Mycological Society the British lant

S/eriges My0ologis0a 1Mrening &,,5'1%( 9Swe"ish Mycological Society< ?ienna !ustriaIPrint 7ffice Berger British Mycological Society 1926 1%96 19%%'19(

?orld Journal of 2ungal and Biology @?J2 BA *eitschrift f<r il)+unde

Bern 9Eeutsche 3esellschaft fNr My0ologieI3er#an Mycological 19&+ Society<

[edit] Notes
1K &K +K 2K 5K 6K 6K %K 9K 1,K 11K 1&K ^ re*lace" by Mycosystema ^ continue" as Sydo5ia ^ Continue" as $e(ista Me.icana de Micolog-a ^ re*lace" by Mycologist ^ Publishe" in three series that inclu"e $e(ue ,ryologi0ue et lic/nologi0ueB CDEF=CDGDB and 4e/ue "e #ycologie 19+6.1969K ^ Continue" by 2ungal genetics and ,iology ^ Past 19%1 this $ournal was incor*orate" into the !ordic Journal of Botany 9Co*enhagen<K ^ Continues 4.perimental Mycology ^ re*lace" by Mycologia ^ ?olu#e 1.&+ *ublishe" as Sa,ouraudia an" ?olu#es &2.++ *ublishe" as Journal of Medical and Heterinary Mycology ^ re*lace" by 2ungal Biology ^ continue" as 2ungal Biology $e(ie5s 11

1+K 12K 15K 16K 16K 1%K 19K

^ ?olu#es 5 9195,< to 52 91962< were *ublishe" as Mycopathologia et Mycologia ApplicataK ^ continue" as *eitschrift f<r il)+unde ^ Hoine" $e(ista %,eroamericana de Micolog-a ^ Continues $e(ista %,/rica de Micolog-a ^ Continues Bolet>n "e la Socie"a" MeLicana "e Micolog>a ^ Continues JordstI>rnan an" ?indahlia ^ continue" as Mycological $esearch

1ro# Gi0i*e"ia the free encyclo*e"ia Hu#* toO na/igation search

Mushroo#s are a 0in" of fungal re*ro"ucti/e structure

%ycology (*rom the )reek UVWXY, mukZs, meaning [*ungus[" is the branch o* biology concerne% with the stu%y o* *ungi, inclu%ing their genetic an% biochemical properties, their ta1onomy an% their use to humans as a source *or tin%er, me%icinals (e.g., penicillin", *oo% (e.g., beer, wine, cheese, e%ible mushrooms" an% entheogens, as well as their %angers, such as poisoning or in*ection. ,rom mycology arose the *iel% o* phytopathology, the stu%y o* plant %iseases, an% the two %isciplines remain closely relate% because the vast maKority o* plant pathogens are *ungi. A biologist who stu%ies mycology is calle% a mycologist. 6istorically, mycology was a branch o* botany because, although *ungi are evolutionarily more closely relate% to animals than to plants, this was not recogni.e% until a *ew %eca%es ago. ?ioneer mycologists inclu%e% Elias $agnus ,ries, +hristian 6en%rik ?ersoon, Anton %e 3ary an% 7ewis 2avi% von Achweinit.. To%ay the most comprehensively stu%ie% an% un%erstoo% *ungi are yeasts an% eukaryotic mo%el organisms Saccharomyces cerevisiae an% Schizosaccharomyces pombe. $any *ungi pro%uce to1ins, antibiotics an% other secon%ary metabolites. ,or e1ample the cosmopolitan (worl%wi%e" genus Fusarium an% their to1ins associate% with *atal outbreaks o* alimentary to1ic aleukia in humans were e1tensively stu%ie%
12

by Abraham 0o**e. ,ungi are *un%amental *or li*e on earth in their roles as symbionts, e.g. in the *orm o* mycorrhi.ae, insect symbionts an% lichens, potency in breaking %own comple1 organic biomolecules such as lignin, the more %urable component o* woo%, an% by playing a role in 1enobiotics, a critical step in the global carbon cycle. ,ungi an% other organisms tra%itionally recogni.e% as *ungi, such as oomycetes an% my1omycetes (slime mol%s", o*ten are economically an% socially important as some cause %iseases o* animals (such as histoplasmosis" as well as plants (such as 2utch elm %isease an% :ice blast". ,iel% meetings to *in% interesting species o* *ungi are known as 8*orays8, a*ter the *irst such meeting organi.e% by the =oolhope >aturalists8 ,iel% +lub in 1 ( an% entitle% [a *oray among the *ungi.[Aome *ungi can cause %isease in humans or other organisms. The stu%y o* pathogenic *ungi is re*erre% to as me%ical mycology.\1]

History
6umans probably starte% collecting mushrooms as *oo% in ?rehistoric times. $ushrooms were *irst written about in the works o* Euripi%es (- '4-'( 3.+.". The )reek philosopher Theophrastos o* Eressos (/714& 3.+." was perhaps the *irst to try to systematically classi*y plants^ mushrooms were consi%ere% to be plants that were missing certain organs. ;t was later ?liny the el%er (&/7! A.2.", who wrote about tru**les in his encyclope%ia >aturalis historia. The $i%%le Ages saw little a%vancement in the bo%y o* knowle%ge about *ungi. :ather, the invention o* the printing press allowe% some authors to %isseminate superstitions an% misconceptions about the *ungi that ha% been perpetuate% by the classical authors.\&] The start o* the mo%ern age o* mycology begins with ?ier Antonio $icheli8s 17/7 publication o* Nova plantarum genera.\-] ?ublishe% in ,lorence, this seminal work lai% the *oun%ations *or the systematic classi*ication o* grasses, mosses an% *ungi. The term mycology an% the complimentary mycologist were *irst use% in 1 /( by $.0. 3erkeley.\5]

Medicinal mycology
Main articleJ Medicinal mushrooms

,or centuries, certain mushrooms have been %ocumente% as a *olk me%icine in +hina, 0apan, an% :ussia.\(] Although the use o* mushrooms in *olk me%icine is largely centere% on the Asian continent, people in other parts o* the worl% like the $i%%le East, ?olan% an% 3elarus have been %ocumente% using mushrooms *or me%icinal purposes.\7]\ ] +ertain mushrooms, especially polypores like :eishi were thought to be able to bene*it a wi%e variety o* health ailments. $e%icinal mushroom research in the Lnite% Atates is currently active, with stu%ies taking place at +ity o* 6ope >ational $e%ical +enter,\!]\1'] as well as the $emorial Aloan5ettering +ancer +enter.\11] +urrent research *ocuses on mushrooms that may have hypoglycemic activity, anti4 cancer activity, anti4pathogenic activity, an% immune system enhancing activity. :ecent research has *oun% that the oyster mushroom naturally contains the cholesterol4lowering %rug lovastatin,\1&] mushrooms pro%uce large amounts o* vitamin 2 when e1pose% to LH light,\1/] an% that certain *ungi may be a *uture source o* ta1ol.\1-] To %ate, penicillin, lovastatin, ciclosporin, griseo*ulvin, cephalosporin, ergometrine, an% statins are the most *amous pharmaceuticals which have been isolate% *rom the *ungi king%om. A f"ng"s (pronounce% IPfQRSTsI^ pl. *ungi\/] or *unguses\-]" is a member o* a large group o* eukaryotic organisms that inclu%es microorganisms such as yeasts an% mol%s (3ritish EnglishT moul%s", as well as the more *amiliar mushrooms. These organisms are classi*ie% as a king%om, F"ngi, which is separate *rom plants, animals, an% bacteria. Cne maKor %i**erence is
13

that *ungal cells have cell walls that contain chitin, unlike the cell walls o* plants, which contain cellulose. These an% other %i**erences show that the *ungi *orm a single group o* relate% organisms, name% the Eumycota (true fungi or Eumycetes", that share a common ancestor (a monophyletic group". This *ungal group is %istinct *rom the structurally similar my1omycetes (slime mol%s" an% oomycetes (water mol%s". The %iscipline o* biology %evote% to the stu%y o* *ungi is known as mycology, which is o*ten regar%e% as a branch o* botany, even though genetic stu%ies have shown that *ungi are more closely relate% to animals than to plants. Abun%ant worl%wi%e, most *ungi are inconspicuous because o* the small si.e o* their structures, an% their cryptic li*estyles in soil, on %ea% matter, an% as symbionts o* plants, animals, or other *ungi. They may become noticeable when *ruiting, either as mushrooms or mol%s. ,ungi per*orm an essential role in the %ecomposition o* organic matter an% have *un%amental roles in nutrient cycling an% e1change. They have long been use% as a %irect source o* *oo%, such as mushrooms an% tru**les, as a leavening agent *or brea%, an% in *ermentation o* various *oo% pro%ucts, such as wine, beer, an% soy sauce. Aince the 1!-'s, *ungi have been use% *or the pro%uction o* antibiotics, an%, more recently, various en.ymes pro%uce% by *ungi are use% in%ustrially an% in %etergents. ,ungi are also use% as biological pestici%es to control wee%s, plant %iseases an% insect pests. $any species pro%uce bioactive compoun%s calle% mycoto1ins, such as alkaloi%s an% polyketi%es, that are to1ic to animals inclu%ing humans. The *ruiting structures o* a *ew species contain psychotropic compoun%s an% are consume% recreationally or in tra%itional spiritual ceremonies. ,ungi can break %own manu*acture% materials an% buil%ings, an% become signi*icant pathogens o* humans an% other animals. 7osses o* crops %ue to *ungal %iseases (e.g. rice blast %isease" or *oo% spoilage can have a large impact on human *oo% supplies an% local economies. The *ungus king%om encompasses an enormous %iversity o* ta1a with varie% ecologies, li*e cycle strategies, an% morphologies ranging *rom single4celle% aFuatic chytri%s to large mushrooms. 6owever, little is known o* the true bio%iversity o* 5ing%om ,ungi, which has been estimate% at aroun% 1.5 million species, with about 5_ o* these having been *ormally classi*ie%. Ever since the pioneering 1 th an% 1!th century ta1onomical works o* +arl 7innaeus, +hristian 6en%rik ?ersoon, an% Elias $agnus ,ries, *ungi have been classi*ie% accor%ing to their morphology (e.g., characteristics such as spore color or microscopic *eatures" or physiology. A%vances in molecular genetics have opene% the way *or 2>A analysis to be incorporate% into ta1onomy, which has sometimes challenge% the historical groupings base% on morphology an% other traits. ?hylogenetic stu%ies publishe% in the last %eca%e have helpe% reshape the classi*ication o* 5ing%om ,ungi, which is %ivi%e% into one subking%om, seven phyla, an% ten subphyla.

14

Contents
'hi"e(

1 )ty#ology & Characteristics + Ei/ersity 2 Mor*hology

o o

2K1 Microsco*ic structures 2K& Macrosco*ic structures

5 3rowth an" *hysiology 6 4e*ro"uction

o o o o

6K1 !seLual re*ro"uction 6K& SeLual re*ro"uction 6K+ S*ore "is*ersal 6K2 7ther seLual *rocesses

6 )/olution % TaLono#y
o o

%K1 TaLono#ic grou*s %K& 1ungus.li0e organis#s

9 )cology
o

9K1 Sy#biosis

9K1K1 Gith *lants 9K1K& Gith algae an" cyanobacteria 9K1K+ Gith insects 9K1K2 !s *athogens an" *arasites

1, Fu#an use
o o o o o o

1,K1 Erugs 1,K& Culture" foo"s 1,K+ Me"icinal use 1,K2 )"ible an" *oisonous s*ecies 1,K5 Pest control 1,K6 Biore#e"iation 15

Etymology
The English wor% fungus is %irectly a%opte% *rom the 7atin fungus (mushroom", use% in the writings o* 6orace an% ?liny.\5] This in turn is %erive% *rom the )reek wor% sphongos`abcddcY ([sponge[", which re*ers to the macroscopic structures an% morphology o* mushrooms an% mol%s^ the root is also use% in other languages, such as the )erman Schwamm ([sponge[", Schimmel ([mol%[", an% the ,rench champignon an% the Apanish champion (which both mean [mushroom[".\(] The use o* the wor% mycology, which is %erive% *rom the )reek mykes`UVWXY (mushroom" an% logos`efdcY (%iscourse",\7] to %enote the scienti*ic stu%y o* *ungi is thought to have originate% in 1 /( with English naturalist $iles 0oseph 3erkeley8s publication The English Flora of Sir James Edward Smith !ol" #"\(]

Characteristics
3e*ore the intro%uction o* molecular metho%s *or phylogenetic analysis, ta1onomists consi%ere% *ungi to be members o* the ?lant 5ing%om because o* similarities in li*estyleT both *ungi an% plants are mainly immobile, an% have similarities in general morphology an% growth habitat. 7ike plants, *ungi o*ten grow in soil, an% in the case o* mushrooms *orm conspicuous *ruiting bo%ies, which sometimes bear resemblance to plants such as mosses. The *ungi are now consi%ere% a separate king%om, %istinct *rom both plants an% animals, *rom which they appear to have %iverge% aroun% one billion years ago.\ ]\!] Aome morphological, biochemical, an% genetic *eatures are share% with other organisms, while others are uniFue to the *ungi, clearly separating them *rom the other king%omsT Ahare% *eaturesT

