c Department of Ecology, University of Ka University of ofEcology, c Department b SchoolofBiological Sciences,Univer Natu Life Sciences, of a Department Yi Mei Wang Shen Pablo Quintela-Alonso Nikolaeva Ma Honggang Lin Gao Day This article isprotected Allrights bycopyright. reserved. doi: 10.1111/jeu.12391-4831 thisversionandthe between lead todifferences been through the copyediting, typesetting, and proofreading which may pagination process, forpublicati accepted This articlehasbeen Mansergh Carr Alan Warren Ciliated Protists Ciliophora) (Alveolata, in Biodiversity of Documentation and Description tothe AGuide “Code”: the Beyond etal.--- Warren Article type : Original Article 21-Dec-2016 : Date Accepted :27-Oct-2016 Date Revised :22-Apr-2016 Date Received

Acceptedp Article , Rebecca Zufall , Rebecca p k e , Diana Lipscomb , Diana h , Erna Aescht , Erna ff Gong , Jun , John G.Day , John , XinluShi w z k , Geoffrey Odhiambo Ong’ondo Odhiambo , Geoffrey , Mercedes Martín-Cereceda , Mercedes , ThomasWeisse a , David J. Patterson , DavidJ. k , Miroslav Macek , Miroslav

l Beyond the “Code” Beyond the , RenuGupta gg f , Weibo Song , Weibo , Saleh A.Al-Farraj , Saleh i , Marc Dellinger , Marc kk , Sabine Agatha q x Lobban, ChristopherS. , Johana Rotterová , Johana hh m , Krzysztof Wiackowski , Xiaozhong Hu k u , ThorstenStoeck b , Jacqueline Mackenzie-Dodds , Jacqueline , MicahDunthorn

j ral History Museum, London 5BD,UK ral History Museum, SW7 , Hamed A. El-Serehy , Hamed ll

g , SalehAl-Quraishy x sity of Sydney, Sydney NSW 2004, Australia 2004,Australia sity Sydney,NSW of Sydney , NettieMcMiller cc on and undergone full peer review buthasnot review undergone fullpeer on and iserslautern, Kaiserslautern 67663, Germany Germany 67663, Kaiserslautern iserslautern, aa , Luciana Santoferrara , Luciana , Blanca Pérez-Uz k r , PierangeloLuporini , Komal Kamra, Komal Version of Record. PleaseVersion cite thisarticle as c , Antonietta La, Antonietta Terza c , John C. Clamp , John ii , Lei Wu d g , David J. S. Montagnes, DavidJ. g , Yangbo Fan , Yangbo , Khaled Al-Rasheid , Khaled x n , Jasmine Purushothaman , Jasmine , Gaytha Langlois , Gaytha p a , KuidongXu , Seema Makhija , Seema dd , Chen Shao , Chen s d , Denis H. Lynn H. , Denis , Undine E.M.Achilles- s k , Adriana , Adriana Vallesi , Feng Gao jj , Zhenzhen , Zhenzhen ee g , Zhuo , Martin o v , Xiaofeng , Xiaofeng y I., Robert , Svetlana k t , Shan , bb s , , This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted Biology, Univer Integrative t Departmentof Italy (MC), Me Veterinary s SchoolofBiosciences and Univer r DivisionofNaturalSciences, 20052, USA Biological q Departmentof 510631,China SouthChinaNormalUniversity,Life Guangzhou p Schoolof Science, & o DepartmentofScience India 110007, n SGTBUniversity Delhi,Delhi KhalsaCollege, of Indiam Maitreyi 110021, Delhi Delhi,New College, of University China Institutel Yantai ofCoasta University China,Qingdao of 266003,China ArticleLaboratoryk Protozoology,Institute of of j MuséumNationald’Histoire i Scottish Association forMarine Science, 1QA,UK Oban PA37 UK Biological h Departmentof Zoology, Kingg ofSaud Department Upper Au Centerofthe f Biology UK 5BB, BH12 E and Life of e Department Durham, NC27707,USA Biomedical Biological and d Departmentof l Zone ChineseAcad Research, Sciences, George Washington University, Washington, University, DC Washington George Sciences, nvironmental Sciences, Bournem nvironmental Sciences, Technology, Bryant Universi Sciences, University of Huddersfield, Huddersfield HD13DH, Huddersfield of Huddersfield, University Sciences, Naturelle, Paris 75005, France 75005,France Naturelle,Paris strian Museum, Linz, A-4040,Austria strian Museum, University, Riyadh University, 11451,SaudiArabia sity of Guam, Mangilao, GU 96923, USA Mangilao, 96923, sity Guam, GU of EvolutionandBiodiversity, Marine Ocean dicine, University of sity of Guelph, Guelph, ON, N1G 2W1, Canada Canada 2W1, Guelph,ON,N1G of sity Sciences, NorthCarolina University, Central ty, SmithfieldRI USA 02917,

emy of Sciences, Yantai264003, Sciences, emy of outh University, Bournemouthouth University, Camerino, 62032, Camerino Camerino, kk China 266071, Institute Sciences,Qingdao of jj ChineseAcademy ofOceanology, This article is protected by copyright. All rights reserved. copyright. This articleis protectedby 5001, USA Instituteii ofEnvironmental Sciences, InstituteLimnology,Univ for hh Research 310036, China gg andEnvi Life College of 510632,China University, Guangzhou ofHydrobiology, Colle Center ff Research 710049, China ee Key Laboratory of Biomedical Information En Sc dd DepartmentofMarine Univer Zoology, Charles of cc Department bb Protozoology Zoological Section, Survey Sciences Biological of aa Department RussianFederation Federal University, /Kazan Kazan, ICZN Secretariat) Scie DepartmentofEarth z United Kingdom yInstitute of Integrative Biology, Univ Madrid, Madrid28040,Spain Departamento deMicrobiolog x Institutew ofMarine Sciences, University Portsmouth,Portsmouth of PO4 9LY,UK College, Dev Univer Narendra v Acharya Mexico Edo.México, México, Limnologyu Tropical FES Project, Research

AcceptedDepartment of Biology and Article nces, Natural History Museum, London Museum, (formerly 5BD, History SW7 UK nces, Natural ronmental Sciences, Hangzhou Normal University, Hangzhou NormalUniversity, Hangzhou Hangzhou ronmental Sciences, iences, University of Connecticut, GrotonCT06340,USA iences, University of Biochemistry, University of Houston, Houston TX77006- Houston,Houston Biochemistry, of University ía III, Facultad de Biología,III, Facultadde ía , Egerton University, Egerton 20115, Kenya Kenya 20115, Egerton , EgertonUniversity,

Jagiellonian University, Kraków 30-387, Poland, University, 30-387, Jagiellonian Kraków ersity Liverpool ofLiverpool, L69 7ZB sity of Delhi, New Delhi 110019, India NewDelhi110019, sity Delhi, of ersity of Innsbruck, Austria Mondsee5310, of ersity ge of Life Science and Technology, Jinan Jinan andTechnology, Science geLife of sity in Prague, Prague 12744, Czech Republic inPrague,sity Prague 12744,Czech of India, Newalipore, Kolkata -700053, India -700053, Kolkata India, Newalipore, of Iztacala, Universidad National Autonomade National Iztacala, Universidad gineering, Xi’an Jiaotong University, Xi’an University, Xi’an Xi’anJiaotong gineering,

Universidad Complutense de Universidad Complutense This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted identifications andprom andmetada related data IRCN-BC proposestopopulate knowledgestrengthening thatsupports base the BiodiversityCoordination Network ofCilia for GrandChalle ways six explored toimplement of observation anddocumentation presents specific ciliates and taxonomy of information aboutbiodiversity of gaps andinconsistencie large complicated by pursuing a integrative more approach toinvestig Articlebiology including oforganisms, ciliate have technology inmolecular Recent advances ABSTRACT 79425149; Telephone number:+44(0)20 5BD, UK Life Natural Sciences, Dept. A. Warren, Correspondence ll DepartmentofEcol ogy andEvolution,Universityof ogy ta to create a resource thatw a resource ta tocreate ote sharing ofdata. ote sharing The Ciliate Guide ciliates. The present paperre ciliates. Thepresent their biodiversity. Thiseffo s, and created unprecedented opportunities for opportunities unprecedented created s, and History Museum, Cromwell Road, LondonMuseum, Cromwell Road, History SW7 e-mail: [email protected] e-mail:[email protected] recommendations forbe

s that stillexist inthefoundation ofbasic s that nges proposed by the International Research International the proposedby nges tes (IRCN-BC).tes commitment ofits to Aspart research on biodiversity of ciliates, the onbiodiversity of research revolutionized research on all aspectsofthe researchon revolutionized ation of biodiversity. However, this goal ofbiodiversity. is this However, ation , an online database, withbiodiversity- , anonlinedatabase, ill facilitateaccu Salzburg, A-5020 Salzburg, Austria Austria A-5020Salzburg, Salzburg,

rt stems from aworkshopthat rt stemsfrom views issues relating tothe views issues st practice inthe st practice rate taxonomic rate taxonomic This article is protected by copyright. All rights reserved. copyright. This articleis protectedby et al.2016). Simpson2009; Lynn Santoferrara and ciliates, despiterecentre of thesemethodsto application standards for noformal are there but decades, several last the over introduced genes havebeen sequencing descriptions orredescripti stubs) onSEM specimens (e.g., 20 convention fordepositing size meanttherewasno inve DNA for source of apotential and represent of collections provideawealth buthasformedthe names not only hasfixed time and Art.75.3.7)has,over (ICZN 1999,Art.16.4.2 Inprotists. rule the particular, described species.are These deliberatelygeneral andsuited more tothe studyanimals of than establis also it but issues, nomenclatural to thelevelof up taxa rules fornaming Zoolog Codeof International governed the by a ofciliates THE nomenclature taxonomy; systematics; specimens type phylogenetics; Cultivation; information resources; molecu Keywords

Acceptedth Article century, when deposition of permanently st ofpermanently century, whendeposition For ciliatesand many protists,the logistical other difficulties imposed by small their commendations (Aescht 2001, 2008; Foissner 2002; ICZN 2001, 2008; Foissner 2002; 1999; commendations (Aescht ons. In of ons. addition,newmethods to deposit type specimens in todeposittype specimens informationaboutthevariabilit nd other heterotrophic protists(sensuAdletal.2012)is nd otherheterotrophic began to be required as type material for taxonomic fortaxonomic astype material began toberequired family (ICZN 1999). The Code regulates regulates TheCode (ICZN 1999). family hes minimal standards for documenting newly newly documenting hes minimal standardsfor lar phylogeny; morphology; nomenclature; nomenclature; morphology; lar phylogeny; nucleus of large museum collections. These oflarge museumcollections. nucleus taxonomic identifications taxonomic ical Nomenclatureical (‘the ained preparations or other physical orother ained preparations stigations of molecular phylogenetics. stigations phylogenetics. ofmolecular type specimens untilthelatterpartof specimens type , generated a database , generated

visualizing morphology and permanently curated repositories repositories curated permanently y and biogeography ofspecies yand biogeography Code’) thatprovides Code’) ordescriptionsof ofmaterialthat This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedthat willfacilitate and encourage integrativ modern, and resour available methodologies thefirst ofspecies), and redescription three. Furthermore, the latterchallenges three all relate to are challenges The firstthree Articleciliate biodiversity: of Biodiversity ofCiliates (http://ircn-bc.org), (IRCN-BC),NS isjointly the fundedby which • • • • • •

culturing, and long-term storage of samples storage ofsamples culturing, andlong-term characterizati and molecular morphological including minimal standards that mustbe Establish a uniformprotocol fordescribing analyses molecular museum”) Establish arepository (“protist information aboutciliatesthatcansupportin Develop anda implement significant new para for ciliates and diversity Identify patternsofdiversity endemicity,andmechanisms identify dispersal and of rates Determine the biogeographical distributionsof lineages specific lifecycle strategi morphology, development, Understand speciation inciliates by investigating evolutionary rateschanges and in With this in mind, the present paper offers recommendations for using currently forusing this inmind,thepresentWith recommendations offers paper International ResearchCoordina In 2012the theoretical and are supportedby are and theoretical ces to generate afirmbase generate ces to step towards investigating biodiversity. investigating biodiversity. step towards of which six relatewhich six totheof documentation of F and NSFC,F identified20GrandChallenges and met for publication and provide guidance on guidance publication andprovide met for to store DNA and fixed cells for use in cellsfor to storeDNAandfixed ‟ or re-describing species or ciliates, of on, sampling protocols, analytical methods, on, sampling protocols,analytical hot spots”, both geographic and ecological, ecological, and bothgeographic hot spots”, es, and genetics underlying divergence of divergence genetics underlying es, and tegrative research on their biodiversity tegrative researchontheirbiodiversity e research intotheciliates. biodiversity of tion Network for Biodiversity of Ciliates Biodiversity of tion Networkfor digm for capturing and storing biological biological andstoring forcapturing digm speciesciliates, of test hypotheses of

