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Marine Fungal Ecology in the Molecular Era

  • V. Venkateswara Sarma
  • Rajesh Jeewon
Chapter

Abstract

The marine environment is an intriguing one and provides a range of wonderful ecological niches to explore the ecology and biodiversity of marine microorganisms. Fungi are possibly by far the most abundant “lifeforms” in the marine environments but largely unexplored. Most studies on marine fungi were from coastal habitats, and they are mainly surveys employing traditional techniques such as microscopy and/or culture-dependent methods which suggest poor diversity of marine fungi (less than 1%) predominated by Dikarya. In fact, open oceans were largely considered as “fungal desert” given their inaccessibility and lack of appropriate methods to recover these organisms from these harsh environments. With recent technological advances and developments in molecular techniques involving advanced DNA sequencing technologies, marine mycologists have started to unravel unseen microbial species and better understand the structural and functional diversity of environmental fungal communities. These molecular genomic tools provided insights into genetic diversity especially pertaining to recovery of uncultured fungal organisms, discovery of novel fungal lineages, as well as the metabolic diversity of these complex fungal communities. Particularly, the culture-independent techniques involving environmental cloning, next-generation sequencing are revealing a higher fungal diversity from environmental DNA samples collected from surface waters in open seas, sediments in coastal, benthic and deep sea environments, hydrothermal vents and oxygen-deficient environments. In addition to the diversity, whole genome sequencing, RNA-Seq and microarray technologies in transcriptome profiling have provided a better understanding of potentially active fungal communities. With the use of these culture-independent methods, several undescribed fungal taxa termed as “dark matter fungi” belonging mainly to zoosporic fungi such as Blastocladiomycota, Chytridiomycota, Cryptomycota, and Neocallimastigomycota and Zygomycota including Entomophthoromycota, Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina lineages have been retrieved from marine habitats. Many of these nameless and faceless taxa of the early diverging clusters are microscopic in nature with special nutritional requirements and are difficult to isolate in vitro. Cryptomycota, the recently described phylum, established using phylotypes based exclusively on environmental sampling, has been shown to be highly diverse, abundant and ubiquitous in distribution. The marine fungal ecology has changed paradigms in the molecular era. The diversity and ecology of marine fungi recovered from the use of molecular tools are discussed in this book chapter.

Keywords

Next-generation sequencing Phylotypes Environmental DNA Deep-sea environment Sediments Nucleic acid primers Environmental cloning 

Notes

Acknowledgments

VVS would like to dedicate this chapter to Late Prof. B.P.R. Vittal, C.A.S. in Botany, University of Madras, Guindy Campus, Chennai, India, for introducing him to marine mycology and for being a great mentor and to Dr. Seshagiri Raghukumar and Dr. Chandralatha Raghukumar, formerly with National Institute of Oceanography, Goa, India, for their encouragement and inspiration.

References

  1. Abdel-Wahab MA, Pang K-L, Nagahama T, Abdel-Aziz FA, Jones EBG (2010) Phylogenetic evaluation of anamorphic species of Cirrenalia and Cumulospora with the description of eight new genera and four new species. Mycolog Prog 9:537–558CrossRefGoogle Scholar
