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2013 SOUTHEASTERN NATURALIST 12(4):666–683
Chytrid Diversity of Tuscaloosa County, Alabama
William J. Davis1,*, Peter M. Letcher1, and Martha J. Powell1
Abstract - Alabama is a biodiversity hotspot. The diversity of chytrid fungi, however, is
underexplored. For this reason, we used standard bait-culturing techniques to sample habitats
in Tuscaloosa County for chytrids. We cultured 100 isolates; the majority was assigned
to 23 taxa belonging to 6 of the 7 recognized orders. Some could not be assigned to a currently
described taxon. The majority of isolates belonged to one of three taxa: Chytriomyces
hyalinus, Rhizoclosmatium globosum, and Boothiomyces macroporosum. This result demonstrates
that chytrid communities in Tuscaloosa County, as elsewhere, are composed of a
few common and many uncommon to rare taxa. The presence of unidentified chytrid isolates
demonstrates the need for further sampling in Alabama, and the potential for this sampling
to broaden our understanding of chytrid diversity.
Introduction
Alabama is a biodiversity hotspot for several taxa (Boschung and Mayden 2004)
and is home to many endemic, endangered, and threatened animals and plants
(ANHP 2011). Alabama also has a diverse fungal biota (Atkinson 1897, Gray
and Morgan-Jones 1979, Hollis 1954, Morgan-Jones 1974). Our understanding
of the scope of this diversity is limited by a lack of recent activity and attempts
to update the taxonomy of former records. As a result, Alabama’s mycobiota is
poorly documented (Morgan-Jones 1974). Due to the importance of agriculture in
the state, most fungal surveys have focused on pathogens and potential pathogens
(Morgan-Jones 1974), a trend that continues to the present (e.g., Diamond et al.
2006, Palmateer et al. 2004, Rong et al. 2001, Vargas-Ayala et al. 2000). With a better
understanding of fungal taxonomy and new techniques, there have been recent
inventories of other groups, such as salt marsh saprophytes (Walker et al. 2010) and
trichomycetes (Nelder 2003, Nelder et al. 2010). With the exception of Lefèvre et
al. (2012), Nelder (2003), and Nelder et al. (2010), past and contemporary inventories
have excluded the early-diverging fungal lineages, such as the chytrid fungi.
Chytridiomycota (sensu Hibbett et al. 2007, = chytrid fungi) is an early-diverging
lineage of fungi characterized by a motile zoospore with a single, posterior
flagellum (Sparrow 1960). Chytrids are primarily aquatic, although numerous species
survive in the capillary network of water found around soil particles and can
be considered terrestrial (Sparrow 1960). As a group, chytrids appear to be ubiquitous
and cosmopolitan across soil and aquatic ecosystems (Barr 1990, Czeczuga et
al. 2005, Sparrow 1960). Within habitats, some chytrid taxa occur frequently and
regularly while others occur more rarely (Willoughby 1961, 1962); thus, chytrid
communities are structured with a few common taxa and many uncommon to rare
taxa (Letcher and Powell 2001, Marano et al. 2008).
1Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487. *Corresponding
author - wjdavis1@crimson.ua.edu.
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Chytrids are often overlooked due to their inconspicuous, microscopic nature
and difficulties with identification (Powell 1993). Nevertheless, early researchers
recognized that they are potentially key components of aquatic and terrestrial ecosystems
(Christensen 1951, Sparrow 1960). Indeed, chytrids act as important parasites
and saprobes (Powell 1993, Sparrow 1960, Wakefield et al. 2010). Recent molecular
inventories have indicated that chytrids may dominate the fungal communities in the
pelagic zones of lakes (Monchy et al. 2011) and in alpine soils (Freeman et al. 2009,
Schmidt et al. 2012); consequently, they likely impact the flow of nutrients and energy
through the food webs in these habitats. Although research is beginning to unravel
how parasitic chytrids influence aquatic food webs (e.g., Grami et al. 2011, Ibelings
et al. 2004, Kagami et al. 2007, Miki et al. 2011, Niquil et al. 2011, van Donk 1989),
many aspects of chytrid ecology—for example, the abiotic and biotic factors determining
the spatial structure of chytrid communities—remain to be explored.
Prior to molecular inventories, most studies of chytrid diversity were observation-
or culture-based local inventories. For this reason, chytrid diversity has been
well documented in only a few locations, such as the English Lake District (Willoughby
1961, 1962) and the Douglas Lake region of Michigan (Dogma 1969,
Paterson 1967, Sparrow 1952), and poorly documented in others. Recent taxonomic
revisions have sampled more broadly and have included 12 isolates from Alabama
(e.g., Letcher et al 2006, 2012; Simmons 2011; Vélez et al. 2011; Wakefield et al.