α -taxonomy (i.e., thedescription (i.e., -taxonomy implementationofthelast of high-quality primary data primary data high-quality of This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedespeci ofthe world, of someunderstudiedareas et et al.2002,2003;Petz al. 1990,1993;Foissner ofpoor explorations this istheresultofrecent atan described ciliates arebeing (Finlaylivinget al.1996). ciliatespecies truediversity. oftheir only asmallfraction with free-livinginternally. ciliates,the As either commensals orparasites, mostly external surfaces onthe hostsbutsometimes oftheir Finlay(Agatha 2011; et al.1996,2004;Foissner 4,800 Of these,roughly (Lynn 2008). recognized et al.1987). lakes (Finlay i vents,polarsea hydrothermal 2002), deep-sea °C butalsoliveinhabita ofabout45 temperatures Article survival. They are fortheir sufficient water 2002; Dobell1932),they havebeen madeth (1632–1723) Leeuwenhoek Since Antonievan overview Historical DESCRIBING THEBIODIVERSITY OF CILIATES biodiversity ofciliates. that willsupportan of informationresources taxonomic recommendations for redescribi describing and (ICZN 1999)for contai The intentisto:1)supplementguidance Towards theendoflastmillennium, Approximately 8,000 free-living Approximately 8,000 average rate of ~50 per yearInal. 2008). per et part, (Foissner of~50 rate average and observational procedures, and observational discovered in almost every environment where there is wherethere almost every environment in discovered In the new millennium,speciesoffree-livingIn thenew ng species, 2) consolidate and update 2)consolidateandupdate species, ng number of knownsymbiotic speciesisprobablynumber common inalmostall common integrative approach to research into to research integrativeapproach ly known or extreme environments (Agathaet environments orextreme ly known oftheCode inthemostrecentversion ned ce (Petz etal.1995),a (Petz ce ally China and Korea, also has been a major has been amajor also Korea, China and ally there wasanestimated4,300describedfree- et al. 2008). Other ciliates are symbionts, ciliates aresymbionts, al.2008).Other et al. 1995), but a sharp increase in sampling insampling al.1995),butasharpincrease are free-living, butthetotalisdebated free-living, are ts asdiversedesert e first descriptions e firstdescriptions

and epibiotic species are are epibiotic species and

and bodies ofwaterbelow

3) promote the creation thecreation 3) promote nd East Africansoda nd East sands (Foissner et al. (Foissner sands of ciliates(Corliss This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted rationalize and combine application. their to above methodscontinue char andmolecular morphological, morphogenetic ofci and behavior ecophysiology, biogeography, vs.morphological. paths oftraining: molecular ciliates. However, contributed they also tothe heterogeneity by promoting separate ofdata our ability toaddre a leapin fueled decades developmentofP rapid data.The ‘layer’ of microscop application ofelectron 2007;Lynnclassification (Corliss1961;Jankowski 1950s, 2008).Beginning inthe Articleallowed better Lwoff Day 1940;Fauré-Fr and 1930;Coleand of methods providedrecognition In regarding taxa. disconnected information role increating data thisheterogeneity of impact ofglobal climatechange). integrative uses ofdata frominvestigations multicellular organisms (e.g., aconstitutes major impediment This vertebrates). todeveloping such descriptionsofciliatesis environm ofmorphological, body factor. The Over the last century, the stepwiseintr Over thelastcentury, α -taxonomy and stimulated major revi andstimulatedmajor -taxonomy beappliedtociliate fragmentary relative to that of comparable-sized groups of tothatofcomparable-sized relative fragmentary ciliary and patterns yorganelles and toinvestigate by adding chronological ‘layers’ of often ‘layers’ adding chronological by CR and gene sequencing during the past three thepast during CR andgene sequencing ss taxonomic andphylogen ss taxonomic of ciliates toaddress large-scaleissues (e.g., the 1920s–1950s, introductionofsilverstaining the 1920s–1950s, ental, and genetic information arising from arising andgeneticinformation ental, oduction of new methods has played a major new methodshasplayed oduction of emiet 1950;Klein1926);theseobservations taxonomy, there have been fewattemptsto havebeen taxonomy, there Finally, information has been gathered onthe gathered hasbeen information Finally, liates, which has been used tocomplement used whichhasbeen liates, acterization of taxa. Although oftaxa. acterization allofthe details ofnuclear sions ofciliate

ultrastructures added another added ultrastructures taxonomy and taxonomy etic questionsabout etic morphology (Chatton This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted incr same time,theexponential threatensprogress and specifically eukaryotes impediment’ (deCarvalho world. This‘taxonomic a declinein of evidence is, however,anecdotal genetics,morphology, develo ecology, population from multiple and complementary perspectives as such phylogeography, comparative The goal ofintegrative biodiversity has as been delimiting defined the unitsoflife’s diversity ciliates datarelatingtobiodiversity of Documenting andaccessing viable alternative. istheone mostwide the morphospeciesconcept method other difficult toseeany is it present, “at that concluded and niche”, ecological same the occupy tell, we can far as fitintoadefinedra collection offormsthatall ArticleFinlay other. thanany pragmatic probably more in nature,themor function oftheorganism 2014) Species Concept’(Seifert ‘Pragmatic the hasbeentermed that anapproach divergence, evolutionary of evidence or morphological, Meisterfeld 2003).Molecular, consistent with amended tobe evolutionary over as reversals irreversible evolutionary dive cilia constitutes aspeciesof As withother organisms, ithas been difficult The species concept applied tociliates te. Sonneborn (1957) suggeste te. Sonneborn(1957) rgence”. Although “irreversible” may no longer be appropriate beappropriate may nolonger “irreversible” Although rgence”. distance occur (Seifert 2014) (Seifert distanceoccur α ease in metagenomics and e inmetagenomics ease . Insofarmorpholog . asciliate -taxonomy by deleting “irreversible” (Schlegel and (Schlegel “irreversible” -taxonomy deleting by of differentiating andidentifying of differentiating phospecies concept is as valid as any, and any, isasvalid concept phospecies to settle onan acceptable ofwhat definition nge of morphological variation –formsthat,so of morphological variation nge in ciliate biodiversity and evolution. Atthe in ciliatebiodiversity andevolution. taxonomic expertise inmost countriesofthe expertise taxonomic et al. (1996) defined the morphospecies as “a themorphospecies al.(1996)defined et ly adopted in the absence of any pragmatic, pragmatic, any of adoptedintheabsence ly other characters can then be used as then can other characters pment, and behavior (Dayrat 2005). There There (Dayrat 2005). pment, andbehavior et al. 2007) is a concern inrespecttoall et al.2007)isaconcern

d the “principle of minimal “principle d the nvironmental sequence data, nvironmental sequencedata, , Sonneborn’s concept can be canbe concept , Sonneborn’s y tothe related isclosely free-living Thus, ciliates”. This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedinvestigations. and onesthat presented, ciliates, ones that MUST the integrative investigations oftheir biodiversity.These willbe categorized as ones that relate tocilia In wereview sections, thefollowing world-wide). available freely and cost-effective, permanent, efficient, are onesthat (i.e., information for systems available through then bemade ofecol understanding an molecular methodsand Researcher exist. descriptions which only scanty tobediscovere remaining species describing Article 2007). (Godfray moreaccessible and diagnoses) barcodes, tomakeinformati to actasafoundation the gapsintaxonomic knowle problemsinthefuture.Consequent cause serious however, might al. 2012),which, et (Butcher forthisapproach coined taxonomy’ been has and high-res withDNAbarcodes taxonomists conc speciescombines ofnew larger numbers popularstrategy biodiversity. Oneincreasingly isprovi open-access journals, ofmethodsfor combined withthedevelopment be done to satisfy basicre bedonetosatisfy ProgressChallenges withthe Grand Biodiversity of of Ciliates hinges onboth tes and recommend standards recommend tes and SHOULD COULD be done to ensure that thehigh that bedonetoensure ding opportunities for progress progress ding opportunitiesfor be done to maximize thevalu bedonetomaximize quirements for taxonomic identif fortaxonomic quirements dge of ciliates. This willrequi ciliates. of dge on (e.g., digitized images of type specimens, images digitized on (e.g., type specimens, of for generating the foundation of data needed for ofdataneeded thefoundation generating for sharing, archiving, and searching taxonomic d and on redescribing the many species for species onredescribing themany and d olution digital ‘turbo- imaging. term The ise morphological descriptions by expert bymorphological expert descriptions ise for streamlining the formal description of streamlining for theformal

sharing information via the internetandin viathe information sharing s require cross-training in morphological and ogical and behavioral aspects. Datamust aspects. ogical andbehavioral ly, there is a need to move towards closing tomovetowardsclosing isaneed there ly, key issues of taxonomic procedures asthey procedures key taxonomic issuesof

est quality of taxonomic datais oftaxonomic est quality towards documenting ciliate documenting towards e of data to integrative e ofdatato re a solid ‘systematics portal’ portal’ re asolid‘systematics ication or description of redescribinggenera ciliates. species or of with pr forcomplying recommended procedures ofciliates; higher taxa Thefollowing elements. abov onspeciesconcept (seesection level taxa Dubois andAescht(2016). theutilityand applica discussionon For further of zoological nomencl acts nomenclatural This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedpublisher beuna files availableshouldthe archive an (https://www.clockss.org/), CLOCKSS Article required, taxa major journals,publishedfor they atrack copies, unless have identical paper suggest that work taxonomic for certai mattersandnomenclature taxonomic of aregistry (ZooB publications) andtheuse withpubli issuesassociated 2012) addressing the Code(ICZN 1999;http://iczn.org/iczn/inde Nomenclaturalacts relating subspecies withranks totaxa from tosuperfamily Rules ofnomenclature TAXONOMIC PROCEDURES byKey issuesnotregulated theCodeinclud should should be published in online-only journals bepublishedinonline-only ature maintained by the ICZN the ature maintainedby Aescht (2001, 2008) provides a (2001,2008)provides Aescht should be added to ZooBank andMi beaddedto (Pyle should many years). For taxonomic beconsulted:Corliss (1972)pr

be published in journals that printat least some multiple ble to continue supporting thejournal. ble tocontinue ank). Concerns over editorial competence in in competence editorial over Concerns ank). cation practices (inclusi cation practices n electronic-only journals (Dubois etal.2013) journals(Dubois n electronic-only e), taxa abovefamily taxa e), record for handling taxonomic issues(i.e., taxonomic forhandling record x.jsp), which includes amendments (ICZN whichincludesamendments x.jsp), tion of the Code, see Dubois etal.(2016)and oftheCode,see tion ovisions of the Code when describing or describing ovisions oftheCodewhen that guarantees to make archived journal archived journal tomake that guarantees e what criteria define species- to family- to species- define criteria e what (http://iczn.org/cont checklist of required and checklist ofrequired

papers, where longevity is longevity papers, where only if chel 2008), the official registry officialregistry 2008),the chel ovides practical guidelines for guidelines ovides practical they are backed-up by backed-up by they are rank, and rank, and phylogenetic ve of electronic-only ve of ent/about-zoobank). must

All follow This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted acts. andnomenclatural specimen(s) between link weredesignated specimens type orvoucher 2010).Tworeprin (Hawksworth, particular location ina thatitwasfound asevidence orretained study specimen usedinaphysiological a example, for type, may maycategory of notbeanymentioned inawork,which or asanominated isdefined voucher specimen A investigations). ecological (e.g., some beimportant may species of identification accurate practice wherepossiblethis of taxa); data associated otherthanone collection deposited inany should types ifcurati tothesecondary institution Article by curation the institutioninwh for permanent of original withthename along description collection, there inalaboratory types deposited are museum repositories (e.g., curated of not astrictrequirement specimensat so,e.g., doing compelling for reason possibility one ofdesignating ormore hapantotypes totaxono refers concept, the(re)description anomenclatural is type specimen the While ofaspecies. variation of range the documenting not be considered as source ofalldescrip assource beconsidered be placed in a different repository than beplacedinadifferentrepository A type specimen is only the name-bearer of a nominal species. Therefore it it Therefore species. a nominal of name-bearer the only is A type specimen should be deposited when they are used for taxonomic works (e.g., revision (e.g., works usedfortaxonomic beare depositedwhenthey the Code, type specimens theCode,type specimens s), notinprivateortemporar could tive data needed in (re)identification, or needed in(re)identification, tive data on cannotbemaintaine in a majormuseum. V be applied to non-taxonomic works where beappliedtonon-taxonomic mic functions. Thisisthe main reason why the a secondary repository that specifies provisions repository thatspecifies a secondary should unit taxonomic representing the specimen ich the laboratory is housed and for passing and forpassing ich thelaboratory ishoused the onethat housestheholotypethe ifitis dfeetsae nalf yl. Although cycle. differentstagesinalife be sent to each repository, to preserve the the preserve to eachrepository, to besent must ts or a pdf copy of the paper inwhich the of ts orapdfcopy should not must be a formal agreement, citedinthe formal agreement, bea

be deposited in permanently permanently in bedeposited y If collections. name-bearing beusedunlessthereisa oucher specimens and oucher specimens d. Paratype specimens d. Paratype should This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted with affiliation andacomparison Establishment ofnewspecies isusedinstead If aredescription specimens studied match only some ofthe illustrations, published these original thatconfirmitsdiagnos descriptions identifications of few groups of ciliates identifications.Co an impedimenttoaccurate a from only known ciliates are Many identifications accurate Making (Dayrat 2005). analysis for latermolecular Article In generall fact, repository. accessible cells molecularanalysis, not possibletoperforma beused thatcan known species,unlessmaterial gene sequences usage their Descriptive terms protistology eukaryotes. Recentdescriptions descriptions ofciliates and redescriptions (1999)isaninvaluableWinston redescriptions and descriptions Composing must must should should be consistent withinthedescription consistent be known ciliate species must be consulted for guidance be consulted for formattingand inclusion in ofdata. (e.g., Berger 1999;V (e.g., be included in a description ofa beincludedinadescription follow those currently accepted (for a glossary, see Lynn 2008), and Lynn 2008), glossary, see a (for accepted thosecurrently follow should and redescriptions of and redescriptions guide todescribing and species of the original description, this description, of theoriginal morphologically similar species. be accompanied by a justification for the generic generic the for a justification by beaccompanied short original descriptionin short original y, alltype depositions,material for should should ď tic features and add new information. If the information. andaddnew tic features a mprehensive taxonomic sources exist only sourcesexist for taxonomic mprehensive č besupportedby detaile ný & Foissner 2012). Therefore, & Foissner 2012).Therefore, ný for extraction of DNA is unavailable. If itis unavailable. ofDNAis extraction for conform tostandard should ciliatespublishedin (i.e., avoid synonyms). An analysis of Ananalysis (i.e., avoidsynonyms). new species or redescription ofa redescription or new species