Gith other eu0aryotesO !s other eu0aryotes fungal cells contain #e#brane.boun" nuclei with chro#oso#es that contain E-! with nonco"ing regions calle" introns an" co"ing regions calle" eLonsK In a""ition fungi *ossess #e#brane.boun" cyto*las#ic organelles such as #itochon"ria sterol.containing #e#branes an" riboso#es of the %,S ty*eK '1,( They ha/e a characteristic range of soluble carbohy"rates an" storage co#*oun"s inclu"ing sugar alcohols 9eKgK #annitol< "isacchari"es 9eKgK trehalose< an" *olysacchari"es 9eKgK glycogen which is also foun" in ani#als'11(<K Gith ani#alsO 1ungi lac0 chloro*lasts an" are heterotro*hic organis#s reUuiring *refor#e" organic co#*oun"s as energy sourcesK'1&( Gith *lantsO 1ungi *ossess a cell wall '1+( an" /acuolesK'12( They re*ro"uce by both seLual an" aseLual #eans an" li0e basal *lant grou*s 9such as ferns an" #osses< *ro"uce s*oresK Si#ilar to #osses an" algae fungi ty*ically ha/e ha*loi" nucleiK'15( Gith euglenoi"s an" bacteriaO Figher fungi euglenoi"s an" so#e bacteria *ro"uce the a#ino aci" =.lysine in s*ecific biosynthesis ste*s calle" the V. a#inoa"i*ate *athwayK'16('16( The cells of #ost fungi grow as tubular elongate" an" threa".li0e 9fila#entous< structures an" are calle" hy*hae which #ay contain #ulti*le nuclei an" eLten" at their ti*sK )ach ti* contains a set of aggregate" /esiclesWcellular structures consisting of *roteins li*i"s an" other organic #oleculesWcalle" S*it5en0Mr*erK'1%( Both fungi an" oo#ycetes grow as 16

fila#entous hy*hal cellsK'19( In contrast si#ilar.loo0ing organis#s such as fila#entous green algae grow by re*eate" cell "i/ision within a chain of cellsK'11(

In co##on with so#e *lant an" ani#al s*ecies #ore than 6, fungal s*ecies "is*lay the *heno#enon of biolu#inescenceK'&,(

LniFue *eaturesT

So#e s*ecies grow as single.celle" yeasts that re*ro"uce by bu""ing or binary fissionK Ei#or*hic fungi can switch between a yeast *hase an" a hy*hal *hase in res*onse to en/iron#ental con"itionsK '&1( The fungal cell wall is co#*ose" of glucans an" chitin; while the for#er co#*oun"s are also foun" in *lants an" the latter in the eLos0eleton of arthro*o"s '&&('&+( fungi are the only organis#s that co#bine these two structural #olecules in their cell wallK In contrast to *lants an" the oo#ycetes fungal cell walls "o not contain celluloseK'&2(

#mphalotus nidiformis a biolu#inescent #ushroo#

$ost *ungi lack an e**icient system *or long4%istance transport o* water an% nutrients, such as the 1ylem an% phloem in many plants. To overcome these limitations, some *ungi, such as $rmillaria, *orm rhi.omorphs,\&5] that resemble an% per*orm *unctions similar to the roots o* plants. Another characteristic share% with plants inclu%es a biosynthetic pathway *or pro%ucing terpenes that uses mevalonic aci% an% pyrophosphate as chemical buil%ing blocks.\&(] 6owever, plants have an a%%itional terpene pathway in their chloroplasts, a structure *ungi %o not possess.\&7] ,ungi pro%uce several secon%ary metabolites that are similar or i%entical in structure to those ma%e by plants. \&(] $any o* the plant an% *ungal en.ymes that make these compoun%s %i**er *rom each other in seFuence an% other characteristics, which in%icates separate origins an% evolution o* these en.ymes in the *ungi an% plants.\&(]\& ]

i!ersity
,ungi have a worl%wi%e %istribution, an% grow in a wi%e range o* habitats, inclu%ing e1treme environments such as %eserts or areas with high salt concentrations\&!] or ioni.ing ra%iation,\/'] as well as in %eep sea se%iments.\/1] Aome can survive the intense LH an% cosmic ra%iation encountere% %uring space travel.\/&] $ost grow in terrestrial environments, though several species live partly or solely in aFuatic habitats, such as the chytri% *ungus %atrachochytrium
17

dendrobatidis, a parasite that has been responsible *or a worl%wi%e %ecline in amphibian populations. This organism spen%s part o* its li*e cycle as a motile .oospore, enabling it to propel itsel* through water an% enter its amphibian host.\//] Cther e1amples o* aFuatic *ungi inclu%e those living in hy%rothermal areas o* the ocean.\/-] Aroun% 1'',''' species o* *ungi have been *ormally %escribe% by ta1onomists,\/5] but the global bio%iversity o* the *ungus king%om is not *ully un%erstoo%.\/(] Cn the basis o* observations o* the ratio o* the number o* *ungal species to the number o* plant species in selecte% environments, the *ungal king%om has been estimate% to contain about 1.5 million species. \/7] ;n mycology, species have historically been %istinguishe% by a variety o* metho%s an% concepts. +lassi*ication base% on morphological characteristics, such as the si.e an% shape o* spores or *ruiting structures, has tra%itionally %ominate% *ungal ta1onomy.\/ ] Apecies may also be %istinguishe% by their biochemical an% physiological characteristics, such as their ability to metaboli.e certain biochemicals, or their reaction to chemical tests. The biological species concept %iscriminates species base% on their ability to mate. The application o* molecular tools, such as 2>A seFuencing an% phylogenetic analysis, to stu%y %iversity has greatly enhance% the resolution an% a%%e% robustness to estimates o* genetic %iversity within various ta1onomic groups.\/!]

Mor"hology

%icroscopic str"ct"res

!n en/iron#ental isolate 1K hy*ha &K coni"io*hore +K *hiali"e 2K coni"ia 5K se*ta

of

enicillium

$ost *ungi grow as hyphae, which are cylin%rical, threa%4like structures &1' gm in %iameter an% up to several centimeters in length. 6yphae grow at their tips (apices"^ new hyphae are typically *orme% by emergence o* new tips along e1isting hyphae by a process calle% branching, or occasionally growing hyphal tips bi*urcate (*ork" giving rise to two parallel4 growing hyphae.\-'] The combination o* apical growth an% branching`*orking lea%s to the %evelopment o* a mycelium, an interconnecte% network o* hyphae.\&1] 6yphae can be either septate or coenocyticT septate hyphae are %ivi%e% into compartments separate% by cross walls (internal cell walls, calle% septa, that are *orme% at right angles to the cell wall giving the hypha its shape", with each compartment containing one or more nuclei^ coenocytic hyphae are not compartmentali.e%.\-1] Aepta have pores that allow cytoplasm, organelles, an% sometimes nuclei to pass through^ an e1ample is the %olipore septum in the *ungi o* the phylum 3asi%iomycota.\-&] +oenocytic hyphae are essentially multinucleate supercells.\-/] $any species have %evelope% speciali.e% hyphal structures *or nutrient uptake *rom living hosts^ e1amples
18

inclu%e haustoria in plant4parasitic species o* most *ungal phyla, an% arbuscules o* several mycorrhi.al *ungi, which penetrate into the host cells to consume nutrients. \--] Although *ungi are opisthokonts#a grouping o* evolutionarily relate% organisms broa%ly characteri.e% by a single posterior *lagellum#all phyla e1cept *or the chytri%s have lost their posterior *lagella.\-5] ,ungi are unusual among the eukaryotes in having a cell wall that, in a%%ition to glucans (e.g., h41,/4glucan" an% other typical components, also contains the biopolymer chitin.\-(]

%acroscopic str"ct"res

Armillaria solidipes

,ungal mycelia can become visible to the nake% eye, *or e1ample, on various sur*aces an% substrates, such as %amp walls an% on spoile% *oo%, where they are commonly calle% mol%s. $ycelia grown on soli% agar me%ia in laboratory petri %ishes are usually re*erre% to as colonies. These colonies can e1hibit growth shapes an% colors (%ue to spores or pigmentation" that can be use% as %iagnostic *eatures in the i%enti*ication o* species or groups. \-7] Aome in%ivi%ual *ungal colonies can reach e1traor%inary %imensions an% ages as in the case o* a clonal colony o* $rmillaria solidipes, which e1ten%s over an area o* more than !'' ha (/.5 sFuare miles", with an estimate% age o* nearly !,''' years.\- ] The apothecium#a speciali.e% structure important in se1ual repro%uction in the ascomycetes#is a cup4shape% *ruiting bo%y that hol%s the hymenium, a layer o* tissue containing the spore4bearing cells. \-!] The *ruiting bo%ies o* the basi%iomycetes (basi%iocarps" an% some ascomycetes can sometimes grow very large, an% many are well4known as mushrooms.

#ro$th and "hysiology

The growth o* *ungi as hyphae on or in soli% substrates or as single cells in aFuatic environments is a%apte% *or the e**icient e1traction o* nutrients, because these growth *orms have high sur*ace area to volume ratios.\5'] 6yphae are speci*ically a%apte% *or growth on soli% sur*aces, an% to inva%e substrates an% tissues.\51] They can e1ert large penetrative mechanical *orces^ *or e1ample, the plant pathogen &agnaporthe grisea *orms a structure calle% an appressorium which evolve% to puncture plant tissues.\5&] The pressure generate% by the appressorium, %irecte% against the plant epi%ermis, can e1cee% megapascals (1,&'' psi".\5&] The *ilamentous *ungus 'aecilomyces lilacinus uses a similar structure to penetrate the eggs o* nemato%es.\5/]

19

Mol" co/ering a "ecaying *eachK The fra#es were ta0en a**roLi#ately 1& hours a*art o/er a *erio" of siL "aysK

The mechanical pressure e1erte% by the appressorium is generate% *rom physiological processes that increase intracellular turgor by pro%ucing osmolytes such as glycerol.\5-] $orphological a%aptations such as these are complemente% by hy%rolytic en.ymes secrete% into the environment to %igest large organic molecules#such as polysacchari%es, proteins, lipi%s, an% other organic substrates#into smaller molecules that may then be absorbe% as nutrients.\55]\5(]\57] The vast maKority o* *ilamentous *ungi grow in a polar *ashion#i.e., by e1tension into one %irection#by elongation at the tip (ape1" o* the hypha. \5 ] Alternative *orms o* *ungal growth inclu%e intercalary e1tension (i.e., by longitu%inal e1pansion o* hyphal compartments that are below the ape1" as in the case o* some en%ophytic *ungi,\5!] or growth by volume e1pansion %uring the %evelopment o* mushroom stipes an% other large organs. \('] )rowth o* *ungi as multicellular structures consisting o* somatic an% repro%uctive cells#a *eature in%epen%ently evolve% in animals an% plants \(1]#has several *unctions, inclu%ing the %evelopment o* *ruiting bo%ies *or %issemination o* se1ual spores (see above" an% bio*ilms *or substrate coloni.ation an% intercellular communication.\(&] Tra%itionally, the *ungi are consi%ere% heterotrophs, organisms that rely solely on carbon *i1e% by other organisms *or metabolism. ,ungi have evolve% a high %egree o* metabolic versatility that allows them to use a %iverse range o* organic substrates *or growth, inclu%ing simple compoun%s such as nitrate, ammonia, acetate, or ethanol.\(/]\(-] ,or some species it has been shown that the pigment melanin may play a role in e1tracting energy *rom ioni.ing ra%iation, such as gamma ra%iation^ however, this *orm o* [ra%iotrophic[ growth has only been %escribe% *or a *ew species, the e**ects on growth rates are small, an% the un%erlying biophysical an% biochemical processes are not known.\/'] The authors speculate that this process might bear similarity to +C& *i1ation via visible light, but instea% utili.ing ioni.ing ra%iation as a source o* energy.\(5]

20

%e"roduction

olyporus s0uamosus

,ungal repro%uction is comple1, re*lecting the %i**erences in li*estyles an% genetic makeup within this king%om o* organisms.\((] ;t is estimate% that a thir% o* all *ungi repro%uce by %i**erent mo%es o* propagation^ *or e1ample, repro%uction may occur in two well4 %i**erentiate% stages within the li*e cycle o* a species, the teleomorph an% the anamorph.\(7] Environmental con%itions trigger genetically %etermine% %evelopmental states that lea% to the creation o* speciali.e% structures *or se1ual or ase1ual repro%uction. These structures ai% repro%uction by e**iciently %ispersing spores or spore4containing propagules.

Asex"al reprod"ction
Ase1ual repro%uction via vegetative spores (coni%ia" or through mycelial *ragmentation is common^ it maintains clonal populations a%apte% to a speci*ic niche, an% allows more rapi% %ispersal than se1ual repro%uction.\( ] The [,ungi imper*ecti[ (*ungi lacking the per*ect or se1ual stage" or 2euteromycota comprise all the species which lack an observable se1ual cycle.\(!]

2ex"al reprod"ction
Ae1ual repro%uction with meiosis e1ists in all *ungal phyla (with the e1ception o* the )lomeromycota".\7'] ;t %i**ers in many aspects *rom se1ual repro%uction in animals or plants. 2i**erences also e1ist between *ungal groups an% can be use% to %iscriminate species by morphological %i**erences in se1ual structures an% repro%uctive strategies. \71]\7&] $ating e1periments between *ungal isolates may i%enti*y species on the basis o* biological species concepts.\7&] The maKor *ungal groupings have initially been %elineate% base% on the morphology o* their se1ual structures an% spores^ *or e1ample, the spore4containing structures, asci an% basi%ia, can be use% in the i%enti*ication o* ascomycetes an% basi%iomycetes, respectively. Aome species may allow mating only between in%ivi%uals o* opposite mating type, while others can mate an% se1ually repro%uce with any other in%ivi%ual or itsel*. Apecies o* the *ormer mating system are calle% heterothallic, an% o* the latter homothallic.\7/] $ost *ungi have both an haploi% an% %iploi% stage in their li*e cycles. ;n se1ually repro%ucing *ungi, compatible in%ivi%uals may combine by *using their hyphae together into an interconnecte% network^ this process, anastomosis, is reFuire% *or the initiation o* the se1ual cycle. Ascomycetes an% basi%iomycetes go through a %ikaryotic stage, in which the nuclei inherite% *rom the two parents %o not combine imme%iately a*ter cell *usion, but remain separate in the hyphal cells (see heterokaryosis".\7-]
21

The %.s*ore" asci of Morchella elata /iewe" with *hase contrast #icrosco*y

;n ascomycetes, %ikaryotic hyphae o* the hymenium (the spore4bearing tissue layer" *orm a characteristic hook at the hyphal septum. 2uring cell %ivision, *ormation o* the hook ensures proper %istribution o* the newly %ivi%e% nuclei into the apical an% basal hyphal compartments. An ascus (plural asci" is then *orme%, in which karyogamy (nuclear *usion" occurs. Asci are embe%%e% in an ascocarp, or *ruiting bo%y. 5aryogamy in the asci is *ollowe% imme%iately by meiosis an% the pro%uction o* ascospores. A*ter %ispersal, the ascospores may germinate an% *orm a new haploi% mycelium.\75] Ae1ual repro%uction in basi%iomycetes is similar to that o* the ascomycetes. +ompatible haploi% hyphae *use to pro%uce a %ikaryotic mycelium. 6owever, the %ikaryotic phase is more e1tensive in the basi%iomycetes, o*ten also present in the vegetatively growing mycelium. A speciali.e% anatomical structure, calle% a clamp connection, is *orme% at each hyphal septum. As with the structurally similar hook in the ascomycetes, the clamp connection in the basi%iomycetes is reFuire% *or controlle% trans*er o* nuclei %uring cell %ivision, to maintain the %ikaryotic stage with two genetically %i**erent nuclei in each hyphal compartment.\7(] A basi%iocarp is *orme% in which club4like structures known as basi%ia generate haploi% basi%iospores a*ter karyogamy an% meiosis.\77] The most commonly known basi%iocarps are mushrooms, but they may also take other *orms (see $orphology section". ;n glomeromycetes (*ormerly .ygomycetes", haploi% hyphae o* two in%ivi%uals *use, *orming a gametangium, a speciali.e% cell structure that becomes a *ertile gamete4pro%ucing cell. The gametangium %evelops into a .ygospore, a thick4walle% spore *orme% by the union o* gametes. =hen the .ygospore germinates, it un%ergoes meiosis, generating new haploi% hyphae, which may then *orm ase1ual sporangiospores. These sporangiospores allow the *ungus to rapi%ly %isperse an% germinate into new genetically i%entical haploi% *ungal mycelia.\7 ]

2pore dispersal
3oth ase1ual an% se1ual spores or sporangiospores are o*ten actively %isperse% by *orcible eKection *rom their repro%uctive structures. This eKection ensures e1it o* the spores *rom the repro%uctive structures as well as travelling through the air over long %istances.