  2. Aleem AA (1980) Distribution and ecology of marine fungi in Sierra Leone (Tropical WestAfrica). Bot Mar 23:679–688Google Scholar
  3. Alexander E, Stock A, Breiner H-W, Behnke A, Bunge J, Yakimov MM, Stoeck T (2009) Microbial eukaryotes in the hypersaline anoxic L’Atalante deep-sea basin. Environ Microbiol 11:360–381PubMedCrossRefGoogle Scholar
  4. Alias SA, Jones EBG (2000) Colonization of mangrove wood by marine fungi at Kuala Selangor mangrove stand. Malaysia Fungal Divers 5:9–21Google Scholar
  5. Alias SA, Kuthubutheen AJ, Jones EBG (1995) Frequencyofoccurrenceoffungi onwood in Malaysian mangroves. Hydrobiologia 295:97–106CrossRefGoogle Scholar
  6. Alker AP, Smith GW, Kim K (2001) Characterization of Aspergillus sydowii (Thom et Church), a fungal pathogen of Caribbean Sea fan corals. Hydrobiologia 460:105–111CrossRefGoogle Scholar
  7. Amend AS, Barshis DJ, Oliver TA (2012) Coral associated marine fungi form novel lineages and heterogeneous assemblates. ISME J 6:291–301CrossRefGoogle Scholar
  8. Arfi Y, Marchand C, Wartel M, Record E (2012) Fungal diversity in anoxic-sulfidic sediments in a mangrove soil. Fungal Ecol 5:282–285CrossRefGoogle Scholar
  9. Bass D, Howe A, Brown N, Barton H, Demidova M, Michelle H, Li L, Sanders H, WatkinsonSCC WS, Richards TAA (2007) Yeast forms dominate fungal diversity in the deep oceans. Proc R Soc B 274:3069–3077PubMedCrossRefGoogle Scholar
  10. Beakes GW, Honda D, Thines M (2014) Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota, and Oomycota. In: McLaughlin DJ, Spatafora JW (eds) The Mycota VII. Part A. Systematics and evolution, 2nd edn. Springer, Berlin/Heidelberg, pp 39–96CrossRefGoogle Scholar
  11. Bills GF, Polishook JD (1994) Abundance and diversity of microfungi in leaf litter of a lowland rain forest in Costa Rica. Mycologia 86:187–198CrossRefGoogle Scholar
  12. Bonthond G, Merselis DG, Dougan KE, Graff T, Todd W, Fourqurean JW, Rodriguez-Lanetty M (2018) Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats. Peer J 6:e4323.  https://doi.org/10.7717/peerj.4323CrossRefPubMedGoogle Scholar
  13. Booth T & Kenkel N (1986) Ecological studies of lignicolous marine fungi: a distribution model based on coordination and classification. In The Biology of Marine Fungi (ed.S.T. Moss), Cambridge University Press, Cambridge, pp. 297-310Google Scholar
  14. Borse BD (1988) Frequency of occurrence of marine fungi from Maharashtra coast, India. Ind J Mar Sci 17:165–167Google Scholar
  15. Burgaud G, Le Calvez T, Arzur D, Vandenkoornhuyse P, Barbier G (2009) Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environ Microbiol 11:1588–1600PubMedCrossRefGoogle Scholar
  16. Cai L, Jeewon R, Hyde KD (2006) Molecular systematics of Zopfiella and allied genera: evidence from multigene sequence analyses. Fungal Biology 110:359–368Google Scholar
  17. Cawthorn RJ (2011) Diseases of American lobsters (Homarus americanus): a review. J Invertebr Pathol 106:71–78PubMedCrossRefGoogle Scholar
  18. Cury JC, Araujo FV, Coelho-Souza SA, Peixoto RS, OliveiraJAL SHF, Davila AMR, Rosado AS (2011) Microbial diversity of a Brazilian coastal region influencedby an upwelling system and anthropogenic activity. PLoS One 6:e16553PubMedPubMedCentralCrossRefGoogle Scholar
  19. Damare SR, Nagarajan M, Raghukumar C (2008) Spore germination of fungi belonging to Aspergillus species under deep-sea conditions. Deep-Sea Res 55:670–678CrossRefGoogle Scholar
  20. Danovaro R, Pusceddu A (2007) Biodiversity and ecosystem functioning in coastal lagoons: does microbial diversity play any role? Estuar Coast Shelf Sci 75:4–12CrossRefGoogle Scholar