bedepositedina publicly- should should the older literature, whichis the older s applied toother applied s d comparisons withthe d comparisons be justified. befollowed,as should should major journalsof beitemized. bedeposited This article is protected by copyright. All rights reserved. copyright. This articleis protectedby AcceptedAt aminimum,vouchers literature much oftheecological Thishasnotbeenacommon practic preservation. ecology) functional DNAbarcoding, (e.g., should a sour cannotbe type slides Type specimens. and fade that samples in result carbonate) silver ammoniacal othersmay become although (Foissner 2014), thatfulfillthese criteri present, thetwomethods taxonomicallycritical features ofthe major tax identification and,therefore, diag sufficient revealing by Aescht (2008)] International Commissi type see definitions, Article re however, has concept, the hapantotype (Art.72.5.4 nominaltaxon the holotype ofthe cycle, life the in stages different representing One ormorepreparatio of theCode(Art.73.2). mig sample aheterogeneous uncertain, although at diffe not specimenscollected These slides isdesignated, a neotype where uponwhichdescripti Stained permanentslides Depositing type andvoucher specimens incollections be deposited for future analysis (e.g., in 95% alcoholat in95% (e.g., bedepositedforfutureanalysis In general, voucher material representing representing material voucher Ingeneral, preparations Permanent should constitute ahomogenous sa could should must consistofphotomicrographs videosdisplaying or the rent places or at different at different placesor rent must must contains taxonomic identifica containstaxonomic be fixed and stained by a method that shows a methodthat andstainedby befixed be deposited (Aescht 2008; Lynn and Simpson 2009). Lynn and (Aescht2008; bedeposited conform to the basic definiti conform tothebasic cently been questioned (Dubois et al. 2016). questioned(Duboiset been cently could toallowunambiguous characters nostic on for (1999)and Zoological Nomenclature ce of DNA for sequencing, so additional cells so DNAforsequencing, of ce may be designated as a hapantotype, whichis a hapantotype, bedesignatedas may appropriate. Somestai appropriate. ons ofnoveltiesarebase ons and Art. 73.3). The continued acceptance of continued acceptance and Art.73.3).The on ofciliates towhich the species belongs. At ns of directly related related ofdirectly ns a most reliably are protargol andsilvernitrate most reliably areprotargol a mple of the specimens used for the work and forthework ofthespecimensused mple ht be designated as a syntype under the rules underthe a syntype bedesignatedas ht be submitted toa repositoryfor long-term populations examined for special purposes forspecial populations examined e for ciliates, with the consequence that that consequence e forciliates,withthe

times whose conspecificity is conspecificity times whose should not tions that cannot be verified. tions thatcannot ˗ 20 °C or cryopreserved). cryopreserved). 20 °Cor on of a type specimen [for [for specimen on ofatype individuals, for example individuals, forexample ning methods (e.g., d, and redescriptions be used to prepare be usedtoprepare This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted Articlepublicly accessibleciliate collections, ofwhich followingare the especially notable. available. Severaluniversities,world’s major museums, ofthe and institutes research hold showing cells th barcodes, preserved plusmeasur taxonomically features relevant • • • • •

type slides, most of which were collected in France France collected in type were slides, mostofwhich Muséum Nationald’Histoi (http://www.nhm.ac.uk/research-curation/ slides ofotherprotistsandove (http://www.nhm.ac.uk/research-curation/re orvouchers) paratypes, neotypes, slides (holotypes, hapantotypes, London, (h Natural History UK Museum, species nominal 28synt tenhapantotypes, paralectotypes, 119holot representing specimens) preserved slides (470microscope as type material 20013-7012, USA(http://invertebrates.si.edu/ National MuseumofNatura International Type Protozoan SlideCollec slides of830nominalspecies,including slides 420type 2,500 about (http://www.ouc.edu.cn/english/); China, Qingdao,University of China Laboratory Protozoology,Institute of of about and 150families; 420 genera or paratypes) neotypes, hapantotypes, (http://www.landesmuseum.at/): Au Upper Biology ofthe Centre re Naturelle, Paris, France (http://www.mnhn.fr/fr); 114 (http://www.mnhn.fr/fr); France Paris, re Naturelle, e taxonomically relevant structure structure relevant e taxonomically l History, Smithsonian Institution,l History, Smithsonian Washington, DC r 1,000 video sequences ofprotists r 1,000videosequences strian Museum, Linz, Austria Linz, strian Museum, approximately 3,500 slides(holotypes, approximately syntypes, 3,500 ements oftheorganisms. For documenting ements 20.000 voucherslidesofprotists of 990 species representing approximately approximately representing of 990species , six SEM stubs, 42alcohol-orformalin- , six Evolution and Marine Biodiversity, Ocean Biodiversity, andMarine Evolution ypes) and 111 vouchers of more than 350 than 111vouchersofmore ypes)and ttp://www.nhm.ac.uk/); approximately 500 ttp://www.nhm.ac.uk/); approximately research/projects/protistvideo/) research/projects/protistvideo/) tion, Department of Invertebrate Zoology, Invertebrate of tion, Department search/projects/protists/), about22,000 search/projects/protists/), ypes, 135 paratypes, 34 lectotypes, 34 ypes, 34lectotypes, 135paratypes, collections.htm); 518itemsdeposited

should bemade This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedfocal planesallow assembly to into3-D composites. Such imagesbe adaptable may then to would betoprovide Bestaccessible. practice This issue those notlistedas other potentialusers,e.g., totaxonomic are useful slides and voucher Type videos, Photomicrographs, consideredancillary such providing when They materials. available tofutureinvestigatorsand the public. There are three that major mustbe issues Beyond asoutlinedabove, depositing material considerations General Article OF MATERIAL ANCILLARY DEPOSITION, ANDCURATION CONSERVATION, • • •

ofsufficient quality quantity and tobe ofutility offered by the facility curation be ina available formthat will at nocost tostakeholders methodologies with provided andmaintained • • •

including holotyp slides(one 12type (http://www.mabik.re.kr/en/mai National Marine Biodiversity Institute in70%ethanol preserved crustaceans registered specimens, mainly Australian epibiotic freshwater speciesfrom Australian Museum, Sydney,Australia (http://australianmuseum.net.au/); lotsof 59 and104paratypes 1,130 slides,49holotypes India(http://www.zsi.gov.in); Kolkata, India, approximately Zoological of Survey could be addressed by making beaddressedby

or line drawings of cellsor linedrawings of forethought to the development of new technologies or tothedevelopmentofnewtechnologies forethought high-resolution digital high-resolution imagesthe specimen(s) of n.do); slides of approximately 80 marine species, species, 80marine n.do); slidesofapproximately ‘approved users’ of certain museumcollections. certain users’of ‘approved images of the specimen(s) taken at different atdifferent taken thespecimen(s) images of e and 11 paratypes) of ten species tenspecies of and 11paratypes) e researchers canmake researchers but also including 13 type slides slides 13type but alsoincluding of Korea, Chungcheongnam-do, Korea Korea Chungcheongnam-do, ofKorea, specialists but are not readily accessible to accessible specialists butarenotreadily

should be: material anddata material This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedthis respect, they are similar totraditional museum specimens. oraccession a registration suchas identifier, an given are specimens Molecular researchers. to accessible readily them make to conditions a material samples offrozen hous Madrid (http://www.mncn.csic.es/).These (http://www.nhm.ac.uk/our-science.html), andthe biologiques-cellules-vivant Naturelle, Paris(https://www.mnhn.fr/fr/collect (http://www.mnh.si.edu/rc/biorepository/index Smithsonian NationalMuseum of ofNaturalHistory,Ne American Museum the are among these Prominent investigations. molecular in used canbe that specimens natural history have museums invirtually allar nowused are Molecular data Article important as integrative approaches tothe inve terms of revealing ecological orphysiological functionalityand willbecome increasingly beha morphological, morphogenetic, At present, thiskindofability isbeing created mainly formolecular however, data; specimens, using a bioinformatic investigations, newlyallowing collected mate we Here, suggest that a wouldfacilitate single portal a variety integrative of ofrawand3-D deposition by be accompanied more sophisticatedfuturemethodologies, in Molecular specimens Molecular

es-cryoconservees), the Natural History Museum, London NaturalHistory Museum, the es-cryoconservees), nd environmental samples that nd environmentalsamples established facilities tohous establishedfacilities nd image-resolution software or dedicated search engines. engines. search softwareordedicated nd image-resolution Natural History,Natural Washington, DC vioral, or physical datahave vioral, orphysical w York (https://research.amnh.org/amcc/), the (https://research.amnh.org/amcc/), w York which physical type or voucher specimenswill voucher physical or type which number, allowing further genetic analyses. In genetic analyses. further number, allowing rial to be compared with type andvoucher with type to becompared rial eas of biological resear .html), theMuséumNa holographic images in databases (e.g., GBIF). GBIF). (e.g., images indatabases holographic stigation ofbiodiversit e permanently curated repositories for repositories curated e permanently ions/ensembles-collections/ressources- Museo Nacional de Ciencias Naturales, CienciasNaturales, Museo Nacionalde

e collections of physical e collectionsof are maintained undercontrolled are maintained their own intrinsic valuein theirown ch. Consequently, major major ch. Consequently, y continue to evolve. y toevolve. continue tional d’Histoire This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted sort. ofany with physical specimens but mostarenotassociated ofthes (Lynn 2008).Many known ciliatesspecies 850namedspecies approximately Curr analysis. identification andphylogenetic thesmallsubunitribosomal gene for coding Lynn(e.g., andSimpson2009).Mostindividual (e databases available Althoughadditional notregulated bytheCode, analyses and data Molecular room temperature. on FTAat cards roomtemperature; stored lyophilized/freeze-dried and 10) material stored at Article libraries (cDNA) libraries samples culture;(cDNA) inbacterial and 9)DNA/RNA expression genomic RNA storedat-80°C;7) phage/BAC °C; 5) at -20 in waterorbuffers at-20°C;4)DNA specimensstored preserved at -196°C;2) inliquidnitrogendeep-frozen stored in natural history repositories andciliates be that used could for 1)specimens includes: et al NaCl (DESS)(Gray DMSO/EDTA/saturated RNAlater® (Ambion,Carlsbad, (Whatman/GE Healthca FTA Cards Reliablemethodsofpreser applied tociliates (eitheras samples ofwhole

.g. NCBI GenBank)

silica-dried material storedat silica-driedmaterial CA). Another method potentiall CA). Anothermethod ving cells or extracted DNA and RNA that have been DNA andRNAthathave cells orextracted ving of ciliates (Fig. 1). Thisre (Fig. of ciliates re Life Sciences,Pittsburg re should whole cells stored at -80 °C;3)alcohol- cellsstoredat whole DNA (SSUrDNA),whichis ently, there are SSU rDNA sequences linkedto rDNAsequences SSU thereare ently, cells orwithin an environmental sample) are extracted from nucleia extracted libraries stored at -80 °C; 8) expression expression at -80°C;8) libraries stored deposition of genetic information inpubliclydeposition ofgenetic information sequences that have been deposited are the deposited arethe sequences thathavebeen beincludedindescri . 2013). The range of materials that can be thatcanbe ofmaterials . 2013).Therange e are associated with deposited material, with deposited associated e are

presents only ~10% ofthe only ~10% presents room temperature; 6) extracted 6)extracted room temperature; h, PA; Hide et al.2003)and h, PA;Hide y for use with ciliatesis y with foruse nd mitochondria stored nd mitochondria ption or redescription ption orredescription useful forciliate useful This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted studiedsofar. ecosystems of and hiddendiversity a large Anal higher or taxa. pseudocryptic species, between ofdivergence value forthedegree b itself, cannotsubstituteforactualcharacters ITS, CO1),by gene SSUrRNA, (e.g., akey of sequences between divergence degree of as ofinquiry such avenues narrow also trueforrelatively evolution, populationstructure,andfu convergent processe questions aboutcomplex mustbeevalua Geneticdata Article curators. alignments mustbecapable should Analytical materialas files nexus ofalignments such orNewick phylogenetic files trees of to namesofspeciesor belinked can where data suggest that the online but thiswillscatter information among sources are that noteasily Hence,we searched. Itand Hunt2009). ispossibletolinkda (Anwar by intended tofillthisrole,isnotsearchable trees.TreeBASE alignments andphylogenetic alsobedeposited in TreeBASE, asitpr databa searchable isnoeasily To date,there Ciliate Guide Ciliate

of being opened in Mesquite) openedin Mesquite) of being ciliates that is rarely reporte ciliates thatisrarely ted in context ofmorphological ted incontext s that involve multiple factors s thatinvolvemultiple (http://ciliateguide.myspecies.info/) ysis of DNA from environmental samplesreveals ysisDNA fromenvironmental of congeneric species, including cryptic and cryptic including species, congeneric taxonomic category or using names of species category using ofspecies taxonomic or names ecause there is no genera ecause thereisno (http://treebase.org/treebase-web/about.html), (http://treebase.org/treebase-web/about.html), ovides quality control (e quality control ovides higher-order taxa in a searchable database. database. inasearchable taxa higher-order ta to a publication as supplementary material, to apublicationassupplementary ta nctional ecology acting in concert.Thisis actingnctional ecology in se for housing analyses of data suchas ofdata housingfor analyses se

