Mycologia, 98(6), 2006, pp. 860–871.

# 2006 by The Mycological Society of America, Lawrence, KS 66044-8897

A molecular phylogeny of the flagellated fungi (Chytridiomycota) and

description of a new phylum (Blastocladiomycota)

Timothy Y. James1 its morphological circumscription. The Blastocla-

Department of Biology, Duke University, Durham, diales appears to be the sister taxon of most
North Carolina 27708 nonflagellated fungi. Based on molecular phyloge-
Peter M. Letcher netic and ultrastructural characters this order is
Department of Biological Sciences, University of elevated to a phylum, the Blastocladiomycota.
Alabama, Tuscaloosa, Alabama 35487 Key words: Blastocladiomycota, Chytridiales,
holocarpic, kinetosome, phylogeny, zoospore
Joyce E. Longcore
ultrastructure
Department of Biological Sciences, University of Maine,
Orono, Maine 04469
INTRODUCTION
Sharon E. Mozley-Standridge
David Porter The Chytridiomycota is a phylum of Fungi that
Department of Plant Biology, University of Georgia, reproduces through the production of motile spores
Athens, Georgia 30605 (zoospores), typically propelled by a single, poster-
Martha J. Powell iorly directed flagellum. These organisms, often
Department of Biological Sciences, University of referred to as chytrid fungi or chytrids, have a global
Alabama, Tuscaloosa, Alabama 35487 distribution with approximately 1000 described spe-
cies. Based on biochemical characteristics, including
Gareth W. Griffith
chitin in cell walls, the a-aminoadipic acid lysine
Institute of Biological Sciences, University of Wales,
Aberystwyth, Ceredigion, Wales SY23 3DA, UK synthetic pathway and storage carbohydrates as
glycogen, Bartnicki-Garcia (1970) classified the Chy-
Rytas Vilgalys tridiomycota as true Fungi. Others considered chy-
Department of Biology, Duke University, Durham, trids as a transitional group between protists and
North Carolina 27708
Fungi because of their production of motile zoo-
spores (Barr 1990). Phylogenetic studies with ribo-
somal RNA genes unified these views and conclusively
Abstract: Chytridiomycota (chytrids) is the only demonstrated that chytrids were true Fungi that
phylum of true Fungi that reproduces with motile
occupied a basal position in the fungal tree (e.g.
spores (zoospores). Chytrids currently are classified
Förster et al 1990).
into five orders based on habitat, zoospore characters
Chytrids are essentially ubiquitous, occurring in
and life cycles. In this paper we estimate the
diverse and unique habitats from the tropics to the
phylogeny of the chytrids with DNA sequences from
arctic regions (Powell 1993). They are found in
the ribosomal RNA operon (18S+5.8S+28S subunits).
aquatic systems such as streams, ponds, and estuarine
To our surprise the morphologically reduced para-
and marine ecosystems primarily as parasites of algae
sites Olpidium and Rozella comprise two entirely new,
and plankton components. Perhaps the majority of
and separate, lineages on the fungal tree. Olpidium
chytrid species occur in terrestrial habitats (Barr
brassicae groups among the Zygomycota, and Rozella
spp. are the earliest branch to diverge in the fungal 2001) such as forest, agricultural and desert soils,
kingdom. The phylogeny also suggests that Chytri- and acidic bogs as saprotrophs of refractory substrata
diomycota is not monophyletic and there are four including pollen, chitin, keratin and cellulose. In soil
major lineages of chytrids: Rozella spp., Olpidium chytrids are obligate parasites of a wide variety of
brassicae, the Blastocladiales and a ‘‘core chytrid vascular plants, including potatoes (Synchytrium) and
clade’’ containing the remaining orders and families curcurbits (Olpidium). The only known chytrid
and the majority of flagellated fungi. Within the core parasite of vertebrates is Batrachochytrium dendrobati-
chytrid group 11 subclades can be identified, each of dis (Longcore et al 1999), considered the causative
which correlates well with zoospore ultrastructure or agent of die-offs and population declines of amphib-
morphology. We provide a synopsis of each clade and ian species (Berger et al 1998). In most habitats a few
chytrid species are relatively frequent and abundant
Accepted for publication 6 September 2006. (i.e. Chytriomyces hyalinus in freshwater and Rhizoph-
1
Corresponding author. E-mail: [email protected] lyctis rosea in agricultural and perturbed soils),

