The recently proposed new phylum name Cryptomycota phyl. nov. is validly published in order to facilitate its use in future discussions of the ecology, biology, and phylogenetic relationships of the constituent organisms. This name is preferred over the previously tentatively proposed “Rozellida” as new data suggest that the life-style and morphology of Rozella is not representative of the large radiation to which it and other Cryptomycota belong. Furthermore, taxa at higher ranks such as phylum are considered better not based on individual names of included genera, but rather on some special characteristics – in this case the cryptic nature of this group and that they were initially revealed by molecular methods rather than morphological discovery. If the group were later viewed as a member of a different kingdom, the name should be retained to indicate its fungal affinities, as is the practice for other fungal-like protist groups

AA Held

D Moore

E Lara

HA Bold

International Commission on Zoological Nomenclature

J McNeill

JA Arx von

LF Kneipp

MDM Jones

RH Whittaker

TY James

IMA Fungus

English

PubMed

Meredith D. M. Jones

Thomas A. Richards

David L. Hawksworth

David Bass

Crossref

Validation and justification of the phylum name Cryptomycota phyl. nov.

This is the final published version. Available from International Mycological Association via the DOI in this record.The recently proposed new phylum name Cryptomycota phyl. nov. is validly published in order to facilitate its use in future discussions of the ecology, biology, and phylogenetic relationships of the constituent organisms. This name is preferred over the previously tentatively proposed "Rozellida" as new data suggest that the life-style and morphology of Rozella is not representative of the large radiation to which it and other Cryptomycota belong. Furthermore, taxa at higher ranks such as phylum are considered better not based on individual names of included genera, but rather on some special characteristics - in this case the cryptic nature of this group and that they were initially revealed by molecular methods rather than morphological discovery. If the group were later viewed as a member of a different kingdom, the name should be retained to indicate its fungal affinities, as is the practice for other fungal-like protist groups.Ministerio de Ciencia e Innovación in Spai