22

The bir"Xs nest fungus Cyathus stercoreus

Apeciali.e% mechanical an% physiological mechanisms, as well as spore sur*ace structures (such as hy%rophobins", enable e**icient spore eKection.\7!] ,or e1ample, the structure o* the spore4bearing cells in some ascomycete species is such that the buil%up o* substances a**ecting cell volume an% *lui% balance enables the e1plosive %ischarge o* spores into the air. \ '] The *orcible %ischarge o* single spores terme% ballistospores involves *ormation o* a small %rop o* water (3uller8s %rop", which upon contact with the spore lea%s to its proKectile release with an initial acceleration o* more than 1',''' g^\ 1] the net result is that the spore is eKecte% '.'1 '.'& cm, su**icient %istance *or it to *all through the gills or pores into the air below. \ &] Cther *ungi, like the pu**balls, rely on alternative mechanisms *or spore release, such as e1ternal mechanical *orces. The bir%8s nest *ungi use the *orce o* *alling water %rops to liberate the spores *rom cup4shape% *ruiting bo%ies.\ /] Another strategy is seen in the stinkhorns, a group o* *ungi with lively colors an% putri% o%or that attract insects to %isperse their spores.\ -]

-ther sex"al processes

3esi%es regular se1ual repro%uction with meiosis, certain *ungi, such as those in the genera 'enicillium an% $spergillus, may e1change genetic material via parase1ual processes, initiate% by anastomosis between hyphae an% plasmogamy o* *ungal cells.\ 5] The *reFuency an% relative importance o* parase1ual events is unclear an% may be lower than other se1ual processes. ;t is known to play a role in intraspeci*ic hybri%i.ation \ (] an% is likely reFuire% *or hybri%i.ation between species, which has been associate% with maKor events in *ungal evolution.\ 7]

E!olution
Main articleJ 4(olution of fungi

;n contrast to plants an% animals, the early *ossil recor% o* the *ungi is meager. ,actors that likely contribute to the un%er4representation o* *ungal species among *ossils inclu%e the nature o* *ungal *ruiting bo%ies, which are so*t, *leshy, an% easily %egra%able tissues an% the microscopic %imensions o* most *ungal structures, which there*ore are not rea%ily evi%ent. ,ungal *ossils are %i**icult to %istinguish *rom those o* other microbes, an% are most easily i%enti*ie% when they resemble e1tant *ungi.\ ] C*ten recovere% *rom a perminerali.e% plant or animal host, these samples are typically stu%ie% by making thin4section preparations that can be e1amine% with light microscopy or transmission electron microscopy.\ !] +ompression *ossils are stu%ie% by %issolving the surroun%ing matri1 with aci% an% then using light or scanning electron microscopy to e1amine sur*ace %etails.\!'] The earliest *ossils possessing *eatures typical o* *ungi %ate to the ?rotero.oic eon, some 1,-/' million years ago ($a"^ these
23

multicellular benthic organisms ha% *ilamentous structures with septa, an% were capable o* anastomosis.\!1] $ore recent stu%ies (&''!" estimate the arrival o* *ungal organisms at about 7('1'(' $a on the basis o* comparisons o* the rate o* evolution in closely relate% groups. \!&] ,or much o* the ?aleo.oic Era (5-&&51 $a", the *ungi appear to have been aFuatic an% consiste% o* organisms similar to the e1tant +hytri%s in having *lagellum4bearing spores.\!/] The evolutionary a%aptation *rom an aFuatic to a terrestrial li*estyle necessitate% a %iversi*ication o* ecological strategies *or obtaining nutrients, inclu%ing parasitism, saprobism, an% the %evelopment o* mutualistic relationships such as mycorrhi.a an% licheni.ation.\!-] :ecent (&''!" stu%ies suggest that the ancestral ecological state o* the Ascomycota was saprobism, an% that in%epen%ent licheni.ation events have occurre% multiple times.\!5] The *ungi probably coloni.e% the lan% %uring the +ambrian (5-&- ./ $a", long be*ore lan% plants.\!(] ,ossili.e% hyphae an% spores recovere% *rom the Cr%ovician o* =isconsin (-(' $a" resemble mo%ern4%ay )lomerales, an% e1iste% at a time when the lan% *lora likely consiste% o* only non4vascular bryophyte4like plants.\!7] ?rotota1ites, which was probably a *ungus or lichen, woul% have been the tallest organism o* the late Ailurian. ,ungal *ossils %o not become common an% uncontroversial until the early 2evonian (-1(/5!.& $a", when they are abun%ant in the :hynie chert, mostly as Oygomycota an% +hytri%iomycota.\!(]\! ]\!!] At about this same time, appro1imately -'' $a, the Ascomycota an% 3asi%iomycota %iverge%,\1''] an% all mo%ern classes o* *ungi were present by the 7ate +arboni*erous (?ennsylvanian, /1 .1 &!! $a".\1'1] 7ichen4like *ossils have been *oun% in the 2oushantuo ,ormation in southern +hina %ating back to (/5551 $a.\1'&] 7ichens were a component o* the early terrestrial ecosystems, an% the estimate% age o* the ol%est terrestrial lichen *ossil is -'' $a^\1'/] this %ate correspon%s to the age o* the ol%est known sporocarp *ossil, a 'aleopyrenomycites species *oun% in the :hynie +hert.\1'-] The ol%est *ossil with microscopic *eatures resembling mo%ern4 %ay basi%iomycetes is 'alaeoancistrus, *oun% perminerali.e% with a *ern *rom the ?ennsylvanian.\1'5] :are in the *ossil recor% are the homobasi%iomycetes (a ta1on roughly eFuivalent to the mushroom4pro%ucing species o* the agaricomycetes". Two amber4preserve% specimens provi%e evi%ence that the earliest known mushroom4*orming *ungi (the e1tinct species $rchaeomarasmius legletti" appeare% %uring the mi%4+retaceous, !' $a.\1'(]\1'7] Aome time a*ter the ?ermian4Triassic e1tinction event (&51.- $a", a *ungal spike (originally thought to be an e1traor%inary abun%ance o* *ungal spores in se%iments" *orme%, suggesting that *ungi were the %ominant li*e *orm at this time, representing nearly 1''_ o* the available *ossil recor% *or this perio%.\1' ] 6owever, the relative proportion o* *ungal spores relative to spores *orme% by algal species is %i**icult to assess,\1'!] the spike %i% not appear worl%wi%e, \11']\111] an% in many places it %i% not *all on the ?ermian4Triassic boun%ary.\11&]

24

Ta&onomy
Although commonly inclu%e% in botany curricula an% te1tbooks, *ungi are more closely relate% to animals than to plants an% are place% with the animals in the monophyletic group o* opisthokonts.\11/] Analyses using molecular phylogenetics support a monophyletic origin o* the ,ungi.\/!] The ta1onomy o* the ,ungi is in a state o* constant *lu1, especially %ue to recent research base% on 2>A comparisons. These current phylogenetic analyses o*ten overturn classi*ications base% on ol%er an% sometimes less %iscriminative metho%s base% on morphological *eatures an% biological species concepts obtaine% *rom e1perimental matings. \11-] There is no uniFue generally accepte% system at the higher ta1onomic levels an% there are *reFuent name changes at every level, *rom species upwar%s. E**orts among researchers are now un%erway to establish an% encourage usage o* a uni*ie% an% more consistent nomenclature.\/!]\115] ,ungal species can also have multiple scienti*ic names %epen%ing on their li*e cycle an% mo%e (se1ual or ase1ual" o* repro%uction. =eb sites such as ;n%e1 ,ungorum an% ;T;A list current names o* *ungal species (with cross4re*erences to ol%er synonyms". The &''7 classi*ication o* 5ing%om ,ungi is the result o* a large4scale collaborative research e**ort involving %o.ens o* mycologists an% other scientists working on *ungal ta1onomy.\/!] ;t recogni.es seven phyla, two o* which#the Ascomycota an% the 3asi%iomycota#are containe% within a branch representing subking%om 2ikarya. The below cla%ogram %epicts the

25

maKor *ungal ta1a an% their relationship to opisthokont an% unikont organisms. The lengths o* the branches in this tree are not proportional to evolutionary %istances.

(axonomic gro"ps
See alsoJ List of fungal orders

The maKor phyla (sometimes calle% %ivisions" o* *ungi have been classi*ie% mainly on the basis o* characteristics o* their se1ual repro%uctive structures. +urrently, seven phyla are propose%T $icrospori%ia, +hytri%iomycota, 3lastocla%iomycota, >eocallimastigomycota, \/!] )lomeromycota, Ascomycota, an% 3asi%iomycota.

Ar,uscular mycorrhi)a seen un"er #icrosco*eK 1laL root cortical cells containing *aire" arbusculesK

?hylogenetic analysis has %emonstrate% that the $icrospori%ia, unicellular parasites o* animals an% protists, are *airly recent an% highly %erive% en%obiotic *ungi (living within the tissue o* another species".\!/]\11(] Cne &''( stu%y conclu%es that the $icrospori%ia are a sister group to the true *ungi, that is, they are each other8s closest evolutionary relative. \117] 6ibbett an% colleagues suggest that this analysis %oes not clash with their classi*ication o* the ,ungi, an% although the $icrospori%ia are elevate% to phylum status, it is acknowle%ge% that *urther analysis is reFuire% to clari*y evolutionary relationships within this group. \/!] The +hytri%iomycota are commonly known as chytri%s. These *ungi are %istribute% worl%wi%e. +hytri%s pro%uce .oospores that are capable o* active movement through aFueous phases with a single *lagellum, lea%ing early ta1onomists to classi*y them as protists. $olecular phylogenies, in*erre% *rom r:>A seFuences in ribosomes, suggest that the +hytri%s are a basal group %ivergent *rom the other *ungal phyla, consisting o* *our maKor cla%es with suggestive evi%ence *or paraphyly or possibly polyphyly.\!/] The 3lastocla%iomycota were previously consi%ere% a ta1onomic cla%e within the +hytri%iomycota. :ecent molecular %ata an% ultrastructural characteristics, however, place the 3lastocla%iomycota as a sister cla%e to the Oygomycota, )lomeromycota, an% 2ikarya (Ascomycota an% 3asi%iomycota". The blastocla%iomycetes are saprotrophs, *ee%ing on %ecomposing organic matter, an% they are parasites o* all eukaryotic groups. Lnlike their close relatives, the chytri%s, which mostly e1hibit .ygotic meiosis, the blastocla%iomycetes un%ergo sporic meiosis.\!/] The >eocallimastigomycota were earlier place% in the phylum +hytri%omycota. $embers o* this small phylum are anaerobic organisms, living in the %igestive system o* larger herbivorous mammals an% possibly in other terrestrial an% aFuatic environments. They lack mitochon%ria but contain hy%rogenosomes o* mitochon%rial origin. As the relate% chrytri%s,
26

neocallimastigomycetes *orm .oospores that are posteriorly uni*lagellate or poly*lagellate. \/!] $embers o* the )lomeromycota *orm arbuscular mycorrhi.ae, a *orm o* symbiosis where *ungal hyphae inva%e plant root cells an% both species bene*it *rom the resulting increase% supply o* nutrients. All known )lomeromycota species repro%uce ase1ually. \7'] The symbiotic association between the )lomeromycota an% plants is ancient, with evi%ence %ating to -'' million years ago.\11 ] ,ormerly part o* the Oygomycota (commonly known as 8sugar8 an% 8pin8 mol%s", the )lomeromycota were elevate% to phylum status in &''1 an% now replace the ol%er phylum Oygomycota.\11!] ,ungi that were place% in the Oygomycota are now being reassigne% to the )lomeromycota, or the subphyla incertae se%is $ucoromycotina, 5ick1ellomycotina, the Ooopagomycotina an% the Entomophthoromycotina.\/!] Aome well4known e1amples o* *ungi *ormerly in the Oygomycota inclu%e black brea% mol% ( (hizopus stolonifer", an% 'ilobolus species, capable o* eKecting spores several meters through the air.\1&'] $e%ically relevant genera inclu%e &ucor, (hizomucor, an% (hizopus.