860
 JAMES ET AL: PHYLOGENY OF CHYTRID FUNGI 861

whereas most species are infrequent and scarce to Chytridiales is the largest of the orders (more than 75
rare (Letcher and Powell 2001, Letcher et al 2004a). genera) and the classification of this group has been
The most prominent morphological feature of the variously approached using developmental, sporan-
chytrid body, or thallus, is the sporangium (FIG. 1). gial and more recently ultrastructural characters.
The sporangium is a sac-like structure in which Sparrow (1960) considered the operculum to be
internal divisions of the protoplasm result in pro- a defining characteristic and created two series of
duction of zoospores. These zoospore-producing families based on whether sporangia were operculate.
sporangia (zoosporangia) are thin-walled (FIG. 1k) In contrast Whiffen (1944), Roane and Paterson
whereas resting spores are thick-walled structures (1974) and Barr (1978) suggested development could
(FIG. 1a, l) that may germinate to produce a sporan- be used to divide the Chytridiales into families.
gium after a dormant period. Zoosporangia always are Systems of classification based on morphology and
produced asexually, but resting spores may be those based on development of the thallus and
sexually or asexually formed. Eucarpic chytrids are sporangium both have been shown by molecular
those that consist of a sporangium and filamentous phylogenetics to be inaccurate in defining genera and
rhizoids (FIG. 1k). In contrast holocarpic chytrids families of Chytridiales (James et al 2000, Letcher et al
produce thalli that are entirely converted to sporangia 2004b).
during reproduction. Chytrid thalli can be either Molecular phylogenies with 18S rDNA have sug-
monocentric, in which an individual produces only gested that both the Chytridiomycota and Chytri-
a single sporangium (FIG. 1g), or polycentric, in diales might not be monophyletic ( James et al 2000).
which an individual is composed of multiple sporan- Phylogenies based on data from entire mitochondrial
gia produced on a network of rhizoids termed genomes (Seif et al 2005) have suggested strongly that
a rhizomycelium (FIG. 1j). Classically chytrids also two main lineages exist within the Chytridiomycota—
were described on the basis of whether they grow on the Blastocladiales and the remaining four orders
(epibiotic, FIG. 1h) or within (endobiotic, FIG. 1a) (the ‘‘core chytrid clade’’). In this paper we present
their substrate. Other characteristics historically used a new dataset that includes an analysis of most chytrid
for taxonomy include the presence of a lid-like 18S rDNA data in conjunction with sequence data for
operculum (FIG. 1e), which opens to allow zoospore the entire rRNA operon (18S, 28S and 5.8S). These
release from a sporangium (Sparrow 1960), and the data provide a comprehensive view of chytrid phylog-
apophysis (FIG. 1i), which is a subsporangial swelling. eny and define four major lineages of flagellated
Zoospores are unwalled cells, usually 2–10 mm Fungi.
diam, which contain a single nucleus and, with the
exception of some genera of the Neocallimastigales, MATERIALS AND METHODS
are propelled by a single posteriorly oriented whip-
lash flagellum (FIG. 1b, m). Considerable effort has Our dataset consists of taxa for which most of the rRNA
been placed on understanding the ultrastructure of operon was sequenced (18S+28S+5.8S subunits, n 5 54) as
the zoospore with electron microscopy; these studies well as chytrid taxa represented only by 18S data (n 5 49)
and additional fungal, animal and Mesomycetozoae taxa (n
have produced a wealth of information about the
5 21; complete operon with one exception, Diaphanoeca
complexity of the internal contents of the spores. Two
grandis). GenBank accession numbers and strain/voucher
character-rich components of the zoospores can be data are provided (SUPPLEMENTARY TABLE I). Data gathered
identified: the flagellar apparatus, basal bodies and for the full operon were obtained by PCR, primarily with
associated structures (Barr 1981), and the microbody- primers SR1R and LR12 (Vilgalys and Hester 1990) using
lipid globule complex (MLC, Powell 1978). LATaq (TaKaRa), with these thermocycling conditions:
The Chytridiomycota is divided into five orders 94 C for 1 min followed by 35 cycles of denaturing at 94 C
based primarily on the mode of reproduction and for 30 s, annealing at 55 C for 30 s, extension at 72 C for
ultrastructure of the zoospore. Three groups can be 5 min and a 10 min final extension at 72 C. Amplicons
distinguished largely on the basis of life cycle and generally were cloned into pCR2.1-TOPO (Invitrogen).
gross morphology: the oogamous Monoblepharidales; The three gene regions were aligned by eye with GeneDoc
the Blastocladiales displaying sporic meiosis and the v2.6 (http://www.cris.com/,Ketchup/genedoc.shtml) and
combined into one supermatrix with MacClade 4.05 (Maddi-
alternation of sporophytic and gametophytic genera-
son and Maddison 2002). Regions of ambiguous alignment
tions; and the Chytridiales, a group characterized by were excluded from further analysis leaving 4109 included
zygotic meiosis. A fourth order, Spizellomycetales, was characters, 1388 of which are parsimony informative. We
separated from the Chytridiales on the basis of estimated the phylogeny with MrBayes v3.1 (Huelsenbeck
distinctive ultrastructural character states (Barr and Ronquist 2001) by four independent runs with the
1980), and a fifth order, Neocallimastigales, occurs GTR+I+C model of evolution, sampling trees every 500
exclusively as anaerobic symbionts of the rumen. generations for 10 3 106 generations. We also assessed
862 MYCOLOGIA

FIG. 1. Light micrographs of representative chytrids. a. Rozella allomycis isolate UCB-47-54 (Clade 1) parasitizing hyphae of
Allomyces. The parasite grows inside the host and causes it to produce hypertrophied, highly septate cells within which the
parasite may form thick-walled resting spores (RS) or unwalled zoosporangia (ZS) that use the host’s cell wall as its own. b.
Neocallimastix sp. (Clade 2A) monocentric thallus with profusely branched rhizoids, inset: multiflagellate zoospores (by Gary
Easton). c. Monoblepharis polymorpha (Clade 2B) mature zygote or oospore (OS), empty and mature antheridia (AN) and
antherozoids (AT) or male gametes emerging from antheridium; photo by Marilyn M. N. Mollicone. d. Polychytrium
aggregatum isolate JEL109 (Clade 2C) finely branched rhizomycelium. e. Catenochytridium sp. (Clade 2D) monocentric,
operculate (OP) zoosporangium with catenulate rhizoids (RH). f. Chytriomyces angularis isolate JEL45 (Clade 2F)
monocentric, operculate sporangium with thread-like rhizoids that branch several mm from the sporangial base (arrow). g.
Terramyces subangulosum isolate PL 076 (Clade 2G) monocentric, inoperculate sporangium with a thick rhizoidal axis, and
densely branched rhizoids (RH) that taper to ,0.5 mm at tips. h. Blyttiomyces helicus (Clade 2H) forming epibiotic,
 JAMES ET AL: PHYLOGENY OF CHYTRID FUNGI 863