  21. Dawson SC, Pace NR (2002) Novel kingdom-level eukaryotic diversity in anoxic environments. Proc Natl Acad Sci USA 99:8324–8329CrossRefGoogle Scholar
  22. Devadatha B, Sarma VV, Wasnasinghe DN, Hyde KD & Jones EBG (2017) Introducing the new Indian mangrove species, Vaginatispora microarmatispora (Lophiostomataceae) based on morphology and multigene phylogenetic analysis. Phytotaxa. 329: 139-149.  https://doi.org/10.11646/phytotaxa.329.2.4CrossRefGoogle Scholar
  23. Devadatha B, Sarma VV, Ariyawansa HA, Jones EBG (2018a) Deniquelata vittalii sp. nov., a novel Indian saprobic marine fungus on Suaeda monoica and two new records of marine fungi from Muthupet mangroves, East coast of India. Mycosphere 9:565–582.  https://doi.org/10.5943/mycosphere/9/3/8CrossRefGoogle Scholar
  24. Devadatha B, Sarma VV, Jeewon R, Jones EBG (2018b) Morosphaeria muthupetensis sp.nov. (Morosphaeriaceae) from India: Morphological characterisation and multigene phylogenetic inference. Bot Mar 61(4):395–405.  https://doi.org/10.1515/bot-2017-0124CrossRefGoogle Scholar
  25. Devadatha B, Sarma VV, Jeewon R, Wanasinghe DN, Hyde KD, EBG J (2018c) Thyridariella, a novel marine fungal genus from India: morphological characterization and phylogeny inferred from multigene DNA sequence analyses. Mycolog Progr 17:791–804.  https://doi.org/10.1007/s11557-018-1387-4CrossRefGoogle Scholar
  26. Duong LM, Lumyong S, Hyde KD, Jeewon R (2004) Emarcea castanopsicola gen. et sp. nov. from Thailand, a new xylariaceous taxon based on morphology and DNA sequences. Stud Mycol 50:253–260Google Scholar
  27. Edgcomb VP, Beaudoin D, Gast R, Biddle JF, Teske A (2011) Marine subsurface eukaryotes: the fungal majority. Environ Microbiol 13:172–183PubMedCrossRefGoogle Scholar
  28. Fell JW, Master IM (1980) The association and potential role of fungi in mangrove detrital systems. Bot Mar 23:257–263Google Scholar
  29. Fryar SC (2002) Fungal succession or sequence of fruit bodies? In: Hyde KD, Jones EBG (eds) Fungal succession. Fungal Divers 10:5–10Google Scholar
  30. Gadanho M, Sampaio JP (2005) Occurrence and diversity of yeasts in the mid-Atlantic ridge hydrothermal fields near the Azores Archipelago. Microb Ecol 50:408–417PubMedCrossRefGoogle Scholar
  31. Gao Z, Li BL, Zheng CC, Wang G (2008) Moleculardetection of fungal communities in the Hawaiian marine sponges Suberites zeteki and Mycale armata. Appl Environ Microbiol 74:6091–6101PubMedPubMedCentralCrossRefGoogle Scholar
  32. Gao Z, Johnson ZI, Wang G (2010) Molecular characterizationof the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. ISME J 4:111–120PubMedCrossRefGoogle Scholar
  33. Gojkovic Z, Knecht W, Zameitat E, Warneboldt J, Coutelis JB, Pynyaha Y, Neuveglise C, Moller K, Loffler M, Piskur J (2004) Horizontal gene transfer promoted evolution of the ability to propagate under anaerobic conditions in yeasts. Mol Genet Genom 271:387–393CrossRefGoogle Scholar
  34. Hatai K (2012) Diseases of fish and shell fish caused by marine fungi. In: Raghukumar C (ed) Biology of marine fungi. Springer, Berlin, pp 15–52CrossRefGoogle Scholar
  35. Hongsanan S, Maharachchikumbura S, Hyde KD, Samarakoon M, Jeewon R, Zhao Q, Bahkali A (2017) An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence. Fungal Divers 84:84.  https://doi.org/10.1007/s13225-017-0384-2CrossRefGoogle Scholar
  36. Hongsanan S, Jeewon R, Purahong W, Xie N, Liu J-K, Jayawardane RS, Ekanayake RS, Dissanayake A, Raspe O, Hyde KD, Stadler M, Persoh D (2018) Can we use environmental DNA as holotypes? Fungal Divers 92:1–30CrossRefGoogle Scholar
  37. Hughes GC (1974) Geographical distribution of the higher marine fungi. Veroeffentlichender Institute ftir Meeres forschung, Bremerhaven Supplement 5:419–441Google Scholar