Eiagra# of an a*otheciu# 9the ty*ical cu*.li0e re*ro"ucti/e structure of !sco#ycetes< showing sterile tissues as well as "e/elo*ing an" #ature asciK

The Ascomycota, commonly known as sac *ungi or ascomycetes, constitute the largest ta1onomic group within the Eumycota.\/ ] These *ungi *orm meiotic spores calle% ascospores, which are enclose% in a special sac4like structure calle% an ascus. This phylum inclu%es morels, a *ew mushrooms an% tru**les, single4celle% yeasts (e.g., o* the genera Saccharomyces, )luyveromyces, 'ichia, an% *andida", an% many *ilamentous *ungi living as saprotrophs, parasites, an% mutualistic symbionts. ?rominent an% important genera o* *ilamentous ascomycetes inclu%e $spergillus, 'enicillium, Fusarium, an% *laviceps. $any ascomycete species have only been observe% un%ergoing ase1ual repro%uction (calle% anamorphic species", but analysis o* molecular %ata has o*ten been able to i%enti*y their closest teleomorphs in the Ascomycota.\1&1] 3ecause the pro%ucts o* meiosis are retaine% within the sac4like ascus, ascomycetes have been use% *or eluci%ating principles o* genetics an% here%ity (e.g. Neurospora crassa".\1&&] $embers o* the 3asi%iomycota, commonly known as the club *ungi or basi%iomycetes, pro%uce meiospores calle% basi%iospores on club4like stalks calle% basi%ia. $ost common mushrooms belong to this group, as well as rust an% smut *ungi, which are maKor pathogens o* grains. Cther important basi%iomycetes inclu%e the mai.e pathogen +stilago maydis,\1&/] human commensal species o* the genus &alassezia,\1&-] an% the opportunistic human pathogen, *ryptococcus neoformans.\1&5]

F"ng"s like organisms

27

3ecause o* similarities in morphology an% li*estyle, the slime mol%s (my1omycetes" an% water mol%s (oomycetes" were *ormerly classi*ie% in the king%om ,ungi. Lnlike true *ungi the cell walls o* these organisms contain cellulose an% lack chitin. $y1omycetes are unikonts like *ungi, but are groupe% in the Amoebo.oa. Comycetes are %iploi% bikonts, groupe% in the +hromalveolate king%om. >either water mol%s nor slime mol%s are closely relate% to the true *ungi, an%, there*ore, ta1onomists no longer group them in the king%om ,ungi. >onetheless, stu%ies o* the oomycetes an% my1omycetes are still o*ten inclu%e% in mycology te1tbooks an% primary research literature.\1&(] The nuclearii%s, currently groupe% in the +hoano.oa, may be a sister group to the eumycete cla%e, an% as such coul% be inclu%e% in an e1pan%e% *ungal king%om.\1&7]

Ecology
Although o*ten inconspicuous, *ungi occur in every environment on Earth an% play very important roles in most ecosystems. Along with bacteria, *ungi are the maKor %ecomposers in most terrestrial (an% some aFuatic" ecosystems, an% there*ore play a critical role in biogeochemical cycles\1& ] an% in many *oo% webs. As %ecomposers, they play an essential role in nutrient cycling, especially as saprotrophs an% symbionts, %egra%ing organic matter to inorganic molecules, which can then re4enter anabolic metabolic pathways in plants or other organisms.\1&!]\1/']

2ymbiosis
$any *ungi have important symbiotic relationships with organisms *rom most i* not all 5ing%oms.\1/1]\1/&]\1//] These interactions can be mutualistic or antagonistic in nature, or in the case o* commensal *ungi are o* no apparent bene*it or %etriment to the host.\1/-]\1/5]\1/(] 'ith plants $ycorrhi.al symbiosis between plants an% *ungi is one o* the most well4known plant*ungus associations an% is o* signi*icant importance *or plant growth an% persistence in many ecosystems^ over !'_ o* all plant species engage in mycorrhi.al relationships with *ungi an% are %epen%ent upon this relationship *or survival.\1/7]

28

The "ar0 fila#ents are hy*hae of the en"o*hytic fungus !eotyphodium coenophialum in the intercellular s*aces of tall fescue leaf sheath tissue

The mycorrhi.al symbiosis is ancient, %ating to at least -'' million years ago. \11 ] ;t o*ten increases the plant8s uptake o* inorganic compoun%s, such as nitrate an% phosphate *rom soils having low concentrations o* these key plant nutrients.\1&!]\1/ ] The *ungal partners may also me%iate plant4to4plant trans*er o* carbohy%rates an% other nutrients. Auch mycorrhi.al communities are calle% [common mycorrhi.al networks[.\1/!] A special case o* mycorrhi.a is myco4heterotrophy, whereby the plant parasiti.es the *ungus, obtaining all o* its nutrients *rom its *ungal symbiont.\1-'] Aome *ungal species inhabit the tissues insi%e roots, stems, an% leaves, in which case they are calle% en%ophytes.\1-1] Aimilar to mycorrhi.a, en%ophytic coloni.ation by *ungi may bene*it both symbionts^ *or e1ample, en%ophytes o* grasses impart to their host increase% resistance to herbivores an% other environmental stresses an% receive *oo% an% shelter *rom the plant in return.\1-&] 'ith algae and cyanobacteria

The lichen Lo,aria pulmonaria a sy#biosis of fungal algal an" cyanobacterial s*ecies

7ichens are *orme% by a symbiotic relationship between algae or cyanobacteria (re*erre% to in lichen terminology as [photobionts[" an% *ungi (mostly various species o* ascomycetes an% a *ew basi%iomycetes", in which in%ivi%ual photobiont cells are embe%%e% in a tissue *orme% by the *ungus.\1-/] 7ichens occur in every ecosystem on all continents, play a key role in soil *ormation an% the initiation o* biological succession,\1--] an% are the %ominating li*e *orms in e1treme environments, inclu%ing polar, alpine, an% semiari% %esert regions.\1-5] They are able to grow on inhospitable sur*aces, inclu%ing bare soil, rocks, tree bark, woo%, shells, barnacles an% leaves.\1-(] As in mycorrhi.as, the photobiont provi%es sugars an% other carbohy%rates via photosynthesis, while the *ungus provi%es minerals an% water. The *unctions o* both symbiotic organisms are so closely intertwine% that they *unction almost as a single organism^ in most cases the resulting organism %i**ers greatly *rom the in%ivi%ual components. 7icheni.ation is a common mo%e o* nutrition^ aroun% &'_ o* *ungi#between 17,5'' an% &',''' %escribe% species#are licheni.e%.\1-7] +haracteristics common to most lichens inclu%e obtaining organic carbon by photosynthesis, slow growth, small si.e, long li*e, long4lasting (seasonal" vegetative repro%uctive structures, mineral nutrition obtaine% largely *rom airborne sources, an% greater tolerance o* %esiccation than most other photosynthetic organisms in the same habitat.\1- ]

29

'ith insects $any insects also engage in mutualistic relationships with *ungi. Aeveral groups o* ants cultivate *ungi in the or%er Agaricales as their primary *oo% source, while ambrosia beetles cultivate various species o* *ungi in the bark o* trees that they in*est. \1-!] Aimilarly, *emales o* several woo% wasp species (genus Sire," inKect their eggs together with spores o* the woo%4 rotting *ungus $mylostereum areolatum into the sapwoo% o* pine trees^ the growth o* the *ungus provi%es i%eal nutritional con%itions *or the %evelopment o* the wasp larvae. \15'] Termites on the A*rican savannah are also known to cultivate *ungi,\151] an% yeasts o* the genera *andida an% -achancea inhabit the gut o* a wi%e range o* insects, inclu%ing neuropterans, beetles, an% cockroaches^ it is not known whether these *ungi bene*it their hosts.
\15&]

As pathogens and parasites

The *lant *athogen Aecidium magellanicum causes calafate rust seen here on a Ber,eris shrub in ChileK

$any *ungi are parasites on plants, animals (inclu%ing humans", an% other *ungi. Aerious pathogens o* many cultivate% plants causing e1tensive %amage an% losses to agriculture an% *orestry inclu%e the rice blast *ungus &agnaporthe oryzae,\15/] tree pathogens such as .phiostoma ulmi an% .phiostoma novo/ulmi causing 2utch elm %isease,\15-] an% *ryphonectria parasitica responsible *or chestnut blight,\155] an% plant pathogens in the genera Fusarium, +stilago, $lternaria, an% *ochliobolus.\1/5] Aome carnivorous *ungi, like 'aecilomyces lilacinus, are pre%ators o* nemato%es, which they capture using an array o* speciali.e% structures such as constricting rings or a%hesive nets.\15(] Aome *ungi can cause serious %iseases in humans, several o* which may be *atal i* untreate%. These inclu%e aspergilloses, can%i%oses, cocci%ioi%omycosis, cryptococcosis, histoplasmosis, mycetomas, an% paracocci%ioi%omycosis. ,urthermore, persons with immuno4%e*iciencies are particularly susceptible to %isease by genera such as $spergillus, *andida, *ryptoccocus,\1/(]\157]\15 ] 0istoplasma,\15!] an% 'neumocystis.\1('] Cther *ungi can attack eyes, nails, hair, an% especially skin, the so4calle% %ermatophytic an% keratinophilic *ungi, an% cause local in*ections such as ringworm an% athleteis *oot.\1(1] ,ungal spores are also a cause o* allergies, an% *ungi *rom %i**erent ta1onomic groups can evoke allergic reactions.\1(&]

30

Human use

Saccharomyces cere(isiae cells shown with EIC #icrosco*yK

The human use o* *ungi *or *oo% preparation or preservation an% other purposes is e1tensive an% has a long history. $ushroom *arming an% mushroom gathering are large in%ustries in many countries. The stu%y o* the historical uses an% sociological impact o* *ungi is known as ethnomycology. 3ecause o* the capacity o* this group to pro%uce an enormous range o* natural pro%ucts with antimicrobial or other biological activities, many species have long been use% or are being %evelope% *or in%ustrial pro%uction o* antibiotics, vitamins, an% anti4cancer an% cholesterol4lowering %rugs. $ore recently, metho%s have been %evelope% *or genetic engineering o* *ungi,\1(/] enabling metabolic engineering o* *ungal species. ,or e1ample, genetic mo%i*ication o* yeast species\1(-]#which are easy to grow at *ast rates in large *ermentation vessels#has opene% up ways o* pharmaceutical pro%uction that are potentially more e**icient than pro%uction by the original source organisms.\1(5]

Dr"gs
$any species pro%uce metabolites that are maKor sources o* pharmacologically active %rugs. ?articularly important are the antibiotics, inclu%ing the penicillins, a structurally relate% group o* h4lactam antibiotics that are synthesi.e% *rom small pepti%es. Although naturally occurring penicillins such as penicillin ) (pro%uce% by 'enicillium chrysogenum" have a relatively narrow spectrum o* biological activity, a wi%e range o* other penicillins can be pro%uce% by chemical mo%i*ication o* the natural penicillins. $o%ern penicillins are semisynthetic compoun%s, obtaine% initially *rom *ermentation cultures, but then structurally altere% *or speci*ic %esirable properties.\1((] Cther antibiotics pro%uce% by *ungi inclu%eT ciclosporin, commonly use% as an immunosuppressant %uring transplant surgery^ an% *usi%ic aci%, use% to help control in*ection *rom methicillin4resistant Staphylococcus aureus bacteria.\1(7] =i%esprea% use o* these antibiotics *or the treatment o* bacterial %iseases, such as tuberculosis, syphilis, leprosy, an% many others began in the early &'th century an% continues to play a maKor part in anti4bacterial chemotherapy. ;n nature, antibiotics o* *ungal or bacterial origin appear to play a %ual roleT at high concentrations they act as chemical %e*ense against competition with other microorganisms in species4rich environments, such as the rhi.osphere, an% at low concentrations as Fuorum4sensing molecules *or intra4 or interspecies signaling. \1( ] Cther %rugs pro%uce% by *ungi inclu%e griseo*ulvin isolate% *rom 'enicillium griseofulvum, use% to treat *ungal in*ections,\1(!] an% statins (6$)4+oA re%uctase inhibitors", use% to inhibit cholesterol synthesis. E1amples o* statins *oun% in *ungi inclu%e mevastatin *rom 'enicillium citrinum an% lovastatin *rom $spergillus terreus an% the oyster mushroom.\17']

31

C"lt"red foods
3aker8s yeast or Saccharomyces cerevisiae, a single4celle% *ungus, is use% to make brea% an% other wheat4base% pro%ucts, such as pi..a %ough an% %umplings.\171] Reast species o* the genus Saccharomyces are also use% to pro%uce alcoholic beverages through *ermentation.\17&] Ahoyu koKi mol% ($spergillus oryzae" is an essential ingre%ient in brewing Ahoyu (soy sauce" an% sake, an% the preparation o* miso,\17/] while (hizopus species are use% *or making tempeh.\17-] Aeveral o* these *ungi are %omesticate% species that were bre% or selecte% accor%ing to their capacity to *erment *oo% without pro%ucing harm*ul mycoto1ins (see below", which are pro%uce% by very closely relate% $spergilli.\175] Euorn, a meat substitute, is ma%e *rom Fusarium venenatum.\17(]

%edicinal "se
See alsoJ Medicinal mushrooms

The #e"icinal fungi 1anoderma lucidum 9left< an" Cordyceps sinensis 9right<K

+ertain mushrooms enKoy usage as therapeutics in *olk me%icines, such as Tra%itional +hinese me%icine. >otable me%icinal mushrooms with a well4%ocumente% history o* use inclu%e $garicus subrufescens,\177]\17 ] 1anoderma lucidum,\17!] an% *ordyceps sinensis.\1 '] :esearch has i%enti*ie% compoun%s pro%uce% by these an% other *ungi that have inhibitory biological e**ects against viruses\1 1]\1 &] an% cancer cells.\177]\1 /] Apeci*ic metabolites, such as polysacchari%e45, ergotamine, an% h4lactam antibiotics, are routinely use% in clinical me%icine. The shiitake mushroom is a source o* lentinan, a clinical %rug approve% *or use in cancer treatments in several countries, inclu%ing 0apan.\1 -]\1 5] ;n Europe an% 0apan, polysacchari%e45 (bran% name 5restin", a chemical %erive% *rom Trametes versicolor, is an approve% a%Kuvant *or cancer therapy.\1 (]

#dible and poisono"s species

32

Amanita phalloides accounts for the #a$ority of fatal #ushroo# *oisonings worl"wi"eK

E%ible mushrooms are well4known e1amples o* *ungi. $any are commercially raise%, but others must be harveste% *rom the wil%. $garicus bisporus, sol% as button mushrooms when small or ?ortobello mushrooms when larger, is a commonly eaten species, use% in sala%s, soups, an% many other %ishes. $any Asian *ungi are commercially grown an% have increase% in popularity in the =est. They are o*ten available *resh in grocery stores an% markets, inclu%ing straw mushrooms (!olvariella volvacea", oyster mushrooms ('leurotus ostreatus", shiitakes (-entinula edodes", an% enokitake (Flammulina spp.".\1 7] There are many more mushroom species that are harveste% *rom the wil% *or personal consumption or commercial sale. $ilk mushrooms, morels, chanterelles, tru**les, black trumpets, an% porcini mushrooms (%oletus edulis" (also known as king boletes" %eman% a high price on the market. They are o*ten use% in gourmet %ishes.\1 ] +ertain types o* cheeses reFuire inoculation o* milk cur%s with *ungal species that impart a uniFue *lavor an% te1ture to the cheese. E1amples inclu%e the blue color in cheeses such as Atilton or :oFue*ort, which are ma%e by inoculation with 'enicillium ro2ueforti.\1 !] $ol%s use% in cheese pro%uction are non4to1ic an% are thus sa*e *or human consumption^ however, mycoto1ins (e.g., a*lato1ins, roFue*ortine +, patulin, or others" may accumulate because o* growth o* other *ungi %uring cheese ripening or storage.\1!']