support for nodes with parsimony bootstrap as imple- of RNA polymerase II suggest that microsporidia
mented in PAUP v4.0b10 (Swofford 2002) and maximum might belong to this lineage (T.Y. James and R.
likelihood bootstrap as implemented in RAxML-VI-HPC Vilgalys, unpublished data).
v2.0 (Stamatakis et al 2005).
Clade 2A. Neocallimastigales.—It is supported as the
RESULTS AND DISCUSSION most basal group of the core chytrid clade (Clade 2)
by Bayesian posterior probability. Members of this
The phylogeny (FIG. 2) is the consensus of credible clade are characterized by obligate anaerobic growth
trees derived from the Bayesian analysis of rDNA and are found in the rumen and hindgut of many
genes from Chytridiomycota. These analyses confirm larger mammalian herbivores. They are morpholog-
the basal position of this group among the Fungi and ically similar to other chytrid orders and may be
provide support for at least four major clades of monocentric or polycentric. The rumen chytrids
Chytridiomycota. Clade 1 is the earliest diverging possess an organelle called a hydrogenosome that
lineage in the Fungi and comprises Rozella spp. The generates ATP and appears to be a degenerate
largest, Clade 2 or the ‘‘core chytrid clade,’’ mitochondrion lacking a genome (van der Giezen
comprises Chytridiales, Spizellomycetales pro parte, 2002). Rumen chytrid zoospores may be multiflagel-
Monoblepharidales and Neocallimastigales and can late or uniflagellate (FIG. 1b). The zoospore of rumen
be subdivided further into 11 clades (clades 2A–2K). chytrids lacks the nonflagellated centrioles (nfc) and
Clade 3 represents the Blastocladiales, grouping sister lipid globules that are found in most other members
of the Dikarya+Glomeromycota+Zygomycota, and of Clade 2 but possesses a microtubulular root
Clade 4 is represented solely by Olpidium brassicae, emanating from a kinetosome associated spur (Heath
which groups among the Zygomycota. These results et al 1983). Six described genera are circumscribed
further suggest that Chytridiomycota is polyphyletic on the basis of number of flagella and sporangial
or at least paraphyletic. As suggested by a phylogenetic characters (Ho and Barr 1995, Ozkose et al 2001).
study of Opisthokonts, the amoeba Nuclearia simplex
appears to be the closest known sister taxon of the Clade 2B. Monoblepharidales.—It is monophyletic and
Fungi (Steenkamp et al 2005). Below we discuss the sister of the clade of Chytridiales+Spizellomycetales.
membership of each clade, providing a brief state- Monoblepharidales is a small order consisting only of
ment on the systematics of each group in light of our six genera. The earliest diverging lineage is the
phylogenetic findings. species Hyaloraphidium curvatum, once believed to
be a colorless, unicellular green alga (Ustinova et al
Clade 1. Rozella.— Two isolates of Rozella are 2000). The planktonic H. curvatum has a lunate
supported strongly as the earliest diverging lineage thallus superficially similar to that of some Harpochy-
in the fungi. Rozella is a holocarpic parasite, primarily trium species, but zoospores have not been observed
of chytrids and Oomycetes, that grows inside its host in H. curvatum. The genera Oedogoniomyces, Hyalor-
as a walless trophic form (Held 1981) until it aphidium and Harpochytrium all grow vegetatively as
produces thick-walled resting spores or zoosporangia simple, unbranched thalli lacking rhizoids, whereas
that fill the host cell (FIG. 1a). The two strains in the the remaining three genera, Gonapodya, Monoble-
rDNA phylogeny are parasites on other chytrids pharis and Monoblepharella, are polycentric species
(Allomyces and Rhizoclosmatium). The ultrastructure with a well developed coenocytic mycelium. In poly-
of R. allomycis zoospores presents a unique combina- centric genera oogamous reproduction occurs in
tion of characters including a striated rhizoplast which a motile male gamete (antherozoid) fuses with
connecting the kinetosome (the basal body of the a nonmotile female gamete (egg, FIG. 1c). Hyphae of
flagellum) to a large, spheroidal mitochondrion, Monoblepharidales have a foamy or reticulate ap-
which abuts a helmet-shaped nucleus (Held 1975). pearance. Zoospores of Monoblepharidales have
Phylogenetic analyses using the two largest subunits a fenestrated cisterna called a rumposome (Fuller

r
inoperculate sporangium with distinct helical pattern on pollen grain. i. Spizellomyces plurigibbosus isolate SW 001 (Clade 2I)
monocentric, inoperculate zoosporangium (ZS), with swollen, apophysate rhizoidal axis (AP) and branched rhizoids that are
blunt at the tips. j. Catenomyces persicinus (Clade 2J) polycentric thallus with intercalary zoosporangia. k. Chytriomyces hyalinus
isolate MP 004 (Clade 2K) monocentric, operculate zoosporangium (ZS) with long branched rhizoids that taper to , 0.5 mm
at the tips. l. Coelomomyces stegomyiae (Clade 3) elliptical resting spores inside the anal gills of mosquito host. m. Olpidium
bornovanus (Clade 4) zoospores labeled with a FITC/Conconavalin A conjugate; photo by D’Ann Rochon. Approximate sizes
relative to scale bar in FIG. 1a 5 10 mm (e, g, h), 15 mm (a, i, m), 20 mm (b, f), 25 mm (c, k), 45 mm (d), 50 mm ( j), and 150
mm (l).
864 MYCOLOGIA

