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Revisiting Salisapiliaceae

June 2019
Fungal Systematics and Evolution

June 2019

DOI:10.3114/fuse.2019.03.10

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CC BY-NC-ND 4.0

Authors:

Reuel M. Bennett

University of Santo Tomas

Marco Thines

Goethe-Universität Frankfurt am Main

Of the diverse lineages of the Phylum Oomycota, saprotrophic oomycetes from the salt marsh and mangrove habitats are still understudied, despite their ecological importance. Salisapiliaceae, a monophyletic and monogeneric taxon of the marine and estuarine oomycetes, was introduced to accommodate species with a protruding hyaline apical plug, small hyphal diameter and lack of vesicle formation during zoospore release. At the time of description of Salisapilia, only few species of Halophytophthora, an ecologically similar, phylogenetically heterogeneous genus from which Salisapilia was segregated, were included. In this study, a revision of the genus Salisapilia is presented, and five new combinations (S. bahamensis, S. elongata, S. epistomia, S. masteri, and S. mycoparasitica) and one new species (S. coffeyi) are proposed. Further, the species description of S. nakagirii is emended for some exceptional morphological and developmental characteristics. A key to the genus Salisapilia is provided and its generic circumscription and character evolution in cultivable Peronosporales are discussed.

Phylogenetic tree based on concatenated ITS and LSU alignments based on Minimum Evolution (ME) inference, with bootstrap support values from ME and Maximum Likelihood, as well as posterior probabilities from Bayesian Inference, in the respective order. (-) indicates support below 50 % (bootstrap) or 0.8 (posterior probability), or alternating but not strongly supported topology (support below 70 % bootstrap or 0.9 posterior probability). The scale bar indicates the number of nucleotide substitutions per site.

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Salisapilia elongata NBRC 100786. Colony patterns on A. Vegetable juice agar. B. Potato carrot agar. C. Mature sporangium; hyaline apical plug (inset). D. Mature sporangium releasing zoospores through a tubular vesicle. Scale bars: A, B = 30 mm, C, D. = 20 µm.

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Salisapilia sapeloensis CBS 127946. Colony patterns on A. Vegetable juice agar. B. Potato carrot agar. C. Peptone yeast glucose agar. D. Potato dextrose agar. E. Mature sporangium. F, G. Oogonia. Scale bars: A-D = 30 mm, E-G = 20 µm.

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Salisapilia tartarea CBS 208.95. Colony patterns on A. Vegetable juice agar. B. Potato carrot agar. C. Peptone yeast glucose agar. D. Potato dextrose agar. E, F. Mature sporangia. Scale bars: A-D = 30 mm, E, F = 20 µm.

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Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

Fungal Systemacs and Evoluon

doi.org/10.3114/fuse.2019.03.10

VOLUME 3

JUNE 2019

PAGES 171–184

INTRODUCTION

The Phylum Oomycota      

    Straminipila (Beakes & Thines

       





et

al. 



Phytophthora

et al. 1989).

       

        

Halophytophthora

Halophytophthora

    et al.    

 

     Halophytophthora s. str 

H. vesicula    H. avicenniaeH.

batemanensis H. polymorphica  et al.   

et al.

H. uvialis 

 

 Halophytophthora

   Phytopythium (Phytopythium kandeliae

basionym: H. kandeliaeSalispina (Salispina

lobata  Phytophthora spinosa  lobata 

Salispina spinosa basionym: Phytophthora spinosa   

spinosa) (Li et al.      

  Phytophthora  Salisapilia   

et al. et al. et

al. 2017).

  Salisapilia    Salisapilia

sapeloensis    Sparna alterniora 

       

Halophytophthora





 Salisapilia nakagirii    

  et al.      

        

  

    Salisapiliaceae 

et al

Halophytophthora 

        

   Halophytophthora    

    Salisapilia  





MATERIALS AND METHODS

Acquision of strains and sporulaon

Halophytophthora Salisapilia





Revising Salisapiliaceae



1

2



3



Abstract: Oomycota

Salisapiliaceae

             



SalisapiliaHalophytophthora

SalisapiliaSalisapilia 

S. bahamensisS. elongataS. epistomiaS. masteri S. mycoparasica)  

(S. coeyiS. nakagirii 

        Salisapilia       

Peronosporales

Key words:



Halophytophthora







Salisapilia

Effectively published online:

Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

172





  

      





  



          

   

      

      



        

        

    

et al. 2009).

DNA extracon, PCR, and phylogenec reconstrucon

         

  



et al.   



        

      et al.  

et al

et al

   

2     

Taq 









   

    



  





       

       

        

  

        

 

 Phytophthora

    

     



    et al.    



     et al.   

       

       



      et al.   

         



        

   et al.     

   



   

       

       



et al.  



      

et al. 2013).

Ancestral state reconstrucon for papilla and hyaline

apical plug

 



Halophytophthora     

Salisapilia 

 Peronosporaceae  Phytophthora Phytopythium 

Pythiumet al. 

et al

et alet al.

et al.

         

     

 









RESULTS

Phylogenec reconstrucons



Halophytophthora

bahamensis  

H. bahamensis

H. elongata  H.

epistomia     H. masteri   

  H. mycoparasica      

       Salisapiliaceae

        

S. nakagirii 

S. sapeloensis    S. tartarea



Morphology

Halophytophthora bahamensis    

H. elongata     H. epistomia 

   H. masteri      H.

mycoparasica   

           

S. sapeloensis 

S. tartarea 

S. nakagirii    





Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

173

Table 1.Salisapilia 

Structure S. sapeloensis

et al.

2010)

S. coeyi (This



S. bahamensis





S. elongata

et al. 2003)

S. epistomia



et al.

1990a)

S. nakagirii

et all.



b)

S. masteri

et al.

1994)

S. mycoparasica





S. tartarea

et al.

1994)

 1–2 1–3 1–3 3–9 2–4 1–2 2–10 2–9 1–3(–9)

 





































 







   























hyphae





hyphae





hyphae





hyphae





hyphae





hyphae





hyphae





hyphae





hyphae



  















32–64





63.3)























6–18 



3.12)

3–7   



b

  





     b  

 



    b 

spines



      b  

 

hyaline

     b   

      b  

 



























































b





 



Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

174

Table 1.

Structure S. sapeloensis

et al.

2010)

S. coeyi (This



S. bahamensis





S. elongata

et al. 2003)

S. epistomia



et al.

1990a)

S. nakagirii

et all.



b)

S. masteri

et al.

1994)

mycoparasica





S. tartarea

et al.