2010). Some of these isolates are phylogenetically unique, such as unidentified
species WB235A in Fig. 1 of Vélez et al. (2011), and may represent new species.
A recent report from AL has expanded the known range of Blyttiomyces spinulosus
(Blytt) Bartsch (Blackwell et al. 2011). Lefèvre et al. (2012) inventoried two lakes
in Tuscaloosa County, AL using a combination of culture-based and molecular
techniques. Their results indicated that chytrids dominated the fungal communities
in these lakes. Moreover, approximately half of the chytrid sequences found did not
cluster with currently described taxa (Lefèvre et al. 2012). This finding suggests
that an exploration of chytrid diversity in AL would benefit a broader understanding
of chytrid diversity as well as add to the knowledge of Alabama’s mycobiota. Thus,
the purpose of this study was to investigate the chytrid diversity within Tuscaloosa
County, with an emphasis on Lake Lurleen. We predicted that chytrids found in
Tuscaloosa County consist of an assemblage of a few common and many uncommon
to rare taxa, with some unique taxa, and that the common taxa are the same as
those found globally.
Study Sites
Soil and water samples were collected from a variety of locations and habitats
around Tuscaloosa County. Tuscaloosa County has a total area of approximately
3500 km2 and is located in west-central AL. Soils in the northeast portion of the
county are derived from the Appalachian Highlands, while soils to the west and
south are part of the Gulf Coast Plain (Johnson et al. 1981).
Four main aquatic sites were sampled: Lake Lurleen, Lake Nicol, the Black Warrior
River, and Marr’s Spring. Lake Lurleen (33.291014, -87.511253) is a 101-ha
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reservoir located in a 658-ha acre state park. Lake Nicol (33.307315, -87.479989)
is a 156-ha reservoir. According to Johnson et al. (1981), the soils surrounding both
reservoirs are mainly acidic, well-drained loams with moderate to high water capacity.
Lefèvre et al. (2012) designated Lake Lurleen as meso-eutrophic and found
it to have a metalimnetic oxygen maximum during the stratified period (May to November).
To date, basic limnological data for Lake Nicol have not been measured.
The Black Warrior River is a 268-km tributary of the Tombigbee River and part of
the Mobile River drainage basin (Ward et al. 2005). It begins in the Appalachian
Plateau region of AL (northeast corner) and crosses the Fall Line, the transition
from the Appalachian Plateau to the Coastal Plain, near the city of Tuscaloosa
(Ward et al. 2005). The Black Warrior River has a mean flow of 277 m3s-1 with
maximum flow occurring in March (Ward et al. 2005). Unfortunately, the Black
Warrior River has been heavily impacted by activities associated with urban centers,
such as Tuscaloosa and Birmingham, mining activity, and agriculture (Mette
et al. 1989). The Black Warrior River has been impounded by a system of locks and
dams and is kept at a width of 61 m and a depth of 3 m for the transportation of coal
(Mette et al. 1989). Marr’s Spring is a modified spring located on the University
of Alabama campus. It has a concrete bottom and is surrounded by flower beds. In
addition, a few samples were taken opportunistically from roadside ditches, ponds,
yards, and pastures across Tuscaloosa County, AL.
Methods
Sampling and isolation
Soil and aquatic samples were opportunistically collected from the banks, shallows,
and pelagic regions of Lake Lurleen, Lake Nicol, the Black Warrior River,
Marr’s Spring, and other locations across Tuscaloosa County. Collections of approximately
200 mL of water or 200 g of soil were made by hand (i.e., dipping a
container in the water or scooping soil into a bag). Samples were stored in whirl-top
plastic bags, kept cool with ice, and transferred to the laboratory. In the laboratory,
portions of each sample were placed in Petri dishes, and sterile water was added to
the soil samples. Samples were baited with sterile pollen from Pinus spp. (pine) and
Liquidambar styraciflua L. (Sweetgum), cellulose (onion epidermal cells), keratin
(snake skin), and chitin (shrimp exoskeleton; Couch 1939, Sparrow 1960). Baits
(added substrates) and natural substrates already present (e.g., senescing or dead
algae, insect exuviae, etc.) were examined microscopically and periodically for
chytrid thalli. Standard techniques (Couch 1939, Sparrow 1960) were used to bring
observed chytrids into pure culture. Due to the limitations of the methods employed,
only saprophytic chytrids were brought into culture and used in subsequent analyses.
Any chytrid that was observed but not brought into culture was not included in the
analyses. Chytrids brought into pure culture, hereafter isolates, were maintained on
PmTG (1 g peptonized milk, 1 g tryptone, 5 g glucose, and 8 g agar per liter of water),
mPmTG (0.4 g peptonized milk, 0.4 g tryptone, 2 g glucose, and 8 g agar per liter of
water), or Archimycete Media (2 g peptonized milk, 3 g malt extract, 5 g glucose, and
8 g agar per liter of water) nutrient agar plates (CBS 2013) and transferred at 2 month
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intervals to maintain viability. Plates were sealed and maintained in the dark at room
temperature. Isolates were tentatively identified using morphological features with
the aid of Sparrow (1960), Karling (1977), and relevant literature.
