Handbook of the protists

1662 Pages·2017·54.443 MB·English

by  Archibald, John M., Simpson, Alastair G. B., Slamovits, Claudio H

John M. Archibald
Alastair G.B. Simpson
Claudio H. Slamovits
Editors
Handbook of
the Protists
Second Edition
Handbook of the Protists
(cid:129)
John M. Archibald Alastair G. B. Simpson
Claudio H. Slamovits
Editors
Handbook of the Protists
Second Edition
With383Figuresand51Tables
Editors
JohnM.Archibald AlastairG.B.Simpson
DepartmentofBiochemistryand DepartmentofBiology
MolecularBiology DalhousieUniversity
DalhousieUniversity Halifax,NS,Canada
Halifax,NS,Canada
ClaudioH.Slamovits
DepartmentofBiochemistryand
MolecularBiology
DalhousieUniversity
Halifax,NS,Canada
HonoraryEditors
LynnMargulis(representedbyJenniferMargulis)
MichaelMelkonian
DavidJ.Chapman
JohnO.Corliss(representedbyYuemeiCorliss)
ISBN978-3-319-28147-6 ISBN978-3-319-28149-0 (eBook)
ISBN978-3-319-28148-3(printandelectronicbundle)
DOI10.1007/978-3-319-28149-0
LibraryofCongressControlNumber:2017945328
1stedition:#JonesandBartlettPublishers1990
#SpringerInternationalPublishingAG2017
2ndEditionofTheHandbookofProtoctista.TheStructure,Cultivation,Habitats,andLifeHistoriesofthe
EukaryoticMicroorganismsandtheirDescendantsExclusiveofAnimals,Plants,andFungi.AGuideto
the Algae, Ciliates, Foraminifera, Sporozoa, Water Molds, Slime Molds, and Other Protoctists. Lynn
Margulis,JohnO.Corliss,MichaelMelkonian,DavidJ.Chapman(eds.),JonesandBartlettPublishers,
Boston,1990.
Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthe
materialisconcerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,
broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionorinformation
storageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology
nowknownorhereafterdeveloped.
Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublication
doesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevant
protectivelawsandregulationsandthereforefreeforgeneraluse.
Thepublisher,theauthorsandtheeditorsaresafetoassumethattheadviceandinformationinthisbook
arebelievedtobetrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsorthe
editorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinorforanyerrors
oromissionsthatmayhavebeenmade.Thepublisherremainsneutralwithregardtojurisdictionalclaims
inpublishedmapsandinstitutionalaffiliations.
Printedonacid-freepaper
ThisSpringerimprintispublishedbySpringerNature
TheregisteredcompanyisSpringerInternationalPublishingAG
Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland
In memory of Lynn Margulis (1938–2011),
tireless champion of the microbial biosphere
Foreword
Beitfortheirimportanceintheplanet’sfoodweb,fortheiroriginalityincarryingout
their cellular processes, or for their Haeckelian elegance, one writing about the
protists soon finds oneself composing a paean. As is true for any of the large
groupings of living organisms, protists are varied, complex, and beautiful – only
moreso.Theyareagrabbagofhugelydistinctorganisms,butwhatagrabtheyare!
Theirendlessfascinationbeguilesstudentsofallaspectsoflife,thosewithorderly,
aswellasthosewithunrulyminds.
Protist varietyiseasily told bythevastrange oftheirdimensions.Evenleaving
aside the giant algae, readily visible with the naked eye, many (e.g., Ostreococcus
tauri)areminimalistshoveringattheonemicrometerlowerlimitofeukaryoticsize.
Some have very large genomes – the claim has been made that the appropriately
named amoeba Polychaos dubium has 670 billion base pairs! Others, such as the
parasitic microsporidian Encephalitozoon cuniculi, manage with a minute 2.9 mil-
lionbasepairs.
Cellular complexity is carried to extremes by the protists. The ciliates and
flagellates(mastigotes),forexample,possess–toshamelesslyuseanthropomorphic
terms – a mouth (some with fancy lips), a stomach, an anus, a bladder, multiple
propulsion devices, and an armamentarium of weapons that allow them to feed on
othermicrobes.Andsomedinoflagellatessportthatmostamazingofcellstructures,
theeye-likeocelloid.Inmulticellularorganisms,suchstructuresandtheirfunctions
are assigned to specialized cells; in the protists, one cell does it all by itself. One
wonders about the trade-off involved, in doing everything yourself versus
employingadifferentiatedconsortiumtodothework.Theveryexistenceofprotist
complex body plans brings up the distinction between unicellularity and multi-
cellularity, a blurry one at best, but one especially relevant to this field. Multi-
cellularity has originated on multiple occasions within the protists, hence they are
mostlikelytoproviderelevantanswerstoourconjectures.