1994)































































b







































      

like b

  



     a   33–66

  a 

  a  



     a   

  a28–44 24–62

 2–9 a1–7 3–10

     a   



 2–9 

12–6 a

3–10 4–10

 



a









aet al. (1990).

bS. nakagirii

Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl



         

Salisapilia 

         

      H. bahamensis 



       

       

     

 

   H. bahamensis    

       



 



        



  

       





  





 

Salisapilia.

Taxonomy

      

  

Salisapilia 

Halophytophthora 

  S. bahamensis S. elongata S. epistomiaS.

masteri  S. mycoparasica     S. coeyi)

Salisapilia





Salisapilia  et al Persoonia 25   emend.



Coloniesaerial hyphae

vegetave hyphae

hyphal swellingssporangia

       

proliferaondehiscence or

Phytophthora

Halophytophthora batemanensis NBRC 32616

Halophytophthora vesicula CBS 152.96

Halophytophthora avicenniae CBS 188.85

Halophytophthora vesicula CBS 393.81

Halophytophthora polymorphica NBRC 32619

Phytopythium

Salisapilia tartarea CBS 208.95

Salisapilia sapeloensis LT6440

Salisapilia nakagirii LT6456

Salisapilia bahamensis NBRC 32556

Salisapilia coffeyi NBRC 32557

Salisapila mycoparasitica NBRC 32967

Salisapilia mycoparasitica NBRC 32966

Salisapilia masteri NBRC 32604

Salisapilia elongata NBRC 100786

Salisapilia epistomia CBS 590.85

Salisapilia epistomia NBRC 32617

Globisporangium

Elongisporangium

Pythium

s.str.

Saprolegnia

100/100/1.0

100/99/1.0

100/100/1.0

100/88/0.99

100/100/1.0

100/99/1.0

100/100/1.0

100/-/1.0

100/56/1.0

100/100/1.0

100/99/1.0

54/93/1.0

99/86/0.99

100/99/1.0

66/99/-

95/98/0.99

100/97/0.99 96/97/1.0

0.020

Peronosporaceae

Salisapiliaceae

Pythiaceae

Fig. 1.

     





Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

176

discharge tube

zoospore release

  



gametangiaantheridial

aachment   oogonia 

oospores

Type species: Salisapilia sapeloenesis et al.

Synopsis of species included in Salisapilia

Salisapilia bahamensis       

comb. nov.

Basionym: Phytophthora bahamensis    Canad. J.

Bot. 53

Synonym: Halophytophthora bahamensis  

Mycotaxon 36: 381. 1990. MB126014.

Typus: Holotype     



 

Philippines.

Distribuon

Salisapilia coeyi     sp. nov. 



E F

A B

Fig. 2. Salisapilia bahamensis A.B.C.D.

E, F.

C D EH

Fig. 3. Salisapilia coeyi  A. B. C.  D.

E. F, G.H.



Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

177

Etymology



Colony paern   

vegetave hyphae

   sporangiogenic hyphae 

sporangia



    

     

dehiscence tube

    dehiscence plug    

  basal plug    

proliferaon  zoospore release   

        vesicle

  chlamydospores   gametangia 



Typus: Bahamas     

  Rhizophora mangle   J.W. Fell & I.M. Master

(holotype



Salisapilia elongata    comb.

nov. 

Basionym: Halophytophthora elongata Mycotaxon

85: 417. 2003. MB372647.

Typus: Holotype      

 



Distribuon

Salisapilia epistomia comb.

nov.

Basionym: Phytophthora epistomium    Canad. J.

Bot. 53

Synonym: Halophytophthora epistomia     

Abstracts IMC-4

Typus: Holotype

  

       

Philippines.

Distribuon: USA.

Salisapilia masteri       

comb. nov.

Basionym: Halophytophthora masteri   

Mycoscience 35: 227. 1994. MB363473.

Typus: Holotype     

  



BCD

Fig. 4. Salisapilia elongata . A.B.C.

D.

Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

178

Distribuon: Bahamas.

Salisapilia mycoparasica 

comb. nov.

Basionym: Phytophthora mycoparasica Canad. J.

Bot. 53

Synonym: Halophytophthora mycoparasica 

Mycotaxon 36: 381. 1990. MB126017.

A B

CDEF

Fig. 5. Salisapilia epistomia A.B.C.D.

E–F. 

B C D

Fig. 6. Salisapilia masteri A.B.C, D.



Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

179

Typus: Holotype lectotype

Canad. J. Bot. 53epitype





Other materials examined     

Tokyo Japan.

Distribuon

Notes

        

    Phytophthora mycoparasica 

   



      lectotype  

      epitype   

ex-epitype culture.

Salisapilia nakagirii  et al Persoonia 25  

emend.

Typus: Holotype     

  



Distribuon: USA.

CDE F

Fig. 7. Salisapilia mycoparasica     A.    B.    C.   

D.E, F.

A B

C D

Fig. 8. Salisapilia nakagirii  A.B.C.  D. 

E.   F–I.        H.  I.



Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

180

Colony paern  

hyphae

  septae   sporangia  

    

  dehiscence tube    

       

hyaline apical plugsporangial wall

 basal plug     proliferaon

 zoospore release    

vesiclegametangiaantheridia

oogonia

oospores



Salisapilia sapeloenesis et alPersoonia 25: 113. 2010.



Typus: Holotype     

   ,   



Distribuon: USA.

Salisapilia tartarea      

comb. nov.

Basionym: Halophytophthora tartarea   

Mycoscience 35: 224. 1994. MB363474.

Synonym: Salisapilia tartarea

et alPersoonia 25



Typus: Holotype



Distribuon: USA.

NotePersoonia 25



DISCUSSION

        



Halophytophthora 

Phytopythium (Bala et al.Salisapilia 

et alSalispina (Li et al Calycofera et

al.Halophytophthora Salisapilia 



et al.



    Salisapiliaceae 

 



 et al      S. nakagirii

         

        

  et al.     

   S. nakagirii has an

   



     et al. (2014)

    S. nakagirii  

          

       

        

Salisapilia



 et al      

       

       

S. nakagirii

A B

Fig. 9. Salisapilia sapeloensisA.B.C.D.

E.F, G.

Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

181

         

Peronosporales  

      

        

    et al   

 et al.et al 

      

      

      Phytophthora  

et al



et al.   et al   et al.

et al. 2011). Halophytophthora elongata  et al.  

H. masteri et al   

      

S. nakagirii

           

Salisapilia



       





et al. et al 



     S. nakagirii  



Salisapilia 





et al.  