α and updating of information by ofinformation and updating -taxonomy. For example, the For example, -taxonomy. d in morphological surveys of d inmorphological characters characters to address broad such as evolutionary rates, evolutionary rates, such as lly accepted lly threshold .g., nexus filesof nexus .g., should beused, This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedextende hasbeen BRCs of role years, the recent of characteristics genotypic and the phenotypic providing w cultures, and role insafeguarding (Müller etal.2008). etal. (McGrath dried cysts onfilterpaper Lee 2000; andSoldo1992;Nerad1991;Tompkins star for for mediaandprotocols theyand depositculturesoftaxa (e.g., ge few ofa members are species cultured Most which they from www.ccap.ac.uk), Protozoa/CCAP; Collection/ATCC; www.lgcstandards-atcc.org/ Type Culture (American protists accept that collections culture in deposited are genera) Article1967). Al 1992; SimonandHwang andNerad1992; (Daggett cryopreservation maintenance ciliate of cellsinan inactive, butviable state has been achieved by prematureaciliates.cultures similar tosuggest role of for However, ina fewcases long-term and the technical difficulty ofmaintaining liv cultures as a name-bearing the type. Given small number ofciliate strains instable cultures ce designating viableprotozoan bacter (e.g., Thus, unlikeothermicroorganisms establishing andmaintaining them Researchaspects intosome ofciliate biodiversityis constrained by the difficulty of cells viable preserved and Cultures Tetrahymena Biological Resource Centers (BRCs), such as the ATCC ortheCCAP,play a key as the (BRCs), such Biological Centers Resource , Paramecium

ting and maintaining cultures (Day et al. 2007; Finlayet al. and maintainingting etal.2007; (Day cultures lls preserved in a metabolicallyalls preserved in , describe; resources are available are resources describe; Euplotes in long-term cultures orpreser in long-termcultures so, few ciliate cultures(~ so, few 1977); and 3) protocols for cryopreservation cryopreservation 1977); and3)protocolsfor ). We recommend that researchers researchers that recommend ). We Müller et al. 2008, 2010; Nerad and Daggett Mülleretal.2008,2010;Nerad e cultures or preserved viable cells, itis viable orpreserved e cultures ith the main objective being the preservation of preservation the ith themainobjectivebeing nera used extensively as modelorganisms usedextensively nera and CultureCollectionof Algae and and ia, algae,traditionia, for fungi), there isno the conserved taxa (Müller et al. 2008). Inet al.2008). (Müller taxa the conserved d, largely as a result of the rapid increase in in increase rapid ofthe result asa d, largely et al. 1995); 2) protocols for preserving forpreserving et al.1995);2)protocols are availableas live cultures or cysts.

700 strainsbelonging to54 inactive state or protozoan orprotozoan state inactive ving cells inaviablestate. cells ving to this end: 1)formulations to thisend: could isolate isolate This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedthe taxonomically charactersrelevant and conditions culture nottypicallyseen innature,so phenotypes itshould However, Quintela-Alonso etal.2013). conditions, includingconditions (e.g., using different cycl polymorphic life Also, somespecieshave therisk that create from fieldsamplesalone (e.g., Gates andBerger 1 rele taxonomically for new search barcoding isozymes, (e.g., characters molecular by recognized havebeen complexes species knowncryptic Where ofmorphology andontogeny, observable detail Articlebiodiversity. Bestpractice should morphological characters about cilia of knowledge entire body Virtually the morphologyDocumenting andontogeny MORPHOLOGICAL ANDONTOGENETIC CHARACTERS et al.2013). (Gachon hyperlinkedcurated tomanually molecular, challenge by developingKnowledgeBase, metagenomics andenvironmen be included with other characteristics wheninvestigating aspects ofciliate A description or redescription A descriptionorredescription If possible,clonalcultures ), adetailedmorphological description cox 1, ITS2; Nanney and McCoy, S 974, 1976;Powelsonetal.1975). must should be studied for species descri studiedforspecies be tal sequencing data. TheCCA data. tal sequencing betomeasure,count,de vant characters that can analyzed by multivariate statistics multivariate by that cananalyzed characters vant should must be used for observations beusedforobservations must for quality-controlled bi for quality-controlled

be based on deposited fi ondeposited bebased bibliographic, and taxonomic information bibliographic, andtaxonomic of confusing morphologically similar species. similar of confusing morphologically es that can only be revealed under culture berevealed canonly es that also be based on live observation (Foissner bebasedonliveobservation also even though all data might notbepublished. thoughalldatamight even be noted that cells in culture may exhibit may exhibit be notedthatcellsinculture tes is linked to morphospecies. Therefore, tes islinkedtomorphospecies.Therefore, should onneborn, references below in below onneborn, references Tetrahymena aquasubterranea Tetrahymena

be carried outwiththe aim to scribe, and illustrateevery scribe, ptions and redescriptions and ptions andredescriptions P has responded tothis P hasresponded must ological material, be described. bedescribed. to avoid reliance ondata to avoidreliance xed materialxed revealing DNA ;

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted liveobservation Information obtainedfrom ArticleInforma 2). seeFig. examples, live therefore, disappear; contract and/or orsw deposited. Cellscanshrink virtual) or material (physical bothofth meeting eitheror where 2014), except • • • • • • • • • • • • •

Composition, shape,andlocation vacuole pore ofc Presence, position,number,andshape extrusomes ofmature location and shape, size, Presence, plastids sequestered or bacteria, algae, symbiotic of Presence granules ofcortical arrangement and color, Presence, Contractility and flexibility ofcell Cytoplasm color Cilia lengths (oral, brush,etc.) somatic, andshape size Cell activity) interactwithab local conditionsandmay to according may vary offoodeaten thatthetypes food web—withthecaveat (indicatingContents offoodvacuoles the lipiddroplets,crystals, or otherinclusions Presence of Position andshapeofthecytopyge environmental conditions shapeasso and Variations incellsize allowing a reinvestigation of the diagnostic features is ofthediagnostic features a reinvestigation allowing tion obtained from live observation tion obtainedfromlive ell during fixation, and the characters of some taxa can taxa ofsome andthecharacters fixation, ell during observations provide useful information (for provideusefulinformation observations of the nuclear apparatus apparatus of thenuclear could ese requirements is not reasonable andother isnotreasonable requirements ese ciated with division, life cycles, or withdivision,lifecycles, ciated alsoinclude: ontractile vacuoles and the contractile contractile vacuolesandthe ontractile iotic factors to affect morphology or morphology toaffect iotic factors role of the organism in the microbial organism inthemicrobial role ofthe

should include: This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedhalteriids by Res Song1993). groups, in well-knownciliate Hill 1995);otherwise,theinvestiga and (Borror cirrusin afrontoventral 2004) andthelackof features, e.g., theis diagnostic positionofthe oral primordium inoligotrichid ciliates (Agatha structures) division including stomatogenesis, morphoge Article stained preparations enabling detailed examination by confocalInformation microscopy. recorded fromsilver- to stainingapply ofstructures fluorescent must stainsmay used toaugment Silver carbonate be diagnostic features type this isnot fixed materialbutwhere be documented photographically (Fig. 2). Inthe future,it (Fig. 2). documentedphotographically be There is a range of other features that may also be examined. Ontogenesis (i.e., cell cell (i.e., Ontogenesis examined. be also may that features other of range a There is • • • • with protargolAt present,staining orsilvernitrate

argyrophilicgranules fibrillar and structures) aspositions such Miscellaneous features, shape ofnucleoli) apparatu Structure ofnuclear organelles) Pattern oforal ciliature arrangement, (i.e., number,and structure ciliary of kinetid andbrush(ifpresent) orientation ofkinetie Pattern ofsomatic should beincludedindescriptionswhen must must should be applied providing permanent type permanent be appliedproviding include: ciliature to include genera toinclude ciliature ting cysts, ifpresent, new patterns of cell division cell new patternsof s; numberandspacing kinetids of s (i.e., number, shape, size s (i.e.,number,shape, reasonable, equivalent reasonable, augment descriptions (Arregui et al.2002), et descriptions(Arregui augment nesis, and the regeneration of parental of andtheregeneration nesis, a certain positionisinfo a tion of this process is recommended as even ofthisprocessisrecommendedaseven tion descriptions, but these fade and theirresults butthesefade descriptions, and appearance of organelles (e.g., (e.g., oforganelles andappearance should it provides taxonomically relevant relevant itprovidestaxonomically l configuration, number,and

beexamined asmorphological must may (e.g., in discovered be material (physical or virtual). or material(physical methods revealing the the methods revealing could toprovide performed be in kineties,andstructureof , andlocationofnuclei be more appropriate to bemoreappropriate rmative ineuplotids This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedallow theclosely speciesfrom other tobe related separated thiswillvary taxa; depending on oriented morphostaticsp mo Data obtainedby data Morphometric abbreviations, andother for the arrangemen style (Arregui etal.2002).The microscopy, toassess ofciliature patterns and infraciliature during the identification process tomicrotubules bind specifically composite image.Fluorescently labelled such taxoids as FLUTAX (Calbiochem, USA)that the cell, image-stacking software ofsilver-sta Asphotomicrographs line drawings. Silver-stained preparations (Ridgway others are source, butthere Article thedefinitive Illustrators theGuild(Hodges(https://gnsi.org/). 2003)is handbookof The for illustrationsacceptable techniques toproduce illustrations and basisof Observations thatformthe Illustrating morphology that capacity 1978). Finally, sometaxa interactions etal. al. 2002;Katz et species (Foissner morphospecies, whic diversity insome occurs

could should should provide insights intothea breeding species(Nobili et al. structure of be documented. bedocumented. rphometric studies rphometric be accompanied by photomicrographs. A useful source regarding source regarding Auseful photomicrographs. by be accompanied stylistic conventions ecimens to provide information on ecimens toprovideinformation (e.g., dileptids;Vd’a (e.g., should could could be usedprimary as the basis ofillustrating specimens with descriptions or redescriptions orredescriptions descriptions 1978; Wood andMcDonne 1978;Wood alsobeused,possibly in beusedtoassembleseve must 2005; Xu and Foissner 2005). Mating type type Mating 2005; XuandFoissner 2005). be on a sufficient number of appropriately- of asufficientnumber beon should h may suggest the existence of pseudocryptic theexistence suggest h may č ný and Foissner 2012) display a regenerative displaya regenerative and Foissner 2012) ný ined specimens show only one focal plane of focal plane one ined specimensshowonly publication is the Guild of Natural Science publication istheGuildofNaturalScience t ofillustrationsandpl follow those in the recent literature. followthoseintherecentliterature.

the range of the characters and characters ofthe the range conjunction withconfocal conjunction ral planes into asingle ral planesinto ll 1994; Zweifel 1988). ll 1994; must be documented by documented by be ates, useofstandard This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedsorts ofcharacters, reliabilitycharacters ofmolecular char and molecular set withfurthermorphologic should must of categories other from different materially not are characters molecular In practice, They criteria. analytical by same the constrained are they because evidence evolutionary al. 2003;Pröscholdet2001;S a protists (Dunthornetal.2014;Hoef-Emden fo precedents already are failed. There characters molecular with above) (described features other relate to trial every if andonly caution beusedwith must taxa fordefining alone characters molecular Accordingly, emerge. to itisevolving forobtaining the technology rapidl methods forstudying morphologic Article inthecla scale readjustments char fornew the search create debate relative regarding the approaches, meritsofthese butindoing sothey initiate with cla disagree that Molecular phylogenies Using molecular dataas MOLECULAR CHARACTERS raw data diagnostic, the not as measurements However, range). error, appropriate. Data measurements butbetween10and30 andthefeature, the taxon critically be evaluated like other characters (i characters other like beevaluated critically

beusedtoformulate hypothese phylogenetic should acters. Certainly, the new molecu thenew acters. Certainly, should be presented as standard descrip asstandard bepresented taxonomic characters taxonomiccharacters ssification of ciliates like the ciliates ssification of besubmitted assupplementary material. un et al. 2012; Zhan et al. 2009). un etal.2012;Zhan etal.2009). al features. Molecular eviden al features.Molecular ssifications based on morphological characters basedonmorphologicalssifications characters nd Melkonian 2003;Hussetal.1999;Marin nd provided in the description may emerge as mayemerge providedinthedescription acters and taxa (Neff 1986). Aswithother 1986). (Neff andtaxa acters y; therefore, pitfalls y; therefore, r this, bothinciliates r .e., a priori vs. a posteriori weighting)and .e., apriorivs.posteriori s that can be tested by enlarging the data data the enlarging by canbetested s that must lar technologies ca lar technologies

