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New
Phytologist
Letters
Fungal associations of basal
vascular plants: reopening a
closed book?
Introduction
The widely held hypothesis that Glomeromycota fungi alone
formed the ancestral land plant—fungus symbiosis (Pirozynski &
Da!pi, 1989; Selosse & Le Tacon, 1998; Wang & Qiu, 2006;
Parniske, 2008) has recently been challenged by new lines of
evidence from molecular, cytological, functional and palaeonto-
logical studies. First, liverworts of the earliest divergent Glade, the
Haplomitriopsida, form a mutualistic mycorrhiza-like relation-
ship, whereby there is reciprocal exchange of plant carbon (C) for
fungal nitrogen (N) and phosphorus (P), with members of the
Mucoromycotina (Bidartondo et al, 2011; Field et
2014), a
fungal lineage considered basal or sister to the Glomeromycota
(James etal., 2006; Lin nal, 2014). Second, other basal plants,
including complex and simple thalloid liverworts and homworts,
enter into associations with both Mucoromycotina and Glomer-
omycota fungi, sometimes simultaneously (Bidartondo et at,
2011; Desire, eta!, 2013). Third, dual partnerships involving
fungi with affinities to Glomeromycota and Mucoromycotina have
been reported in fossils of early vascular plants from the Devonian
(Strullu-Derrien et al, 2014).
Turning to the fungal associations of the extant representatives of
the early diverging vascular plant lineages, the glomeromycete
identity of fungi in ferns (Monilophyta) has never been questioned
—a consensus borne out by cytology and limited DNA sequencing
data (Wang & Qiu, 2006; Ogura-Tsujita etal., 2013). By contrast,
the unusual cytology of fungal colonization in lycopods
(Lycopodiophyra), highly reminiscent of the cytology reported in the
Haplomitriopsida genus Treubia (Duckett et al, 2006), suggested
unique fungal partnerships or ilycopodioid mycothallus interac-
tions' (Duckett & Ligrone, 1992; Schmid & Oberwinlder, 1993)
until a molecular study detected Glomeromycota in this group
(Winther & Friedman, 2008), thus 'laying to rest over a century of
speculations and uncertainty' surrounding their identity (Leake
et al, 2008). However, Windier & Friedman's study, and a more
recent investigation proposing a basidiomycete as the main
symbiont in a member of the Lycopodiaceae (Horn eta!, 2013;
but see rebuttal in Strullu-Derrien eta& 2014 criticizing their
limited molecular and microscopical data), used methods that do
not detect Mucoromycotina fungi. Therefore, it remains to be
determined whether members of the Mucoromycotina related to
the fungi known to enter into mutualism with basal liverworts
(Field et al, 2014) also form associations with vascular plants. To
test this possibility, we carried out molecular and microscopical
analyses of the fungal associations of all the major lineages of
lycopods and ferns.
Materials and Methods
Sampling sites were globally distributed (Supporting Information
Table S1). At least one mature plant colony was collected from each
site. Plants were processed for cytological and molecular analyses
within 1 wk of collection by removing and cleaning roots with
forceps and sterile water. Roots were prepared for scanning and
transmission electron microscopy as previously described (Pressel
et al, 2010; Desire end, 2013). Extraction and sequencing of
genomic fungal DNA were performed using the method of
Bidartondo et al (2011). In brief, the universal fungal 18S primer
combination NS1 (White et 4, 1990) and EF3 (Smit et at, 1999)
was used to amplify DNA which was cloned (TOPO TA;
Invitrogen) and sequenced using an Applied Biosystems Genetic
Analyser 3730 (Waltham, MA, USA). Between four and eight
clones were sequenced for each sample and identified using NCBI
BLAST (Altschul et al, 1997). Sequence editing and assembly were
performed in Geneious v5.6 (http://www.geneious.com). The
alignment algorithms of MUSCLE were used within MEGA v5.1
(Tamura et al, 2011), with reference sequences from GenBank.
Using UCHIME (Edgar et al, 2011) within MOTHUR (http://
www.mothur.org), confirmed sequences were not chimeric. Evo-
lutionary models were tested in MEGA. Bayesian inference was
carried out using MrBayes (Huelsenbeck & Ronquist, 2001) and
FigTree v1.4 (http://tree.bio.ed.ac.uk) for visualization and edit-
ing. Representative DNA sequences have been deposited in
GenBank (KJ952212—KJ952241).
Results
Molecular and cytological analyses showed that both Mucoromy-
cotina and Glomeromycota fungi associate with lycopods and ferns
(Figs 1, 2). We examined samples from 20 lycopod and 18 fern
species, and detected fungi in seven and 13 species, respectively
(Table S1). Glomeromycota fungi were present in three lycopod
species while Mucoromycotina were found in four. Fungal
colonization was detected in only 17 of the 101 lycopod samples
analysed. Diverse Mucoromycotina fungi colonized lycopods,
sometimes occurring within the same species, and even the same
plant, and six new Mucoromycotina clades were discovered (Fig.