S. nakagirii, 

Salisapilia.

 Salisapiliaceae    

        Peronosporaceae 

Pythiaceaeet al et al. (2010)

  H. bahamensis H. epistomia H. exoprolera,

H. operculata Salisapilia

     

et al

        Halophytophthora

operculata       Calycofera

et. al 

Phytopythiumet alH. epistomia





H. epistomia   Salisapilia.



one.

CDE

Fig. 10. Salisapilia tartarea A. B. C.D.

E, F.

Key to the species of Salisapilia

 ................................................................................................................. S. nakagirii

 ........................................................................................................................................ 2

 ............................................................................................................................. 3

 ..................................................................................................................... 4

Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

182



 ........................................................................................................... S. masteri



 ................................................................................................................................................... S. elongata

 .......................................................................................................................................................................

 ................................................................................................................................................................ 6



 ............................................................................................................................................. S. bahamensis



 ..................................................................................................................... S. coeyi

 ......................................................... S. mycoparasica

 ...................................................................... 7

 ........................................................................................................................................................... S. tartarea

 ............................................................................................................................................................................. 8



 ................................................................................................................. S. sapeloensis



 .......................................................................................................... S. epistomia

Salisapilia

Phytopythium

Halophytophthora

Phytophthora

Pythium s.lat.

CBS 382.34 Pythium oligandrum

CBS 377.34 Pythium acanthicum

CBS 158.73 Pythium monospermum

CBS 118.80 Pythium aphanidermatum

CBS 574.85 Pythium insidiosum

CBS 222.94 Pythium capillosum

CBS 188.68 Pythium dissotocum

CBS 772.81 Pythium apleuroticum

CBS 215.80 Pythium aquatile

CBS 295.37 Pythium vanterpoolii

CBS 699.83 Pythium volutum

CBS 237.62 Pythium graminicola

CBS 168.68 Pythium inflatum

CBS 316.33 Pythium torulosum

CBS 842.68 Pythium catenulatum

CBS 406.72 Elongisporangium dimorphum

CBS 157.69 Elongisporangium undulatum

CBS 285.31 Elongisporangium anandrum

CBS 393.54 Elongisporangium helicandrum

CBS 845.68 Elongisporangium prolatum

CBS 698.83 Globisporangium paddicum

CBS 574.80 Globisporangium macrosporum

CBS 275.67 Globisporangium spinosum

CBS 250.28 Globisporangium irregulare

CBS 453.67 Globisporangium sylvaticum

CBS 450.67 Globisporangium heterothallicum

CBS 122650 Globisporangium ultimum

CBS 398.51 Globisporangium ultimum

CBS 811.70 Globisporangium polymastum

CBS 674.85 Globisporangium perplexum

CBS 281.64 Globisporangium echinulatum

CBS 470.50 Globisporangium multisporum

CBS 776.81 Globisporangium pleroticum

CBS 540.67 Saprolegnia parasitica s.lat.

CBS 127041 Saprolegnia parasitica.

NBRC 32617 Salisapilia epistomia

CBS 590.85 Salisapilia epistomia

NBRC 32604 Salisapilia masteri

NBRC 100786 Salisapilia elongata

NBRC 32967 Salisapilia mycoparasitica

NBRC 32966 Salisapilia mycoparasitica

NBRC 32557 Salisapilia coffeyi

NBRC 32556 Salisapilia bahamensis

NBRC LT6456 Salisapilia nakagirii

CBS 127946 Salisapilia sapeloensis

CBS 208.95 Salisapilia tartarea

CBS 119.80 Phytopythium vexans

CBS 286.31 Phytopythium helicoides

CCIBt 3981 Phytopythium palingenes

CBS 111349 Phytopythium montanum

CBS 768.73 Phytopythium ostracodes

CBS 112351 Phytopythium megacarpum

CBS 113.91 Phytopythium kandeliae

AJM 26 Phytopythium kandeliae

CBS 393.81 Halophytophthora vesicula

BRC 32619 Halophytophthora polymorphica

CBS 188.85 Halophytophthora avicenniae

BRC 32616 Halophytophthora batemanensis

CBS 152.96 Halophytophthora ‘vesicula’

IMI 288805 Phytophthora insolita

P15005 Phytophthora polonica

CBS 406.48 Phytophthora quininea

CBS 291.29 Phytophthora boehmeriae

PD 00105 Phytophthora kernoviae

PD 00133 Phytophthora ilicis

CBS 101553 Phytophthora ramorum

CBS 144.22 Phytophthora cinnamomi

P6317 Phytophthora colocasiae

CBS 554.88 Phytophthora mexicana

CBS 128.23 Phytophthora capsici

PD 00177 Phytophthora idaei

PD 00134 Phytophthora clandestina

PD 00173 Phytophthora iranica

PD 00067 Phytophthora phaseoli

PD 00078 Phytophthora ipomoeae

CBS 366.51 Phytophthora infestans

Revisiting Salisapiliaceae

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

183

ACKNOWLEDGEMENTS



        



        

        







        



REFERENCES

         

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   Molekularbiologische Populaonsstudien an

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

  et al. (2010). Phytopythium

       gen. nov 

Phytopythium sindhum     sp. nov.

Persoonia 24: 136–137.

 HyphochytriomycotaOomycota. In:

Handbook of the Prosts



       Phytophthora elongata

(Peronosporaceae

Mycosphere 8

et al. (2017b). Calycofera

Phytopythium, Peronosporaceae.

Mycological Progress 16

 et al 

Phytophthora      

Fungal Genecs and Biology 45: 266–277.

et al

 Phytophthora    Fungal Genecs and

Biology 30: 17–32.

      et al. (2009). Fungal

Biodiversity. CBS Laboratory Manual 1: 1–269. 



et al. (1987). Pythium insidiosum

       Journal of Clinical

Microbiology 25: 344–349.

       et al.   Phytopythium:

Persoonia 34

      Diseases Worldwide.



 Phytophthora

PythiumRhizophora

mangleCanadian Journal of Botany 53: 2908–2922.

Phytophthora

Mycotaxon 19

   

Phytophthora. Experimental Mycology 3: 321–339.

Halophytophthora elongata

Mycotaxon 85: 417–422.

Halophytophthora epistomium

Mycologia 82

Halophytophthora

Pythiaceae. Mycotaxon 36: 377–382.

et al. (2010). Salisapiliaceae



Persoonia 25: 109–116.

et al. (2017). Nothophytophthora

Phytophthora

Persoonia 39: 143–174.

et al.  