DNA extraction, PCR, and sequencing
For DNA extractions, isolates were grown in 50 mL of nutrient broth, which is the
same as nutrient agar without the agar. Broth cultures were then centrifuged in 50-mL
Falcon tubes for 20 minutes at 3000 rpm in a ThermoIEC I-703a centrifuge (ThermoIEC,
Needham Heights, MA) to pellet chytrid thalli. DNA was extracted from
the pellet using the NucleoSpin Plant II DNA extraction kit (Macherey-Nagel, Inc.,
Bethlehem, PA) and the NucleoSpin protocol for fungal cultures (Macherey-Nagel,
Inc. 2008). DNA concentration was determined with spectrophotometry using a
Nanodrop (Nanodrop, Wilmington, DE). The DNA was diluted to 10 ng/μL for PCR.
The D1/D2 region of the 28s large ribosomal subunit (800–900bp from the 5’
end) has been used as a molecular marker to delineate taxa within Chytridiomycota
(e.g., Letcher et al. 2006, Longcore and Simmons 2012, Simmons 2011, Simmons
et al. 2009, Vélez et al. 2011, Wakefield et al. 2010), and phylogenies inferred with
this region are congruent with those inferred from zoospore ultrastructure (Letcher
et al. 2005). As a result, there is a database of taxonomically reliable sequences
available, and we chose this region for use in our study. The region was amplified
using the LROR/LR5 primer pair (Rehner and Samuels 1994, Vilgalys and Hester
1990) for 30 cycles of 1 min at 94 °C, 1 min at 50 °C, 1 min at 72 °C with an initial
denaturing at 94 °C for 2 mins, and final elongation at 72 °C for 5 mins. Four
replicate amplifications were pooled and cleaned following the protocols of the Nucleospin
Extraction II kit (Macherey-Nagel, Inc. 2009). Amplicons were sequenced
(Macrogen USA, Rockville, MD) and assembled into contiguous sequences using
Sequencher 4.5 (Genecodes) as described by Letcher et al. (2004b). Sequences
were searched against the GenBank database using the blastn algorithm (Altschul
et al. 1990) to corroborate the tentative morphology-based iden tification.
Alignment and phylogenetic analysis
Taxonomically reliable reference sequences used in revisions of the Chytridiomycota
were downloaded from GenBank. In two cases (MP53 and EL102), the
reference sequences were also obtained from the study area and so were included
in subsequent calculations. All sequences were aligned with ClustalX (Thompson
et al. 1997) and manually adjusted with BioEdit (Hall 1998).
Maximum parsimony (MP) trees were inferred using PAUPRat (Sikes and
Lewis 2002), and maximum likelihood (ML) trees were inferred using RAxML
7.0.3 (Stamatakis 2006) under the GTR + G model of nucleotide substitution as
determined by ModelTest 3.7 (Posada and Crandall 1998). A 50% majority rule
consensus-tree was generated from the MP trees and bootstrapped in PAUP* (Swofford
2002). The best ML-tree was bootstrapped with 1000 replicates using the
rapid bootstrap option (Stamatakis et al. 2008). The inferred trees were rooted with
Monoblepharella mexicana (UCB 78-1 from James et al. 2006), a member of the
Monoblepharidiomycota (Doweld 2001), the sister group of Chytridiomycota.
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2013 Southeastern Naturalist Vol. 12, No. 4
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Results
Phylogenetic analysis
The alignment contained 100 isolates and 992 characters, of which 521 were
parsimony-informative. The inferred MP (2615 steps, CI = 0.408, RI = 0.891) and
ML (-lnL = 14427.072300) trees were incongruent concerning the placement of
the Spizellomycetales and Polychytriales. Neither could resolve the relationships
between the orders. However, the trees were congruent concerning the placement of
taxa into families, genera, and species. Thus, only the ML tree is illustrated (Fig. 1).
Phylogenetic distribution
The 100 isolates were delineated into taxa at the order, family, genus, and species
level using the monophyletic phylogenetic species concept (Mayden 1999).