S2). Colonization rates in ferns were higher (33 out of 58 samples)
and showed specificity to Glomeromycota (Fig. SI). Ferns
exclusively contained members of the order Glomerales, with the
exception of one Ophioglossum (Diversisporales), one Psi/arum
(Archaeosporales), one Tmetipteris (Archaeosporales), and three
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Fig. 1 Representative fungal associates of basal vascular plants in a Bayesian full 18S nrDNA analysis. Both lycopods and ferns harbou rdivene Mucoromycotina
and Glomeromycota fungi. Reference sequences from GenBan k are highlightedin grey.Analysiswasperformed using an HKY85 model (nit = 2)and invgamma
rates. Four heated chains were run simultaneously with a chain length of 1.1 x 106.
Anogramme (Mucoromycotina and Diversisporales) specimens;
Anogramme was the only fern genus harbouring Mucoromycotina
fungi. All samples analysed were sporophytes, with the exception of
one fern gametophyte (Presents sp.), which contained Gigaspora-
ceae fungi. This investigation added two new samples to the still
limited database of Endogone fruiting body DNA sequences
(including the first E. incresram) and supported the placement of
Spharrortrar pubes-nu (Hirose etal., 2014) in Mucoromycotina
Group L (ram Desire et al, 2013).
The cytology of fern—fungal associations hitherto undescribed is
illustrated in Fig. 2. In Anogramma colonized by Mucoromycotina
(Fig. 22,6), the exclusively intracellular fungus produces large
hyphae, finer short-lived coils and vesicles (Fig. 2b). Fungal
structures are surrounded by host plasma membrane and healthy
host cytoplasm packed with mitochondria (Fig. 2a). Fungal
associations in both the roots and gametophytes of Anima
(Fig. 2c—g) comprise structures typical of Glomeromycota coloni-
zation, including arbuscules, large vesicles and hyphal coils, which
are intimately associated with the plant cell wall.
Discussion
This study demonstrates for the first time that the extant
representatives of the earliest diverging clades of vascular plants,
lycopods and ferns, form associations with both Mucoromycotina
and Glomeromycota fungi. Lycopod sporophytes rely on a variety
of strategies, entering into partnership with either Glomeromycota
or Mucoromycotina, both or often neither. By contrast, all the ferns
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sampled associated exclusively with Glomeromycota, with the
exception of the derived gen US Anogramma where dual partnerships
were detected. Our discovery finally provides an explanation for the
unusual colonization patterns reported before in some lycopods
(Duckett & Ligrone, 1992; Schmid & Obenvinkler, 1993),
consisting of an intracellular phase and extensive fungal prolifer-
ation in gametophytic mucilage-filled intercellular spaces, as also
reported in other Mucoromycotina-associated groups: the Haplo-
miotriopsida liverwort genus Treubia (Duckett a al., 2006), several
hornwort genera (Desire eta!, 2013), and the Devonian fossil
plant Horneoplryton hstneri (Strullu-Derrien etnl., 2014). We
hypothesize that the associations between Mucoromycotina fungi
and vascular plants are mutualistic. Beyond microscopy, our main
line of evidence is the recent demonstration of mutualism between
Haplomitriopsida liverworts and Mucoromycotina fungi (Field
a al., 2014) closely related to those now detected in vascular plants.
Our observations demonstrate that intercellular fungal prolif-
eration is a signature of Mucoromycotina colonization, and lend
further support to the hypothesis that the early Devonian vascular
plant Nothia, which also harboured inter- and intracellular fungi
Fig. 2 Fungal colonization in ferns.
(a, b) Transmission electron micrographs of
Anogramma leptophyna colonized by
Mucoromycotina fungi. Fungal colonization is
largely confined to a zone where the tubers
join the main root system and the lipid-filled
tubers, as in hornworts and liverworts, are
fungus-free. (a) Early stage in fungal
colonization showing living farrowed) and
collapsed (9 hyphae surrounded by healthy
host cytoplasm packed with mitochondria
(M). (b) Later stage of colonization showing a
large hypha, clusters of collapsed short-lived
hyphae and a vesicle farrowed).
(c-g) Scanning electron micrographs of
Ptisana purpurascern colonized by
Glomeromycota fungi. (c) Fungal structures
(indicated by arrows) in root inner cortex cells
packed with amyloplasts. (d) Large vesicle and
fine hyphal coil. (e) Hyphae tightly appressed
to the inner walls of colonized cells (indicated
by arrows). (f) Arbuscules. (g) Fungal entry is
via the root hairs (indicated by arrows). Bars:
(O 50 pm; (d-g) 20 pm.