  38. Hyde KD (1988a) Studies on the tropical marine fungi of Brunei. Bot J Linn Soc 98:135–151CrossRefGoogle Scholar
  39. Hyde KD (1988b) Observations on the vertical distribution of marine fungi on Rhizophora spp. at Kampong Danau mangrove, Brunei. Asian Mar Biol 5:77–81Google Scholar
  40. Hyde KD (1989a) Ecology of tropical marine fungi. Hydrobiologia 178:199–208CrossRefGoogle Scholar
  41. Hyde KD (1989b) Intertidal mangrove fungi from North Sumatra. Can J Bot 67:3078–3082CrossRefGoogle Scholar
  42. Hyde KD (1989c) Vertical zonation of intertidal mangrove fungi. In: Hattori T, lshida Y, Maruyama Y, Moria R, Uchida A (eds) Recent advances in microbial ecology. Japan Scientific Societies Press, Tokyo, pp 302–306Google Scholar
  43. Hyde KD (1990a) A comparison of the intertidal mycota of five mangrove tree species. Asian Mar Biol 7:93–107Google Scholar
  44. Hyde KD (1990b) A study of the vertical zonation of intertidal fungi on Rhizophora apiculata at Kampong Kapok mangrove, Brunei. Aquat Bot 36:255–262CrossRefGoogle Scholar
  45. Hyde KD (1991) Fungal colonization of Rhizophora apiculata and Xylocarpus granatumpoles in Kampong Kapok mangrove Brunei. Sydowia 43:31–38Google Scholar
  46. Hyde KD (1992) Intertidal mangrove fungi from the West Coast of Mexico including onenew genus and two new species. Mycol Res 96:25–30CrossRefGoogle Scholar
  47. Hyde KD, Alias SA (2000) Biodiversity and distribution of fungi associated with decomposing Nypafruticans. Biodivers Conserv 9:393–402CrossRefGoogle Scholar
  48. Hyde KD, Jones EBG(1988) Marine mangrove fungi. Marine Ecol (P.S.Z.N.I.) 9:15–33CrossRefGoogle Scholar
  49. Hyde KD, Jones EBG (1989) Ecological observations on marine fungi from the Seychelles. Bot J Linn Soc 100:237–254CrossRefGoogle Scholar
  50. Hyde KD, Lee SY (1995) Ecology of mangrove fungi and their role in nutrient cycling. What gaps occur in our knowledge? Hydrobiologia 295:107–118CrossRefGoogle Scholar
  51. Hyde KD, Sarma VV (2006) Biodiversity and ecological observations on filamentous fungi of Nypa fruticans along the Tutong River, Brunei. Ind J Mar Sci 35(4):297–307Google Scholar
  52. Hyde KD, Chalermongse A, Boonthavikoon T (1990) Ecology of intertidal fungi at Ranong mangrove, Thailand. Trans Mycol Soc Japn 31:17–28Google Scholar
  53. Hyde KD, Jones EBG, Leano E, Pointing SB, Poonyth AD, Vrijmoed LLP (1998) Role of marine fungi in marine ecosystems. Biodivers Conserv 7:1147–1161CrossRefGoogle Scholar
  54. Hyde KD, Sarma VV, Jones EBG (2000) Morphology and taxonomy of higher marine fungi. In: Hyde KD, Pointing SB (eds) Marine mycology a practical approach. Fungal Diversity Press, Hong Kong, pp 172–204Google Scholar
  55. Jebaraj CS, Raghukumar C (2009) Anaerobic denitrification in fungi from the coastal marine sediments off Goa, India. Mycol Res 113:100–109CrossRefGoogle Scholar
  56. Jebaraj CS, Raghukumar C, Behnke A, Stoeck T(2009) Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 71:399–412PubMedCrossRefGoogle Scholar
  57. Jebaraj CS, Raghukumar C, Behnke A, Stoeck T (2010) Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiol Ecol 71:399–412PubMedCrossRefGoogle Scholar
  58. Jeewon R, Hyde KD (2007). Detection and diversity of fungi from environmental samples: traditional versus molecular approaches. In: Varma A, Oelmüller R (eds) Advanced techniques in soil microbiology. Soil biology, vol 11. Springer, Berlin/Heidelberg, pp 427.  https://doi.org/10.1007/978-3-540-70865-0_1
  59. Jeewon R, Hyde KD (2016) Establishing species boundaries and new taxa among fungi: recommendations to resolve taxonomic ambiguities. Mycosphere 7(11):1669–1677CrossRefGoogle Scholar