Nucleic Acid Research 30

et al. 

  Phytophthora     

Fungal Genecs and Biology 41: 766–782.

et al.Phytophthora

anno 2012. Phytopathology 102: 348–364.

 

Fungal Diversity 49: 93–100.

et al.

      Fungal

Diversity 78: 1–237.

   Mesquite: a modular system for

evoluonary analysis

       et al.    

 Peronosporales (Oomycetes, Straminipila  

Fungal Ecology 19: 77–88.

      et al.  

  Pythiales  Peronosporales (Oomycetes,

Straminipila  Freshwater

fungi and fungal-like organisms      





Ganoderma

Mycologia 87: 223–238.

Halophytophthora

H. tartarea H. masteri 

Mycoscience 35: 223–232.

      et al.    

       Recent Advances in

Microbial Ecology       et al 



   Pythium montanum

         Mycological

Progress 2: 73–80.

          

Fungal Ecology 6

       Pythium

  Transacons of the Brish Mycological Society 89:



Fig. 11.ElongisporangiumGlobisporangium HalophytophthoraPhytophthora

PhytopythiumPythium Salisapilia 

 



Bennett & Thines

Editor-in-Chief

Prof. dr P.W. Crous,Westerdijk Fungal BiodiversityInstitute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.

E-mail:p.crous@westerdijkinstitute.nl

184

         Pythium megacarpum sp.

FEMS

Microbiology Leers 186: 229–233.

Pythium prolatum

FEMS Microbiology

Leers 173

     Phytophthora operculata    

Mycotaxon 15: 99–102.

         



Molecular Biology and Evoluon 26

          

PLoS ONE 5: e9490.

      et al.  

   Peronosporales  

Mycologia

84: 834–849.

        et al.   

 

Systemac Biology 61

et al.

 

Phytophthora. IMA Fungus 2: 163–171.

et al.

  Phytophthora. CMI Mycological Papers 162:

1–28.

      et al.   

  Molecular Biology and

Evoluon 30

        

European Journal of Plant Pathology

138: 431–447.

          

PythiumMycoscience 51

 



Cladiscs 27: 171–180.

Pythium.

Studies in Mycology 21: 1–244.

PhytophthoraCMI

Mycological Papers 92: 1–22.

     Halophytophthora uvias   

FEMS Microbiology Leers 352: 230–237.



Phytophthora. IMA Fungus 8

Supplementary Material: hp://fuse-journal.org/

Table S1.

Fig. S1.        

        

        









Fig. S2.        

        



Table S1. GenBank numbers of sequences used in this study.

Species

Strain information

Other strain no.