(Berbee & Taylor, 2007; Krings ttat, 2007a,b), formed associa-
tions with Mucoromycotina fungi (Pressel etal., 2010; Strullu-
Derrien et al, 2014). Nonetheless, where the fungi are exclusively
intracellular (e.g. Anogramma), it is impossible to ascertain from
cytology alone to which fungal group they belong, as both
Glomeromycota and Mucoromycotina produce vesicles and
hyphal coils. The short-lived fungal swellings or lumps typical of
Mucoromycotina colonization in the Haplomitriopsida (Carafa
et al, 2003; Duckett et al, 2006) are unique to this group, the only
land plant lineage to date known to associate exclusively with
Mucoromycotina fungi (Field cal, 2014). Arbuscules, the
signature of Glomeromycota colonization in angiosperms, are
produced in some lycopod and fern—Glomeromycota associations
(e.g. Ptisana, Angioptens, °mune& — Ogura-Tsujita et A, 2013)
but are lacking in others (see Strullu-Derrien cal, 2014 and
references therein), as is also often the case in liverworts and
hornworts.
The presence of Glomeromycota and Mucoromycotina fungi in
lycopods and the predominance of Glomeromycota in the later
diverging ferns fit the phylogenetic distribution of these fungi in
New Ph )tologht (2015) 205: 1394-1398
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Lams
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other 'lower land plant groups. As such, dual partnerships are the
norm in basal thalloid liverworts, while more derived clades have,
like ferns, the specificity to Glomeromycota typical of later vascular
plant lineages (Smith & Read, 2008). Together with the occurrence
of multiple fungal associations in Devonian plants (Strullu-Derrien
mat, 2014), this lends further weight to the notion of shifting
symbiotic encounters between early land colonists and soil-
dwelling fungi before the Glomeromycota became dominant.
The presence of Mucoromycotina in Anogramma may be a recent
reacquisition, on a par with Endogone forming ectomycorrhizas
with pines (Walker, 1985), and probably relates to its unique life
cycle among ferns — comprising short-lived sporophytes and
aestivating tubers (Goebel, 1905). It is also possible that associa-
tions with Mucoromycotina in lycopods and other plants represent
recent acquisitions. However, this seems unlikely, given that the
genes required for mycorrhiza formation in angiosperms are highly
conserved across major plant lineages and that mycorrhizal genes
from Mucoromycotina-associated Haplomitriopsida liverworts
recovered the Glomeromycota mycorrhizal phenotype in a trans-
formed mutant of the angiosperm Medicago minnow& (Wang
mat, 2010). These finding', coupled with the occurrence of
Mucoromycotina in extant basal groups of both nonvascular and
vascular plants. as well as fossil plants (Strullu-Derrien et
2014),
indicate that associations between Mucoromycotina and land
plants are extremely ancient.
During this investigation, we examined sporophytes only and it
would be desirable now to study the cryptic nonphotosynthetic
gametophytes of a range of lycopods and ferns, which are expected
to be more heavily and consistently colonized by fungi (Read eta!,
2000; Ogura-Tsujita et al, 2013). Nevertheless, our discovery that
lycopods enter into partnerships with both Mucoromycotina and
Glomeromycota fungi opens a new chapter in understanding the
origins and evolution of fungal symbioses in vascular plants.
Functional studies into the nature of these associations, like those
conducted by Field etal. (2014) on Haplomitriopsida—Mucoro-
mycotina symbioses, are now needed.
Acknowledgements
M.i.B. and S.P. thank NERC for grants NEJI027193/1 and NE/
I025360/1. J.G.D. thanks the Leverhulme Trust for an Emeritus
Fellowship. A Darwin Initiative Grant enabled S.P. and J.G.D. to
collect fungal samples from Ascension Island. We thank Jim
Trappe (Oregon State University) and Maria Martin (Royal
Botanic Garden of Madrid) for fungal fruiting bodies, and Tatiana
Solovieva (supported by the Society for Biology and Imperial
College Undergraduate Research Opportunities Programme) for
analysing Ascension Island samples. Our thanks go to the Editor
and three anonymous referees for their comments.
William R. Rim ington 11213*, Silvia Breese"), Jeffrey G. Duckett3
and Martin I. Bidartondola
'Department of Life Sciences, Imperial College London, London,
SW7 2AZ, UK;
2Jodrell Laboratory. Royal Botanic Gardens, ICew,TW9 3DS, UK;
3 Department of Life Sciences, Plants Division, Natural History
Museum, Cromwell Road, London, SW7 5BD, UK
("Author for correspondence: tel +44 (0)20 8332 5379;
email [email protected])
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Supporting Information
Additional supporting information may be found in the online
version of this article.
Fig. Si Glomeromycota associates of basal vascular plants in a
Bayesian full 18S nrDNA analysis.
Fig. S2 Mucoromycotina associates of basal vascular plants in a
Bayesian full I 85 nrDNA analysis.
Table SI Lycopod, fern and fungal fruiting body samples analysed
with their origin and fungi detected
Please note: Wiley Blackwell are not responsible for the content or
functionality of any supporting information supplied by the
authors. Any queries (other than missing material) should be
directed to the New Phytologist Central Office.
Key words: ferns. Glomeromycota. lycopods. Mucoromycotina. myconhin.
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0p
DOJ Data Set 11OtherUnknown
EFTA02514132
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DOJ Data Set 10CorrespondenceUnknown
EFTA Document EFTA02107688
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DOJ Data Set 11OtherUnknown
EFTA02389606
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