FIG. 2. Phylogeny of chytrid fungi based on rDNA operon. Shown is a majority-rule consensus phylogram computed from
the set of 36 000 credible trees. A ‘‘+’’ above a node indicates branch was supported by $ 95% Bayesian posterior probability
(BPP); ‘‘++’’ indicates branch supported by $ 95% BPP and maximum likelihood bootstrap (MLBS) $ 70%. Branches
supported by BPP, MLBS and parsimony bootstrap $ 70% are indicated by thickened lines. Branches with double diagonal
hash marks have been shortened four times to aid viewing. The schematic illustrations diagram the ultrastructural details of
 JAMES ET AL: PHYLOGENY OF CHYTRID FUNGI 865

1966) and most have an electron opaque core in the Clade 2E. Chytridiales.—Synchytrium. This genus
transitional zone of the axoneme similar to the one contains more than 200 species that are obligate
found in some members of the Chytridiales. parasites of green plants, particularly angiosperms.
The four species of Synchytrium are monophyletic in
Clade 2C. Chytridiales.—Polychytrium clade. The two the rDNA phylogeny (FIG. 2). The distinguishing
monotypic, polycentric genera Polychytrium and La- feature of Synchytrium is colonial asexual reproduction
custromyces and several monocentric species of Karlin- by a sorus, a cluster of sporangia. The sorus of
giomyces make up the Polychytrium clade (formerly Synchytrium is derived by the internal cleavage of the
termed the Lacustromyces clade, James et al 2000). common membrane of a single thallus into multiple
Polychytrium and Lacustromyces possess a rhizomyce- sporangia. Synchytrium is included among Chytri-
lium that lacks swellings containing nuclei (FIG. 1d). diales, and the zoospore ultrastructure of two of the
Polychytrium aggregatum is found in acidic lakes and species generally conforms to the chytridialean type
bogs; Lacustromyces hiemalis occurs in lakes or (Lange and Olson 1978, Montecillo et al 1980). The S.
commonly wet areas and Karlingiomyces can be endobioticum (Lange and Olson 1978) zoospore con-
isolated from aquatic or terrestrial habitats. Both the tains an electron opaque plug at the base of the
monocentric and polycentric species of this clade grow flagellum but lacks a fenestrated cisterna; in contrast
on chitin baits. Zoospores are spherical when in the S. macrosporum zoospore has a fenestrated cisterna
motion and usually larger than 4 mm diam. The but lacks the electron opaque plug (Montecillo et al
unique ultrastructural feature of the clade is the 1980). Both species lack aggregated ribosomes ob-
composition of the kinetosome and its associated served in most other Chytridiales. Synchytrium spp.
structures (Longcore 1993 unpublished). The nfc is as host ranges vary from broad (Karling 1964, S.
long as the kinetosome and the connection of the nfc macrosporum can be inoculated onto 165 different
to the kinetosome is distinctive. Densely staining plant families) to narrow (S. decipiens is restricted to
material extends about 0.1 mm into the zoospore from the genus Amphicarpaea).
kinetosome triplets 1 and 9; the primary microtubule
root arises between these extensions. At the same level Clade 2F. Chytridiales.—C. angularis. Chytriomyces
within the kinetosome is a scalloped ring (Longcore angularis is a monocentric, epibiotic, operculate
1993). fungus distinguished by a gibbous zoosporangium
with thread-like rhizoids (FIG. 1f). Secondary rhizoids
Clade 2D. Chytridiales.—Cladochytrium. This clade usually form several micrometers from the sporangial
(formerly Nowakowskiella) (James et al 2000) is a well base and branch perpendicularly from the initial
supported lineage with a zoospore ultrastructure rhizoidal axis (FIG. 1f). In the literature fungi with
similar to Nowakowskiella elegans and Cladochytrium this description were considered possibly to be an
replicatum (Lucarotti 1981). It includes eight genera: alternate form of C. poculatus. These fungi are
Allochytridium, Catenochytridium, Chytridium (?) pro recovered on pollen and snakeskin baits from soils
parte, Cladochytrium, Endochytrium, Nephrochytrium, or boggy areas and seem to be more abundant in
Nowakowskiella and Septochytrium. Species in this acidic environments. This clade also includes Chytri-
group may be monocentric or polycentric and often dium polysiphoniae, a parasite of the marine brown alga
are characterized by the presence of swellings in the Pylaiella littoralis. Although C. angularis was classified
rhizoids or rhizomycelium (FIG. 1e). They occur as a member of Chytriomyces based on its morphology
primarily on cellulose-rich substrates in aquatic and and development, its zoospore (Longcore 1992) lacks
soil habitats. Members of the Cladochytrium clade have features found in the Chytridiaceae (Letcher et al
a zoospore that is typical for Chytridiales and most 2005); instead it is characterized by a unique connec-
similar to that of the Chytriomyces clade (2K). One tion of the kinetosome and nfc (Longcore 1992).
distinctive feature of the zoospore is that the micro-
tubular root arising from the kinetosome is a cord-like Clade 2G. Chytridiales.—Rhizophydium. This clade
bundle interconnected by fine fibrillar bridges (Lucar- is composed primarily of members of the morpho-
otti 1981, Barr 1986). Two major subclades were genus Rhizophydium, which is characterized by a mono-
recovered in our phylogenetic analysis. Nephrochytrium centric, epibiotic, inoperculate sporangium, an endo-
and Cladochytrium form a clade that is sister of a clade biotic rhizoidal axis that branches (FIG. 1g) and an
containing the remaining genera. epibiotic resting spore. Molecular studies with 28S