33

Stilton cheese /eine" with enicillium ro0ueforti

$any mushroom species are poisonous to humans, with to1icities ranging *rom slight %igestive problems or allergic reactions as well as hallucinations to severe organ *ailures an% %eath. )enera with mushrooms containing %ea%ly to1ins inclu%e *onocybe, 1alerina, -epiota, an% most in*amously, $manita.\1!1] The latter genus inclu%es the %estroying angel 3$" virosa4 an% the %eath cap 3$" phalloides4, the most common cause o* %ea%ly mushroom poisoning. \1!&] The *alse morel (1yromitra esculenta" is occasionally consi%ere% a %elicacy when cooke%, yet can be highly to1ic when eaten raw.\1!/] Tricholoma e2uestre was consi%ere% e%ible until being implicate% in serious poisonings causing rhab%omyolysis.\1!-] ,ly agaric mushrooms ($manita muscaria" also cause occasional non4*atal poisonings, mostly as a result o* ingestion *or use as a recreational %rug *or its hallucinogenic properties. 6istorically, *ly agaric was use% by %i**erent peoples in Europe an% Asia an% its present usage *or religious or shamanic purposes is reporte% *rom some ethnic groups such as the 5oryak people o* north4eastern Aiberia.\1!5] As it is %i**icult to accurately i%enti*y a sa*e mushroom without proper training an% knowle%ge, it is o*ten a%vise% to assume that a wil% mushroom is poisonous an% not to consume it.\1!(]\1!7]

,est control

3rassho**ers 0ille" by Beau(eria ,assiana

;n agriculture, *ungi may be use*ul i* they actively compete *or nutrients an% space with pathogenic microorganisms such as bacteria or other *ungi via the competitive e1clusion principle,\1! ] or i* they are parasites o* these pathogens. ,or e1ample, certain species may be use% to eliminate or suppress the growth o* harm*ul plant pathogens, such as insects, mites, wee%s, nemato%es an% other *ungi that cause %iseases o* important crop plants.\1!!] This has generate% strong interest in practical applications that use these *ungi in the biological control o* these agricultural pests. Entomopathogenic *ungi can be use% as biopestici%es, as they actively kill insects.\&''] E1amples that have been use% as biological insectici%es are %eauveria bassiana, &etarhizium spp, 0irsutella spp, 'aecilomyces (5saria" spp, an% -ecanicillium lecanii.\&'1]\&'&] En%ophytic *ungi o* grasses o* the genus Neotyphodium, such as N" coenophialum, pro%uce alkaloi%s that are to1ic to a range o* invertebrate an% vertebrate herbivores. These alkaloi%s protect grass plants *rom herbivory, but several en%ophyte alkaloi%s can poison gra.ing animals, such as cattle an% sheep. \&'/] ;n*ecting cultivars o* pasture or *orage grasses with Neotyphodium en%ophytes is one approach being use% in grass bree%ing programs^ the *ungal strains are selecte% *or pro%ucing only alkaloi%s that increase resistance to herbivores such as insects, while being non4to1ic to livestock.\&'-]

34

Bioremediation
See alsoJ Mycoremediation

+ertain *ungi, in particular [white rot[ *ungi, can %egra%e insectici%es, herbici%es, pentachlorophenol, creosote, coal tars, an% heavy *uels an% turn them into carbon %io1i%e, water, an% basic elements.\&'5] ,ungi have been shown to biominerali.e uranium o1i%es, suggesting they may have application in the bioreme%iation o* ra%ioactively pollute% sites.\&'(]
\&'7]\&' ]

%odel organisms
Aeveral pivotal %iscoveries in biology were ma%e by researchers using *ungi as mo%el organisms, that is, *ungi that grow an% se1ually repro%uce rapi%ly in the laboratory. ,or e1ample, the one gene4one en.yme hypothesis was *ormulate% by scientists who use% the brea% mol% Neurospora crassa to test their biochemical theories.\&'!] Cther important mo%el *ungi are $spergillus nidulans an% the yeasts, Saccaromyces cerevisiae an% Schizosaccharomyces pombe, each o* which has a long history o* use to investigate issues in eukaryotic cell biology an% genetics, such as cell cycle regulation, chromatin structure, an% gene regulation. Cther *ungal mo%els have more recently emerge% that each a%%ress speci*ic biological Fuestions relevant to me%icine, plant pathology, an% in%ustrial uses^ e1amples inclu%e *andida albicans, a %imorphic, opportunistic human pathogen,\&1'] &agnaporthe grisea, a plant pathogen,\&11] an% 'ichia pastoris, a yeast wi%ely use% *or eukaryotic protein e1pression.\&1&]

-thers
,ungi are use% e1tensively to pro%uce in%ustrial chemicals like citric, gluconic, lactic, an% malic aci%s,\&1/] an% in%ustrial en.ymes, such as lipases use% in biological %etergents,\&1-] cellulases use% in making cellulosic ethanol\&15] an% stonewashe% Keans,\&1(] an% amylases,\&17] invertases, proteases an% 1ylanases.\&1 ] Aeveral species, most notably 'silocybin mushrooms (colloFuially known as magic mushrooms", are ingeste% *or their psyche%elic properties, both recreationally an% religiously.

35

Mycoto&ins

)rgota#ine a #a$or #ycotoLin *ro"uce" by Cla(iceps s*ecies which if ingeste" can cause gangrene con/ulsions an" hallucinations

$any *ungi pro%uce biologically active compoun%s, several o* which are to1ic to animals or plants an% are there*ore calle% mycoto1ins. C* particular relevance to humans are mycoto1ins pro%uce% by mol%s causing *oo% spoilage, an% poisonous mushrooms (see above". ?articularly in*amous are the lethal amato1ins in some $manita mushrooms, an% ergot alkaloi%s, which have a long history o* causing serious epi%emics o* ergotism (At Anthony8s ,ire" in people consuming rye or relate% cereals contaminate% with sclerotia o* the ergot *ungus, *laviceps purpurea.\&1!] Cther notable mycoto1ins inclu%e the a*lato1ins, which are insi%ious liver to1ins an% highly carcinogenic metabolites pro%uce% by certain $spergillus species o*ten growing in or on grains an% nuts consume% by humans, ochrato1ins, patulin, an% trichothecenes (e.g., T4& mycoto1in" an% *umonisins, which have signi*icant impact on human *oo% supplies or animal livestock.\&&'] $ycoto1ins are secon%ary metabolites (or natural pro%ucts", an% research has establishe% the e1istence o* biochemical pathways solely *or the purpose o* pro%ucing mycoto1ins an% other natural pro%ucts in *ungi.\&&1] $ycoto1ins may provi%e *itness bene*its in terms o* physiological a%aptation, competition with other microbes an% *ungi, an% protection *rom consumption (*ungivory".\&&&]\&&/]

#!ol"tion of f"ngi
The e!ol"tion of f"ngi has been going on since *ungi %iverge% *rom other li*e aroun% 1,5'' million years ago, (=ang et al., 1!!!"\1] with the glomaleans branching *rom the [higher *ungi[ at j57' million years ago, accor%ing to 2>A analysis. (AchQkler et al., &''1^ Tehler et al., &'''"\1] ,ungi probably colonise% the lan% %uring the +ambrian, over 5'' million years ago, (Taylor l Csborn, 1!!("\1] but *ossils only become uncontroversial an% common %uring the 2evonian, -'' million years ago.\1] Early *ungi A rich %iversity o* *ungi is known *rom the lower 2evonian :hynie chert, an earlier recor% is absent. Aince *ungi %o not biomineralise, they %o not rea%ily enter the *ossil recor%^ there are only three claims o* early *ungi. Cne *rom the Cr%ovician\&] has been %ismisse% on the groun%s that it lacks any %istinctly *ungal *eatures, an% is hel% by many to be contamination^ \/] the position o* a [probable[ ?rotero.oic *ungus is still not establishe%,\/] an% it may represent a stem group *ungus. There is also a case *or a *ungal a**inity *or the enigmatic micro*ossil .rnatifilum. Aince the *ungi *orm a sister group to the animals, the two lineages must have %iverge% be*ore the *irst animal lineages, which are
36

known *rom *ossils as early as the E%iacaran.\-] ;n contrast to plants an% animals, the early *ossil recor% o* the *ungi is meager. ,actors that likely contribute to the un%er4representation o* *ungal species among *ossils inclu%e the nature o* *ungal *ruiting bo%ies, which are so*t, *leshy, an% easily %egra%able tissues an% the microscopic %imensions o* most *ungal structures, which there*ore are not rea%ily evi%ent. ,ungal *ossils are %i**icult to %istinguish *rom those o* other microbes, an% are most easily i%enti*ie% when they resemble e1tant *ungi.\5] C*ten recovere% *rom a perminerali.e% plant or animal host, these samples are typically stu%ie% by making thin4 section preparations that can be e1amine% with light microscopy or transmission electron microscopy.\(] +ompression *ossils are stu%ie% by %issolving the surroun%ing matri1 with aci% an% then using light or scanning electron microscopy to e1amine sur*ace %etails. \7] The earliest *ossils possessing *eatures typical o* *ungi %ate to the ?rotero.oic eon, some 1,-/' million years ago ($a"^ these multicellular benthic organisms ha% *ilamentous structures with septa, an% were capable o* anastomosis.\/] $ore recent stu%ies (&''!" estimate the arrival o* *ungal organisms at about 7('1'(' $a on the basis o* comparisons o* the rate o* evolution in closely relate% groups.\ ] ,or much o* the ?aleo.oic Era (5-&&51 $a", the *ungi appear to have been aFuatic an% consiste% o* organisms similar to the e1tant +hytri%s in having *lagellum4bearing spores.\!] The evolutionary a%aptation *rom an aFuatic to a terrestrial li*estyle necessitate% a %iversi*ication o* ecological strategies *or obtaining nutrients, inclu%ing parasitism, saprobism, an% the %evelopment o* mutualistic relationships such as mycorrhi.a an% licheni.ation.\1'] :ecent (&''!" stu%ies suggest that the ancestral ecological state o* the Ascomycota was saprobism, an% that in%epen%ent licheni.ation events have occurre% multiple times.\11] The *ungi probably coloni.e% the lan% %uring the +ambrian (5-&- ./ $a", long be*ore lan% plants.\1] ,ossili.e% hyphae an% spores recovere% *rom the Cr%ovician o* =isconsin (-(' $a" resemble mo%ern4%ay )lomerales, an% e1iste% at a time when the lan% *lora likely consiste% o* only non4vascular bryophyte4like plants.\1&] ?rotota1ites, which was probably a *ungus or lichen, woul% have been the tallest organism o* the late Ailurian. ,ungal *ossils %o not become common an% uncontroversial until the early 2evonian (-1(/5!.& $a", when they are abun%ant in the :hynie chert, mostly as Oygomycota an% +hytri%iomycota.\1]\1/]\1-] At about this same time, appro1imately -'' $a, the Ascomycota an% 3asi%iomycota %iverge%,\15] an% all mo%ern classes o* *ungi were present by the 7ate +arboni*erous (?ennsylvanian, /1 .1 &!! $a".\1(] 7ichen4like *ossils have been *oun% in the 2oushantuo ,ormation in southern +hina %ating back to (/5551 $a.\17] 7ichens were a component o* the early terrestrial ecosystems, an% the estimate% age o* the ol%est terrestrial lichen *ossil is -'' $a^\1 ] this %ate correspon%s to the age o* the ol%est known sporocarp *ossil, a 'aleopyrenomycites species *oun% in the :hynie +hert.\1!] The ol%est *ossil with microscopic *eatures resembling mo%ern4 %ay basi%iomycetes is 'alaeoancistrus, *oun% perminerali.e% with a *ern *rom the ?ennsylvanian.\&'] :are in the *ossil recor% are the homobasi%iomycetes (a ta1on roughly eFuivalent to the mushroom4pro%ucing species o* the agaricomycetes". Two amber4preserve% specimens provi%e evi%ence that the earliest known mushroom4*orming *ungi (the e1tinct species $rchaeomarasmius legletti" appeare% %uring the mi%4+retaceous, !' $a.\&1]\&&] Aome time a*ter the ?ermian4Triassic e1tinction event (&51.- $a", a *ungal spike (originally thought to be an e1traor%inary abun%ance o* *ungal spores in se%iments" *orme%, suggesting that *ungi were the %ominant li*e *orm at this time, representing nearly 1''_ o* the available *ossil recor% *or this perio%.\&/] 6owever, the relative proportion o* *ungal spores relative to spores *orme% by algal species is %i**icult to assess,\&-] the spike %i% not appear worl%wi%e, \&5]\&(] an% in many places it %i% not *all on the ?ermian4Triassic boun%ary.\&7] mycotoxin