Theprotistsalsomakeeccentricusesofchemicals,includingsomeelementsthat
are seldom employed in the biological world. Diatoms use silica for their shells
(tests),whichisexcitingenough,butotherplanktonicorganisms(theacanthariaor
“ray animalcules”) make skeletons out of strontium sulfate (celestite)! Yet others
formintracellularcrystalsofbariumsulfate(barite).Andmanytherearethatmake
structures of imposing beauty. Some, such as the radiolarians, coccolithophorids,
vii
viii Foreword
and diatoms, are pure eye candy. Moreover, their skeletons have accumulated in
formationsofsuchmassivedimensionsthattheyhavechangedtheEarth’sgeology.
Photosynthetic protists (algae) account for perhaps half the world’s total photo-
synthesis and are indispensable for life on Earth. The others, the heterotrophic
protists, make their living largely by eating other microbes and also play a huge
roleinthemovementofnutrientsontheplanet.Theygrazeonprokaryotes,whichby
andlargetheyregardaspacketsofnutrients,andintheprocessregulateprokaryotic
populationdensitiesinmanynaturalenvironments.Theyarethemselveseaten,often
byotherprotists.Onewondershowmanylayerstherearetothis.
Lettingmymindwander...aboutwhatwouldhappenifNobelPrizesweregiven
toorganismsforhavingevolvedimportantandreadilyascertainablephenomena,as
well as to the researchers who discovered such evolutionary achievements. Surely,
Tetrahymena warrant multiple prizes for contributing the first known example of
splicing and ribozymes, plus telomeres and telomerases. And Paramecium also
comestomindforcorticalinheritanceandothergeneticmarvels.Also,doesn’tthe
invention of the macronucleus – that talented device that permits rapid growth of
intricate cells – deserve a special accolade? Someday, as researchers continue to
delve into this rich treasure trove, many more organisms will qualify. Possibly
Oxytrichia, Cyanidioschyzon, Ostreococcus or, closer to immediate human con-
cerns, Giardia, trypanosomes, and Toxoplasma. Make your own list of protists
deservingtobecomeNobelists.
Whateverphylogeneticdiagramyouprefer,mostoftheeukaryoticlineagesbyfar
will be of protists. Their evolution started at the very emergence of the eukaryotic
cell and has repeatedly involved the lateral transfer of whole genomes. In some
instances, endosymbiotic events have occurred not just once, but twice and even
threetimesinthesamelineage.Itisevidentthatevolutionheredidnotproceedby
timidjumps,butratherbyboldleaps.
ForthesereasonsandmanyothersIhavenotbroughtup,protistsarethebasisfor
the understanding of all eukaryotic life in both time and space. So, the study of
protistsisnotanobscuretopictobelefttoafewspecialists.Itistheconcernofall
biologistsaswellasplanetaryscientistsandwhoknowswhoelse?
IwasaskedtowritethispiecebythelateLynnMargulis,afriendofold.Itriedto
wiggle out of it, but those of you who reacted in such manner to a request of hers
shouldbesmilingbynow.Inallways,scientific,intellectual,andpersonal,shewas
utterly irresistible. It worked out – I am glad to contribute to this work, a fitting
tribute to her unique contribution to the field in which she started in science and
whichsheneverforsook.
MoselioSchaechter
Preface to the Second Edition
This Handbook of the Protists is the 2nd edition of the Handbook of Protoctista,
whichwaspublishedin1990andeditedbyLynnMargulis,JohnO.Corliss,Michael
Melkonian, and David J. Chapman. The subject is the biology, diversity, and
evolutionofeukaryotic(nucleus-containing)microbesandtheirdescendants,exclu-
sive ofanimals, landplants,andtypical fungi.Thenew edition largelyfollows the
structure of the original Handbook, but its content has changed dramatically to
reflect 27 years of progress in many areas of life science research, including
microscopy,microbialecology,biochemistry,molecularbiology,andphylogenetics.