ITS

LSU

Halophytophthora

H. bahamensis

NBRC 32557

IFO 32557 ATCC28297

P3931*

MF979510

MF979503

H. bahamensis T

NBRC 32556

IFO 32556

ATCC 28296

CBS 586.85

IMI 330182

P3930*

MF979511

MF979504

H. batemanensis T

NBRC 32616

CBS 679.84

NBRC 32616

MG 25-3

MG 33-5

DAR 41559

IMI 327602

ATCC 56965

AF271223

DQ361227

H. elongata T

NBRC 100786

BCRC 33983

MF979512

MF979505

H. epistomia

CBS 590.85

NBRC 32617

HQ643220

HQ665279

H. epi stomia T

NBRC 32617

IFO 32617

ATCC 28293

IMI 330183

CBS 590.85

MF979513

MF979506

H. masteri T

NBRC 32604

IFO 32604

ATCC 96906

CBS 207.95

MF979514

MF979507

H. mycoparasitica

NBRC 32967

IFO 32967

MF979515

MF979508

H. mycoparasitica

NBRC 32966

IFO 32966

MF979516

MF979509

H. polymorphica T

CBS 680.84

DAR 41562 IFO 32619

ATCC 56966

NBRC 32619

HQ643313

HQ665288

H. vesicula T

NBRC 32216

IFO 32216

CBS 393.81

JF750389

KT455418

H. vesicula

CBS 152.96

HQ232472

HQ232463

Phytopythium

P. helicoides

CBS 286.31

HQ643383

HQ665186

P. kandeliae

AJM26

KJ399962

KJ399965

P. kandeliae

CBS 113.91

KJ399961

HQ665079

P. megacarpum

CBS 112351

AB725881

HQ665067

P. montanum

CBS 111349

AB725883

HQ665064

P. ostracodes

CBS 768.73

HQ643395

HQ665295

P. palingenes

CCIBt 3981

KR092139

KR092143

P. ve xans

CBS 119.80

AY598713

HQ665090

Salisapilia

S. nakagirii T

LT6456

CBS 127947

NBRC 108757

HQ232467

HQ232458

S. sapeloensis T

LT6440

CBS 127946

NBRC 108756

HQ232466

HQ232457

S. tartarea T

CBS 208.95

IFO 32606

NBRC 32606

ATCC 96905

HQ232473

HQ232464

Saprolegnia

S. parasitica

CBS 540.67

AY310504

HQ665256

S. parasitica

CBS 127041

HQ111458

HQ395663

Phytophthora

P. boehmeriae

CBS 291.29

PD 00181

P6950

NR147884

HQ665190

P. capsici

CBS 128.23

DQ464056

HQ665120

P. cinna momi

CBS 144.22

KC478663

HQ665126

P. cland estina

CBS 349.86

P3942

PD_00134

P. colo casiae

P6317

PD_00139

P. idaei

CBS 971.95

P6767

IMI 313728

PD_00177

P. ilicis

P3939

PD_00133

P. infestans

CBS 366.51

HQ643247

HQ665217

P. insolita

IMI 288805

PD 00175

P6195

NR147858

EU080180

P. ipomoeae

P10225

PD_00078

P. iranica

CBS 374.72

P3882

PD_00173

P. kernoviae

P10958

PD_00105

P. Mexicana

CBS 554.88

P0646

PD_00061

P. phaseoli

P10145

PD_00067

P. polonica

P15005

PD_01107

P. quininea

CBS 406.48

P3247

PD_00126

P. ramorum

CBS 101553

PD 00065

P10103

NR147877

HQ665053

Pythium

P. acanthicum

CBS 377.34

HQ643409

HQ665222

P. aphanidermatum

CBS 118.80

AY598622

HQ665084

P. apleroticum

CBS 772.81

AY598631

HQ665296

P. aquatile

CBS 215.80

AY598632

HQ665153

P. capillosum

CBS 222.94

AY598635

HQ665164

P. catenulatum

CBS 842.68

AY598675

HQ665302

P. dissotocum

CBS 166.68

AY598634

HQ665139

P. graminicola

CBS 327.62

HQ643545

HQ665211

P. inflatum

CBS 168.68

AY598626

HQ665140

P. insidiosum

CBS 574.85

AY598637

HQ665273

P. monospermum

CBS 158.73

AY598621

HQ665137

P. oligandrum

CBS 382.34

AY598618

HQ665223

P. torulosum

CBS 316.33

AY598624

HQ665206

P. vanterpoolii

CBS 295.37

AY598685

HQ665193

P. volutum

CBS 699.83

AY598686

HQ665291

Globisporangium

G. echinulatum

CBS 281.64

AY598639

HQ665183

G. heterothallicum

CBS 450.67

AY598654

G. irregulare

CBS 250.28

AY598702

HQ665172

G. macrosporum

CBS 574.80

AY598646

HQ665272

G. multisporum

CBS 470.50

AY598641

HQ665239

G. paddicum

CBS 698.83

AY598707

HQ665290

G. perplexum

CBS 674.85

AY598658

HQ665283

G. pleroticum

CBS 776.81

AY598642

HQ665298

G. polymastum

CBS 811.70

AY598660

HQ665301

G. spinosum

CBS 275.67

AY598701

HQ665181

G. sylvaticum

CBS 453.67

AY598645

HQ665236

G. ultimum

CBS 122650

HQ643864

HQ665103

G. ultimum

CBS 398.51

AY598657

HQ665227

Elongisporangium

E. anandrum

CBS 285.31

AY598650

HQ665185

E. dimorphum

CBS 406.72

AY598651

HQ665229

E. helicandrum

CBS 393.54

AY598653

HQ665225

E. prolatum

CBS 845.68

AY598652

HQ665303

E. undulatum

CBS 157.69

AY598708

HQ665134

Strain information and abbreviation

T – ex-Type specimen

ATCC – American Type Culture Collection, USA

BCR C – Bioresource Collection and Research Center, Taiwan

CBS – Westerdijk Fungal Biodiversity (formerly Centraalbureau voor Schimmelcultures), The Netherlands

NBRC – NITE Biological Resource Centre, Japan

IMI – CABI Bioscience, part of the United Kingdom National Culture Collection

IFO – Institute for Fermentation Osaka, Japan

PD – sequence strains obtained from the Phytophthora database (http://www.phytophthoradb.org/)

*information obtained from the Phytophthora WOC Database, World Phytophthora Genetic Resource Collection

(http://phytophthora.ucr.edu/)

Phytophthora

Halophytophthora avicenniae CBS 188.85

Halophytophthora avicenniae NBRC 32614

Halophytophthora fluviatilis 57A9

Halophytophthora vesicula CBS 152.96

Halophytophthora batemanensis NBRC 32616

Halophytophthora polymorphica NBRC 32619

Halophytophthora vesicula CBS 393.81

Phytopythium

Globisporangium

Elongisporangium

Pythium

Salisapilia sapeloensis LT6440

Salisapilia tartarea CBS 208.95

Salisapilia bahamensis NBRC 32556

Salisapilia nakagirii LT6456

Salisapilia coffeyi NBRC 32557

Salisapilia elongata NBRC 100786

Salisapilia masteri NBRC 32604

Salisapilia epistomium CBS 590.85

Salisapilia epistomium NBRC 32617

Salisapilia mycoparasitica NBRC 32966

Salisapilia mycoparasitica NBRC 32967

Saprolegnia parasitica CBS 540.67

Saprolegnia parasitica CBS 127041

100/100/1.0

100/99/1.0

100/-/1.0

98/-/-

95/-/1.0

100/100/1.0

100/99/1.0

99/-/1.0

100/100/1.0

100/98/1.0

85/-/-

67/51/-

100/100/1.0

53/-/-

77/-/-

70/-/-

60/-/-

99/92/1.0

95/64/1.0 100/100/1.0

0.050

Fig. S1

Phytophthora

Halophytophthora polymorphica NBRC 32619

Halophytophthora vesicula CBS 393.81

Halophytophthora avicenniae CBS 188.85

Halophytophthora batemanensis NBRC 32616

Halophytophthora vesicula CBS 152.96

Phytopythium

Elongisporangium

Globisporangium

Pythium

Salisapilia coffeyi NBRC 32557

Salisapilia sp. NBRC 32607

Salisapilia bahamensis NBRC 32556

Salisapilia sapeloensis CBS 127946

Salisapilia tartarea CBS 208.95

Salisapilia nakagirii LT6456

Salisapilia mycoparasitica NBRC 32967

Salisapilia mycoparasitica NBRC 32966

Salisapilia masteri NBRC 32604

Salisapilia elongata NBRC 100786

Salisapilia epistomia NBRC 32617

Salisapilia epistomia CBS 590.85

Sapromyces elongatus CBS 213.82

Salispina intermedia CCIBt 4155

Salispina spinosa CBS 591.85

Saprolegnia parasitica CBS 540.67

Saprolegnia parasitica CBS 127041

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Fig. S2

Neofunctionalization of Glycolytic Enzymes: An Evolutionary Route to Plant Parasitism in the Oomycete Phytophthora nicotianae

Article

Full-text available

Jan 2022

Oomycetes, of the genus Phytophthora, comprise of some of the most devastating plant pathogens. Parasitism of Phytophthora results from evolution from an autotrophic ancestor and adaptation to a wide range of environments, involving metabolic adaptation. Sequence mining showed that Phytophthora spp. display an unusual repertoire of glycolytic enzymes, made of multigene families and enzyme replacements. To investigate the impact of these gene duplications on the biology of Phytophthora and, eventually, identify novel functions associated to gene expansion, we focused our study on the first glycolytic step on P. nicotianae, a broad host range pathogen. We reveal that this step is committed by a set of three glucokinase types that differ by their structure, enzymatic properties, and evolutionary histories. In addition, they are expressed differentially during the P. nicotianae life cycle, including plant infection. Last, we show that there is a strong association between the expression of a glucokinase member in planta and extent of plant infection. Together, these results suggest that metabolic adaptation is a component of the processes underlying evolution of parasitism in Phytophthora, which may possibly involve the neofunctionalization of metabolic enzymes.