tive statistics(e. previous introductionsofnew be evaluated by a thorough athorough evaluated by be ce isstillrelatively and new should and limitations continue and limitations and in othergroupsof generally be generally g., mean,standard use similarlarge- This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted c markers includethe barcoding candidates for as barcodes coding may be needed regions Owi et al.2013). 2010;ZhaoLynn and Strüder-Kypke Kher etal.2011;Sa Guggiari andPeck2008; ciliates (Barth of barcoding rela (Corliss 2002).Despitetheseadvantages, that allows most fo morphology character-rich and re are monophyletic be identified.They Ciliates exhibit a number offeatures that make barcode itlikely thatwill aDNA suitable (Pawlowski etal.2012). defined se being then barcodes group-specific 18S V4region ofthe the ~500bplong variable (http://www.barcodeoflife.or applying theCBOL group-sp using a assignment, species-level Articlepreliminary identification: usa universal eukary The CBOL su ProWG (Pawlowski etal.2012). for regions in 2012toidentify barcode standard Life Protist of Consortium fortheBarcode it hasbeenimpossibletoidentifyDNA asingle tothei owing diverse Protists aresogenetically DNA barcoding characters molecular withthegoalhomoplasies orpolymorphisms, of suchas elements discover to analyses cladistic andwith taxa andbetween within comparison

must be described, illustrated, and discussed. et al. 2006; Chantangsi etal et al.2006;Chantangsi ecific barcode. Based on comparative studies, Based oncomparative barcode. ecific for different groupsfor different of Working Group (CBOL ProWG) was established wasestablished ProWG) (CBOL Working Group latively well-studied and have a complex, complex, a andhave well-studied latively ntoferrara et al. 2013; Stoeck et al.2014; etal.2013;Stoeck ntoferrara tively few studies have focused ontheDNA focused studieshave few tively parately for each major protistan group group majorprotistan each for parately rms to be identified reliably to morphospecies to to beidentifiedreliably rms oding regions for the small subunit ribosomal forthesmall subunit regions oding rDNA as the universal pre-barcode, with pre-barcode, astheuniversal rDNA r long independent evolu independent r long ggests a two-step barcoding approach of approachof ggests atwo-stepbarcoding otic barcode(theotic pre- the allofthem.Consequently, for barcode protists and to assemble a reference library andtoassembleareference protists discovering robustsyna discovering g/) selection criteria, the ProWG suggests theProWG g/) selectioncriteria, ng to their genetic diversity, different different genetic diversity, ng totheir . 2007; Gentekaki and Lynn. 2007;Gentekakiand 2012;

ciliates.

barcode) followwitha tionary historiesthat tionary pomorphies. Finally, pomorphies. Potential This article is protected by copyright. All rights reserved. copyright. This articleis protectedby temporary attachment, alternation of rests and movements. The speed swimming of helical trajectories),escape and jumping feeding, behaviour, contractility, formation ofstalks, feature. Anecdotal observations could include: patterns ofcrawling (e.g., swimming or behaviour canat be least similar incongeners. Behaviour may thusbe diagnostic a poor light, type, etc.), pH,substrate temperature, dependent onth that suchbehavioursare characters Such surfaces. to adhering “body in such asjumping lengths” several explicitly supportthisapproach. descriptions ofprotistswithancillaryon their behaviour, does the not information Code complementing Leeuwenhoek, of van toAntonie Although isahistory, back dating there Behavior OTHER CHARACTERS should wh from DNA extracted the barcode sequence, taxonomically features relevant asi Furthermore, barcodes. documented by of oftheprocess them through aspart names and the (seeabove) taxa traditionally described Seberg etal.2003;Willand intoaccountthemorpholog and adjustedtaking ( internal transcribed spacers (I subunit large DNA (SSUrDNA,18SrDNA), Accepted Articlecox 1). Proofed genetic distances for genetic distances 1). Proofed be deposited, and fixed bedeposited,andfixed

Rubinoff 2004).Barcodedata TS1 and ITS2),cytochrome b( TS1 and cells and/or live or cryopreserved cultures cryopreserved cells and/orliveor should Some ciliates, however, ex Someciliates,however, members of individual majormembers taxa ofindividual could be deposited as a means of cross-referencing a new anew ofcross-referencing bedepositedasameans e environment (food type and abundance, abundance, and (foodtype environment e a fraction of a second, spiral swimming, or swimming, ofasecond,spiral a fraction convergent behaviours occur across taxa, and taxa, across occur behaviours convergent ndicated above, voucher material showing the material above,voucher ndicated be included in descriptions. It iscriticalto note beincludedindescriptions. inferring ecological roles from occurrences occurrences from roles ecological inferring ribosomal DNA (LSU rDNA, 28SrDNA), ribosomal DNA(LSU rDNA, ich the barcode sequence was derivedalso was sequence thebarcode ich ical data (Lee 2004; Lipscomb etal.2003; Lipscomb data(Lee 2004; ical autecological information associated with informationassociated autecological

should hibit characteristic behaviour, hibit characteristic cyt b) , be correlated with becorrelated and cytochrome c oxidase coxidase cytochrome and should could beestablished bedeposited. could be This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptednourishing integrative as biodiversity resources Information accurately. and knowledge quickly heterogeneous, making itdifficult orimpossible forresearchers toidentify andfillgaps in andnon-taxonomic Both taxonomic Overview INFORMATION RESOURCES culture conditions sediment, orsoilfromwhich samples are taken physical datasuch Therefore, on growth/size. can astemperature such factors environmental environment,as thetype Beyond describing data Environmental Articleresults). exa descriptive whenitisnotrigorously de be tiedtotaxonomic therefore, encourage detailed studies ofciliate behaviour and ecophysiology, then which may identification oflive materiala and pa play of behaviour the characterises (Oliveira-Pintoet cell motion,areavailable sophisticated methods,suchas trajectorieson peculiarities plusremarks ofmovement may sufficient, more be but ofthefieldview dish, orknowing thewidth roughly estimated,for example, using stripofscaled a small beneath placed paper a Petri must

scriptions. However, we caution caution scriptions. However,we be presented in the methods of inthemethods bepresented a taxon, then these data thenthese ataxon, image analysis of video sequenc of image analysis data relating to biodiversit datarelating to an investigative approach, but data approach, butdata an investigative mined (withfulldocumentationofmethodsand rt in future research on functionality. We, We, onfunctionality. research rt infuture outlined in the Code (Recommendation 76A), intheCode(Recommendation outlined al. 1993). Ina study fully contrast,if al. 1993). at lower microscope ma at lowermicroscope as temperature, salinity, and pH of the water, pH ofthewater, and salinity, as temperature, affect behavior and have a significant impact impact asignificant and have behavior affect should should be recorded. Likewise, detailed berecorded. described species (see above). (see above). describedspecies against providing information as against providing

could beusedtoaidinthe y are often fragmentary and fragmentary y often are es and computer modelling of es andcomputer reduce thisissueby reduce gnifications. Simple gnifications. must bereliableand This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedguidelines: onlineand/ordifficu items thatareunavailable acommunity, we as them. Atthevery least, above ofthe thedispersednature However, (http://www.biodiversitylibrary.org/ andth Articledigitizing initiatives such as the BiodiversityLibrary Heritage makesomeof to efforts been Therehave illustrations that constitute the functional oftype equivalent material. thatincludenomen treatments inolderjournals Al research onciliates. othermaterial slides,or cells,type preserved time,noknowledge atthis (Table 1).However, object aremany there Beyond material, type Thes but notduplicationofsuchresources. information resource interdisciplin toabroad, accessible readily • • • • •

Marine Benthic Ciliates (http://www2.ouc.edu.cn/ak Free-Living Ciliatesinthe Seas, BohaiandYellow China http://protist.i.hosei.ac.jp/pdb/images/menuE.html) Specimen Archives Digital Microbial The Planktonic Ciliate Project http://ciliateguide.myspecies.info/ciliates-activated-sludge) Ciliates inActivated Sludge should so itisdifficulttofindsome publis encourage an increasing array of array encourage anincreasing (http://ciliate.myspecies.info/en) (http://ciliate.z (software package available for download from fordownloadfrom available package (software fs/ciliate/asp/) fs/ciliate/asp/) ary community. research Furthermore, a good rough taxon-specific websites such as: as: such websites taxon-specific rough e are the aspirations we promote below. aspirationswepromote are the e resources reduces the potential to interrogate thepotential reduces resources s needed to ensure high quality taxonomic taxonomic quality toensurehigh s needed should these resources more available, through available, through more resources these lt to obtain in hard copy, following these following obtain inhardcopy, lt to clatural actsordescri clatural resource like GenBank or ZooBank exists for exists ZooBank or resource likeGenBank s that havevalueto s that ooplankton.cn) (Protist information Server: (Protist supplement these efforts by digitizing supplementtheseefforts

hed material, such as taxonomic hed material,suchastaxonomic links to other expert sources expert linkstoother taxonomy of ciliates taxonomy ptions/revisions plus This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted it that suggest We species. templateforkeys, providing anomenclatural (http://ciliateguide.myspecies.info/), which development of To thisend,wepropose It aresource. developing such single thecriteri following onlineresource, weHere suggest that integrative biodiversity of species identifying and information sharing for resources of Development Article • • • • • • • • •

Provide quality control for online Provide quality control for physiological data/metadata tofacilitate large-scale studies Enable taxonomic data/metadatacombined tobe reliable with ecological and Allow new investigations taxonomic to Facilitate continua Standards forsupplementa the ConventiononBiological (http://www.cbd.int/) Diversity Documentation al. 2013) et interrogation (Gachon Sites providing ac cu ona be madeavailable anddatali Supplementary information (Droege et al. 2014) etal.2014) (Droege Global Genome Biodiversity Network [GGBN] Reliable metadata community research should should l, accurate identification of c identificationof accurate l, cessmetadata to should should be providedsothatcollecti beusedasthesoftware plat be made available via a dedicated web-portal, e.g., The e.g., dedicatedweb-portal, viaa bemadeavailable rated open-access website website rated open-access ry materials anddata ry materials : The

a outlined above. There are four reasons for reasons for four are a outlinedabove.There materialsother web sites from is a Scratchpad/Biodiversityis resource, online

Ciliate Guide should descriptions, andmetada descriptions, ciliates would benefit from developmentofa wouldbenefitfrom ciliates

nked with type or voucher specimens specimens voucher nked withtype or build on be organized toallowremote beorganized iliates collected from nature nature collectedfrom iliates

Data Portal (http://data.ggbn.org) Portal(http://data.ggbn.org) Data all should prior work priorwork ons of specimens comply with ons ofspecimenscomply form for the following reasons: following reasons: form forthe be agreed upon by the the uponby beagreed ta to the levelta to of

should

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted type Todevelop specimens. museum”, making itmucheasier tolocate specimens and linkmetadatadigitized to images of physical of database searchable identifying species and assembling data/metadata, membership and integrative focus on biodive Article IRCN-BC the suggest also that We • • • • • • • •

Establish means to provide credit for contributions contributions Establish meanstoprovide creditfor to accommodate features Identify andadd of thesite update Ensure anactive Promote participationtoga rights toa committee experts of Establish a registration system allowing registered users tocontribute, limiting editorial Identify complementary initiatives and establish information-flow Configure group toproposeth Establish asteering • • • • • • •

Provides the capacity data tosubmit and metadata Provides an ability tocreate keys foridentification porta Provides ataxonomic materials that are vetted by ase vetted materials thatare Iscommunal environmentthat suitedtoa from material access Can Is accessible freely http://scratchpads.eu/) hostingProvides guaranteedpermanent The Ciliate Guide The Ciliate Guide specimens and type slides. It asa“virtual can thusfunction slides. andtype specimens ther and review resources and reviewresources ther accordingly accordingly should independent sources independentsources l for entry of content content of forentry l assume this task because of its broad, inclusive broad,inclusive its becauseof task assumethis lect group of authoritative users users group authoritative lect of rsity. Aside from providing a resource for resource a Asidefromproviding rsity. e initialrequirements the IRCN-BC developments in methodology and needs needs inmethodologyand developments The Ciliate Guide (EU-sponsored Scratchpads project: project: Scratchpads (EU-sponsored allows a registered user to contribute contribute userto a registered allows

will : and set priorities and setpriorities also can be used as a canbeusedas also This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedthe British Societyfor ProtistBiology Protistology-UK), (nowcalled at their efforts for Holloway,University Royal staffof conference Also,special ZSI slidecollection. protozoa Director Song.Weibo thankDr.K.Chandra, We fromtheNationalNatu and grantno.31111120437 fromtheU.S. grant 1136580 provided by DEB ofparticipants theconsensus and reflects etal.2015).Thepresent September 2014(Dunthorn London, UKfrom1–3 ProtistBiologySociety of University for thatmetatRoyal Holloway, This reviewistheproductofaworkshopspons ACKNOWLEDGMENTS IRCN-BC (http://ircn-bc.org). me checklists forobservational Article re A biodiversity ofciliates. forbestpracti recommendations of specific needsintheform articulated this end,wehave whileassembling uniform standardsofpractice observations ofmicroorganisms. duetohi information abouttheirbiodiversity Intaxa. essence,research onciliate biodiversityconstrained basic is by a deficit in protists has,ofcourse thebiodiversityabout of progress inknowledge de over thelastseveral advances Technological CONCLUSIONS