37

(*rom )reek UVWXY (mykes, mukos" m*ungusn an% 7atin (to1icum" mpoisonn" is a to1ic secon%ary metabolite pro%uce% by organisms o* the *ungus king%om, commonly known as mol%s.\1]\&] The term omycoto1ini is usually reserve% *or the to1ic chemical pro%ucts pro%uce% by *ungi that rea%ily coloni.e crops.\1] $ost *ungi are aerobic (use o1ygen" an% are *oun% almost everywhere in e1tremely small Fuantities %ue to the minute si.e o* their spores. They consume organic matter wherever humi%ity an% temperature are su**icient. Cne mol% species may pro%uce many %i**erent mycoto1ins an%`or the same mycoto1in as another species.\/] =here con%itions are right, *ungi proli*erate into colonies an% mycoto1in levels become high. The reason *or the pro%uction o* mycoto1ins is not yet known^ they are neither necessary *or growth nor the %evelopment o* the *ungi.\-] 3ecause mycoto1ins weaken the receiving host, the *ungus may use them as a strategy to better the environment *or *urther *ungal proli*eration. The pro%uction o* to1ins %epen%s on the surroun%ing intrinsic an% e1trinsic environments an% the to1ins vary greatly in their severity, %epen%ing on the organism in*ecte% an% its susceptibility, metabolism, an% %e*ense mechanisms.\5] Aome o* the health e**ects *oun% in animals an% humans inclu%e %eath, i%enti*iable %iseases or health problems, weakene% immune systems without speci*icity to a to1in, an% as allergens or irritants. Aome mycoto1ins are harm*ul to other micro4organisms such as other *ungi or even bacteria^ penicillin is one e1ample.\(] $ycoto1ins can appear in the *oo% chain as a result o* *ungal in*ection o* crops, either by being eaten %irectly by humans, or by being use% as livestock *ee%. $ycoto1ins greatly resist %ecomposition or being broken %own in %igestion, so they remain in the *oo% chain in meat an% %airy pro%ucts. Even temperature treatments, such as cooking an% *ree.ing, %o not %estroy mycoto1ins. Although various wil% mushrooms contain an assortment o* poisons that are %e*initely *ungal metabolites causing noteworthy health problems *or humans, they are rather arbitrarily e1clu%e% *rom %iscussions o* mycoto1icology. ;n such cases the %istinction is base% on the si.e o* the pro%ucing *ungus an% human intention. \7] $ycoto1in e1posure is almost always acci%ental whereas with mushrooms improper i%enti*ication an% ingestion causing mushroom poisoning is commonly the case. ;ngestion o* misi%enti*ie% mushrooms containing mycoto1ins may result in hallucinations. The cyclopepti%e4pro%uce% $manita phalloide is well known *or its to1ic potential an% is responsible *or appro1imately !'_ o* all mushroom *atalities. \ ] The other primary mycoto1in groups *oun% in mushrooms inclu%eT orellanine, monomethylhy%ra.ine, %isul*iram4like, hallucinogenic in%oles, muscarinic, iso1a.ole, an% gastrointestinal ();"4speci*ic irritants.\!] The bulk o* this article is about mycoto1ins that are *oun% in micro*ungi other than poisons *rom mushrooms or macroscopic *ungi.\7] $any international agencies are trying to achieve universal stan%ar%i.ation o* regulatory limits *or mycoto1ins. +urrently, over 1'' countries have regulations regar%ing mycoto1ins in the *ee% in%ustry, in which 1/ mycoto1ins or groups o* mycoto1ins are o* concern.\1'] The process o* assessing a nee% *or mycoto1in regulation inclu%es a wi%e array o* in4laboratory testing which inclu%es e1tracting, clean4up an% separation techniFues. \11] $ost o**icial regulations an% control metho%s are base% on high4per*ormance liFui% techniFues (e.g., 6?7+" through international bo%ies.\11] ;t is implie% that any regulations regar%ing these to1ins will be in co4or%inance with any other countries with which a tra%e agreement e1ists. $any o* the stan%ar%s *or the metho% per*ormance analysis *or mycoto1ins is set by the European +ommittee *or Atan%ar%i.ation (+E>".\11] 6owever, one must take note that scienti*ic risk assessment is commonly in*luence% by culture an% politics which, in turn, will a**ect tra%e regulations o* mycoto1ins.\1&] ,oo%4base% mycoto1ins were stu%ie% e1tensively worl%wi%e throughout the &'th century. ;n Europe, statutory levels o* a range o* mycoto1ins permitte% in *oo% an% animal *ee% are set by a range o* European %irectives an% +ommission regulations. The L.A. ,oo% an% 2rug A%ministration has regulate% an% en*orce% limits on concentrations o* mycoto1ins in *oo%s an% *ee% in%ustries since 1! 5. ;t is through various compliance programs that the ,2A monitors these in%ustries to guarantee that mycoto1ins are kept at a practical
38

level. These compliance programs sample *oo% pro%ucts inclu%ing peanuts an% peanut pro%ucts, tree nuts, corn an% corn pro%ucts, cottonsee%, an% milk. There is still a lack o* su**icient surveillance %ata on some mycoto1ins that occur in the L.A. which is largely %ue to the lack o* reliable analytical metho%s.\1/]

Contents

1 Ma$or grou*s & Bin"ing agents "eacti/ators

an"

+ In the in"oor en/iron#ent 2 Fu#an health effects 5 In *et foo" 6 In fiction 6 See also % 4eferences 9 )Lternal lin0s

Ma'or grou"s
Aflatoxins are a type o* mycoto1in pro%uce% by $spergillus species o* *ungi, such as $" flavus an% $" parasiticus.\1-] The umbrella term a*lato1in re*ers to *our %i**erent types o* mycoto1ins pro%uce%, which are 31, 3&, )1, an% )&. \15] A*lato1in 31, the most to1ic, is a potent carcinogen an% has been %irectly correlate% to a%verse health e**ects, such as liver cancer, in many animal species.\1-] A*lato1ins are largely associate% with commo%ities pro%uce% in the tropics an% subtropics, such as cotton, peanuts, spices, pistachios an% mai.e.\1-]\15] -chratoxin is a mycoto1in that comes in three secon%ary metabolite *orms, A, 3, an% +. All are pro%uce% by 'enicillium an% $spergillus species. The three *orms %i**er in that Cchrato1in 3 (CT3" is a nonchlorinate% *orm o* Cchrato1in A (CTA" an% that Cchrato1in + (CT+" is an ethyl ester *orm Cchato1in A.\1(] $spergillus ochraceus is *oun% as a contaminant o* a wi%e range o* commo%ities inclu%ing beverages such as beer an% wine. $spergillus carbonarius is the main species *oun% on vine *ruit, which releases its to1in %uring the Kuice making process. \17] CTA has been labele% as a carcinogen an% a nephroto1in, an% has been linke% to tumors in the human urinary tract, although research in humans is limite% by con*oun%ing *actors.\1(]\17] Citrinin is a to1in that was *irst isolate% *rom 'enicillium citrinum, but has been i%enti*ie% in over a %o.en species o* 'enicillium an% several species o* $spergillus. Aome o* these species are use% to pro%uce human *oo%stu**s such as cheese ( 'enicillium camemberti", sake, miso, an% soy sauce ($spergillus oryzae". +itrinin is associate% with yellow rice %isease in 0apan an% acts as a nephroto1in in all animal species teste%. Although it is associate% with many human *oo%s (wheat, rice, corn, barley, oats, rye, an% *oo% colore% with $onascus pigment" its *ull signi*icance *or human health is unknown. +itrinin can also act synergistically with Cchrato1in A to %epress :>A synthesis in murine ki%neys.\7]

39

#rgot Alkaloids are compoun%s pro%uce% as a to1ic mi1ture o* alkaloi%s in the sclerotia o* species o* *laviceps, which are common pathogens o* various grass species. The ingestion o* ergot sclerotia *rom in*ecte% cereals, commonly in the *orm o* brea% pro%uce% *rom contaminate% *lour, cause ergotism the human %isease historically known as At. Anthonyis ,ire. There are two *orms o* ergotism gangrenous a**ecting bloo% supply to e1tremities an% convulsive which a**ects the central nervous system. $o%ern metho%s o* grain cleaning have signi*icantly re%uce% ergotism as a human %isease, however it is still an important veterinarian problem. Ergot alkaloi%s have been use% pharmaceutically.\7] ,at"lin is a to1in pro%uce% by the '" e,pansum, $spergillus, 'enicillium, an% 'aecilomyces *ungal species. '" e,pansum is especially associate% with a range o* mol%y *ruits an% vegetables, in particular rotting apples an% *igs.\1 ]\1!] ;t is %estroye% by the *ermentation process an% so is not *oun% in apple beverages, such as ci%er. Although patulin has not been shown to be carcinogenic, it has been reporte% to %amage the immune system in animals.\1 ] ;n &''-, the European +ommunity set limits to the concentrations o* patulin in *oo% pro%ucts. They currently stan% at 5' Ug`kg in all *ruit Kuice concentrations, at &5 Ug`kg in soli% apple pro%ucts use% *or %irect consumption, an% at 1' Ug`kg *or chil%ren8s apple pro%ucts, inclu%ing apple Kuice.\1 ]\1!] F"sari"m to1ins are pro%uce% by over 5' species o* Fusarium an% have a history o* in*ecting the grain o* %eveloping cereals such as wheat an% mai.e.\&']\&1] They inclu%e a range o* mycoto1ins, such asT the f"monisins, which a**ect the nervous systems o* horses an% may cause cancer in ro%ents^ the trichothecenes, which are most strongly associate% with chronic an% *atal to1ic e**ects in animals an% humans^ an% zearalenone, which is not correlate% to any *atal to1ic e**ects in animals or humans. Aome o* the other maKor types o* Fusarium to1ins inclu%eT beauvercin an% enniatins, butenoli%e, eFuisetin, an% *usarins.\&&]

(inding agents and deacti!ators

;n the *ee% an% *oo% in%ustry it has become common practice to a%% mycoto1in bin%ing agents such as $ontmorillonite or bentonite clay in or%er to a**ectively a%sorb the mycoto1ins. \&/] To reverse the a%verse e**ects o* mycoto1ins, the *ollowing criteria are use% to evaluate the *unctionality o* any bin%ing a%%itiveT

)fficacy of acti/e co#*onent /erifie" by scientific "ata ! low effecti/e inclusion rate Stability o/er a wi"e *F range Figh ca*acity to a"sorb high concentrations of #ycotoLins Figh affinity to a"sorb low concentrations of #ycotoLins !ffir#ation of che#ical interaction between #ycotoLin an" a"sorbent Pro/en in (i(o "ata with all #a$or #ycotoLins -on.toLic en/iron#entally frien"ly co#*onent

Aince not all mycoto1ins can be boun% to such agents, the latest approach to mycoto1in control is mycoto1in %eactivation. 3y means o* en.ymes (esterase, epo1i%ase", yeast (Trichosporon mycoto,invorans" or bacterial strains (Eubacterium 33A6 7!7", mycoto1ins can be re%uce%
40

%uring pre4harvesting contamination. Cther removal metho%s inclu%e physical separation, washing, milling, heat4treatment, ra%iation, e1traction with solvents, an% the use o* chemical or biological agents. ;rra%iation metho%s have proven to be e**ective treatment against mol% growth an% to1in pro%uction.\&/]

)n the indoor en!ironment

3uil%ings are another source o* mycoto1ins an% people living or working in areas with mol% increase their chances o* a%verse health e**ects. $ol%s growing in buil%ings can be %ivi%e% into three groups # ?rimary, Aecon%ary, an% Tertiary coloni.ers. Each group is categori.e% by the ability to grow at a certain water activity reFuirement. ;t has become %i**icult to i%enti*y mycoto1ins pro%uction by in%oor mol%s *or many variables, such as (i" they may be maske% as %erivatives (ii" they are poorly %ocumente% an% (iii" the *act that they are likely to pro%uce %i**erent metabolites on buil%ing materials. Aome o* the mycoto1ins in the in%oor environment are pro%uce% by Alternaria, Aspergillus (multiple *orms", ?enicillium, an% Atachybotrys.\&-] Atachybotrys chartarum contains a higher number o* mycoto1ins than other mol%s grown in the in%oor environment an% has been associate% with allergies an% respiratory in*lammation. \&5] The in*estation o* A. chartarum in buil%ings containing gypsum boar%, as well as on ceiling tiles, is very common an% has recently become a more recogni.e% problem. =hen gypsum boar% has been repeate%ly intro%uce% to moisture A. chartarum grows rea%ily on its cellulose *ace.\&(] This stresses the importance o* moisture controls an% ventilation within resi%ential homes an% other buil%ings. The negative health e**ects o* mycoto1ins are a *unction o* the concentration, the %uration o* e1posure an% the subKect8s sensitivities. The concentrations e1perience% in a normal home, o**ice or school are o*ten too low to trigger a health response in occupants.;n the 1!!'s, public concern over mycoto1ins increase% *ollowing multi4million %ollar to1ic mol% settlements. The lawsuits took place a*ter the +enter *or 2isease +ontrol (+2+" %i% a stu%y in +levelan% Chio an% claime% that there was an association between mycoto1ins *rom Stachybotrys spores an% pulmonary hemorrhage in in*ants. 6owever in &''', base% on internal an% e1ternal reviews o* their %ata, the +2+ conclu%e% that because o* *laws in their metho%s the association was not proven. Stachybotrys spores in animal stu%ies have been shown to cause lung hemorrhaging but only at very high concentrations. \&7]Cne stu%y by the +enter o* ;ntegrative To1icology at $ichigan Atate Lniversity investigate% the causes o* 2amp 3uil%ing :elate% ;llness (23:;". They *oun% that Stachybotrys is possibly an important contributing *actor to 23:;. Ao *ar animal mo%els in%icate that airway e1posure to S" chartarum can evoke allergic sensiti.ation, in*lammation, an% cytoto1icity in the upper an% lower respiratory tracts. Trichothecene to1icity appears to be an un%erlying cause o* many these a%verse e**ects. :ecent *in%ings in%icate that lower %oses (stu%ies usually involve high %oses" can cause these symptoms.\&5]Aome to1icologists have use% the +oncentration o* >o To1icological +oncern (+o>T+" measure to represent the airborne concentration o* mycoto1ins that are e1pecte% to cause no ha.ar% to humans (e1pose% continuously throughout a 7'yr li*etime". The resulting %ata o* several stu%ies have thus *ar %emonstrate% that common e1posures to airborne mycoto1ins in the built in%oor environment are below the +o>T+, however agricultural environments have potential to pro%uce levels greater than the +o>T+.\& ]