Jones, MDM

Richards, TA

Hawksworth, DL

Bass, D

Open Research Exeter

ARTICLEv o l u m e  2  ·  n o .  2  173© 2011 International Mycological AssociationYou are free to share - to copy, distribute and transmit the work, under the following conditions:Attribution:	 	 You	must	attribute	the	work	in	the	manner	specified	by	the	author	or	licensor	(but	not	in	any	way	that	suggests	that	they	endorse	you	or	your	use	of	the	work). Non-commercial:		 You	may	not	use	this	work	for	commercial	purposes.	No derivative works:	 You	may	not	alter,	transform,	or	build	upon	this	work.	For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.INtroductIoNThe designation “cryptomycota” was introduced by Jones et al.	 (2011)	 to	accommodate	a	well-supported	clade	 (using	ribosomal	DNA	 (rDNA)	phylogenies)	of	organisms	putatively	branching	deep	within	the	fungal	radiation.	The	rank	of	phylum	is the most appropriate for this group as current results show that it has fungal characteristics but is distinct from other fungi in	not	having	a	chitin-rich	cell	wall	in	the	major	stages	of	its	life-cycle	so	 far	 identified,	 including	putative	 trophic	 interactions.	However,	 Cryptomycota	 was	 not	 validly	 published	 as	 a	scientific	name	in	that	work	as	no	Latin	diagnosis	was	provided	(McNeill	et al.	2006:	Art.	36).	A	Latin	diagnosis	is	provided	here	in	order	to	formally	establish	the	name.	In	addition,	comments	are made on our decision to introduce this name rather than take up the earlier informal name “Rozellida”, and on the distinctive	features	of	the	phylum	and	its	position.tAXoNoMYcryptomycota M.	D.	M.	Jones	&	T.	A.	Richards,	phyl. nov.MycoBank	MB563383Etymology: crypto- – hidden; and -mycota,	a	phylum	of	fungi.Fungi	unicellulares,	zoosporis	unicellularis,	uniflagellatibus,	flagellis	microtubularis,	cystes	sine	tunica	chitinosa	vel	cellulosa.	Consortia	epibiontica	formata.Fungi unicellular, zoospores single-celled with a single microtubular	 flagellum,	 and	 cysts	 without	 a	 chitin/cellulose	cell	wall.	Forming	epibiontic	associations.Representatives:	 GenBank	 accession	 nos	 AJ130857,	AJ130849.1,	AJ130850,	FJ687265,	FJ687267	and	FJ687268,	and Rozella.Illustrations: Jones et al.	(2011:	figs	1d,	2a–e).dIScuSSIoNIt	 has	 been	 demonstrated	 that	 Rozella occupies a deep branching position in phylogenetic analyses of kingdom Fungi	(James	et al.	2006a,	b),	although	bootstrap	support	for	this relationship is inconsistent and often weak in the most comprehensively	sampled	phylogenies	 (James	et al.	2006a,	b, Jones et al.	 2011).	The	 name	 “Rozellida”	was	 coined	 by	Lara	et al.	(2010)	to	accommodate	Rozella and a number of environmental	 sequences	 that	 form	 a	 distinct	 clade,	 but	we	refer to this group henceforth as Cryptomycota for reasons indicated	below.	Jones	et al.	(2011)	showed	that	Cryptomycota are	 more	 diverse	 than	 previously	 recognised	 and	 that	 the	molecular	diversity	of	this	group	may	be	as	diverse	as	the	rest	of the known Fungi	according	to	rDNA	gene	markers.Members	 of	 Cryptomycota are found in freshwater, soil, sediment,	and	some	marine	habitats.	Jones	et al.	(2011)	used	Validation and justification of the phylum name Cryptomycota phyl. nov.Meredith	D.	M.	Jones1,2,	Thomas	A.	Richards1,2,	David	L.	Hawksworth3,	and	David	Bass21School	of	Biosciences,	University	of	Exeter,	Exeter	EX4	4QD,	UK;	corresponding	author	e-mail:	d.bass@nhm.ac.uk2	Department	of	Zoology,	Natural	History	Museum,	Cromwell	Road,	London	SW7	5BD,	UK3	Departamento	de	Biología	Vegetal	II,	Facultad	de	Farmacia,	Universidad	Complutense	de	Madrid,	Plaza	Ramón	y	Cajal,	28040	Madrid,	Spain;	and	Department	of	Botany,	Natural	History	Museum,	Cromwell	Road,	London	SW7	5BD,	UKAbstract: The recently proposed new phylum name Cryptomycota	phyl.	nov.	is	validly	published	in	order	to	facilitate	its	use	in	future	discussions	of	the	ecology,	biology,	and	phylogenetic	relationships	of	the	constituent	organisms.	