r
the kinetosome, nonflagellated centriole and associated structures. ‘‘N’’ indicates nucleus; ‘‘M’’ indicates mitochondrion.
Ultrastructures are indicated for all clades except 2H (B. helicus) for which information is not available.
866 MYCOLOGIA

rDNA indicate that the genus Rhizophydium is more counterparts in the Chytridiales with similar morphol-
variable than previously understood and actually ogy and development (e.g. Spizellomyces has Phlyctochy-
represents multiple genera (Letcher and Powell trium morphology and development [FIG. 1i] but each
2005b). The genus Kappamyces was circumscribed on possesses the distinctive Spizellomycetalean zoospore).
the bases of molecular monophyly and zoospore At the ultrastructural level the nucleus is spatially or
ultrastructure (Letcher and Powell 2005b). Species structurally associated with the kinetosome, the nfc lies
showing none of the usual Rhizophydium generic at an angle to the kinetosome, organelles of the MLC
characters also are in this clade (FIG. 2), including are loosely associated and ribosomes are not aggregat-
endobiotic species (Batrachochytrium dendrobatidis and ed around the nucleus (Barr 1980). Under a light
Entophlyctis helioformis), species with multiple rhizoidal microscope spizellomycetalean zoospores are recogniz-
axes ( JEL142), species with swollen basal rhizoids (e.g. able because they can be amoeboid while swimming,
Rhizophydium brooksianum) and operculate species are irregularly shaped and the flagellar insertion may
(e.g. JEL223). move to a lateral position. The rDNA phylogeny
Although thallus morphology among most mem- (FIG. 2) suggests two groupings within this clade, one
bers of the Rhizophydium clade is relatively conserved, in which the nucleus possesses a heel that extends to
zoospore ultrastructure is divergent. A key feature of the kinetosome (Powellomyces and Spizellomyces) and
the zoospore is the absence of an electron opaque another in which this character is absent (Gaertner-
plug in the base of the flagellum, which distinguishes iomyces and Triparticalcar).
it from most members of the Chytridiales (Letcher et
al 2006). Other zoospore ultrastructural features that Clade 2J. Spizellomycetales.—Rhizophlyctis clade. This
may be present include a kinetosome-associated group is a heterogenous assemblage of five strains that
structure (KAS) as a spur or shield (Letcher et al is not well supported as a clade but possesses some
2004b), a microtubular root in which four to five morphological similarities. Rhizophlyctis is a diverse
microtubules are stacked and a vesiculated, cup- and polyphyletic group based on zoospore ultrastruc-
shaped, invaginated region of the endoplasmic re- ture (Barr and Désaulniers 1986) and 18S rDNA
ticulum that surrounds the ribosomal aggregation, phylogeny ( James et al 2000). In Rhizophlyctis rosea the
adjacent to the proximal end of the kinetosome. kinetosome is connected to the nucleus with a striated
Character states of zoospore ultrastructural features rhizoplast (Barr and Désaulniers 1986). The R. rosea
are correlated with well supported clades of isolates zoospore shares similarities with other members of the
within the Rhizophydium clade. The diversity of the Spizellomycetales, and Barr (1980) placed Rhizophlyctis
Rhizophydium clade, as revealed by 18S, 28S, and with Entophlyctis, Olpidium and Rozella in Spizellomy-
ITS1–5.8S–ITS2 rDNA molecular analyses and zoo- cetales based on the shared characters of association of
spore ultrastructural analyses (Letcher et al 2004b), the nucleus with the basal body and dispersed
support naming the clade a new order Rhizophy- ribosomes. The Rhizophlyctis clade groups with the
diales, which contains many families and genera Spizellomyces clade (2I), albeit with no statistical
(Letcher et al 2006). support. The genera Rozella and Olpidium, which also
have a striated rhizoplast associated with their kineto-
Clade 2H. Chytridiales.—Blyttiomyces helicus. This somes, are unrelated to the Rhizophlyctis clade, in-
is a distinctive species that has a sporangium traversed dicating that this feature is homoplasious. Catenomyces
by spiral thickenings. It grows saprotrophically on persicinus, currently assigned to the Blastocladiales, is
pollen (FIG. 1h) but has not been isolated into pure in this clade (FIG. 1j). It resembles R. rosea and also
culture (J.E. Longcore unpublished). The rDNA degrades cellulose; however, rather than being a soil
sequencing for the species was from an enriched organism like R. rosea, we have found it from aquatic
unifungal culture on pollen. The placement of B. habitats.
helicus in our analysis is uncertain, but additional data
suggest a grouping with Catenomyces persicinus (see Clade 2K. Chytridiales.—Chytriomyces. It is com-
Clade 2J. Spizellomycetales.—Rhizophlyctis clade, below, posed of members of 13 studied genera (Asterophlyctis,
T.Y. James unpublished). Chytridium, Chytriomyces, Entophlyctis, Obelidium,
Phlyctochytrium, Phlyctorhiza, Physocladia, Podochy-
Clade 2I. Spizellomycetales.—Spizellomyces. This is trium, Polyphlyctis, Rhizidium, Rhizoclosmatium and
a well supported lineage that appears to have diverged Siphonaria). These genera exhibit diverse thallus
from among the lineages of Chytridiales. The clade forms that include inoperculate or operculate sporan-
contains the majority of the genera in the Spizellomy- gia (FIG. 1k), often apophysate rhizoidal axes, varia-
cetales: Gaertneriomyces, Kochiomyces, Powellomyces, tion in sporangial ornamentation and monocentric or
Spizellomyces and Triparticalcar. Most members of this polycentric thalli. Because of this morphological
clade are saprophytic in soil. All these genera have diversity many species are identifiable with light
 JAMES ET AL: PHYLOGENY OF CHYTRID FUNGI 867