Human health e**ects

$ycoto1icoses is the term use% *or poisoning associate% with e1posures to mycoto1ins. The symptoms o* a mycoto1icosis %epen% on the type o* mycoto1in^ the concentration an% length o* e1posure^ as well as age, health, an% se1 o* the e1pose% in%ivi%ual. \7] The synergistic e**ects
41

associate% with several other *actors such as genetics, %iet, an% interactions with other to1ics have been poorly stu%ie%. There*ore it is possible that vitamin %e*iciency, caloric %eprivation, alcohol abuse, an% in*ectious %isease status can all have compoun%e% e**ects with mycoto1ins. \7] ;n turn, mycoto1ins have the potential *or both acute an% chronic health e**ects via ingestion, skin contact, an% inhalation. These to1ins can enter the bloo% stream an% lymphatic system, they inhibit protein synthesis, %amage macrophage systems, inhibit particle clearance o* the lung, an% increase sensitivity to bacterial en%oto1in. \&(]>otably Aevere +ases o* A*lato1in ;ngestionT ;n &''- in 5enya 1&5 people %ie% an% nearly &'' others were treate% a*ter eating a*lato1in contaminate% mai.e.\&!] The %eaths were mainly associate% with homegrown mai.e that ha% not been treate% with *ungici%es or properly %rie% be*ore storage. 2ue to *oo% shortages at the time, *armers may have been harvesting mai.e earlier than normal to prevent the*ts *rom their *iel%s, so that the grain ha% not *ully mature% an% was more susceptible to in*ection.

[edit] )n "et *ood

There have been outbreaks o* pet *oo% containing mycoto1ins in >orth America.\/']

[edit] )n *iction
A *ictional use o* a mycoto1in occurs in =illiam )ibson8s seminal novel Neuromancer" A [:ussian war4time mycoto1in[ is a%ministere% to +ase, the novel8s protagonist

$ist of deadly f"ngi

,rom =ikipe%ia, the *ree encyclope%ia

0ump toT navigation, search Although many people have a *ear o* mushroom poisoning by [toa%stools[, only a small number o* the many macroscopic *ruiting bo%ies commonly known as mushrooms an% toa%stools have proven *atal to humans.

42

2ea%ly ,ungi

43

,ungi with signi*icant risk o* %eath i* consume% Common 2cientific name Acti!e Agent (oxicity name

)abitat

2imilar edible ,ict"re species

abrupt4 $manita abrupta bulbe% ?eck 7epi%ella

non4protein amino aci%s

liver

$i1e% woo%lan%s, eastern >orth America an% eastern Asia

$manita arocheae

7atin American Tulloss, Cvrebo l %eath cap 6alling

amato1ins

liver

=oo%lan% (oak" $e1ico

$manita bisporigera
). ,. Atk.

Eastern >orth American %estroying angel

amato1ins

liver

=oo%lan% (pine an% $garicus oak" silvicola, Eastern !olvariella >orth volvacea America

$manita e,itialis )uang.hou Ohu 7. Rang l T.6. %estroying 7i angel

amato1ins\1]\&] liver

2eci%uous woo%lan% )uang%ong province, +hina^ ;n%ia >orth America, )uatemala

$manita magnivelaris
?eck

)reat *elt skirt amato1ins\/] %estroying angel

liver

44

=estern >orth American $manita ocreata %estroying amato1ins ?eck angel (also known as $e%usoi% $ycelulem"

liver

=oo%lan% (oak" ?aci*ic >orthwest >orth America =oo%lan% (various" !olvariella Europe, volvacea, >orth (ussula A*rica, virescens >orth $manita lanei America, Tricholoma Australia e2uestre (AE", >ew Oealan%

$manita phalloides
(Haill. e1 ,r." 7ink

%eath cap

amato1ins an% liver phalloto1ins

$manita smithiana
3as

unknown

ki%ney

=oo%lan% 0apan an% ?aci*ic >orthwest

$manita sub6un2uillea
A. ;mai

East Asian amato1ins %eath cap

liver

=oo%lan% East an% Aoutheast Asia, 0apan, ;n%ia

$manita

(3ull.T ,r." 7am.

verna *ools mushroom

amato1ins

liver

$garicus arvensis =oo%lan% $garicus (various" campestris Europe -ycoperdon spp.

45

$manita
(,r." 3ertillon

European virosa %estroying angel

amato1ins

liver

$garicus arvensis =oo%lan% $garicus (various" campestris Europe -ycoperdon spp. grasslan% Europe, >orth America grasslan% Europe, >orth America

*litocybe dealbata
(Aowerby" )illet

ivory *unnel muscarine

+>A

&arasmius oreades

*litocybe rivulosa
(?ers." ?. 5umm.

*alse muscarine champignon

+>A

&arasmius oreades

*onocybe
(,ries" 5Qhner

filaris

amato1ins

liver

grasslan%, lawns 'silocybe spp. >orth America

*ortinarius gentilis
(,r." ,r.

orellanine

ki%ney

*ortinarius orellanus
,ries

,ool8s webcap

orellanine

ki%ney

+oni*erous woo%lan% >orthern Europe +oni*erous woo%lan% >orthern Europe

*ortinarius rubellus
+ooke

%ea%ly webcap

orellanine

ki%ney

*ortinarius splendens
:ob. 6enry

splen%i% webcap, orellanine yellow clubbe% *oot

ki%ney

46

1alerina marginata
(3atsch" 5Qhner

autumn skullcap

amato1ins

liver

)uehneromyces mutabilis

1alerina sulciceps
(3atsch" 5Qhner

amato1ins

liver

;n%onesia

1yromitra esculenta
(?ers. e1 ?ers." ,r.

*alse morel

$$6

liver

+oni*erous woo%lan% &orchella spp. >orthern latitu%es

5nocybe erubescens
A. 3lytt

re%4staining inocybe muscarine (prev. 5" patouillardii"

+>A

*alocybe 2eci%uous gambosa, woo%lan% $garicus spp., (beech" *ortinarius Europe caperatus\-] +oni*erous woo%lan% Europe +oni*erous woo%lan% Europe +oni*erous woo%lan% Europe +oni*erous woo%lan% >orth America

-epiota %ea%ly brunneoincarnata %apperling

+ho%at l +. $artpn

amato1ins

liver

-epiota helveola
3res.

amato1ins

liver

-epiota castanea chestnut Eu<l %apperling

amato1ins

liver

-epiota 6osserandi -epiota ,anthophylla

?.2. Crton

%ea%ly parasol

amato1ins

liver

47

'odostroma cornu/damae
(?atouillar%" l ;.awa 6ongo

mycoto1ins

0apan

,ungi where isolate% %eaths have been reporte% Common 2cientific name Acti!e Agent (oxicity name

)abitat

2imilar edible ,ict"re species

%oletus pulcherrimus
,r.

$uscarine

=oo%lan% severe =estern %oletus spp. gastrointestinal >orth America

Entoloma sinuatum
(3ull." ?. 5umm.

unknown

2eci%uous woo%lan% severe >orth gastrointestinal America, Europe =oo%lan% severe =estern gastrointestinal >orth America

*litopilus prunulus *alocybe gambosa

0ypholoma fasciculare
(6u%s.T,r." ?. 5umm.

sul*ur tu*t

*asciculol

$rmillaria mellea 0ypholoma capnoides

-actarius torminosus
(Achae**." )ray

woolly milk4 unknown cap

=oo%lan% severe -actarius >orthern gastrointestinal deliciosus Europe cultivate% groun%, lawns >orth America

-epiota subincarnata
0.E. 7ange

%ea%ly parasol

amato1ins\5]

liver

'a,illus involutus brown (3atsch e1 ,r." ,r. rim

roll4

unknown

autoimmune, haemolysis

grasslan% Europe

48

(ussula subnigricans
6ongo

Tricholoma e2uestre
(7." ?. 5umm.

cycloprop4&4 0apan, ene +hina an% rhab%omyolysis carbo1ylic >orth aci% America cycloprop4&4 yellow ene woo%lan% knight, man4 rhab%omyolysis carbo1ylic Europe on4horseback aci%

&nternal transcribed spacer

,rom =ikipe%ia, the *ree encyclope%ia

0ump toT navigation, search &(2 (*or internal transcribe% spacer" re*ers to a piece o* non4*unctional :>A situate% between structural ribosomal :>As (r:>A" on a common precursor transcript. :ea% *rom 58 to /8, this polycistronic r:>A precursor transcript contains the 58 e1ternal transcribe% seFuence (58 ETA", 1 A r:>A, ;TA1, 5. A r:>A, ;TA&, & A r:>A an% *inally the /8ETA. 2uring r:>A maturation, ETA an% ;TA pieces are e1cise% an% as non f"nctional mat"ration by prod"cts rapi%ly %egra%e%. )enes enco%ing ribosomal :>A an% spacers occur in tan%em repeats that are thousan%s o* copies long, each separate% by regions o* non4transcribe% 2>A terme% intergenic spacer (;)A" or non/transcribed spacer (>TA". AeFuence comparison o* the ;TA region is wi%ely use% in ta1onomy an% molecular phylogeny because it a" is (%ue to the high copy number o* r:>A genes" easy to ampli*y even *rom small Fuantities o* 2>A, an% b" has a high %egree o* variation even between closely relate% species. This can be e1plaine% by the relatively low evolutionary pressure acting on such non4*unctional seFuences\citation needed]. ,or e1ample, ;TA has proven especially use*ul *or eluci%ating relationships among congeneric species an% closely relate% genera in Asteraceae \1](3al%win, 1!!&^ 3al%win et al., 1!!5^ 5im et al., 1!!(" as well as clinically important yeast species.\&] The ;TA region is now perhaps the most wi%ely seFuence% 2>A region in *ungi. \citation needed] ;t has typically been most use*ul *or molecular systematics at the species level, an% even within species (e.g., to i%enti*y geographic races". 3ecause o* its higher %egree o* variation than other genic regions o* r2>A (*or small4 an% large4subunit r:>A", variation among in%ivi%ual r2>A repeats can sometimes be observe% within both the ;TA an% ;)A regions. ;n a%%ition to the stan%ar% ;TA1q;TA- primers use% by most labs, several ta1on4speci*ic primers have been %escribe% that allow selective ampli*ication o* *ungal seFuences (e.g., see )ar%es l 3runs
49

1!!/ paper %escribing ampli*ication o* basi%iomycete ;TA seFuences *rom mycorrhi.a samples".\/] ;TA region is nowa%ays being use% to know the genetic %iversity among %i**erent strains o* bacteria by seFuencing the ;TA gene.\citation needed].

D*A barcoding
D*A barcoding is a ta1onomic metho% that uses a short genetic marker in an organism8s 2>A to i%enti*y it as belonging to a particular species. ;t %i**ers *rom molecular phylogeny in that the main goal is not to %etermine classi*ication but to i%enti*y an unknown sample in terms o* a known classi*ication.\1] Although barco%es are sometimes use% in an e**ort to i%enti*y unknown species or assess whether species shoul% be combine% or separate%,\&] the utility o* 2>A barco%ing *or these purposes is subKect to %ebate.\/] Applications inclu%e, *or e1ample, i%enti*ying plant leaves even when *lowers or *ruit are not available, i%enti*ying insect larvae (which typically have *ewer %iagnostic characters than a%ults", i%enti*ying the %iet o* an animal base% on stomach contents or *aeces, \-] an% i%enti*ying pro%ucts in commerce (*or e1ample, herbal supplements or woo%".\1]

50

Contents
'hi"e(

1 Choice of =ocus o 1K1 Mitochon"rial E-!

o

1K& I"entifying flowering *lants

& ?ouchere" s*eci#ens + 7rigin 2 Case stu"ies

o o o o

2K1 I"entification of bir"s 2K& Eeli#iting cry*tic s*ecies 2K+ Cataloguing ancient life 2K2 The Moorea Bioco"e Pro$ect

5 Criticis#s 6 E-! Barco"ing Software 6 See also % 4eferences 9 )Lternal lin0s

Choice o* Locus
A %esirable locus *or 2>A barco%ing shoul% be stan%ar%i.e% (so that large %atabases o* seFuences *or that locus can be %evelope%", \5] present in most o* the ta1a o* interest an% seFuencable without species4speci*ic ?+: primers,\5] short enough to be easily seFuence% with current technology,\(] an% provi%e a large variation between species yet a relatively small amount o* variation within a species.\7] Although several loci have been suggeste%, a common set o* choices areT

1or ani#als an" #any other eu0aryotes the #itochron"rial C71 gene 1or lan" *lants the concatenation of the rbc= an" #at; chloro*last genes'5(

%itochondrial D*A
2>A barco%ing is base% on a relatively simple concept. $ost eukaryote cells contain mitochon%ria, an% mitochon%rial 2>A (mt2>A" has a relatively *ast mutation rate, which results in signi*icant variation in mt2>A seFuences between species an%, in principle, a comparatively small variance within species. A (- 4bp region o* the mitochon%rial cytochrome c o1i%ase subunit ; (+C;" gene was propose% as a potential 8barco%e8.
51

