and green algal endosymbionts (Jiang and Tyler
2012 ; Maruyama et al. 2009 ;Richardsetal. 2006 ;
2011 ;Soanesetal. 2007 ).
This account presents an updated phyloge-
netic and taxonomic overview of these organ-
isms based primarily on molecular sequence
data and then briefly reviews the biology and
evolutionary history of these organisms in the
context of our revised phylogenetic framework.
II. Molecular Phylogeny
and Systematics
A. Higher-Level Relationships
Apart from the posteriorly uniflagellate
chytrids (see Powell and Letcher 2014 ; James
et al. 2014 ), all of the zoosporic organisms
traditionally studied by mycologists can now
be placed in the recently definedstrameno-
pile/alveolate/rhizaria (SAR) superkingdom
(Burki et al. 2008 ; Hackett et al. 2007 ; Reeb
et al. 2009 ). Thecryptophytesandhaptophytes
are now generally excluded from this assem-
blage (Dorrell and Smith 2011 ; Reeb et al.
2009 ). All of the flagellate osmotrophic organ-
isms traditionally studied by mycologists,
except theplasmodiophorids, fall within the
Straminipila/Heterokontabranch of the SAR
assemblage (Fig.3.1).
Dick (2001a) argued that the kingdom name
Straminipila (which is the etymologically correct
version of the stamenopile name), should be adopted
for the lineage, which encompasses all of the non-
photosynthetic osmotrophic groups, instead of the
nameChromista, because the name implies photosyn-
thetic pigmentation. However, Cavalier-Smith and
Chao ( 2006 ) still considered theStraminipilaas defined
by Dick (2001a) to be synonymous with their kingdom,
Chromista. However, the original concept of the
Chromista (Cavalier-Smith 1986 ) no longer fits with
theSAR superkingdom, and its usage is now generally
discontinued. Anderson and Cavalier-Smith ( 2012 )
consider theHeterokontato be synonymous with the
stramenopilesdefined by Adl et al. ( 2012 ). In this
mycological treatise, we continue to useStraminipila
(as defined by Dick2001a) as a formal kingdom
designation but use the more widely adoptedstrame-
nopiles(Adl et al. 2012 ;Le ́vesque 2011 ) when generally
referring to these organisms.
The overall relationships between the major
groups within theSAR lineage,and the strame-
nopiles in particular (Fig.3.1a), have recently
been resolved using multiple protein-encoding
genes (Reeb et al. 2009 ; Riisberg et al. 2009 ; Tsui
et al. 2009 ). The statistically well-supported
alveolate clade, comprised of the apicocom-
plexans, dinoflagellates, and ciliates, forms the
sister clade to the heterokont stramenopiles
(Keeling 2009 ). These can be divided into two
main lineages (Fig.3.1a). The first, theBOL
clade(Fig. 3.1a), encompasses the bacterio-
trophic flagellate Bicosoecida, the protistan
gut-inhabitingOpalinida (plus proteromonads
andBlastocystis), and theLabyrinthulomycota
(Reeb et al. 2009 ; Riisberg et al. 2009 ; Tsui et al.
2009 ); the second, theHOOf clade(Fig.3.1a),
includes the osmotrophicHyphochytriomycota
andOomycota, the photosyntheticOchrophyta,
and the phagotrophicflagellatesDevelopayella
andPirsonia.Developayellais usually given as
the sister clade to the Oomycota in small
subunit (SSU) ribosomal RNA (rRNA) trees
(Leipe et al. 1994 ; Tong 1995 ). However, recent
molecular ecological studies have revealed that
a number of unknown marinepicoeukaryote
stramenopiles (Massana et al. 2002 , 2004 ,
2006 ) form a clade (e.g. the oomycete-related
group) (Fig.3.1b) that is sister to the Oomy-
cota, and so their closest relatives remain a
mystery. In this account theLabyrinthulomy-
cota,Hyphochytriomycota,andOomycotaare
assigned phylum rank within Kingdom
Straminipila.B. Systematics of LabyrinthulomycotaThe Labyrinthulomycota consists of a
relatively small group of what, at least until
recently (Anderson and Cavalier-Smith 2012 ),
were considered exclusively marine genera
(Figs.3.1band3.2, Table3.1). They typically
feed saprotrophically and are key players in the
detrital food web, breaking down often
intractable plant and animal remains and
making these substrates more accessible to
grazing amoebae and ciliates (Bongiorni 2012 ;
Raghukumar 2002b). Some thraustochytrids
feed bacteriotrophically (Raghukumar2002a),Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota, and Oomycota 41