This	name	is	preferred	over	the	previously	tentatively	proposed	“Rozellida”	as	new	data	suggest	that	the	life-style	and	morphology	of Rozella is	not	representative	of	the	large	radiation	to	which	it	and	other	Cryptomycota	belong.	Furthermore,	taxa	at	higher	ranks	such	as	phylum	are	considered	better	not	based	on	individual	names	of	included	genera,	but	rather	on	some	special	characteristics	–	in	this	case	the	cryptic	nature	of	this	group	and	that	they	were	initially	revealed	by	molecular	methods	rather	than	morphological	discovery.	If	the	group	were	later	viewed	as	a	member	of	a	different	kingdom,	the	name	should	be	retained	to	indicate	its	fungal	affinities,	as	is	the	practice	for	other	fungal-like	protist	groups.Article info:	Submitted	26	September	2011;	Accepted	2	November	2011;	Published	11	November	2011.Key words: chitinchytridFungiphylogenyRozellaRozellidadoi:10.5598/imafungus.2011.02.02.08 IMA FuNguS · voluMe 2 · No 2: 173–175Jones et al.ARTICLE174  i m a  f u n G u Slineage-specific	 fluorescence	 in situ	 hybridization	 (FISH),	 cell	wall	 stains,	 and	 immuno-fluorescence	 staining	 to	 show	 two	distinct lineages within Cryptomycota,	which	comprised	ovoid	cells of ca.	5	µm	diam,	existing	in	at	least	three	morphologies	in	 freshwater	 environments:	 uniflagellate	 zoospores,	 more	variably-shaped	cells	without	flagella	attached	to	other	eukaryotic	microscopic	organisms	(e.g.	diatom	hosts),	and	non-flagellate	cysts.	None	of	these	stages	were	shown	to	possess	a	chitin	or	cellulose	wall,	although	other	life-cycle	phases	with	a	chitin	and/or	cellulose	cell	wall	may	remain	undetected.	A	chitin	cell	wall	is	sometimes	cited	as	defining	feature	of	kingdom	Fungi, although we note that this is not a reliable diagnostic feature as distantly related protist groups also possess chitin on their cell surface (e.g.	Kneipp	et al.	1998).The	name	“Rozellida”	was	applied	to	this	phylum	by	Lara	et al.	(2010)	but	in	an	informal	way	between	inverted	commas	and	with	no	formal	diagnosis.	The	ICZN	(International	Code	of	 Zoological	 Nomenclature;	 International	 Commission	 on	Zoological	 Nomenclature	 1999)	 does	 not	 apply	 to	 names	above	the	rank	of	family-group,	but	if	it	were	in	those	ranks	it	 would	 be	 viewed	 as	 unavailable	 as	 a	 conditional	 name	(Art.	 15.1).	 For	 names	 introduced	 under	 the	 ICZN	 which	later are found to belong to Fungi,	 the	 ICN	 (International	Code	 of	 Nomenclature	 for	 algae,	 fungi,	 and	 plants)	 now	accepts	them	as	available	under	Art.	45.4	(as	revised	at	the	Melbourne	Congress	in	July	2011;	McNeill	et al.	2011).	Thus,	no	Latin	diagnosis	was	required,	as	it	was	for	fungal	names	introduced	between	1935	and	1	January	2012).	However,	we	are inclined not to accept “Rozellida” because of the use of the	 inverted	commas	suggesting	the	usage	was	a	tentative	suggestion and in any case note that it is not mandatory to follow	the	principle	of	priority	of	publication	for	names	above	the	rank	of	family	(ICN)	or	family	group	(ICZN).	Indeed,	the	ICZN	does	not	cover	ranks	higher	than	family	group.We	 decided	 that	 it	 would	 be	 better	 not	 to	 definitely	establish a name based on Rozella	for	several	reasons:(1)	 The	 fungal	 termination	 to	be	used	 for	names	 in	 the	rank of phylum is “-mycota”	under	the	ICN	(McNeill	et al.	2006;	Art	16.4),	and	that	termination	has	also	been	used	for	phyla	traditionally studied by mycologists but which are no longer considered Fungi	 but	 placed	 in	 other	 kingdoms.	 Examples	include Hyphochytriomycota R.H.	Whittaker	(Whittaker	1969:	154)	now	placed	in	Straminipila	M.W.	Dick	2001,	Myxomycota Bold	(Bold	1957:	152)	for	slime	moulds	in	the	Protozoa, and Oomycota Arx	 (Arx	 1967:	 16)	 for	 fungal	 analogues	 in	 the	Straminipila.	 This	 practice	 has	 been	 employed	 in	 standard	reference	 works	 (e.g.	 