  60. Jeewon R, Liew ECY, Hyde KD (2002) Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters. Mol Phylogenet Evol 25:378–392PubMedCrossRefGoogle Scholar
  61. Jeewon R, Liew ECY, Simpson JA, Hodgkiss IJ, Hyde KD (2003a) Phylogenetic significance of morphological characters in the taxonomy of Pestalotiopsis species. Mol Phylogenet Evol 27:372–383PubMedCrossRefGoogle Scholar
  62. Jeewon R, Cai L, Zhang K, Hyde KD (2003b) Dyrithiopsis lakefuxianensis gen et sp. nov. from Fuxian Lake, Yunnan, China and notes on the taxonomic confusion surrounding Dyrithium. Mycologia 95:911–920PubMedCrossRefGoogle Scholar
  63. Jeewon R, Yeung QSY, Hyde KD (2009) Novel phylogenetic group within Thozetella (Chaetosphaeriaceae): a new taxon based on morphology and DNA sequence analyses. Can J Microbiol 55:680–687PubMedGoogle Scholar
  64. Jeewon R, Ittoo J, Mahadeb D, Jaufeerally-Fakim Y, Kai WH, Liu A-R (2013) DNA based identification and phylogenetic characterisation of endophytic and saprobic fungi from Antidesma madagascariense, a medicinal plant in Mauritius. J Mycol 2013:1.  https://doi.org/10.1155/2013/781914CrossRefGoogle Scholar
  65. Jeewon R, Wanasinghe DN, Rampadaruth S, Puchooa D, Zhou L-G, Liu A-R, Wang H-K (2017) Nomenclatural and identification pitfalls of endophytic mycota based on DNA sequence analyses of ribosomal and protein genes phylogenetic markers: A taxonomic dead end? Mycosphere 8(10):1802–1817CrossRefGoogle Scholar
  66. Jeewon R et al (2018) Hidden mycota of pine needles: Molecular signatures from PCR-DGGE and Ribosomal DNA phylogenetic characterization of novel phylotypes. Sci Rep 8:18053.  https://doi.org/10.1038/s41598-018-36573-zCrossRefPubMedPubMedCentralGoogle Scholar
  67. Jones EBG, Alias SA (1997) Biodiversity of mangrove fungi. In: Hyde KD (ed) Biodiversity of tropical microfungi. Hong Kong University Press, Hong Kong, pp 71–92Google Scholar
  68. Jones EBG, Hyde KD (2002) Succession: where do we go from here? In Hyde KD, Jones EBG (eds) Fungal succession. Fungal Divers 10:241–253Google Scholar
  69. Jones EBG, Tan TK (1987) Observations on manglicoIous fungi from Malaysia. Tran Br Mycol Soc 89:390–392CrossRefGoogle Scholar
  70. Jones EBG, Sakayaroj J, Suetrong S, Somrithipol S, Pang KL (2009) Classification of marine Ascomycota, anamorphic taxa and Basidiomycota. Fungal Divers 35:1–187Google Scholar
  71. Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:200–203PubMedCrossRefGoogle Scholar
  72. Jones EBG, Suetrong S, Sakayaroj J, Bahkali AH, Abdel-Wahab MA, Boekhout T, Pang K-L (2015) Classification of marine Ascomycota, Basidiomycota, Blastocladiomycota and Chytridiomycota. Fungal Diver 73:1–72CrossRefGoogle Scholar
  73. Karunarathna A, Papizadeh M, Senanayake IC, Jeewon R, Phookamsak R, Goonasekara ID, Wanasinghe DN, Wijayawardene NN, Amoozegar MA, Shahzadeh Fazeli SA, Camporesi E, Hyde KD, Weerahewa HLD, Lumyong S, McKenzie EHC (2017) Novel fungal species of Phaeosphaeriaceae with an asexual/sexual morph connection. Mycosphere 8(10):1818–1834CrossRefGoogle Scholar
  74. Kim K, Alker AP, Shuster K, Quirolo C, Harvell CD (2006) Longitudinal study ofaspergillosis in sea fan corals. DisAquat Organ 69:95–99CrossRefGoogle Scholar
  75. Kis-Papo T (2005) Marine fungal communities. In: Dighton J, White JF, Oudemans P (eds) The fungal community: its organisation and role in the ecosystem. Boca Raton, Taylor & Francis, pp 61–92CrossRefGoogle Scholar
  76. Kodsueb R, McKenzie EHC, Lumyong S, Hyde KD, Jeewon R (2007) Molecular phylogeny of Aquaticheirospora broccolii; a new synnematous hyphomycete taxon from Thailand and its teleomorphic affinities to Massarinaceae. Bot J LinnSoc 155:283–296Google Scholar