Adding a missing piece to the puzzle of oomycete phylogeny: the placement of Rhipidium interruptum (Rhipidiaceae)

Article

Full-text available

Jun 2023

Oomycetes are a group of fungus-like organisms, which phylogenetically comprise early diverging lineages that are mostly holocarpic, and two crown classes, the Peronosporomycetes and Saprolegniomycetes, including many well-investigated pathogens of plants and animals. However, there is a poorly studied group, the Rhipidiales, which placement amongst the crown oomycetes is ambiguous. It accommodates several taxa with a sophisticated vegetative and reproductive cycle, as well as structural organisation, that is arguably the most complex in the oomycete lineage. Despite the remarkable morphological complexity and their notable perseverance in the face of faster-growing saprotrophic oomycetes and fungi, the knowledge on Rhipidiales is limited to date, as the most complex members are not easily cultured, even by targeted approaches. This also leads to inadequate sequence data for the order, which was sourced from only the two least complex out of seven introduced genera, i.e. Sapromyces and Salispina. In the present study, ex-situ baiting was done using various fruit substrates, and naturally-shed twigs or fruits acquired from water bodies were examined. As a result of these efforts, the species Rhipidium interruptum was obtained and gross cultivation was accomplished using poplar (Populus nigra) twigs as substrate, which allowed further documentation of both asexual and sexual reproduction. This enabled phylogenetic and detailed morphological study, as well as an epitypification of the species. Phylogenetic analyses based on cox2 and nrLSU sequences revealed Rhipidium as the sister genus of Sapromyces. The morphological studies done support a conspecificity of R. interruptum and R. continuum, which might in turn be conspecific with R. americanum. Though several further studies will be required to fit the scattered missing pieces of knowledge on Rhipidiales together revealing a more complete picture of oomycete evolution, we hope that the current study can serve as a cornerstone for future investigations in the group.

Unravelling the Lipids Content and the Fatty Acid Profiles of Eight Recently Described Halophytophthora Species and H. avicennae from the South Coast of Portugal

Article

Full-text available

Mar 2023
MAR DRUGS

In this study, mycelia of eight recently described species of Halophytophthora and H. avicennae collected in Southern Portugal were analysed for lipids and fatty acids (FA) content to evaluate their possible use as alternative sources of FAs and understand how each species FAs profile relates to their phylogenetic position. All species had a low lipid percentage (0.06% in H. avicennae to 0.28% in H. frigida). Subclade 6b species contained more lipids. All species produced monounsaturated (MUFA), polyunsaturated (PUFA) and saturated (SFA) FAs, the latter being most abundant in all species. H. avicennae had the highest FA variety and was the only producer of γ-linolenic acid, while H. brevisporangia produced the lowest number of FAs. The best producer of arachidonic acid (ARA) and eicosapentaenoic acid (EPA) was H. thermoambigua with 3.89% and 9.09% of total FAs, respectively. In all species, palmitic acid (SFA) was most abundant and among the MUFAs produced oleic acid had the highest relative percentage. Principal component analysis (PCA) showed partial segregation of species by phylogenetic clade and subclade based on their FA profile. H. avicennae (Clade 4) differed from all other Clade 6 species due to the production of γ-linolenic and lauric acids. Our results disclosed interesting FA profiles in the tested species, adequate for energy (biodiesel), pharmaceutical and food industries (bioactive FAs). Despite the low amounts of lipids produced, this can be boosted by manipulating culture growth conditions. The observed interspecific variations in FA production provide preliminary insights into an evolutionary background of its production.

Eight new Halophytophthora species from marine and brackish-water ecosystems in Portugal and an updated phylogeny for the genus

Article

Mar 2022

During an oomycete survey in December 2015, 10 previously unknown Halophytophthora taxa were isolated from marine and brackish water of tidal ponds and channels in saltmarshes, lagoon ecosystems and river estuaries at seven sites along the Algarve coast in the South of Portugal. Phylogenetic analyses of LSU and ITS datasets, comprising all described Halophytophthora species, the 10 new Halophytophthora taxa and all relevant and distinctive sequences available from GenBank, provided an updated phylogeny of the genus Halophytophthora s.str. showing for the first time a structure of 10 clades designated as Clades 1–10. Nine of the 10 new Halophytophthora taxa resided in Clade 6 together with H. polymorphica and H. vesicula. Based on differences in morphology and temperature-growth relations and a multigene (LSU, ITS, Btub, hsp90, rpl10, tigA, cox1, nadh1, rps10) phylo-geny, eight new Halophytophthora taxa from Portugal are described here as H. brevisporangia, H. celeris, H. frigida, H. lateralis, H. lusitanica, H. macrosporangia, H. sinuata and H. thermoambigua. Three species, H. frigida, H. macrosporangia and H. sinuata, have a homothallic breeding system while the remaining five species are sterile. Pathogenicity and litter decomposition tests are underway to clarify their pathological and ecological role in the marine and brackish-water ecosystems. More oomycete surveys in yet undersurveyed regions of the world and population genetic or phylogenomic analyses of global populations are needed to clarify the origin of the new Halophytophthora species. Citation: Maia C, Horta Jung M, Carella G, et al. 2022. Eight new Halophytophthora species from marine and brackish-water ecosystems in Portugal and an updated phylogeny for the genus. Persoonia 48: 54 – 90. https://doi.org/10.3767/persoonia.2022.48.02..

Multigene analyses with a broad sampling in Phytophthora and related genera provide evidence for the monophyly of downy mildews

Article

Full-text available

Nov 2023

Downy mildews are the most species-rich group of oomycetes, with more than 700 known species. The relationships within the main downy mildew lineages (i.e. the downy mildews with pyriform haustoria, the downy mildews with coloured conidia, and the brassicolous downy mildews) are increasingly well resolved, and 20 well-characterised monophyletic genera have been described. However, their relationships to each other, the various lineages of graminicolous downy mildews, and to the species subsumed in Phytophthora are still unresolved. Recent phylogenomic studies have suggested a polyphyly of the downy mildews, but with a limited taxon sampling within Phytophthora . As taxon sampling is crucial for inferring relationships between large groups, we have conducted a multigene analysis with a set of 72 Phytophthora species and included all known downy mildew lineages. In addition, we performed approximately unbiased (AU) testing as an additional approach to evaluate major nodes. Our analyses resolve the downy mildews as a monophyletic assemblage in all phylogenetic algorithms used. We thus conclude that the evolution of the obligate biotrophy characteristic of downy mildews was a singular event and that all downy mildew pathogens can be traced to a single ancestor.