Kirk	 et al.	 2001)	 and	 also	 the	 most	recent	textbooks	(e.g.	Moore	et al.	2011).(2)	 Cryptomycota	 represent	 a	 very	 diverse	 radiation,	potentially	equivalent	to	or	larger	than	the	rest	of	the	known	fungi.	 Of	 the	 three	 lineages	 within	 the	 radiation	 for	 which	morphological	data	exist,	Rozella	appears	to	be	exceptional	in that it is primarily an intracellular parasite; indeed the possession of intracellular sporangia is included in the generic description of Rozella species	(Held	1981).	To	extend	the implication of this life-cycle characteristic across the rest of	 the	 radiation	 –	 where	 there	 is	 no	 evidence	 of	 this	 life-cycle	characteristic	–	would	be	misleading.	Lara	et al.	(2010)	were also hesitant commending the use of the proposed name	 “between	quotation	marks	until	morphological	and/or	ultrastructural	synapomorphies	are	defined	to	diagnose	and	validate	 this	entire	group”.	Jones	et al.	 (2011)	demonstrate	that this key characteristic of Rozella	does	not	seem	to	extend	across the whole group and therefore the name “Rozellida” is not	representative	of	the	group	as	a	whole.(3)	 It	is	important	to	recognize	that	our	current	knowledge	of	 the	 life	 stages	 of	 the	 newly	 discovered	 Cryptomycota and of Rozella	 is	 very	 incomplete.	As	 Jones	 et al.	 (2011)	suggest, chitin may be present in the walls of some currently unknown Cryptomycota	 life-cycle	stage(s)	and/or	present	in	uncharacterized lineages within Cryptomycota,	and	even	 in	currently unknown stages in Rozella.	It	would	be	premature,	therefore, to separate Cryptomycota from the kingdom Fungi on the single character that they do not possess chitin walls (which,	as	mentioned	above	is	not	diagnostic	for	Fungi).	(4)	 Cryptomycota	 have	 some	 strong	 resemblances	 to	Chytridiomycota (‘chytrids’)	 in	 both	 structure	 (e.g.	 flagellar	apparatus)	and	ecology,	if	not	in	cell	wall	chemistry.	There	is	no	agreed	defining	non-molecular	characteristic	for	identifying	the boundaries of kingdom Fungi.	Therefore,	as	several	other	key characteristics are shared by Cryptomycota and some Fungi, the former are most sensibly and parsimoniously considered as belonging to the latter as they form the closest branches	 on	 phylogenetic	 trees	 (James	 et al.	 2006a,	 b,	Lara	et al. 2010,	Jones	et al.	2011).	This	stance	 is	entirely	consistent with the historical position regarding Rozella: for the	 last	 40	 years	 leading	 mycologists	 have	 classified	 this	genus within Fungi	(e.g.	Held,	1981;	Kirk	et al.	2008).	(5)	 Cryptomycota	(including	Rozella)	consistently	branch	with Fungi	in	all	phylogenies	so	far	constructed.	However,	their	position as the primary branch within fungi is much weaker (e.g.	James	et al.	2006;	Jones	et al.	2011).	Indeed,	they	could	actually occupy a higher branching position within Fungi.	 If	this is the case, their lack of some traditionally diagnostic fungal features such as a chitin cell wall may be the result of secondary losses, which would not preclude them from being considered Fungi.	In	this	case,	excluding	Cryptomycota from the Fungi could potentially make the rest of fungi paraphyletic –	a	highly	undesirable	and	not	logically	sustainable	situation.	In	the	absence	of	a	strong	morphological	argument	to	exclude	this group from the fungal kingdom – we must therefore look to	the	only	available	data,	which	is	phylogenetic,	and	argues	that Cryptomycota are most reasonably considered to be within	Fungi.(6)	 Consequently,	we	agree	with	Lara	et al.	 (2010)	 that	there are sound reasons for considering Rozella	 (and	now	we suggest other Cryptomycota)	 as	Fungi.	