, benefited from this trend, but not fromthistrend,but , benefited gularly updated listingofreco gularly updated thodologies madeava willbe The best remedy is an organized, sustained pushtofollow sustained is anorganized, The bestremedy in the workshop. Funding for the workshop was Funding forthe in theworkshop. ce and a proposal to populate a database onthe a proposaltopopulate ce and thanks are owed toEmily and the Perrier thanks areowed storical difficulties in making systematic difficultiesinmaking storical of Grand Challenges that are addressed by sets by addressed are that Grand Challenges of ored jointlyIRCN-BC andtheBritish by the of London, and to Martin Carr, Treasurer of London, and toMartinCarr,Treasurer of cades have made itpossi havemade cades National Science Foundation to John Clamp toJohn ScienceFoundation National organisms. Research on ciliates andother onciliates Research organisms. data that will form a future foundation.To thatwillformafuture data of ZSI, Kolkata, for providing details providing Kolkata,of ZSI, ofthe for ral Science Foundation ofChina to Foundation ral Science paper reviews topics that were discussed were discussed topicsthat paper reviews to the degree seen in multicellular to thedegree seen

mmendations accompaniedby mmendations ilable on the website ofthe ilable onthe ble to achieve rapid ble toachieverapid

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby AcceptedImproved data & Hunt,E.2009. Anwar, N. Agatha, S.,Spindler,M.& Wilbert,N.1993. Agatha, S.,Wilbert,N.,Spindler,M.& Elbräc O aloricate diversity of Agatha, S.2011.Global for th approach Agatha, S.2004.Acladistic of“type catalogue Aescht, E.2008.Annotated Article of Aescht, E.2001.Catalogue Adl, S.M.,Simpson,A.Lane,Lukeš, Bass,Bowser,G., S.S.,Brown, C.E., J., D., M.W., LITERATURE CITED comments. constructive for reviewer andananonymous editor ofJEM arrangements making thatallofthe sure linguistic data enrichment. ice. (Antarctica). Sea Weddell the water. sea in marineandbrackish (Ciliophora: Spirotricha). for “typification” species. of AustrianMuse further protistsattheUpper 1:1–350. 493. ofeukaryotes. 2012.Therevisedclassification W. Rueckert,S.,Shadwic Pawlowski, W., J., H., Mitchell,E.A. H., McManus, Lynn, D. Hampl, V.,Heiss, Burki,Dunthorn, M., F., Acta Protozool ., 32:261–268. the Namesof Generic Cilia Acta Protozool. BMC Evol.Biol Denisia Acta Protozool for the workshop went smoothly. We thankthe We wentsmoothly. theworkshop for

PLoS One, e classification of oligotrichid ciliates ofoligotrichid classification e retrieval fromTreeBASE retrieval ,

23:125–234. Ciliated protozoa(Cili hter, M.1990.Euplotidciliatesinseaiceof material” of ciliates of material” ligotrichea (Protista,C ligotrichea k, L.,Spiegel, C.,Smirnov,A.&F.k, Schoch, , 43:201–217. ., 9:93. um in Linzaum in(Austria) guideline including A., Hoppenrath, M., Lara, E., Le Gall, L.,Le Gall, Lara, E., M., A., Hoppenrath, D., Mozley-Stanridge, S. E., Parfrey, L. S.E.,Parfrey, D., Mozley-Stanridge, 6:e22466. 6:e22466. ., 29:221–228.

tes (Protozoa,Ciliophora). J. Eukaryot.Microbiol., (Ciliophora) and some (Ciliophora) andsome ophora) from Arctic sea ophora) fromArctic via taxonomic and viataxonomic iliophora, Spirotricha) 59:429- Denisia , This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted Theuseofsilv Cole, R.&F. 1940. Day, M. Chatton, E. & Lwoff, A.1930.Imprégnation, par M.T., H.,Brandl, Lynn,Chantangsi, D. C., A., Smith,M.Butcher, B. A.,Sharkey, M. (Ciliophora):taxonomy, withdivision Euplotida F.Hill, B. 1995.Theorder A.C.&Borror, Article oftheOxytrichid Berger, H.1999.Monograph ofoccurren 2010.Organization S.J. Baskauf, I. S. & S.,Fokin, Berendonk,T. Barth,Krenek, D., C.,SerranoS., L,Arregui, Muñoz-Fontela, technique. Abstract 47. technique. Abstract Séanc. Soc.Biol., fi douce, après ciliés marinsetded’eau Int. J.Syst.Evol.Microbiol Barcoding ciliates: a comprehensivegenus ofthe study of75isolates descriptions of179newspecies. based largely Braconidae: Rogadinae) study ofThai of 78:1–1080. nodes and theroleof creation process oftheir Eukaryot. Microbiol Paramecium taxoid. visualization ofthemicrotubularcytoskelet Euplotes . Biodivers.Inf., J. Eukaryot.Microbiol into several genera. intoseveral revealed by mitochondrial cytochrome c oxidase I coxidase mitochondrialcytochrome sequences. by revealed Aleiodes 104:834–836. 104:834–836. ., 53:20–25. 7:17–44. ( J. Parasitol J. Aleiodes ., 57:2412–2425. ., 49:312–318. J. Eukaryot. Microbiol J. Eukaryot. ) and Zootaxa, ., 26(Suppl.6):30–31. J. & Quicke, D. L. J. 2012. A turbo-taxonomic 2012.Aturbo-taxonomic L. D.J. & Quicke, J. Barasoain, I.Barasoain, & Guinea, A. Direct 2002. er albumose (Protargol Cole, J. C., Hetrick, N. & Ikonomi, C.,Hetrick,N.& P.2007. Cole, J. ce-related biodiversity resources basedonthe biodiversity resources ce-related Aleiodes on COI barcoded specimens, with rapid with rapid specimens, barcoded on COI ae (Ciliophora, Hypotrichia).Biol., Monogr. ae (Ciliophora, xation cytologiquexation etsansdesiccation. individual organisms as resource relationship relationship organismsasresource individual 3457:1–232. diffusion argentique, de l’infraciliature de l’infraciliature diffusion argentique, de on of ciliated protozoa on of U. 2006. Intraspecific genetic variation in genetic variation Intraspecific U.2006. ( Arcaleiodes

., 42:457–466. ) in protozoological ) inprotozoological ) (Hymenoptera: ) (Hymenoptera: with a fluorescent withafluorescent Tetrahymena. J. C. R.

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedand Leeuwenhoek van Dobell, C.1932.Antony F. A.,Amorim, de Carvalho,M.R.,Bockmann, integrative taxonomy B.Dayrat, 2005.Towards Article U.,Brown, G.,Achilles-Day, S. Day, J. LongDaggett,T. A.1992. ma P.-M.& term Nerad, O.2002.AsalutetoAntonyCorliss, va J. innomenclaturaltaxonomy. O.1972.CommonCorliss, senseandcourtesy J. O.1961.TheCiliatedProtozoa:Char Corliss, J. Inc., New York. p. vii + 435. York.p.vii+ Inc., New automation paradigm. impediment totaxonomy? Acommentary onsystematics and the cybertaxonomic- DeSalle, R., Ebach,M.C.& Nels J., C.,Faivovich, W. R., Page,J L. M.,Wheeler, Lundberg, G.,Gill,A.C.,Britz, J. R.,Wheeler E.M.,Crisci, L., N.,Cancello, Papavero, L., H.A.,dePinna,M. Britski, Figueiredo, J. Washington. 79–92. ManualofE (ed.), L.& D. Stetzenbach, protozoa. Protozoology.Protozoologists, Lawrence, Kansas.A93.1–A93.6. of Society cryopreservation. drying and Century founding fatherof protistology. 21:117–122. p.1–310 London New York. Literature. Press, Pergamon and In:

Hurst, C. J., Crawford, R. L., Garland, J. L., Lipson, D. A., Mills, A. L. L., A. Lipson, J. L., D.A.,Mills, Crawford,R. Garland, Hurst,C.J., Evol. Biol Evol. In : Lee, J. J. & Lee, Soldo, J. : A.T.(ed.),Protocolsin J. ., 34:140–143. & Warren, A.2007.Cultivationofalgaeand & Warren, n Leeuwenhoek ofDelft, Leeuwenhoek n on, G. J. 2007. Taxonomic impediment or 2007.Taxonomic on, G.J. nvironmental Microbiology. 3rd ed. ASM, ed. Microbiology. 3rd nvironmental acterization, Classifica Protist, his “Little Publications Animals”.Dover Biol. J.Linn.Soc Biol. D. S.,Branda, C.R.F.,Vivo,M.,de de J. V., McEachran, J. D., Schelly, R. C., D.,Schelly, V.,McEachran, J. J. intenance ofselected C. C., Menezes, N. A., Marques, F. P. N.A.,Marques, C.C.,Menezes, ., Vari, R. P., Grande, L., C. ., Vari,R.P.,Grande, Humphries, , Q. D., Stiassny, M. L. J., Parenti, L., Q.D.,Stiassny,L.Parenti, M. J., 153:177–190.

., mostversatile17th

85:407–415. tion andGuidetothe encysting ciliatesby Syst. Zool.,

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Acceptedcomp MorphologieFauré-Fremiet, E.1950. Lobban, C. Dunthorn, M.,Zufall, R.A.& 2014). (9–10 July Nomenclature Berger,Dunthorn, M.,Otto,J., S.A.,Stamatak Linz The ofzoological nomenclature. Dickinson, E. & Dubois A.,AeschtE. Article Dickinson,E.C Dubois, A.,Crochet,P.-A., Sessions1–6oftheLinzDubois A.& Zoocode E.2016. Committee Aescht Bartels, J., Astrin, J. Droege, P.,Butler,G., Barker, K., C.,Cantrill, D. Fr. British Societyfor ProtistBiology. International Research Netw Coordination context frommicr amplicons generation sequencing & F. Sto Audic, S.,Stock,A.,Kauff, on thesituationinbotany. actsinzoology, nomina andnomenclatural Nomenclaturaland problems taxonomic rela Löbl,A. 2013. Schatz,H.&Lavilla, E.O., I.,Koyamba, Ohler, V., V., Malécot, P., Frétey,T., Jaeger, Laure, D., deCarvalho,M.R., Bour, R., Blagoderov, V., 2016). (February–June Biodiversity Network (GGBN) data portal Petersen, G.,Sanjur,O., O´Tuama,E., J., D.,Mackenzie-Dodds, B., Hobern, F., Gemeinholzer, Forest, , 75:109–122. . Mol.Biol.Evol ., 31:993–1009. Dumerilia, Schindel, D. & Seberg, O. 2014. The Global Genome O. 2014.TheGlobalGenome Schindel, D.& Seberg, Zootaxa C. 2016. Burning questions and problems C. 2016.Burningandproblems questions Dumerilia , 3735:1–94. 6:38–70. 2015. Report of the 2014 joint workshop ofthe 2015. Reportofthe2014jointworkshop Eur. J. Protistol Eur. J. arée etsystéma ., Nemésio, A., Aescht, E., Bauer, A.M., A.,Aescht,E., ., Nemésio, eck, T. 2014. Placing environmental next- Placing environmental eck, T.2014. International Workshop ofZoological Workshop International is, A., Mahé, F., Romac, S., de Vargas, C. F., Romac,S.,deVargas, A., Mahé, is, . ork for Biodiversity Ciliates of ork for andthe

, 6:24–34. Nucleic Acids Res Acids Nucleic with brief comments on optical discs and with briefcommentsonoptical obial eukaryotes into a phylogenetic obial eukaryotes intoaphylogenetic ted to the electronic publication ofnew the electronicpublication ted to

tique des ciliés. tique des ., 51:118–119. ., 42 (D1):D607–D612. ., 42(D1):D607–D612. , Coddington, J., Coddington, J., Bull. Soc.Zool. This article is protected by copyright. All rights reserved. copyright. This articleis protectedby AcceptedF. Gachon, C.M.M.,Heesch, S.,Küpper, L.Foissner, W.,Chao,A.&Katz, A. 2008.Dive Staa M.,Vander Strüder-Kypke, Foissner, W., & H.2002. Foissner, Berger, W.,Agatha, S. light of‘basic 2014.Anupdate Foissner, W. ArticleFoissner, W.2002.Neotypificati diversity F.Fenchel, isdifferent? &Finlay, T.2004.Protist Esteban,G. B. J., Brown,I. S.,Clarke, J., H. Finlay, Black, B. J., F.Fenchel, & T.1996.BiodiversityFinlay, O., Esteban,G. Corliss,J. B.at themicrobial J., Finlay, Curds,C.R.,Bamforth, B. J., S.S., Campbell, C.N.,Clarke, A., (Protista: Ciliophora). study. acombined bromeliads (Bromeliaceae): H.P.2003.Endemiccilia Hackstein, J. Desert. Namib Etosha Region andthe withEmphasi Namibia (SouthwestAfrica), studiesofciliated protozoa’. taxonomic Bull. Zool.Nomencl 155:15–22. community L., K.2000.Estima Vickerman, Rollett,A.& level: the number offree-living ciliates inthe biosphere. Arch. Protistenkd lake Africansoda microorganisms fromtwo Eur. J. Protistol . Protist, ., 133:81–91. 151:69–80. ., 59:165–169. Biodivers. Conserv ., 39:365–372. on of protists, especially c on ofprotists,especially Dorrell, R. G., Field, J., Gont J., Field, Dorrell, R.G., C., Achilles-Day, U. E. M., Brennan,C., Achilles-Day, U.E.M., D., & Bafort, J. M.1987.Cilia J. Bafort, & Soil Ciliates(Protozoa,Ciliophora) from and scanning electron microscopic methodsfor microscopic electron scanning and Denisia tes (Protozoa, Ciliophora) from tank tes (Protozoa,Ciliophora)fromtank y, G. W. M., Moon-van der Staay,&y, M.,Moon-vander S.-Y. G. W. K. J., Esteban, G. F., Hindle, R. M., Olmo, J. Esteban,G.F., Hindle,R.M.,Olmo,J. J., K. Int. J. Syst. Evol.Microbiol Int. J.Syst. morphological, molecular, and ecological and ecological molecular, morphological, rsity and geographic distribution ofciliates geographic distribution and rsity ., 17:345–363. ., 17:345–363. s on two Contrasting the s ontwo Environments, s (Lake s (Lake Nakuru andLake Simbi, Kenya). tinggrowth ofthesoilprotozoan the , 5:1–1459.

iliates (Protozoa,Ciliophora). Q. Rev. Biol Q. Rev. arek, S., Menendez, C.R., arek, S.,Menendez, ted protozoaandother ., 64:271–292. ., 71:221–237. ., 71:221–237. Protist, This article is protected by copyright. All rights reserved. copyright. This articleis protectedby AcceptedHoef-Emden, K.& Melkonian, Hodges, E.R.S.2003.TheGuildHandbookofSc R.2003.A M.,& McNuff, J. Hide, G.,Hughes, Bionom TermsUsedin L.Hawksworth, D.2010. Guggiari, M.& Peck,R.2008. Article &Z. C. Kellogg, A., Gray, M.A.,Pratte, age. Linnaeus intheinformation 2007. Godfray, H.C.J. Lynn, H.2012.Spatialgene& D. Gentekaki, E. 1976. & Berger,Gates, M.A. J. of ofthreestrains 1974.Abiometricstudy & J. Berger, Gates, M.A. insights intoalong-hidden dimorphism. combination ofmol a (Cryptophyceae): p.1– Hoboken, NJ. 3:7. Blepharisma japonicum Inplant communities).GlobalBiodiversity Protistol sewage treatmentMolecular plant: cy and for environmental bacterial community samples. of theperitr and (Ciliatea: Hymenostomatida withtaxonomic resources 2013. TheCCAPKnowledge G. Day, M.& J. Veszelovszki, K.,Blaxter, R. A.,Guiry,Gharbi, J., Saxon, M.D., P. pentaurelia ., 44:168–180. ichous ciliate .