Fungi and fungus-like microorganisms in Philippine marine ecosystems

Chapter

Jan 2023

Lagena-an overlooked oomycete genus with a wide range of hosts

Article

Full-text available

Jul 2022
MYCOL PROG

Lagena has so far only been known from the scarcely reported but widespread species Lagena radicicola, which is a parasite of root epidermal cells. While it was mostly reported from a wide range of cereals and other grasses, it has been shown to affect some dicot species under, e.g. tobacco and sugar beet. Due to the wide host spectrum under laboratory conditions, there were no attempts to subdivide the genus into several species, even though some morphological differentiation was reported and the species had been found in several continents. During a survey of diatoms, we came across some parasitoids that would have previously been assumed to be members of the genus Lagenidium. The species exhibited rather narrow host specificity in nature. One species was brought into dual culture with host diatoms of the genus Ulnaria, but could not be transferred to other host genera. Surprisingly, phylogenetic analyses revealed that Lagena radicicola was in a sister clade to that formed by the diatom parasitoids, suggesting a versatile pathogenicity of the genus. Interestingly, several phylogenetic lineages only known from environmental sequencing were clustered with the species found in this study, hinting an undiscovered diversity in the genus Lagena.

Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates

Article

Full-text available

Feb 2022
J. Fungi

Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.

Palmitic acid and long-chain polyunsaturated fatty acids dominate in mycelia of mangrove Halophytophthora and Salispina species in Taiwan

Article

Full-text available

Aug 2021
BOT MAR

Marine oomycetous species produce, among other fatty acids, omega-6 arachidonic acid (ARA) and omega-3 eicosapentaenoic acid (EPA), with implications for the industrial potential of this group of organisms and the need to find an isolate with high production. This study screened 14 isolates of marine oomycetous species: Halophytophthora avicenniae , H. batemanensis , H. exoprolifera , H. polymorphica and Salispina spinosa cultured from fallen mangrove leaves in Taiwan for 24 saturated and unsaturated fatty acids in their mycelia. This paper is the first to report C18:1n-7 vaccenic acid, C20:1 eicosenoic acid, C24:1 nervonic acid, C20:2n-6 eicosadienoic acid, C22:4n-6 adrenic acid, C20:4n-3 eicosatetraenoic acid and C22:5n-3 docosapentaenoic acid in mycelia of Halophytophthora and Salispina species, and the fatty acid profiles of H. batemanensis and H. exoprolifera . Five fatty acids were dominant in the mycelia of the isolates, i.e. C16:0 palmitic acid, C18:1n-9 oleic acid, C18:2n-6 linoleic acid, C20:4n-6 arachidonic acid and C20:5n-3 eicosapentaenoic acid. For the essential fatty acids, S. spinosa produced the highest level of arachidonic acid (27–31% of total fatty acid (TFA), 141–188 mg l ⁻¹ yield) while H. avicenniae IMB212 produced the highest percentage of EPA (15% of TFA) while H. polymorphica IMB227 produced the highest yield (96 mg l ⁻¹ ). Different species and isolates of the same species produced different fatty acid profiles, and further research effort may yield a high production isolate of industrial significance and also important fatty acids from the marine environment.

Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae

Article

Full-text available

Apr 2021

Marine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae —one could be assigned to Peronospora verna , an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum . While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae . While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox 2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.

Phylogeny of the genus Pythium and description of new genera

Article

Full-text available

Jan 2010

Phylogeny of the genus Pythium is analyzed based on sequences of the large subunit ribosomal DNA D1/D2 region and cytochrome oxidase II gene region of Pythium isolates and comprehensive species of related taxa belonging to the Oomycetes. The phylogenetic trees show that the genus Pythium is a highly divergent group and divided into five well- or moderately supported monophyletic clades. Each clade is characterized by sporangial morphology such as globose, ovoid, elongated, or filamentous shapes. Based on phylogeny and morphology, the genus Pythium (s. str.) is emended, and four new genera, Ovatisporangium, Globisporangium, Elongisporangium, and Pilasporangium, are described and segregated from Pythium s. lato.

An expanded phylogeny for the genus Phytophthora

Article

Full-text available

Dec 2017

A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

Nothophytophthora gen. nov., a new sister genus of Phytophthora from natural and semi-natural ecosystem

Article

Full-text available

Aug 2017
Persoonia

During various surveys of Phytophthora diversity in Europe, Chile and Vietnam slow growing oomycete isolates were obtained from rhizosphere soil samples and small streams in natural and planted forest stands. Phylogenetic analyses of sequences from the nuclear ITS, LSU, β-tubulin and HSP90 loci and the mitochondrial cox1 and NADH1 genes revealed they belong to six new species of a new genus, officially described here as Nothophytophthora gen. nov., which clustered as sister group to Phytophthora. Nothophytophthora species share numerous morphological characters with Phytophthora: persistent (all Nothophytophthora spp.) and caducous (N. caduca, N. chlamydospora, N. valdiviana, N. vietnamensis) sporangia with variable shapes, internal differentiation of zoospores and internal, nested and extended (N. caduca, N. chlamydospora) and external (all Nothophytophthora spp.) sporangial proliferation; smooth-walled oogonia with amphigynous (N. amphigynosa) and paragynous (N. amphigynosa, N. intricata, N. vietnamensis) attachment of the antheridia; chlamydospores (N. chlamydospora) and hyphal swellings. Main differing features of the new genus are the presence of a conspicuous, opaque plug inside the sporangiophore close to the base of most mature sporangia in all known Nothophytophthora species and intraspecific co-occurrence of caducity and non-papillate sporangia with internal nested and extended proliferation in several Nothophytophthora species. Comparisons of morphological structures of both genera allow hypotheses about the morphology and ecology of their common ancestor which are discussed. Production of caducous sporangia by N. caduca, N. chlamydospora and N. valdiviana from Valdivian rainforests and N. vietnamensis from a mountain forest in Vietnam suggests a partially aerial lifestyle as adaptation to these humid habitats. Presence of tree dieback in all forests from which Nothophytophthora spp. were recovered and partial sporangial caducity of several Nothophytophthora species indicate a pathogenic rather than a saprophytic lifestyle. Isolation tests from symptomatic plant tissues in these forests and pathogenicity tests are urgently required to clarify the lifestyle of the six Nothophytophthora species.