Specifically, an isolate was considered a member of a taxon if it formed a monophyletic
clade with a reference sequence of that taxon. Chytridiomycota contains
seven orders: Chytridiales, Rhizophydiales, Spizellomycetales, Rhizophlyctiales,
Polychytriales, Cladochytriales, and Lobulomycetales. Isolates obtained in this
study grouped with reference sequences in the Chytridiales, Rhizophydiales,
Spizellomycetales, Rhizophlyctidales, Polychytriales, and Cladochytridales. The
isolates were unevenly distributed among these orders (Fig. 1). Lobulomyces
poculatus (Willoughby) Simmons, a representative of the Lobulomycetales, was
observed but attempts to culture it failed. The majority of the isolates (52%) was
placed in Chytridiales and represented one of two families within the order (Vélez
et al. 2011). Approximately one-third (34%) of the isolates represented eight of ten
families within the Rhizophydiales (Letcher et al. 2006, 2008b). All of the families
within Spizellomycetales were represented by 9% of the isolates. Two isolates (2%)
represented one of four families in the Rhizophlyctidales (Letcher et al. 2008a).
Two isolates (2%) also represented the Polychytriales, and one isolate (1%) represented
the Cladochytriales.
The vast majority (96%) of the isolates was assigned to 23 described taxa at the
genus or species level (Appendix 1). The isolates were also unevenly distributed
among these taxa, with 24% of the isolates grouping into the clade corresponding
to the morphospecies Chytriomyces hyalinus Karling, 15% grouping with the
morphospecies Rhizoclosmatium globosum Petersen, and 17% grouping with Boothiomyces
macroporosum (Karling) Letcher (Fig. 1). Most taxa were represented
by few isolates.
Geographic distribution
Thirty-nine of the isolates came from Lake Lurleen (Appendix 1). These
isolates represented nine taxa at the genus and species level: Rhizoclosmatium
globosum, Rhizidium sp., Siphonaria petersenii Karling, Chytriomyces
hyalinus, Geranomyces variabilis (Powell) Simmons, Boothiomyces macroporosum,
Kappamyces laurelensis Letcher, Polychytrium aggregatum Ajello, and
Angulomyces argentinensis Letcher. Two of the Lake Lurleen isolates—WB228
and WB235A— did not form monophyletic clades with currently described taxa.
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2013 Southeastern Naturalist Vol. 12, No. 4
Figure 1. Maximum likelihood tree (-lnL = 14427.072300) of Tuscaloosa County chytrid
isolates. Only clades with >50% bootstrap support are shown, with the exception of the
Rhizophlyctidales. Branches cut with a │are half their original length
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2013 Southeastern Naturalist Vol. 12, No. 4
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Polychytrium aggregatum, Kappamyces laurelensis, and Siphonaria petersenii
were only isolated from Lake Lurleen. Thirteen isolates came from Lake
Nicol (Appendix 1) and were grouped into six taxa: Chytriomyces hyalinus,
Rhizoclosmatium globosum, Globomyces pollinis-pini (Braun) Letcher, Protrudomyces
lateralis (Braun) Letcher, Rhizophydium sp., and Gorgonomyces haynaldii
(Schaaraschm) Letcher. Protrudomyces lateralis and G. haynaldii were only isolated
from Lake Nicol. The Black Warrior River yielded eleven isolates that were
identified as Alphamyces chaetifer (Sparrow) Letcher, Rhizophydium sp., G. pollinis-
pini, C. hyalinus, Rhizidium sp., Fimicolochytrium alabamae Simmons,
and Fimicolochytrium jonesii Simmons (Appendix 1). The Black Warrior River
was the only source of F. jonesii. Nine isolates and eight taxa (Appendix 1) were
from Marr’s Spring: Rhizidium sp., Rhizophydium globosum (Braun) Rabenhorst,
A. chaetifer, Cladochytrium replicatum Karling, Boothiomyces macroporosum,
Gorgonomyces sp., Angulomyces argentinensis, and C. hyalinus. Cladochytrium
replicatum was isolated only from Marr’s Spring.
Discussion
The purpose of our study was to explore chytrid diversity in Tuscaloosa County,
AL. We were motivated by the need to document Alabama’s diverse mycobiota,
specifically the understudied chytrid fungi. Approximately 95% of the isolates
form monophyletic clades with previously identified taxa, which have global distributions.
For example, Boothiomyces macroporosum has been found in Australia,
Argentina, and Canada (Letcher et al. 2006, 2008b). Gaertneriomyces semiglobifer
(Uebelmesser) Barr has been observed or isolated from Germany, Israel, and
Australia (Wakefield et al. 2010). Globomyces pollinis-pini has been observed or
isolated from Russia, China, and Cuba (Sparrow 1960); Douglas Lake, MI (Sparrow
1952); and Argentina (Letcher et al. 2008b). Thus, the chytrid taxa found in
AL are the same as those found globally, which is in agreement with our initial
prediction. This is the first time that many of these taxa have been reported from
AL. Thus, our sampling in AL has expanded the known distribution of these taxa
and has corroborated the view that chytrids are cosmopolitan (Barr 1990, Czeczuga
et al. 2005, Sparrow 1960).