Whether	 or	 not	Cryptomycota other than Rozella	 prove	 to	 be	 phagocytotic	(which	in	itself	would	not	be	a	sufficiently	strongly	deterministic	trait	 for	 inclusion	 in	 –	 or	 exclusion	 from	 –	Fungi, as some plant	 lineages	and	oomycetes	have	also	 lost	phagotrophy),	their	chytrid-like	uniflagellate	zoospore	stage	and	particularly	their phylogenetic position argue most parsimoniously for a fungal	affiliation.Validation  of the phylum name CryptomycotaARTICLE175v o l u m e  2  ·  n o .  2  (7)	 The	names	used	for	taxa	at	the	highest	ranks,	such	as	phylum, are better not based on names of included genera, but rather on some special characteristic, as is the case with, for	 example,	 the	 phyla	Ascomycota and Basidiomycota.	 In	this	 way	 the	 names	 immediately	 convey	 some	 feature	 of	the	 taxon.	 In	 this	 case,	 we	 highlight	 the	 cryptic	 nature	 of	Cryptomycota in that they were hidden from science until revealed	 by	 molecular	 methods	 rather	 than	 morphological	discovery.In	 conclusion,	 we	 consider	 the	 formal	 validation	 of	 the	name Cryptomycota	to	be	justified,	and	commend	it	for	use	for	this	group	of	organisms	as	it	emphasises	the	fungal	affinity	and attributes of the organisms so far known within this group.	Even	if	in	some	future	classification	these	organisms	were placed outside the Fungi, we consider the name should be	retained	to	reflect	their	nature	as	fungal	analogues.AcKNoWledgeMeNtSWe	thank	Ramon	Massana,	Irene	Forn,	Caterina	Gadelha,	and	Martin	Egan	for	useful	discussions,	and	Joost	A	Stalpers	for	checking	the	Latin	diagnosis.	D.	L.	H.	acknowledges	support	from	the	Ministerio	de	Ciencia	e	Innovación	in	Spain	(project	CGL	2008-01600).reFereNceSArx	JA	von	(1967)	Pilzkunde: Ein kurzer Abriss der Mykologie under besonderer Berücksichtigung der Pilze in Reinkultu. Lehre:	 J	Cramer.  Bold	HA	(1957)	Morphology of Plants. New	York:	Harper	Row.Held	AA	(1981)	Rozella and Rozellopsis: naked endoparasitic fungi which	dress	up	as	their	hosts.	Botanical Review 47:	451–515.International	 Commission	 on	 Zoological	 Nomenclature	 (1999)	International Code of Zoological Nomenclature. 4th	edn.	London:	International	Trust	for	Zoological	Nomenclature.James	TY,	Kauff	F,	Schoch	CL,	Matheny	PB,	Hofstetter	V,	Cox	CJ	[and	 	64	others],	 (2006a)	Reconstructing	 the	early	evolution	of	Fungi	using	a	six-gene	phylogeny.	Nature 443:	818–822.James	TY,	Letcher	PM,	Longcore	JE,	Mozley-Standridge	SE,	Porter	D,	 Powell	 MJ,	 Griffith	 GW,	 Vilgalys	 R	 (2006b)	 A	 molecular	phylogeny	 of	 the	 flagellated	 fungi	 (Chytridiomycota)	 and	description	 of	 a	 new	 phylum	 (Blastocladiomycota).	 Mycologia 98:	860–871.Jones	 MDM,	 Forn	 I,	 Gadelha	 C,	 Egan	 MJ,	 Bass	 D,	 Massana	 R,	Richards	 TA	 (2011)	 Discovery	 of	 novel	 intermediate	 forms	redefines	the	fungal	tree	of	life.	Nature 474:	200–203.Kirk	PM,	Cannon	PF,	David	JC,	Stalpers	JA	(eds)	(2001)	Ainsworth & Bisby’s Dictionary of the Fungi. 9th	 edn.	 Wallingford:	 CABI	Publishing.Kirk	PM,	Cannon	PF,	Minter	DW,	Stalpers	JA	(eds)	(2008)	Ainsworth & Bisby’s Dictionary of the Fungi. 10th	 edn.	Wallingford:	 CABI	Publishing.Kneipp	 LF,	 Andrade	 AF,	 de	 Souza	 W,	 Angluster	 J,	 Alviano	 CS,	Travassos	 LR	 (1998)	Trichomonas vaginalis and Trichomonas foetus:	 expression	 of	 chitin	 at	 the	 cell	 surface.	 Experimental Parasitology 89:	195–204.Lara	E,	Moreira	D,	López-Garcia	P	(2010)	The	environmental	clade	LKM11	and	Rozella form the deepest branching clade of Fungi.	Protist 161:	116–121.McNeill	J,	Turland	NJ,	Monro	A,	Lepschi	B	(2011)	XVIII	International	Botanical	Congress:	preliminary	mail	vote	and		report	of	congress	action	on	nomenclature	proposals.	Taxon 60:	1507–1520.	Moore	D,	Robson	GD,	Trinci	APJ	(2011)	21st Century Guidebook to Fungi. Cambridge:	Cambridge	University	Press.Whittaker	 RH	 (1969)	 New	 concepts	 of	 kingdoms	 of	 organisms.	Science 163:	150–160.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3359815

Validation and justification of the phylum name Cryptomycota phyl. nov.

Abstract

Similar works

Full text

Available Versions

Crossref

Open Research Exeter