  77. Kohlmeyer J (1983) Geography of marine fungi. Austr J BotSuppl Ser 10:67–76Google Scholar
  78. Kohlmeyer J (1987) Marine fungi from Aldabra, the Galapagos and other tropical islands. Can J Bot 65:571–582CrossRefGoogle Scholar
  79. Kohlmeyer J, Kohlmeyer E (1979) Marine mycology: The higher fungi. Academic, London/New York/San Francisco, p 690Google Scholar
  80. Kohlmeyer J, Volkmann-Kohlmeyer B (1992) Two Ascomycotina from coral reefs in the Caribbeanand Australia. Cryptogam Bot 2:367–374Google Scholar
  81. Kohlmeyer J, Bebout B, Volkmann-Kohlmeyer B (1995) Decomposition of mangrove wood by marine fungi and teredinids in Belize. Mar Ecol (P.S.Z.N.I.) 16:27–39Google Scholar
  82. Lai X, Cao L, Tan H, Fang S, Huang Y, Zhou S (2007) Fungal communities from methane hydrate bearing deep-sea marine sediments in South China Sea. ISME J 1:756–762PubMedCrossRefGoogle Scholar
  83. Le Calvez T, Burgaud G, Mahé S, Barbier G, Vandenkoornhuyse P (2009) Fungal diversity in deep-seahydrothermal ecosystems. Appl Environ Microbiol 75:6415–6421PubMedPubMedCentralCrossRefGoogle Scholar
  84. Le Campion-Alsumard T, Golubic S, Priess K (1995) Fungi in corals: symbiosis or disease?Interaction between polyps and fungi causes pearl-like skeleton biomineralization. Mar Ecol Progr Ser 117:137–147.  https://doi.org/10.3354/meps117137CrossRefGoogle Scholar
  85. Leong WF, Tan TX, EBG J (1991) Fungal colonization of submerged Bruguiera cylindrica and Rhizophora apiculata wood. Bot Mar 34:69–76CrossRefGoogle Scholar
  86. Li JF, Jeewon R, Phookamsak R, Bhat DJ, Mapook A, Chukeatirote E, Hyde KD, Lumyong S, McKenzie EHC (2018) Marinophialophora garethjonesii gen. et sp. nov.: a new hyphomycete associated with Halocyphina from marine habitats in Thailand. Phytotaxa 345(1):1–12CrossRefGoogle Scholar
  87. Liu AR, Chen SC, Wu SY, Xu T, Guo LD, Jeewon R, Wei JG (2010) Cultural studies coupled with DNA based sequence analyses and its implication on pigmentation as a phylogenetic marker in Pestalotiopsis taxonomy. Mol Phylogenet Evol 57:528–535PubMedCrossRefGoogle Scholar
  88. López-Garcia P, Vereshchaka A, Mozeira D (2007) Eukaryotic diversity associated with carbonatesand fluid-seawater interface in Lost City hydrothermal field. Environ Microbiol 9:546–554PubMedCrossRefGoogle Scholar
  89. Luo ZL, Bhat DJ, Jeewon R, Boonmee S, Bao D-F, Zhao Y-C, Chai H-M, Su H-Y, Su X-J, Hyde KD (2017) Molecular phylogeny and morphological characterization of asexual fungi (Tubeufiaceae) from freshwater habitats in Yunnan, China. Cryptogamie Mycol 38:1–28Google Scholar
  90. Manohar CS, Raghukumar C (2013) Fungal diversity from various marine habitats deduced through culture independent studies. FEMS Microbiol Lett 341:69–78PubMedCrossRefGoogle Scholar
  91. Marano AV, Pires-Zottarelli CLA, de Souza JI, Glockling SL, Leano EM, Gachon CMM,Strittmatter M, Gleason FH (2012) Hyphochytriomycota, Oomycota and Perkinsozoa (SupergroupChromalveolata). In Jones EBG, Pang K-L (eds) Marine fungi andfungal-like organisms. De Gruyter, Berlin/Boston, pp 167–213Google Scholar
  92. Massana R, Pedrós-Alió C (2008) Unveiling new microbial eukaryotes in the surface ocean. Curr Opin Microbiol 11:213–218PubMedCrossRefGoogle Scholar
  93. Morrison-Gardiner S (2002) Dominant fungi from Australian coral reefs. Fungal Divers 9:105–121Google Scholar
  94. Nagahama T, Hamamoto M, Nakase T, Horikoshi K (2003) Rhodotorula benthica sp nov and Rhodotorula calyptogenae sp nov, novel yeast species from animals collected from the deepsea floor, and Rhodotorula lysiniphila sp nov, which is related phylogenetically. Int J Syst Evol Microbiol 53:897–903PubMedCrossRefGoogle Scholar