Approximately half of the isolates belong to the clades of Chytriomyces hyalinus,
Rhizoclosmatium globosum, and Boothiomyces macroporosum. The rest of the
taxa were represented by few isolates. Although frequency and abundance were
not calculated, it can be inferred from the phylogenetic distribution of isolates that
chytrid communities in AL are dominated by a few common species; thus, there
are a few common species and many uncommon to rare species in Alabama. This
is in agreement with general ecological theory, the results of surveys conducted
in Virginia (Letcher and Powell 2001), Australia (Letcher et al. 2004a, b), Brazil
(Nascimento et al. 2011a, b), Argentina (Marano et al. 2008), Canada (Lee 2000),
and Great Britain (Willoughby 1961, 1962), and our initial prediction.
We were able to assign some isolates to a genus but not to a species, e.g., isolates
in the Triparticalcar, Gorgonomyces, Rhizidium, and Rhizophydium clades. This is
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a common occurrence and has been reported for other taxa such as Triparticalcar
and Powellomyces (Wakefield et al. 2010) and Cladochytrium (Mozley-Standridge
et al. 2009). The lack of resolution at the species level could be due to exclusive
use of the D1/D2 region of the 28s rDNA gene, which is good at resolving chytrid
families and genera but may have limited utility at the species level (Letcher et al.
2004b). It could also be the result of an insufficient number of available sequences
from those genera. Alternatively, these isolates could represent unknown phylogenetic
diversity, which could correspond to new species. Such phylogenetic diversity
was previously reported for the genus Powellomyces by Wakefield et al. (2010),
which was delineated into new species by Simmons (2011) and Simmons and Longcore
(2012). Four isolates could not be assigned to a genus or a species: WB228,
WB235A, MP041, and WJD150. Isolate WB235A was previously reported by
Vélez et al. (2011) as sister to Chytriomyces hyalinus. In our study, isolate MP041
is sister to it, and their position within Chytridiales is unresolved. Isolate WB228
is an early diverging lineage within the Chytridiales. Isolate WJD150 is sister to
isolate PL157, an undescribed isolate from Argentina (Letcher et al. 2008b). These
isolates could represent undescribed taxa or described but not sequenced taxa.
Thus, it can also be concluded that AL samples may reveal novel taxa and unknown
phylogenetic diversity within described taxa. As a result, our AL samples can aid in
the current exploration and refinement of chytrid species concepts (Longcore 2004,
Simons and Longcore 2012).
A total of 23 described taxa were isolated in our study. This is comparable to
the diversity reported by other inventories. Marano et al. (2008, 2011) reported 16
species from the Las Cañas stream near Buenos Aires, Argentina. Thirteen species
have been recorded from the Reserva Natural Selva Marginal Punta Lara, Argentina
(Arellano et al. 2009, Marano et al. 2008). Nascimento et al. (2011a, b) have
reported 20 species from the Reserva Biológica de Mogi Guaçu, Brazil. However,
given that 34 species were recorded from the English Lake District by Willoughby
(1961, 1962) and approximately 60 species have been recorded from the Douglas
Lake Region, MI (Dogma 1969, Paterson 1967, Sparrow 1952), it is likely that
Tuscaloosa County is under-sampled for chytrid diversity.
Of the 23 taxa isolated from Tuscaloosa County, nine were reported from Lake
Lurleen, the most heavily sampled site. This number is comparable to the findings
of Kiziewicz and Nalepa (2008), who reported five species from a site on Lake
Michigan near Muskegon, MI. It is also comparable to the numbers reported for
the Reserva Natural Selva Marginal Punta Lara and Las Cañas stream. However, a
comparison of our results for Lake Lurleen to Lefèvre et al.’s (2012) results suggests
much of the chytrid diversity in Lake Lurleen was missed in our study. Lefèvre et
al. (2012) reported 18 unique chytrid phylotypes and 3 cultured chytrids from Lake
Lurleen for a total of 21 taxa. Of those 21 taxa, only three—Chytriomyces hyalinus,
Rhizoclosmatium globosum, and Kappamyces laurelensis—were the same as ones
isolated in our study. Also, the majority of the phylotypes did not form clades with
previously described species or genera (Lefèvre et al. 2012), which further supports
the contention that Lake Lurleen has been under-sampled.
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2013 Southeastern Naturalist Vol. 12, No. 4
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Part of this under-sampling is due to the intensity of sampling. In order to fully
sample chytrid diversity, repeated temporal (Willoughby 1961, 1962) and spatial
(Letcher and Powell 2001) sampling is necessary. Most sites included in this study
were not sampled as intensely as those in Willoughby (1961, 1962) and Letcher and
Powell (2001). Thus, the chytrid diversity at each site was undersampled, resulting
in an overall under-sampling of the chytrid diversity across Tuscaloosa County.