microscopy. Species identified as being in the genus

Chytriomyces occur in several separate, well supported
clades indicating that Chytriomyces as currently defined
is polyphyletic (FIG. 2).
Although thallus morphology is divergent zoospore
ultrastructure is conserved among the members of
this clade. Most isolates from the Chytriomyces clade
possess a Group I-type zoospore (Barr 1980) and form
a clade that has been delineated as the Chytridiaceae
(Letcher et al 2005). Features of that zoospore
include a fenestrated cisterna, a lateral microtubular
root composed of a bundle of approximately seven
microtubules in a cord-like arrangement, and a pair
of three stacked, flat, electron opaque plates adjacent
to the kinetosome, a paracrystalline inclusion in the FIG. 3. Comparison of ultrastructural differences be-
peripheral cytoplasm and an electron opaque plug in tween the Blastocladiales and core chytrids. a. Longitudinal
the base of the flagellum. Phlyctochytrium planicorne section through the closed mitotic pole of Catenaria
(Letcher and Powell 2005a) and Polyphlyctis unispina allomycis with centriole (arrowed) separated from the
(Letcher et al 2005) have a Group II-type zoospore internuclear spindle (Blastocladiales). b. Open mitotic pole
(Barr 1980), distinguishable from the zoospore of the of Powellomyces variabilis (Spizellomyces clade) with the
Chytridiaceae primarily by the structure of the centriole (arrowed) proximate to the mitotic spindle. c.
Unstacked, single cisterna of a Golgi equivalent (arrowed)
electron opaque plates adjacent to the kinetosome.
in Allomyces arbusculus (Blastocladiales) near rough endo-
Isolates with a Group II-type zoospore probably
plasmic reticulum. d. A Golgi apparatus with five stacked
represent a separate family in the Chytridiales. cisternae in Powellomyces variabilis (Spizellomyces clade).
Notice smooth endoplasmic reticulum and small transport
Clade 3. Blastocladiomycota.—Traditionally consid- vesicles at the proximal (upper) side of the stacks and larger
ered among phylum Chytridiomycota, the Blastocla- secretory vesicles at the distal (lower) side of the stack.
diales diverges from the core chytrid clade and is Methods for sample preparation and microscopy are as
sister of a clade including Zygomycota, the chytrid previously published (Powell 1975). Bars: a, b 5 0.25 mm; c,
genus Olpidium, Glomeromycota and Dikarya d 5 0.125 mm.
(FIG. 2). They are saprotrophs as well as parasites of
diales exhibits several ultrastructural features more
fungi, algae, plants and invertebrates, and may be
characteristic of higher filamentous fungi than of the
facultatively anerobic. Two major subclades are re-
core chytrids, including closed nuclear poles during
solved in molecular phylogenetic analyses (FIG. 2),
mitosis (FIG. 3a) rather than open (fenestrate) poles
one composed of the plant parasite Physoderma and
(FIG. 3b) and Golgi equivalents (Bracker 1967,
the other containing the remaining blastocladialean
FIG. 3c) rather than stacked Golgi cisternae (FIG. 3d).
genera. The morphology of thalli of Blastocladiales
A Golgi apparatus with stacked cisternae has been
parallels forms found among the core chytrid clade,
reported in Physoderma (Lange and Olson 1980),
ranging from monocentric to polycentric and myce-
suggesting this subclade might have diverged before
lial. However Coelomomyces produces a tubular un-
the loss of Golgi cisternal stacking in the Blastocla-
walled thallus in its host, reminiscent of hyphal bodies
diales. These distinctive ultrastructural characteristics
in the Zygomycete group Entomophthorales. The
as well as the phylogenetic placement of the group
zoospore is functionally similar to those found among
warrant their elevation to a new phylum, the
core chytrids with a single posteriorly directed
Blastocladiomycota.
flagellum, stored lipid and glycogen reserves, a char-
acteristic assemblage of lipids, microbodies, mem-
brane cisterna called the side-body complex (5micro- Blastocladiomycota T. James, phylum nov.
body-lipid globule complex) and a membrane- Synonyms: Allomycota Cavalier-Smith, BioSystems
bounded ribosomal cap covering the anterior surface 14:465, 1981 (not valid, no Latin diagnosis)
of a cone-shaped nucleus. Archemycota Cavalier-Smith, Biol. Rev. 73:246,
Major evolutionary changes have accompanied the 1998 pro parta
divergence of the Blastocladiales from the core Zoosporum cum flagellum unum, corpus-latus
chytrids. For example the Blastocladiales have a life complexe, nucleus pileus ex ribosomata membrane
cycle with sporic meiosis whereas most core chytrids confinium, nucleus cum conus forma terminari
have zygotic meiosis, where known. The Blastocla- propinquus kinetosoma, microtubuli ex propinqui-
868 MYCOLOGIA