Trans. Am.Microsc.Soc. 656. using PCRandimmobilisation onFTA paper. ciliate The bacterivorous M. 2003.Revisionofthegenus Morphometric inseparability of Morphometric inseparability Carchesium polypinum data. andmolecular ).J. Zool Can. Base: linking and protistan 2013. Comparison of DNA preservation methods 2013.ComparisonofDNApreservation ecular phylogeny and morphology provides provides and morphology ecular phylogeny tic variation, phylogeography and barcoding andbarcoding variation, phylogeography tic Protist, rapid andsimplemet rapid tological descriptions for barcoding. descriptionsforbarcoding. tological enclature: The naming of organisms (and organisms (and enclature: Thenaming of . 52:1167–1183. ientific Illustration. John Wiley & Sons, formation Facility, p.1–215. Copenhagen. formation , 95:507–514. , 95:507–514. Syst. Biodivers., Syst. 154:371–409. . FEMS Microbiol.Ecol FEMS Cyclidium glaucoma Nature,

Eur. J. Protistol., Cryptomonas Cryptomonas cyanobacterial biological biological cyanobacterial Paramecium primaurelia Paramecium 446:259–260. Tetrahymena pyriformis hod ofdetection 11:407–413. 48:305–313. , isolated from a from , isolated BMC Ecol BMC ., 83:468–477. ., 83:468–477. Eur. J. .,

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted & Soldo,A. T. J. Lee,1992. Protocols in J. mit ei Klein, B. M.1926.Ergebnisse Ikonomi,P., Cooper,J., F. Kher, C.P.,Doerder, L.B. L. O. O., Griffin,A.,Pirog, K.,Costas, G. B., Snoeyenbos-West, Katz, A.,McManus, Article A.V.2007.[PhylumJankowski, 1901.ReviewofTaxa]. CiliophoraDoflein, InternationalICZN CommissiononZoolog= International CommissiononZoologicalICZN= C.,Harmann,E.C Huss, V.A.R.,Frank, Lawrence, Kansas. Kansas. Lawrence, 56:243–279. 13. I barcode subunit (cox-1) unknowns using coxidase thecytochrome D. H.2011.Barcoding 65. highgene flowanddiversit for evidence debate: everywhere’ the‘Everything is 2005.Reframing & W. Foissner, Russian withEnglish summary). on (ed.), Protista:Handbook ofpublication. andrefinemethods expand 78 ofth Articles 8,9,10,21and +306. Padova.p.xxix La Garangola, Tipografia International Trus Biological Sciences. edition FourthZoological Nomenclature. the genus E. P.& Kessler, Wenzeler, Chlorella sensu lato(Chlorophyta). Tetrahymena

yciliate morphospecies. in 1999. Biochemical taxonomy and molecular phylogeny of of phylogeny andmolecular taxonomy 1999. Biochemical Zoology. Part 2. Nauka, St. Petersburg. 415–976. (in St.Petersburg.Zoology. 415–976. Part2.Nauka, ner Silbermethode e International Code of Z International Codeof e ., Hirmer, M., Kloboucek, A., Seidel, B. M., M.,Kloboucek,A.,Seidel, ., Hirmer, Protozoology. ofProtozoologists, Society : discriminating species and identifying ical Nomenclature. 2012. Amendment of t for Zoological Nomenclature, London. Zoological Nomenclature, t for P., Achilles-Day, U., Kupper, F. C. & Lynn,& F. C. P., Achilles-Day, U.,Kupper, Nomenclature.Inte1999. adopted by the International Union of Internationaladopted by Union the Bull. Zool. Nomencl., J. Phycol beiCiliaten.

Aquat. Microb.Ecol ., 35:587–598. oological Nomenclature to Nomenclature oological Arch. Protistenkd 69:161–169. rnational Codeof . Protist, . Protist, In : AlimovA.F. ., 41:55– 162:2– .,

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted Catalogue of A. 1991.ATCC Nerad, T. weighting. character basisforapriori A. 1986.Arational Neff, N. ofthespecies 1976.Characterization W. J. &L. McCoy, Nanney, D. G. U.E.M.&Müller, J. H.,Achilles-Day, Day, U.E.M. & J. Day, Müller, H.,Achilles-Day, P.-M.& T. McGrath, M.S.,Daggett, Nerad, ArticleM. Marin, B., M.& Palm,A.,Klingberg, Melkonian, Lynn,H. & Simpson,A.G.B. D. 2009.Desc Protozoa.Charact H. 2008.TheCiliated Lynn, D. Q. N. &Lipscomb, Wheeler, D.,Platnick, molecularisation oftaxonomy. Lee, M.S.Y.2004.The pyriformis andfreezing. Spirotrichea) todesiccation Colpoda inflata vitrification protocols ciliatethe freshwater ciliate Protist, signatures comparisons andsynapomorphic eugl revision ofplastid-containing Eukaryot. Microbiol +605. p.xxxiii Dordrecht. ed.Springer, Literature. 3rd comment onDNAtaxonomy. Didinium nasutum 154:99–145. complex. (Ciliophora,and Colpodea) ., 56:403–405. Trans. Am.Microsc.Soc. Meseres corlissi . CryoLetters . Trans. Am.Microsc.Soc Trends Ecol.Evol., Protists, ATCC, Rockville,MD. Protists, enophytes based on SSU rDNA sequence onSSUrDNAsequence based enophytes , 29:329–338. 2003. The intellectual content of taxonomy: a The intellectualcontentof 2003. A. 1977. Studies on the preservation ofthe Studiesonthepreservation A. 1977. G. 2008. Cryopreservation of resting cysts resting of of G.2008.Cryopreservation by conventional two-st by conventional ribing new taxa of unicellular protists. ofunicellular taxa new ribing

2010. Tolerance of the resting cysts of resting ofthe 2010. Tolerance Eur. J. Protistol Eur. J. erization, ClassificationandGuidetothe in the SSU rRNA secondary structure. SSUrRNAsecondary structure. inthe Meseres corlissi Meseres

, 95:664–682. , 95:664–682. 2003. Phylogeny and taxonomic taxonomic 2003. Phylogeny and Invertebr. Syst., 18:65–66.

., 96:519–525. ., 46:133–142. Syst. Biol. Syst. (Ciliophora, ep methods and one-step ep methodsand 18:1–6. 18:1–6. Tetrahymena , 35:110–123. J. This article is protected by copyright. All rights reserved. copyright. This articleis protectedby AcceptedSchlö Pröschold, T.,Marin,B., 1975. Berger,M. A.& J. Powelson, E.E.,Gates, Petz, W., Song, W.& Wilbert, N.1995.Ta Article Audic, S., Adl,S.,Bass,Pawlowski, J., Be D., L.N. &Oliveira-Pinto, F., Nieri, 1993. Ricci, Nobili, R.,Luporini, P.&Br Dini,F. 1978. P.-M. 1992.Cry Daggett,A. & Nerad, T. taxonomic revisionof taxonomic syngens of Stapfia, Ciliophora)intheEndopagial and (Protozoa, e1001419. theanima beyond eukaryotic richness C.2012.CB Vargas, Schnidel, D.& de L., J., Stoeck,T.,Zimmermann, G. B., Stern,R.F., J. Smirnov,A.V.,Spouge, Nitsche,F., D. G.,Mitchell,E.A.D., Kostka,M., R., Jirku,M.,Keeling, J., P. Dunthorn,M.,Fiore-Donno, J., I.,Decelle, protozoa Evolution (ed.),Ma J. &Battaglia,B. Beardmore, evolutionary marine insome trends species ofEuplotidae (Ciliata Hypotrichida). A92.1–A92.4. Kansas. Lawrence, ProtocolsinProtozoology.& Soldo,A.T.(ed.), Society Protozoologists, of 40:1–23. J. Theor. Biol J. Theor. . Plenum Press, New York. 591–616. PlenumPress, NewYork.591–616. Paramecium aurelia Paramecium Chlamydomonas ., 163:365–372. sser, U. G. & Melkonian, M. & Melkonian, sser, U.G. . Can. J.Zool. opreservation of non-encysting ciliates. ofnon-encysting ciliates. opreservation xonomy and Ecology of xonomyand Ecology eeding system, species relationships and speciesrelationships system, eeding l, plant, and fungal kingdoms.l, plant,and Romeralo, M., Saunders, G. W., Simpson,A. M.,Saunders,G.W., Romeralo, lbahri, L., S.S.,Cepicka, Berney, C.,Bowser, lbahri, Simulation ofcreeping (Chlorophyta). I. Emendationof (Chlorophyta). OL Protist Working Group: barcoding OL Working Group: barcoding Protist rine Organisms: rine Organisms: Ge Kudryavtsev, A., Lara, E., Lukeš,Mann, J., A biometrical analysis A biometricalanalysis A. M., Gile, G. H., Holzmann, M., Jahn, M.,Jahn, Gile, G.H.,Holzmann, A. M., Pelagial of the Weddell Sea, Antarctica. Sea, oftheWeddell Pelagial , 53:19–32.

2001. Molecular phylogeny and 2001. Molecularphylogeny netics, Ecology and netics, Ecology theCiliateFauna movements of ciliated movements of 22stocksoffour of PLoS Biol., In : Lee,: J. J. 10: In:

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted speciesconcept A pragmatic Seifert, B. 2014. St Knapp,S., C. J., Seberg, O.,Humphries, R.2003.Thesp Schlegel, M.& Meisterfeld, L. F.,Bachy, C., V. Santoferrara, Alder, A., Go Article& G.B.L.F., Alde McManus, Santoferrara, L.Illustration.Ridgway, St J. 1978.Scientific Quintela-Alonso, P.,Nitsche,F., Wylezic 2008. ZooBank:L.Pyle, Deve E. R. & Michel, 86:85–93. ofrepr independent fromtheirmode taxonomy. insy Andersen, N.M.2003.Shortcuts Protistol., Ciliophora, Spirotrichea). biodiversity studies inloricate protists:thethe case tintinnids(Alveolata, of A.,X M.C.,Warren, D., Strüder-Kypke, Spirotrichea). w speciesdiscrimination morphology for 1–187. South Africa. Tetrahymena years information. ofbiological Oogamochlamys Chlamydomonas 39:349–355. Trends Ecol. Evol., Trends Ecol. (Ciliophora, Oligohymenophorea) fr Oligohymenophorea) (Ciliophora, J. Eukaryot. Microbiol J. Eukaryot. Protist, gen. nov. and gen. nov. Ehrenberg and Ehrenberg 164:24–36. J. Eukaryot.Microbiol. 18:63–65. Lobochlamys Zootaxa, Chloromonas h, C., Arndt, H.& 2013. Anew h, C.,Arndt, Foissner, W. evenson, D. W., Petersen, G., Scharff, N. & Scharff, G., Petersen, evenson, D.W., oduction orevolutionary history. ., 60:235–246. r, V. A. 2013. Utility of geneticA. 2013.Utility markersand r, V. of ecies problem in protozoa revisited. problem inprotozoa ecies stematics? A commentary on DNA-based A commentary onDNA-based stematics? anford University Press, Redwood City, Press,Redwood CA.p. anford University applicable toalle applicable loping anomenclatural loping ng, J., Kim, Y.-O., Saccà, A., da Silva Neto, I. Neto, A., daSilva Y.-O.,Saccà, Kim, J., ng, u, D., Yi, Z.& S.2016.Updating Agatha, u, D., ithin the order Tintinnida(Ciliophora, 1950:39–50. gen. nov. Gobi, anddescriptionof Gobi, , 63:651–656. ,

om groundwater of Cape Town, Cape om groundwater of Protist, ukaryotic organisms tool for unifying250 tool 152:265–300. Soil Org., Eur. J.