This under-sampling can also be explained by the limitations of a culture-based
inventory, which have been reviewed by Lozupone and Klein (2002). Our results
include only those chytrids capable of saprophytic growth on nutrient media. All
of the parasitic lineages have been excluded, which reduces the total number of
species reported and the phylogenetic diversity sampled (Letcher et al. 2004b).
The inclusion of these taxa will require the development of new techniques in
chytrid isolation and culturing. Alternatively, a molecular inventory would reveal
more diversity because it would include difficult-to-culture taxa, such as those in
the Lobulomycetales (Simmons et al. 2009). However, molecular inventories are
only useful when there is reliable and abundant sequence information available for
a lineage (Lozupone and Klein 2002). This fact is demonstrated by the findings of
Lefèvre et al. (2012). It remains to be seen whether Lefèvre et al.’s (2012) phylotypes
are novel taxa or merely unsequenced, described taxa, and this ambiguity
highlights the need for more taxonomic work in Chytridiomycota and an increase
in the number of taxonomically reliable sequences. Although recent molecular revisions
of Chytridiomycota have greatly increased the number of chytrid sequences
available, these studies were all bait-culture based. Since the majority of chytrid
species are described based on morphological characters (Longcore 1996, Sparrow
1960), bait-culture studies will be crucial to building a molecular database
necessary for molecular inventories to be useful. The sequences we have generated
represent the beginning of such a database for future molecular inventories that
might take place in Alabama.
Our results suggest that the same phylogenetic depth and diversity (Faith 1992)
seen with a global sampling is mirrored on a local scale. Further analysis is required
to determine the amount of biodiversity not detected by local sampling. Increased
sampling of the state will document a previously excluded portion of Alabama’s
mycobiota biodiversity and broaden our understanding of chytrid diversity.
Acknowledgments
Thanks are extended to Dr. Carol Duffy, Rebecca Holland, Sharmeka Lewis, Scotty De-
Priest, Samantha Perkins, Trey Milton, Adam Fuller, Nichole Mattheus, Sarah Duncan, and
Alissa Vincent for help with collecting the samples. Appreciation is expressed to Dr. Will
Blackwell, Antijuan Spivy, Leeanne Bertram, Ben Swann, Keith Atkinson, and Michael
Brooks for help in bringing isolates into culture and to Dr. Satoshi Sekimoto and Dr. Emilie
Lefèvre for help with extractions and sequencing. Special thanks to Jonathan Antonetti
who was involved in multiple areas of the project and to Richard Baird and two anonymous
reviewers for careful review and helpful suggestions. Funding was kindly provided by the
National Science Foundation (NSF REVSYS 0949305), the McNair Graduate Fellowship,
and the Department of Biological Sciences of the University of Alabama.
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2013 Southeastern Naturalist Vol. 12, No. 4
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Appendix 1. List of isolate and reference sequences included in the phylogenetic analysis.
Culture number refers to the identifier given to an isolate by the investigator who isolated
it. Isolates are grouped first by taxa and second by location.
GenBank 28s
Culture number/taxonomic affiliation accession # Location
Isolates
Chytridiales
MP053 Chytriomyces hyalinus JN049526 Lake Lurleen, AL
AQ Chytriomyces hyalinus KC691310 Lake Lurleen, AL
WJD105 Chytriomyces hyalinus KC691369 Lake Lurleen, AL
WJD107 Chytriomyces hyalinus KC691370 Lake Lurleen, AL
WJD108 Chytriomyces hyalinus KC691371 Lake Lurleen, AL
WJD112 Chytriomyces hyalinus KC691375 Lake Lurleen, AL
WJD136 Chytriomyces hyalinus KC691386 Lake Lurleen, AL