ThenewHandbookcontainssome44chapters,eachfocusedonadifferentgroup
ofprotists.Taxonomicrankvariessomewhatfromchaptertochapter;eachincludes
aSummaryClassificationofthelineagesdiscussedtherein.Manyofthechaptersare
thorough updates of those appearing in the original Handbook, although a few are
not retained in the new edition; in most cases these omissions reflect shifts in
knowledge stemming from a more complete understanding of the large-scale phy-
logenetic structure of eukaryotic diversity. For example, Ellobiopsida (“Incertae
Sedis” in the 1st Ed.) are no longer covered as a stand-alone chapter, as the group
is now within Dinoflagellata. The fate of Phylum Myxozoa (original chapter
publishedbythelateJiříLom)revealsastunningtwistinthehistoryofknowledge.
Myxozoan parasites were usually seen as an enigmatic group of spore-forming
“protozoa”; however, molecular phylogenetics confirmed that they are in fact a
highly derived lineage of animals. Still other chapters have no counterpart in the
original – they explore groups of protists that have gained substantially in impor-
tance over the past quarter century. And a handful of chapters address traditional
protist assemblages based on morphology that do not correspond to evolutionarily
unifiedgroups;inthesecasesthedifferentsubgroupsareclearlydistinguished.
The opening chapter, entitled “Protist Diversity and Eukaryote Phylogeny,”
servesasaguidetotheHandbook’soverarchingstructureandcontent.Itsummarizes
the biology of the currently recognized high-level protist lineages and provides
references to the literature for those wishing to learn more about specific groups
thatarenotcoveredindetailinthisHandbook.
Inwritingandupdatingtheirchapters,authorsweregiventhefreedomtoadhere
to terms used in the original Handbook (e.g., “protoctists” = protists,
ix
x PrefacetotheSecondEdition
“undulipodia” = flagella)ornotandencouragedtobringallrelevantresearchtothe
table, including advances coming from molecular biology and molecular
phylogenetics.
Key Features at a Glance
(cid:129) Explores the ecological, medical, and economic importance of major groups of
protists
(cid:129) Covers the morphology, molecular biology, biochemistry, ecology, and fossil
recordofprotists
(cid:129) Collatesworkonanunparalleledbreadthofeukaryoticmicroorganisms
(cid:129) Is organized by current protist systematics, as informed by molecular phyloge-
neticsandgenomics
June2017 JohnM.Archibald
AlastairG.B.Simpson
ClaudioH.Slamovits
List of First Edition Chapters and
Contributors
I. PhylainWhichMembersLackUndulipodiaatAllStagesandWhichLack
ComplexSexualLifeCycles
1. RHIZOPODA,F.L.Schuster
2. HAPLOSPORIDIA,F.O.Perkins
3. PARAMYXEA,I.Desportes,F.O.Perkins
4. MYXOZOA,J.Lom
5. MICROSPORA,E.U.Canning
II. Phyla in Which Members Lack Undulipodia at All Stages of Their Life
CyclesandWhichDisplayComplexSexualLifeCycles
6. ACRASEA,R.L.Blanton
7. DICTYOSTELIDA,J.C.Cavender
8. RHODOPHYTA,P.W.Gabrielson,D.J.Garbary,M.R.Sommerfeld,R.A.
Townsend,P.L.Tyler
9. CONJUGAPHYTA,R.W.Hoshaw,R.M.McCourt,J.C.Wang
III. Phyla in Which Members Display Reversible Formation of Undulipodia
andLackComplexSexualLifeCycles
10. XENOPHYOPHORA,Ø.S.Tendal
11. CRYPTOPHYTA(CRYPTOMONADS),M.Gillott
12. GLAUCOCYSTOPHYTA,L.Kies,B.P.Kremer
13. KARYOBLASTEA,J.M.Whatley,C.Chapman-Andresen
14. ZOOMASTIGINA
Classes:
a. Amebomastigota,B.D.Dyer
b.Bicoecids,B.D.Dyer
c. Choanomastigotes(Choanoflagellates),K.R.Buck
d. Diplomonadida,K.Vickerman
e. Pseudociliata,J.O.Corliss
f. Kinetoplastida,K.Vickerman
g.Opalinata,J.O.Corliss
h.Proteromonadida,G.Brugerolle,J.P.Mignot
i. Parabasalia,B.D.Dyer
j. Retortamonadida,G.Brugerolle,J.P.Mignot
k.Pyrsonymphida,B.D.Dyer
xi