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby V DeVille, M. M.,Day,Tompkins, J., G.& J. 2012. Xu,D.,W. Sun, P.,Clamp, & Miao, J., Kusuoka,Y. H. 2010. Lynn,& D. Strüder-Kypke, M.C. Stoeck, T.,Przybo Sonneborn, T.M.1957.Breeding repr systems, Song, 1993.Studiesonthecortical W. 1967. S. W. Simon, E.M.& Hwang,

Acceptedď Article a č ný, P. & Foissner, W. 2012.MonographW. of Foissner, P.&ný, Rhynchostomatia). Cata and Protozoa 142. fo coding gene derived fromthe Vorticella Pe (Ciliophora, Oligohymenophora, evaluation ofitssuitabilitya biodiversityas marker. cytochrome forciliates. ribosomal DNAasbarcode Washington, 50:155–324. American Association 28–29,1955. December ofScience Advancement forthe Association American ofthe Meeting Atlanta protozoa. 11:122–129. grandinella performance. thawing onbreeding and the families Vorticellidaeand Astylozoidae using molecular characters In: ś (Müller,1773)(Ciliophora,Oligotrichida). , E. & Dunthorn, M. 2014. The D1-D2 region of the large subunit thelarge D1-D2region of , E.&Dunthorn,M.2014.The c Mayr, E. (ed.), The Species Problem. A Symposium Presented atthe ASymposium Presented TheSpeciesProblem. (ed.), Mayr, E. oxidase subunit I gene in subunit (COI) oxidase logue of Strains. Denisia, 31:1–529. Tetrahymena morphogenesis duringcell divisionin morphogenesis r small subunitribosomal RNA. r small

Science, CCAP, Ambleside. CCAP, ritrichia) is a grade not isa ritrichia) Comparative analysis ofthemitochondrial Comparative analysis Turner, M. F. 1995. Culture Collection ofAlgae M.F. 1995.Culture Turner, Mol. Ecol. Res Mol. Ecol. oductive methods, and species problemsin methods,and species oductive the Dileptids(Protista,Ciliophora, the – effect of freezing and subsequent and offreezing –effect 155:694–696. ciliates (Alveolata for the Advancement of Science, ofScience, theAdvancement for

Vorticella Syst. Biodivers ., 14:458–468.

Chin. J. Oceanol. Limnol., Chin. J.Oceanol. a clade: redefinition of clade: redefinition a Linnaeus, 1767 , Ciliophora)and Protist, ., 8:131–148. Halteria 163:129–

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted (http://www.ncbi.nlm.nih.gov; on6/4/2015). accessed Figure 1. FIGURE LEGENDS I ofBiological F. 1988.AHandbook Zweifel, Zhao, Y., E., Yi, Gentekaki, Z. & Lin, X. Article A.& Y. Gong, Z., Xu,K.,Warren, Zhan, Descriptionsof 2005. Foissner,Xu, K.& W. P.&Wood, McDonnell,P.1994.Scie E.1999.Describing Winston, J. Prac Species. K. &Will, W. Rubinoff,D.2004.Myth ofth Press, Chicago, IL. Press, Chicago,p.1–152. PLoS One, cytochrome oxidase subclass MobiliaKahl,1933. small subunitribosomal RNA genesequen relationships ofthesubc morphology. fraterculum p.1–176. Sons, Hoboken,NJ. Techniques, Desig and MedicalRendering +518. Columbia University NewYork.xx Press, for identif morphology replace Ciliate sequences ofthe Ciliatesequences 8: e77044. 8: e77044. n. sp. (Ciliophora, Haptoria), twospeci n.sp.(Ciliophora,Haptoria), J. Eukaryot. Microbiol J. Eukaryot.

c subunit I gene subunit ingenus lass Peritrichia(Ciliophora, lass small subunitribosomalRNAgene intheNCBIGenBank J. Eukaryot.Microbiol., ication andclassification ntific Illustration:ntific Zoological, AGuidetoBiological, 2009. Reconsideration of phylogenetic ofphylogenetic Reconsideration 2009. 2013. Genetic differentiati 2013. Genetic ., 52:298–309. e molecule: DNA barcodes for species cannot species cannot for DNAbarcodes e molecule: Protospathidium serpens Protospathidium tical Taxonomic Procedure for Biologists. Procedurefor Taxonomic tical llustration. 2nd ed. University of Chicago of Chicago 2nded.University llustration. n, Printing, and Display. John Wileyn, Printing, andDisplay.& John ces, with the establishment of a new with theestablishmentofa ces, Paramecium

es based on different resting cyst resting es basedondifferent Oligohymenophorea) based Oligohymenophorea) on 56:552–558. . Cladistics (Protista,Ciliophora). on of the mitochondrial on ofthe (Kahl, 1930)and (Kahl, , 20:47–55. P. This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted used thatare vacuoles inthecell isthemacr structure central cell. Thelarge mouth ( using thebasket-shaped Living ciliate. sp., ahypotrich envelopact fashion, whileanelastic aspiral in contract to it causes that aspasmoneme contains stalk The vacuoles. many food thece theanteriorof aroundtheedge of extend feeding, the one is contracted. tothe left feeding The ciliapolykineties) and (haplokinety interfe under Nomarskidifferential =50µm. bar Scale cell. the bristles) cirri (ciliary cell, are spots near the frontofthe cell, forming margin ofthecellisa front(top) collar aroundthe Pattersoniella vitiphila Article structurenear globular macronucleus isthe formsthecytopha system ofmicrotubulesthat arranged inlongitudinal rows;the oral cilia ar the cilia(basal of thebases impregnates hasbeen Thecell oligohymenophorean ciliate. developing extrusomes ribbonofmacr stained pinkaretheirregular that ofextrusomes band underlain withadense andstainedwithFeulgen The fixed reagent. Homalozoon vermiculare Figure 2. Photomicrographs of representative ciliat ofrepresentative Photomicrographs . Scale bar = 50 µm. = 50µm. . Scalebar , a hypotrichciliate. Fixed cell stained The withprotargol. C-shaped , a crawling, ribbon-shaped litostoma ribbon-shaped , acrawling, D. . The macronuclear nodules areth . Themacronuclearnodules

cell under phase contrast optics. contrast cell underphase Vorticella convallaria upper right). Several ingested diatoms can beseeninsidethe ingested diatomscan Several upper right). for osmoregulation. Scale bar = 50 µm. = 50µm. Scalebar osmoregulation. for rence contrast optics, theone contrast optics, rence s as antagonist. Scale bar = 50 µm. Scalebar=50µm. antagonist. s as bodies) and the nucleus. The somatic ciliaare thenucleus.Thesomatic and bodies) onucleus. Therearemultip the center of the cell. Scale bar = 20 µm. =20µm. Scalebar ofthecell. center the B. onuclear nodules, the micronuclei, and a few andafew nodules,themicronuclei, onuclear anterior mouth,atthetopofimage,is anterior e densely packedand appearas shortbands. A doral zoneofmembrane doral

rynx extends fromthemouthintocell.The rynx fixed andstainedwithprotargolfixed that al bands and a curving row in the center of the in thecenterof row al bandsandacurving Tetrahymena pyriformis are used to capture food. The structures food. The usedtocapture are ll and curveintothemouth.Thecellscontain ll and e taxa (originals from D. J. Patterson). D. J. from (originals e taxa , a peritrich ciliate. living Two cells

tid predator. The cell has been tid predator.Thecellhasbeen Thecelleatssmallalgae, e globular inclusionswithin e to the right is extended and isextended to theright le smallc lles (ciliary fans). The (ciliary fans). lles , an , an E. F.

Trithigmostoma

Paramecium Paramecium ontractile C.

A.

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby zone ofmembranellesthe anterior at cell. also from the extend ofthe remaining Cilia body feedin its posteriorendand,when Nomarski differential interferenc 20 µm. jumpingcilia motion;further lay posterioradpressed portionofthe= tothe body. Scale bar contrast optics.Stiffbundlesof giving the algae endosymbiotic cryptomonad (= = 20µm. Scalebar body. along ofthe thelength (kineties) thatextend optics. The mouthisthe tothe extension anterior right.cilia The formdimpled rows sp., asmallandrarely-encounter in vesicles lieoverthemacronucleus on small cell,and seen aroundthe at thean are twozonesofcilia exte with longitudinal thatformarounded grooves Living contra stomach ofabison. underphase cell µm. =50 bar swarmers. Scale stalk. Ciliaareab a of substrates by means containing extrus apex expanded flagellates that swimintothe extending sticky Nomarski differential interferenc =50µm. bar Scale cytopharynx. the (minuteharpoon-likestru extrusomes optics.The contrast differential interference bursaria

Accepted rubra Myrionecta Article K. , apeniculidciliatewith

Stentor coeruleus Stentor ), a small marine), a small planktonic litostomatid ciliate that contains , a trumpet-shaped heterotr , atrumpet-shaped terior end. The ciliate feedsonb end. The terior H. equatorial cilia extend fromth cilia extend equatorial ed karyorelictean ciliate.Lied karyorelictean omes that catch hold of any prey. The cell is attached to to attached is cell prey.The ofany hold catch that omes e contrast optics. The cell attaches toimmersed surfaces via e contrast optics. Thispredator captures ciliates other and

endosymbiotic zoochlorellae. Eudiplodinium g, the cell has acharacteristic particles of wood. Twocontrac particles ofwood. G. the left cell half. Scale bar = 20 µm. =20µm. half.Scalebar the leftcell ctures). The pear-shaped area in the center of the cell is ofthe inthecenter area pear-shaped ctures). The

Acineta sent in the trophic cell, but present inthe sent inthetrophiccell,butpresent cell surface is underlain with many rod-shaped many rod-shaped isunderlainwith cell surface cell its red color. Living cell under phase Livingcell cell itsredcolor. tentacles. Each tentacle tentacle Each tentacles. sp., asuctoriancilia sp., sp.,anentodiniomorphidciliatefromthe st optics.Thebody isverystiff, sculpted nsion at the posterior end of the cell. There ofthecell.There nsion attheposteriorend ich ciliate. Liich ciliate.

ving cell under phase contrast phase contrast cellunder ving e cellandtheiractioncausesa Living cellunderNomarski acteria, many of which canbe of many acteria, conical form withtheadoral form conical tile vacuoles and associated andassociated tile vacuoles te. Living cellunder te. ving cellunder is a mouth andhasan is a J.

Mesodinium rubrum I.

Cryptopharynx

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted freshwater itfeeds habitats, onpl where leads formthe ofthe anterior cell tothe cytostome. The ciliate ismostly instill- found op Living cellunderdarkfield colpodid ciliate. huge inform the cellgravitational as tothe of direction Scale pull. bar = 50µm. with abright refr buteach of asimilarsize peri and alight core has adark nodules isevidentjust One ofthemacronuclear most which engulfs cell, ofthe the anteriorright Livinghabitats. underphase cell Articlebar =20µm. cell. Scale ofthe surface thatareusedtok underlain withextrusomes from thecell,extending of along thebottomedge nodules macronuclear twolarge optics. Thereare Livingsp., alitostomatidpredatoryciliate. thatextrusomes areto killprey used small ciliates. -often Scale= 50µm. bar thetipofex substrate. Themouthisat theposteriorend while prey, for searching Th contrast optics. under phase 100 µm. = bar Scale cell surface. fromminutepartic color comes Theblue surface. pheral region. Anteriorly andposte Anteriorly pheral region. e extensible andcontractile e extensible contrast optics. The sickle-shaped mouth region is located to mouthregion islocated sickle-shaped optics.The contrast L.

Lacrymaria olor N. anktonic algae. Scale bar = 50 µm. =50µm. Scalebar algae. anktonic

Loxodes Loxodes tensible neck and is expanded because ofthe because tensible neck andisexpanded actile granule. These are Müller’s bodies that are Müller’s granule. These actile of the body oftenremainsof the attached tothe cell seenfromtheside ill prey. Somatic ly algae, such as diatoms, and cyanobacteria. cyanobacteria. as diatoms,and algae,such ly above themid-lineandin in the center of the cell. The mouthlies thecell. inthecenterof les (cortical granules) lying justunderthe granules) (cortical les near the middle to the anterior end, and is end, nearthemiddletoanterior sp., a karyorelictid c sp., akaryorelictid tics. There is a large, curved channel that curved channel tics. Thereisalarge, , a predatory ciliate.Living haptorid cell

anterior portionmovesaround, anterior cilia extend from theventral from cilia extend under phase contrast contrast underphase riorly to it are two vacuoles toitaretwo vacuoles riorly iliate from freshwater iliate fromfreshwater theleftcellhalf;it O.

Bursaria M.

Litonotus sp., a This article is protected by copyright. All rights reserved. copyright. This articleis protectedby 2010) from Baskauf a informationresources Table 1.Categories of hsclojc mtra reat filmnegative material artefact representations specific ofrepresentation form physical object resource of category Accepted Articleinformation digital image file pplicable to biodiversity of ciliates (modified ofciliates tobiodiversity pplicable taxonomic synonymy taxonomic classification phylogenetic tree sequence alignment DNA/RNA sequence specimen data video original illustrations notes laboratory hard-copy field hard-copy notes specimens fixed slides prepared preserved cell/DNA sample living/viable culture film movie photographic print physical-chemical measurements measurements physical-chemical coordinates geographic

This article is protected by copyright. All rights reserved. copyright. This articleis protectedby Accepted Article