WJD139 Chytriomyces hyalinus KC691389 Lake Lurleen, AL
BD Chytriomyces hyalinus KC691311 Lake Nicol, AL
JA003 Chytriomyces hyalinus KC691314 Lake Nicol, AL
MP083 Chytriomyces hyalinus KC691351 Black Warrior River, AL
MP089 Chytriomyces hyalinus KC691354 Black Warrior River, AL
WJD138 Chytriomyces hyalinus KC691388 Black Warrior River, AL
WJD140 Chytriomyces hyalinus KC691390 Black Warrior River, AL
JA001 Chytriomyces hyalinus KC691312 Marr’s Spring Pond, AL
PL181 Chytriomyces hyalinus KC691357 Lake Tuscaloosa, AL
MP004 Chytriomyces hyalinus DQ273836 University of Alabama, AL
MP070 Chytriomyces hyalinus KC691345 Cottondale, AL
MP080 Chytriomyces hyalinus KC691348 Cottondale, AL
WB216 Chytriomyces hyalinus KC691358 Cottondale, AL
MP066 Chytriomyces hyalinus KC691342 Northport, AL
MP068 Chytriomyces hyalinus JX905526 Northport, AL
MP069 Chytriomyces hyalinus KC691344 Northport, AL
WB241 Chytriomyces hyalinus KC691366 Northport, AL
MP081 Chytriomyces hyalinus KC691349 Tuscaloosa, AL
MB001 Rhizoclosmatium globosum KC691318 Lake Lurleen, AL
MB007 Rhizoclosmatium globosum KC691322 Lake Lurleen, AL
MB037 Rhizoclosmatium globosum KC691329 Lake Lurleen, AL
MB038 Rhizoclosmatium globosum KC691330 Lake Lurleen, AL
MB048 Rhizoclosmatium globosum KC6911331 Lake Lurleen, AL
WB219 Rhizoclosmatium globosum KC691360 Lake Lurleen, AL
WJD111 Rhizoclosmatium globosum KC691374 Lake Lurleen, AL
WJD143 Rhizoclosmatium globosum KC691391 Lake Lurleen, AL
WB235C Rhizoclosmatium globosum KC691364 Lake Lurleen, AL
JA002 Rhizoclosmatium globosum KC691313 Lake Nicol, AL
JA004 Rhizoclosmatium globosum KC691315 Lake Nicol, AL
JA005 Rhizoclosmatium globosum KC691316 Lake Nicol, AL
WB236B Rhizoclosmatium globosum KC691365 Lake Nicol, AL
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GenBank 28s
Culture number/taxonomic affiliation accession # Location
WB218 Rhizoclosmatium globosum KC691359 Cottondale, AL
WB224 Rhizoclosmatium globosum KC691361 Cottondale, AL
EL102 Rhizoclosmatium aurantiacum JN049529 Lake Lurleen, AL
MP067 Rhizoclosmatium aurantiacum KC691343 Lake Nicol, AL
MP046 Rhizoclosmatium sp. KC691335 Lake Lurleen, AL
MP056 Rhizoclosmatium sp. KC691339 Marr’s Spring, AL
MB013 Rhizidium sp. KC691324 Lake Lurleen, AL
MP051 Rhizidium sp. KC691338 Lake Lurleen, AL
MP040 Rhizidium sp. KC691332 Marr’s Spring, AL
MP087 Rhizidium sp. KC691352 Black Warrior River, AL
MP088 Rhizidium sp. KC691353 Black Warrior River, AL
WB235A Chytriomyces sp. FJ822968 Lake Lurleen, AL
MP041 Chytriomyces sp. JX905522 Tuscaloosa, AL
WB235B Siphonaria petersenii KC691363 Lake Lurleen, AL
WB228 Unidentified Chytridiales sp. KC691362 Lake Lurleen, AL
Rhizophydiales
MB006 Boothiomyces macroporosum KC691321 Lake Lurleen, AL
MB012 Boothiomyces macroporosum KC691323 Lake Lurleen, AL
MB016 Boothiomyces macroporosum KC691325 Lake Lurleen, AL
MB017 Boothiomyces macroporosum KC691326 Lake Lurleen, AL
MB019 Boothiomyces macroporosum KC691327 Lake Lurleen, AL
MB020 Boothiomyces macroporosum KC691328 Lake Lurleen, AL
MP063 Boothiomyces macroporosum KC691340 Lake Lurleen, AL
MP075 Boothiomyces macroporosum KC691347 Lake Lurleen, AL
WJD102 Boothiomyces macroporosum KC691367 Lake Lurleen, AL
WJD109 Boothiomyces macroporosum KC691372 Lake Lurleen, AL
WJD110 Boothiomyces macroporosum KC691373 Lake Lurleen, AL
WJD117 Boothiomyces macroporosum KC691376 Lake Lurleen, AL
WJD128 Boothiomyces macroporosum KC691381 Marr’s Spring, AL
P065 Boothiomyces macroporosum KC691341 Northport, AL
WJD118 Boothiomyces macroporosum KC691377 Northport, AL
WJD127 Boothiomyces macroporosum KC691380 Northport, AL
PL133 Terramyces subangulosum DQ485584 Northport, AL
JA006 Gorgonomyces haynaldii KC691317 Lake Nicol, AL
WJD130 Gorgonomyces sp. KC691383 Marr’s Spring, AL
MP045 Alphamyces chaetifer JF809855 Black Warrior River, AL
MP048 Alphamyces chaetifer JF809857 Marr’s Spring, AL