tate kinetosomatis per zoosporum radiant circum selection because a name does not have priority
nucleus, flagellum obturamentum nullum. Generare outside its own rank (Article 11.2). As we have
nonsexus cum zoosporae, generare sexus ad conjiun- described the Blastocladiomycota, it is a natural
gare planogametum, orbis vita cum meiosis sporae. group separate from the more heterogeneous phylum
Typus: Blastocladia Reinsch 1878 Archemycota (Cavalier-Smith 1998).
Zoospore with a single flagellum, side-body com-
Clade 4. Olpidium brassicae.—Olpidium brassicae
plex, nuclear cap of membrane-bounded ribosomes,
unexpectedly grouped among the polyphyletic Zygo-
cone-shaped nucleus that terminates near the kinet-
mycota and with the nonzoosporic fungi. O. brassicae
osome, microtubules radiate anteriorly from the
currently is assigned to the Spizellomycetales (Barr
proximal end of the kinetosome around the nucleus,
1980), although this placement was considered
zoospore flagellum lacks electron-opaque plug in
tenuous (Barr 2001). Few ecological and morpholog-
transition zone. Asexual reproduction with zoospores,
ical features unite O. brassicae and Zygomycota; O.
sexual reproduction through fusion of planogametes,
brassicae is a root pathogen of cucurbits, whereas most
life cycle with sporic meiosis.
members of the Zygomycota II lineage (FIG. 2) are
Type: Blastocladia Reinsch 1878 associated with animals. The zoospore of O. brassicae
contains a unique combination of features, cone-
Blastocladiomycetes cl. nov. T. James. Description as shaped striated rhizoplast, gamma-like particles and
for Blastocladiomycota. rough endoplasmic reticulum (Lange and Olson
Reinsch described Blastocladia in 1878, and Peter- 1976). These ultrastructural features as well as
sen (1910) erected the family Blastocladiaceae to holocarpic, endobiotic sporangia had suggested a re-
accommodate this single genus, classifying it in the lationship between Olpidium and Rozella (Held 1975),
class Oomycetes. Kanouse (1927) first used the order but Olpidium differs from Rozella in that sporangia of
name, Blastocladiales (which she credited to Peter- the former develop a cell wall inside the host
sen), and included in it the single family with cytoplasm while sporangia of Rozella do not and
Allomyces and Gonapodya (now removed). Fitzpatrick instead use the host’s cell wall (Held 1981). Further
(1930) placed the Blastocladiales in class Phycomy- data will be needed to determine the exact phyloge-
cetes, a classification Sparrow (1960) followed. Alex- netic position of O. brassicae and whether it shares
opoulos (1966) separated fungi into eight classes, one a common ancestor with the majority of terrestrial
of which was class Chytridiomycetes, including Blas- fungi. We predict that Caulochytrium protostelioides
tocladiales. This placement for the Blastocladiales was with a similar zoosporic ultrastructure and aerially
retained as Chytridiomycetes was elevated to the produced sporangia (Powell 1981) also will be
phylum Chytridiomycota (not validly published, no a member of this currently monotypic clade.
Latin diagnosis; p 15 in von Arx 1967, Margulis et al Toward a phylogenetic classification.—The paraphyly
1990). Chytridiomycota will be validated when the of the Chytridiomycota requires that its current
phylogeny is more clearly resolved. circumscription be redefined to produce a phyloge-
Although Tehler (1988) used Blastocladiomycota netic classification system. Placing all flagellated true
as a division (phylum) name, the taxon was not validly Fungi into one phylum does not reflect shared
published because he did not provide or refer to ancestry of these fungi because the flagellum was
a Latin description or diagnosis or explain the basis of a character possessed by the common ancestor of all
or rationale for this name (Article 36.1, Greuter et al Fungi (i.e. it is a pleisiomorphic character. Further-
2000). Consequently it is nomen nudum and further- more the absence of a flagellated state (as in
more the group that Tehler (1988) circumscribed Hyaloraphidium curvatum) should not prevent the
with this name is not monophyletic. Thus we have inclusion of nonzoosporic fungi among natural
used Blastocladiomycota as a phylum for a mono- groups of Chytridiomycetes. The phylogeny (FIG. 2)
phyletic clade (Clade 3), validated the phylum name suggests the existence of at least four major lineages
with a Latin description and have designated a type. A of chytrids. The distinction of Blastocladiomycota
potentially competing phylum name, Allomycota from other chytrids is clear on the basis of life cycle
(Cavalier-Smith 1981), is invalid because Cavalier- (Sparrow 1960), ultrastructural characters (FIG. 3)
Smith did not include a Latin diagnosis. We may and multiple molecular phylogenetic studies using
select the phylum name Blastocladiomycota however rDNA ( James et al 2000, this study), RPB1 (Tanabe et
because the principle of priority is not mandatory al 2004), RPB2 (T.Y. James unpublished) and whole
above the rank of family (Article 11.1, 11.9). Cavalier- mitochondrial genome sequencing (Seif et al 2005).
Smith (1998) eventually validated class Allomycetes The exact placement of the holocarpic parasites
with Latin; however this validation is moot to our Rozella and Olpidium, formerly included in the
 JAMES ET AL: PHYLOGENY OF CHYTRID FUNGI 869