6owever, because all mt2>A genes are maternally inherite% (%irect evi%ence *or recombination in mt2>A is available in some bivalves such as &ytilus\ ] but it is suspecte% that it may be more wi%esprea%\!]", any occurrences o* hybri%i.ation,\1'] male4killing microoroganisms,\11] cytoplasmic incompatibility4in%ucing symbionts (e.g., 7olbachia\11]", hori.ontal gene trans*er (such as via cellular symbionts\1&]", or other [reticulate[ evolutionary phenomena in a lineage can lea% to mislea%ing results (i.e., it is possible *or two %i**erent species to share mt2>A,\1/] or *or one species to have more than one mt2>A seFuence e1hibite% among %i**erent in%ivi%uals".\1-]\15] As o* &''!, %atabases o* +C1 seFuences inclu%e% at least (&',''' specimens *rom over 5 ,''' species o* animals, larger than %atabases available *or any other gene.\1(]

&dentifying flowering plants

5ress et al" (&''5\1]" suggest that the use o* the +C; seFuence mis not appropriate *or most species o* plants because o* a much slower rate o* cytochrome c o1i%ase ; gene evolution in higher plants than in animalsn. A series o* e1periments was then con%ucte% to *in% a more suitable region o* the genome *or use in the 2>A barco%ing o* *lowering plants (or the larger group o* lan% plants".\(] Cne &''5 proposal was the nuclear internal transcribe% spacer region an% the plasti% trn64psbA intergenic spacer^ \1] other researchers a%vocate% other regions such as mat5.\(] ;n &''!, a collaboration o* a large group o* plant 2>A barco%e researchers propose% two chloroplast genes, rbc7 an% mat5, taken together, as a barco%e *or plants.\5] 0esse Ausubel, a 2>A barco%e researcher not involve% in that e**ort, suggeste% that stan%ar%i.ing on a seFuence was the best way to pro%uce a large %atabase o* plant seFuences, an% that time woul% tell whether this choice woul% be su**iciently goo% at %istinguishing %i**erent plant species.\1(]

+ouchered s"ecimens
2>A seFuence %atabases like )en3ank contain many seFuences that are not tie% to vouchere% specimens (*or e1ample, herbarium specimens, culture% cell lines, or sometimes images". This is problematic in the *ace o* ta1onomic issues such as whether several species shoul% be split or combine%, or whether past i%enti*ications were soun%. There*ore, best practice *or 2>A barco%ing is to seFuence vouchere% specimens.\17]\1 ]

,rigin
The use o* nucleoti%e seFuence variations to investigate evolutionary relationships is not a new concept. +arl =oese use% seFuence %i**erences in ribosomal :>A (r:>A" to %iscover archaea, which in turn le% to the re%rawing o* the evolutionary tree, an% molecular markers (e.g., allo.ymes, r2>A, an% mt2>Avage " have been success*ully use% in molecular systematics *or %eca%es. 2>A barco%ing provi%es a stan%ar%ise% metho% *or this process via the use o* a short 2>A seFuence *rom a particular region o* the genome to provi%e a 8barco%e8 *or i%enti*ying species. ;n &''/, ?aul 2.>. 6ebert *rom the Lniversity o* )uelph, Cntario, +ana%a, propose% the compilation o* a public library o* 2>A barco%es that woul% be linke% to name% specimens. This library woul% mprovi%e a new master key *or i%enti*ying species, one whose power will rise with increase% ta1on coverage an% with *aster, cheaper seFuencingn.

52

Case studies

&dentification of birds
;n an e**ort to *in% a correspon%ence between tra%itional species boun%aries establishe% by ta1onomy an% those in*erre% by 2>A barco%ing, 6ebert an% co4workers seFuence% 2>A barco%es o* &(' o* the ((7 bir% species that bree% in >orth America (6ebert et al" &''-a\1!]". They *oun% that every single one o* the &(' species ha% a %i**erent +C; seFuence. 1/' species were represente% by two or more specimens^ in all o* these species, +C; seFuences were either i%entical or were most similar to seFuences o* the same species. +C; variations between species average% 7.!/_, whereas variation within species average% '.-/_. ;n *our cases there were %eep intraspeci*ic %ivergences, in%icating possible new species. Three out o* these *our polytypic species are alrea%y split into two by some ta1onomists. 6ebert et al"8s (&''-a\1!]" results rein*orce these views an% strengthen the case *or 2>A barco%ing. 6ebert et al" also propose% a stan%ar% seFuence threshol% to %e*ine new species, this threshol%, the so4calle% [barco%ing gap[, was %e*ine% as 1' times the mean intraspeci*ic variation *or the group un%er stu%y.

Delimiting cryptic species

The ne1t maKor stu%y into the e**icacy o* 2>A barco%ing was *ocuse% on the neotropical skipper butter*ly, $straptes fulgerator at the Area +onservacion %e )uanacaste (A+)" in north4western +osta :ica. This species was alrea%y known as a cryptic species comple1, %ue to subtle morphological %i**erences, as well as an unusually large variety o* caterpillar *oo% plants. 6owever, several years woul% have been reFuire% *or ta1onomists to completely %elimit species. 6ebert et al" (&''-b\&']" seFuence% the +C; gene o* - - specimens *rom the A+). This sample inclu%e% mat least &' in%ivi%uals reare% *rom each species o* *oo% plant, e1tremes an% interme%iates o* a%ult an% caterpillar color variation, an% representativesn *rom the three maKor ecosystems where $straptes fulgerator is *oun%. 6ebert et al" (&''-b\&']" conclu%e% that $straptes fulgerator consists o* 1' %i**erent species in north4western +osta :ica. These results, however, were subseFuently challenge% by 3rower (&''(\&1]", who pointe% out numerous serious *laws in the analysis, an% conclu%e% that the original %ata coul% support no more than the possibility o* three to seven cryptic ta1a rather than ten cryptic species. This highlights that the results o* 2>A barco%ing analyses can be %epen%ent upon the choice o* analytical metho%s use% by the investigators, so the process o* %elimiting cryptic species using 2>A barco%es can be as subKective as any other *orm o* ta1onomy. A more recent e1ample use% 2>A barco%ing *or the i%enti*ication o* cryptic species inclu%e% in the ongoing long4term %atabase o* tropical caterpillar li*e generate% by 2an 0an.en an% =innie 6allwachs in +osta :ica at the A+).\&&] ;n &''( Amith et al"\&/] e1amine% whether a +C; 2>A barco%e coul% *unction as a tool *or i%enti*ication an% %iscovery *or the &' morphospecies o* %elvosia \/] parasitoi% *lies (Tachini%ae" that have been reare% *rom caterpillars in A+). 3arco%ing not only %iscriminate% among all 17 highly host4speci*ic morphospecies o* A+) %elvosia, but it also suggeste% that the species count coul% be as high as /& by in%icating that each o* the three generalist species might actually be arrays o* highly host4speci*ic cryptic species.

53

;n &''7 Amith et al" e1pan%e% on these results by barco%ing &,1/- *lies belonging to what appeare% to be the 1( most generalist o* the A+) tachini% morphospecies. \&-] They encountere% 7/ mitochon%rial lineages separate% by an average o* -_ seFuence %ivergence an%, as these lineages are supporte% by collateral ecological in*ormation, an%, where teste%, by in%epen%ent nuclear markers (& A an% ;TA1", the authors there*ore viewe% these lineages as provisional species. Each o* the 1( initially apparent generalist species were categori.e% into one o* *our patternsT (i" a single generalist species, (ii" a pair o* morphologically cryptic generalist species, (iii" a comple1 o* specialist species plus a generalist, or (iv" a comple1 o* specialists with no remaining generalist. ;n sum, there remaine% ! generalist species classi*ie% among the 7/ mitochon%rial lineages analy.e%. 6owever, also in &''7, =hitworth et al" reporte% that *lies in the relate% *amily +alliphori%ae coul% not be %iscriminate% by barco%ing.\1-] They investigate% the per*ormance o* barco%ing in the *ly genus 'rotocalliphora, known to be in*ecte% with the en%osymbiotic bacteria 7olbachia. Assignment o* unknown in%ivi%uals to species was impossible *or ('_ o* the species, an% i* the techniFue ha% been applie%, as in the previous stu%y, to i%enti*y new species, it woul% have un%erestimate% the species number in the genus by 75_. They attribute% the *ailure o* barco%ing to the non4monophyly o* many o* the species at the mitochon%rial level^ in one case, in%ivi%uals *rom *our %i**erent species ha% i%entical barco%es. The authors went on to stateT
The *attern of ?ol,achia infection strongly suggests that the lac0 of within. s*ecies #ono*hyly results fro# introgressi/e hybri"i5ation associate" with ?ol,achia infectionK 3i/en that ?ol,achia is 0nown to infect between 15 an" 65Y of insect s*ecies we conclu"e that i"entification at the s*ecies le/el base" on #itochon"rial seUuence #ight not be *ossible for #any insectsK '12(

$arine biologists have also consi%ere% the value o* the techniFue in i%enti*ying cryptic an% polymorphic species an% have suggeste% that the techniFue may be help*ul when associations with voucher specimens are maintaine%,\17] though cases o* [share% barco%es[ (e.g., non4 uniFue" have been %ocumente% in cichli% *ishes an% cowries\15]

Catalog"ing ancient life

7ambert et al" (&''5\&5]" e1amine% the possibility o* using 2>A barco%ing to assess the past %iversity o* the Earth8s biota. The +C; gene o* a group o* e1tinct ratite bir%s, the moa, were seFuence% using &( sub*ossil moa bones. As with 6ebert8s results, each species seFuence% ha% a uniFue barco%e an% intraspeci*ic +C; seFuence variance range% *rom ' to 1.&-_. To %etermine new species, a stan%ar% seFuence threshol% o* &.7_ +C; seFuence %i**erence was set. This value is 1' times the average intraspecies %i**erence o* >orth American bir%s, which is inconsistent with 6ebert8s recommen%ation that the threshol% value be base% on the group un%er stu%y. Lsing this value, the group %etecte% si1 moa species. ;n a%%ition, a *urther stan%ar% seFuence threshol% o* 1.&-_ was also use%. This value resulte% in 1' moa species which correspon%e% with the previously known species with one e1ception. This e1ception suggeste% a possible comple1 o* species which was previously uni%enti*ie%. )iven the slow rate o* growth an% repro%uction o* moa, it is probable that the interspecies variation is rather low. Cn the other han%, there is no set value o* molecular %i**erence at which populations can be assume% to have irrevocably starte% to un%ergo speciation. ;t is sa*e to say, however, that the &.7_ +C; seFuence %i**erence initially use% was *ar too high.
54

(he %oorea Biocode ,ro:ect

The 3ioco%e ?roKect is a barco%ing initiative to create the *irst comprehensive inventory o* all non4microbial li*e in a comple1 tropical ecosystem, the islan% o* $oorea in Tahiti. Aupporte% by a grant *rom the )or%on an% 3etty $oore ,oun%ation, the $oorea 3ioco%e ?roKect is a /4 year proKect that brings together researchers *rom the Amithsonian ;nstitution, L+ 3erkeley, ,ranceis >ational +enter *or Acienti*ic :esearch (+>:A", an% other partners. The outcome o* the proKect is a library o* genetic markers an% physical i%enti*iers *or every species o* plant, animal an% *ungi on the islan% that will be provi%e% as a publicly available %atabase resource *or ecologists an% evolutionary biologists aroun% the worl%. The so*tware back4en% to the $oore 3ioco%e ?roKect is )eneious ?ro an% two custom4 %evelope% plugins *rom the >ew Oealan%4base% company, 3iomatters. The 3ioco%e 7;$A an% )enbank Aubmission plugins have been ma%e *reely available to the public \&(] an% users o* the *ree )eneious 3asic so*tware will be able to access an% view the 3ioco%e %atabase upon completion o* the proKect, while a commercial copy o* )eneious ?ro is reFuire% *or researchers involve% int %ata creation an% analysis.

Criticisms
2>A barco%ing has met with spirite% reaction *rom scientists, especially systematists, ranging *rom enthusiastic en%orsement to voci*erous opposition.\&7] ,or e1ample, many stress the *act that 2>A barco%ing %oes not provi%e reliable in*ormation above the species level, while others in%icate that it is inapplicable at the species level, but may still have merit *or higher4level groups.\1-] Cthers resent what they see as a gross oversimpli*ication o* the science o* ta1onomy. An%, more practically, some suggest that recently %iverge% species might not be %istinguishable on the basis o* their +C; seFuences. \& ] 2ue to various phenomena, ,unk l Cmlan% (&''/\&!]" *oun% that some &/_ o* animal species are polyphyletic i* their mt2>A %ata are accurate, in%icating that using an mt2>A barco%e to assign a species name to an animal will be ambiguous or erroneous some &/_ o* the time (see also $eyer l ?aulay, &''5 \/']". Atu%ies with insects suggest an eFual or even greater error rate, %ue to the *reFuent lack o* correlation between the mitochon%rial genome an% the nuclear genome or the lack o* a barco%ing gap (e.g., 6urst an% 0iggins, &''5,\1&] =hitworth et al", &''7,\1-] =iemers l ,ie%ler, &''7\/1]". ?roblems with mt2>A arising *rom male4killing microoroganisms an% cytoplasmic incompatibility4in%ucing symbionts (e.g., 7olbachia"\11] are also particularly common among insects. )iven that insects represent over 75_ o* all known organisms, \/&] this suggests that while mt2>A barco%ing may work *or vertebrates, it may not be e**ective *or the maKority o* known organisms. $orit. an% +icero (&''-\//]" have Fuestione% the e**icacy o* 2>A barco%ing by suggesting that other avian %ata is inconsistent with 6ebert et al"8s interpretation, namely, 0ohnson an% +icero8s (&''-\/-]" *in%ing that 7-_ o* sister species comparisons *all below the &.7_ threshol% suggeste% by 6ebert et al" These criticisms are somewhat mislea%ing consi%ering that, o* the /! species comparisons reporte% by 0ohnson an% +icero, only actually use +C; %ata to arrive at their conclusions. 0ohnson an% +icero (&''-\/-]" have also claime% to have %etecte% bir% species with i%entical 2>A barco%es, however, these 8barco%es8 re*er to an unpublishe% 7&/4bp seFuence o* >2( which has never been suggeste% as a likely can%i%ate *or 2>A barco%ing. The 2>A barco%ing %ebate resembles the phenetics %ebate o* %eca%es gone by. ;t remains to be seen whether what is now toute% as a revolution in ta1onomy will eventually go the same
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