WJD154 Kappamyces laurelensis KC691397 Lake Lurleen, AL
MP050 Rhizophydium globosum KC691337 Tuscaloosa, AL
WJD145 Rhizophydium sp. KC691393 Lake Nicol, AL
MP043 Rhizophydium sp. KC691334 Black Warrior River, AL
MP042 Rhizophydium sp. KC691333 Tuscaloosa, AL
MP049 Rhizophydium sp. KC691336 Tuscaloosa, AL
WJD132 Globomyces pollinis-pini KC691384 Lake Nicol, AL
WJD133 Globomyces pollinis-pini KC691385 Lake Nicol, AL
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GenBank 28s
Culture number/taxonomic affiliation accession # Location
MP082 Globomyces pollinis-pini KC691350 Black Warrior River, AL
WJD137 Angulomyces argentinensis KC691387 Lake Lurleen, AL
WJD129 Angulomyces argentinensis KC691382 Marr’s Spring, AL
WJD144 Protrudomyces lateralis KC691392 Lake Nicol, AL
WJD150 Unidentified Rhizophydiales sp. KC691395 University of Alabama, AL
Spizellomycetales
MB004 Geranomyces variabilis KC691319 Lake Lurleen, AL
MB005 Geranomyces variabilis KC691320 Lake Lurleen, AL
PL166 Geranomyces variabilis HQ901699 Tuscaloosa, AL
WJD125 Fimicolochytrium alabamae KC691379 Black Warrior River, AL
WJD152 Fimicolochytrium jonesii KC691396 Black Warrior River, AL
WJD148 Fimicolochytrium jonesii KC691394 Northport, AL
MP074 Gaertneriomyces semiglobifer KC691346 Tuscaloosa Co., AL
WJD101 Triparticalcar sp. KC788571 Duncanville, AL
WJD156 Triparticalcar sp. KC691398 Tuscaloosa Co., AL
Rhizophlyctidales
JM001 Rhizophlyctis rosea EU379183 Tuscaloosa, AL
RT003 Rhizophlyctis rosea EU379197 Tuscaloosa, AL
Polychytriales
PL071 Polychytrium aggregatum KC691355 Lake Lurleen, AL
WJD104 Polychytrium aggregatum KC691368 Lake Lurleen, AL
Cladochytriales
WJD123 Cladochytrium replicatum KC691378 Marr’s Spring, AL
Reference sequences
MP053 Chytriomyces hyalinus JN049526
JEL006 Rhizoclosmatium globosum AY439061
EL102 Rhizoclosmatium aurantiacum JN049529
JEL378 Rhizidium sp. DQ273832
KP013 Rhizophydium phycophilum FJ214802
JEL102 Siphonaria petersenii AY439072
PLAUS021 Boothimyces macroporosum AY439040
ARG026 Gorgonomyces haynaldii EF585607
ARG025 Alphamyces chaetifer EF585606
PL098 Kappamyces laurelensis DQ485581
JEL222 Rhizophydium globosum DQ485551
ARG068 Globomyces pollinis-pini EF585625
ARG008 Angulomyces argentinensis EF585595
ARG071 Protrudomyces lateralis EF585628
PL157 Unidentified Rhizophydiales sp. DQ485594
MP003 Geranomyces variabilis HQ901689
JEL538 Fimicolochytrium alabamae HQ901669
JEL569 Fimicolochytrium jonesii HQ901681
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GenBank 28s
Culture number/taxonomic affiliation accession # Location
BR043 Gaertneriomyces semiglobifer FJ827702
BR059 Triparticalcar arcticum DQ273826
BR186 Rhizophlyctis rosea AY349079
JEL109 Polychytrium aggregatum AY546686
JEL180 Cladochytrium replicatum NG_027614
Outgroup
UCB781 Monoblepharella mexicana DQ273777
Appendix 2. List of described species, with authorities, included in Appendix 1. State
records are designated with (**).
Taxon name
Chytridiales
Chytriomyces hyalinus Karling
Rhizoclosmatium globosum Petersen **
Rhizoclosmatium aurantiacum (Petersen) Sparrow
Siphonaria petersenii Karling **
Rhizophydiales
Boothiomyces macroporosum (Karling) Letcher **
Terramyces subangulosum (Braun) Letcher
Gorgonomyces haynaldii (Schaarschmidt) Letcher **
Alphamyces chaetifer (Sparrow) Letcher
Kappamyces laurelensis Letcher
Rhizophydium globosum (Braun) Rabenhorst **
Globomyces pollinis-pini (Braun) Letcher **
Angulomyces argentinensis Letcher **
Protrudomyces lateralis (Braun) Letcher **
Spizellomycetales
Geranomyces varibilis (Powell) Simmons
Fimicolochytrium alabamae Simmons
Fimicolochytrium jonesii Simmons
Gaertneriomyces semiglobifer Barr **
Triparticalcar arctiacum Barr
Rhizophlyctidales
Rhizophlyctis rosea (de Bary and Woronin) Fischer
Polychytriales
Polychytrium aggregatum Ajello **
Cladochytriales
Cladochytrium replicatum Karling **
Outgroup
Monoblepharella mexicana Shanor