Spizellomycetales, is an open question because of organisms from different lineages but it may be
limited sampling of taxa, a paucity of molecular data a valuable character for taxonomic purposes within
and phylogenetic uncertainty (in the case of O. a lineage. The heuristic exercise of mapping
brassicae). morphological characters on gene trees suggests
Molecular studies have revealed that many current- that some character states have evolved repeatedly in
ly defined genera in Chytridiales are polyphyletic distinct lineages, thus creating an opportunity for
(James et al 2000, Letcher and Powell 2005b, Letcher previous assumptions regarding character homology
et al 2005). Our results show that neither develop- to be reassessed in a phylogenetic context.
mental characters, such as polycentric growth, or
Summary of current phylogenetic knowledge and
sporangial characters, such as presence of an opercu-
remaining questions.—We have identified four major
lum, will be useful in defining families or even
lineages of chytrid fungi, the largest of which can be
genera. These phylogenies demonstrate a repeated
subdivided into 11 additional clades. By increasing
evolution of polycentric growth in nearly every well
the sampling of both rRNA characters and species we
sampled clade, suggesting the evolution of this form
have greatly expanded our knowledge of phylogenetic
of indeterminant growth does not require a complex
diversity and relationships among the groups of
genetic change. Some of the largest genera (e.g.
chytrids. Our results confirm previous phylogenetic
Rhizophydium, Entophlyctis and Chytriomyces) are
studies and ultrastructural information that suggest
based on few distinctive characters and are dramati-
the Blastocladiales is distinct from the remaining
cally in need of revision. Other genera are highly
chytrids and possibly more closely related to the
distinctive (e.g. Loborhiza, Obelidium) but are mono-
nonzoosporic fungi than the core chytrids. Thus we
typic. Current efforts are focused on combining
have elevated the order Blastocladiales to the level of
morphological, ultrastructural and molecular data to
phylum (Blastocladiomycota). Based on the present
use a holistic approach for redefining genera of
research, as well as the results of the Assembling the
Chytridiales (e.g. Letcher and Powell 2005b).
Fungal Tree of Life project (http://ocid.nacse.org/
Application of zoospore ultrastructural characters.—A research/aftol/) and complete sequencing of fungal
resolved phylogeny of the chytrid fungi now permits mitochondrial genomes (Seif et al 2005), the phylog-
the mapping of ultrastructural character states onto eny of the core chytrids is beginning to be resolved
the gene tree to further our understanding of with the Neocallimastigales as the earliest diverging
character evolution. For example the electron-dense lineage and the Monoblepharidales as sister taxon of
plug in the base of the flagellum has been a clade containing Chytridiales+Spizellomycetales.
considered phylogenetically informative (Barr Phylogenetic investigations in the past three years
2001). This structural character state is present in suggest that much of the diversity in the chytrids is
found in species that are not readily cultured (e.g.
all members of the Chytriomyces (2K, Letcher et al
Olpidium, Rozella, Synchytrium). Remaining questions
2005), Cladochytrium (2D) and Polychytrium (2C)
in the chytrid phylogeny are the exact placement of
clades examined thus far. It is absent in the Rozella
Olpidium and whether microsporidia are a part of the
(1), Neocallimastigales (2A), Blastocladiomycota (3)
basal grade of chytrids. Further sampling of DNA
and Olpidium (4) clades (Barr 2001). When the
sequences from species that are obligate biotrophic
presence or absence of this character is mapped
parasites with unique zoospore ultrastructure (e.g.
onto the rDNA phylogeny, it appears that this
Caulochytrium [Powell 1981], Thalassochytrium [Ny-
character was present in the ancestor of the
vall et al 1999] and Zygorhizidium [Beakes et al 1988])
Chytridiales and Monoblepharidales (clades 2B–K)
might yet uncover additional clades. Furthermore,
but has been lost repeatedly in independent
given that a number of chytrid species are facultative
lineages (FIG. 2). For example in the Synchytrium
or obligate anaerobes, sampling of these environ-
clade (2E) this structure may be either present (S.
ments also might uncover additional phylogenetic
endobioticum, Lange and Olsen 1978) or absent (S.
diversity.
macrosporum, Montecillo et al 1980); in the Mono-
blepharidales (2B) it is either present (i.e. Mono-
blepharis polymorpha, Mollicone and Longcore 1994) ACKNOWLEDGMENTS
or lost (Gonapodya polymorpha, Mollicone and Long-
We thank Alison Mao for diligent technical assistance with
core 1999); it has been lost in the Spizellomycetales DNA sequencing. Material in the form of cultures and
(2I and 2J, Barr 1980) and Rhizophydium clades (2G; herbarium material used for these studies was kindly
Letcher et al 2004b, 2006). Thus an apparently provided by Robert Campbell, John W. Taylor and Howard
identical character state, the absence of the flagellar Whisler. We thank Will Blackwell for nomenclatural
plug, is a convergent character state if applied to assistance and Gary Easton, Marilyn R.N. Mollicone and
870 MYCOLOGIA

D’Ann Rochon for providing photos. We thank Carol Fitzpatrick HM. 1930. The lower fungi Phycomycetes. New
Nichols for her help preparing the ultrastructural sche- York: McGraw-Hill. 331 p.
matics. Financial support was provided by the National Förster H, Coffey MD, Elwood H, Sogin ML. 1990. Sequence
Science Foundation through the Assembling the Fungal analysis of the small subunit ribosomal RNAs of three
Tree of Life grant (AFTOL, award DEB-0228668) and the zoosporic fungi and implications for fungal evolution.
Partnership for Enhancing Expertise in Taxonomy grants Mycologia 82:306–312.
(PEET, awards DEB-9978094 and 0529694). This collabora- Fuller MS. 1966. Structure of the uniflagellate zoospores of
tive project would not have been possible without additional aquatic Phycomycetes. In: Madelin M, ed. Colston
support from the Research Coordination Network: A papers. Vol. XVIII. London: Butterworth Science
Phylogeny for Kingdom Fungi grant (Deep Hypha) by Publishers. p 67–84.
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Taylor. blepharella sp. zoospores. Can J Bot 46:279–283.
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