Phytophthora elongata (Peronosporaceae) is present as an estuarine species in Philippine mangroves

Article

Full-text available

Jun 2017

The genus Phytophthora, a group of hemibiotrophic oomycetes, is composed of almost 150 species, most of which are pathogens of terrestrial and freshwater plant species. Of the known taxa of Phytophthora, three species (P. estuarina, P. gemini, and P. rhizophorae) were only recorded in the estuarine or marine environment, while others were recently discovered to be present in these environments as saprotrophs, suggesting that more Phytophthora species might be present in marine or estuarine habitats. Thus, mangrove habitats of the Philippines were surveyed for additional Phytophthora species apart from the previously-reported species, Phytophthora insolita. As a result, Phytophthora elongata, which was reported as a pathogen of Eucalyptus marginata from Western Australia, was isolated from mangrove leaf litter in the coastal area of Cavite, Philippines, as the first Clade 2 species found in saline habitats. This suggests that among Phytophthora species there is the potential to rather easily evolve measures to deal with osmotic pressure, which supports the potential importance of mangroves as a cryptic habitat of Phytophthora.

MEGA6: Molecular evolutionary genetics analysis

Article

Full-text available

Jan 2013

Fungal diversity notes 253–366: taxonomic and phylogenetic contributions to fungal taxa

Article

Full-text available

May 2016

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota.

Phylogenetic relationships in Ganoderma inferred from the internal transcribed spacers and 25S ribosomal DNA sequences

Article

Mar 1995

Over 250 species have been described in Ganoderma. Species identification and species circumscription are often unclear and taxonomic segregation of the genus remains controversial. In this study we sequenced the 5′ half of the 25S ribosomal RNA gene and the internal transcribed spacers to determine appropriate regions to i) discriminate between Ganoderma species and ii) infer taxonomic segregation of Ganoderma s. lato (Ganodermataceae) on a phylogenetic basis. We studied 19 Ganoderma isolates representing 14 species classified in 5 subgenera and sections, one isolate of the related genus Amauroderma, and one isolate of Fomitopsis which served as the out- group in parsimony analysis. Results showed that a transition bias was present in our data, and that rates of nucleotide divergence in the different ribosomal regions varied between lineages. Independent and combined analyses of different data sets were performed and results were discussed. Nucleotide sequences of the internal transcribed spacers, but not those of the coding regions, distinguished between most Ganoderma species, and indicated that isolates of the G. tsugae group were misnamed. Phylogenetic analysis of the combined data sets of the divergent domain D2 of the 25S ribosomal RNA gene and of the internal transcribed spacers indicated that subgenus Elfvingia was monophyletic, whereas sections Characoderma and Phaeonema were not. Combined data from these regions is useful for infrageneric segregation of Ganoderma on a phylogenetic basis. Phylogenetic analysis from data of the D2 region alone strongly supported Amauroderma as a sister taxon of Ganoderma. This suggested that the D2 region should be suitable for systematics at higher taxonomic ranks in the Ganodermataceae. The low sequence variation observed in the 25S ribosomal gene within Ganoderma species suggested that the genus is young.

Calycofera gen. nov., an estuarine sister taxon to Phytopythium, Peronosporaceae

Article

Aug 2017

The genus Halophytophthora is a predominantly marine or estuarine genus of the oomycete family Peronosporaceae. This genus has been revealed as a highly polyphyletic assemblage of largely unrelated species. A new genus of the Peronosporaceae, Calycofera, is introduced in this manuscript to accommodate Halophytophthora operculata. Calycofera is distinct compared to Phytopythium s. str. and to Halophytophthora s. str. on the basis of sporangium morphology, sporangiogenous hyphae, and the development and release of zoospores. Phylogenetic analyses using ITS, cox2 and cox1 sequences strongly supported the establishment of this taxon. In addition, a second species of the genus was found, which is genetically more divergent from C. operculata than most sister species in the sister genus Phytopythium, and is described as C. cryptica based on diagnostic nucleotides.

Hyphochytriomycota and Oomycota

Chapter

Sep 2017

The anteriorally uniflagellate Hyphochytriomycota and biflagellate Oomycota are in the Kingdom Straminipila (commonly referred to as stramenopiles) which are part of the SAR superkingdom. Both appear to be basal to the large assemblage of golden-brown algae, the Ochrophyta. Both feature osmotrophic nutrition and have traditionally been considered as zoosporic “fungi,” but are unrelated to organisms in the monophyletic kingdom Mycota. The Hyphochytriomycota is a small group encompassing around half a dozen genera, which have simple nonmycelial, holocarpic thalli, traditionally encompassing three families: the endobiotic Anisolpidiaceae, the polycentric Hyphochytriaceae, and the monocentric Rhizidiomycetaceae. Recently the former have been shown to be placed among the early diverging Oomycota, leaving just the latter two families in the monophyletic Hyphochytriomycota clade. Hyphochytriomycota are widespread in occurrence, and most are saprotrophs or parasites, infecting the resting spores of Oomycota and Glomeromycota. In contrast, the Oomycota are a large and diverse assemblage, consisting of two major (class level) clades, the Saprolegniomycetes and Peronosporomycetes, and several early diverging classes most of which are simple holocarpic organisms that lack mycelial organisation. Many of these early-diverging clades are as yet poorly resolved because of sparse taxon sampling. The early-diverging orders include the Eurychasmales and Olpidiopsidales, both of which are marine seaweed parasites, the nematode infecting Haptoglossales and crustacean infecting Haliphthorales. The Saprolegniomycetes mostly have fungal-like mycelial thalli and include the orders Atkinsiellales s.lat., Leptomitales, and Saprolegniales, which are mostly saprophytes or parasites of invertebrates and, occasionally, vertebrates such as fish and amphibians. A few species in the Saprolegniales are root infecting parasites of plants. The Peronosporomycetes are the second major fungal-like class, and include the largely saprotrophic Rhipidiales, the facultively parasitic Pythiales s.lat., which can infect both animals and plants and the predominantly plant pathogenic Albuginales and Peronosporales sensu lato. Indeed, the Oomycota are significant parasites of both animals and plants, impacting both natural ecosystems and causing significant economic losses in both aquacultural and agricultural systems. The molecular systematics of the Oomycota is still in a state of flux, and in this account a relatively conservative approach has been taken. It is apparent that most of the early-diverging genera are almost exclusively marine and that the Peronosporales represents the main terrestrial and plant pathogenic lineage. Most early-diverging genera lack the oogamous sexual reproduction that characterizes this group and suggests that the oogenesis evolved around the time of emmergence from the sea to the land and freshwater ecosystems. It is also clear that obligate biotrophy in the white blister rusts (Albuginales) and downy mildews (Peronosporales s.str.) has evolved independently.

Succession of fungi in decomposing mangrove leaves in Japan

Article

Jan 1989

Revisiting Salisapiliaceae

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