  95. Nagahama T, Takahashi E, Nagano Y, Abdel-Wahab MA, Miyazaki M (2011) Molecular evidencethat deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments. Environ Microbiol 13:2359–2370PubMedCrossRefGoogle Scholar
  96. Nagano Y, Nagahama T, Hatada Y, Nunoura T, Takami H, Miyazaki J, Takai K, Horikoshi K (2010) Fungal diversity in deep-sea sediments – the presence of novel fungal groups. Fungal Ecol 3:316–325CrossRefGoogle Scholar
  97. Nagano Y, Miura T, Nishia S, Lima AO, Nakayama C, Pellizari VH, Fujikura K (2018) Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau. Deep-Sea Res Pt II 146:59–67CrossRefGoogle Scholar
  98. Newell SY (1976) Mangrove fungi: the succession in the mycoflora of red mangrove (Rhizophora mangle L.) seedlings. In: Jones EBG (ed) Recent advances in aquatic mycology. Wiley, New York, pp 51–91Google Scholar
  99. Newell SY (1996) Established and potential impacts of eukaryotic mycelial decomposers in marine/terrestrial ecotones. J Exp Mar Biol Ecol 200:187–206CrossRefGoogle Scholar
  100. Nikolcheva LG, Bärlocher F (2004) Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream. Mycol Progr 3:41–49.  https://doi.org/10.1007/s11557-006-0075-yCrossRefGoogle Scholar
  101. Orsi W, Biddle JF, Edgcomb V (2013) Deep sequencing of sub-seafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PLoS One 8(2):e56335.  https://doi.org/10.1371/journal.pone.0056335CrossRefPubMedPubMedCentralGoogle Scholar
  102. Pang K-L, Jones EBG (2017) Recent advances in marine mycology. Bot Mar 60:361–362CrossRefGoogle Scholar
  103. Pang KL, Overy DP, Jones EBG, Calado MDL, Burgaud G, Walker AK, Johnson JA, Kerr RG, Cha HJ, Bills GF (2016) ‘Marine fungi’ and ‘marine-derived fungi’ in natural product chemistry research: toward a new consensual definition. Fungal Biol Rev 30:163–175CrossRefGoogle Scholar
  104. Picard KT (2017) Coastal marine habitats harbor novel early-diverging fungal diversity. Fungal Ecol 25:1–13CrossRefGoogle Scholar
  105. Pinnoi A, Jeewon R, Sakayaroj J, Hyde KD, Jones EBG (2007) Berkleasmium crunisia sp. nov. and its teleomorphic affinities to the Pleosporales based on 18S, 28S and ITS-5.8S rDNA sequence analyses. Mycologia 99:378–384PubMedCrossRefGoogle Scholar
  106. Polishook JD, Bills GF, Lodge DJ (1996) Microfungi from decaying leaves of two rain forest trees in Puerto Rico. J Ind Microbiol Biotechnol 17:284–294CrossRefGoogle Scholar
  107. Poonyth AD, Hyde KD, Peerally A (1999) Intertidal fungi in Mauritian mangroves. Bot Mar 42:243–252CrossRefGoogle Scholar
  108. Porter D (1986) Mycoses of marine organisms: an overview of pathogenic fungi. In: Moss ST (ed) The biology of marine fungi. Cambridge University Press, Cambridge, pp 141–153Google Scholar
  109. Promputtha I, Jeewon R, Lumyong S, McKenzie EHC, Hyde KD (2005) Ribosomal DNA fingerprinting in the identification of non-sporulating endophytes from Magnolia liliifera (Magnoliaceae). Fungal Divers 20:167–186Google Scholar
  110. Promputtha I, Lumyong S, Vijaykrishna D, McKenzie EHC, Hyde KD, Jeewon R (2007) A phylogenetic evaluation of whether endophytes become saprotrophs at host senescence. Microbial Ecol 53:579–590CrossRefGoogle Scholar
  111. Raghukumar C, Ravindran J (2012) Fungi and their role in corals and coral reef ecosystems. In: Raghukumar C (ed) Biology of marine fungi. Springer, Berlin, pp 89–114CrossRefGoogle Scholar
  112. Raghukumar S, Sharma S, Raghukumar C, Sathe-Pathak V (1994) Thraustochytrid and fungal component of marine detritus. IV. Laboratory studies on decomposition of leaves of themangrove Rhizophora apiculata Blume. J Exp Mar Biol Ecol 183:113–131CrossRefGoogle Scholar
  113. Raghukumar S, Sathe-Pathak V, Sharma S, Raghukumar C (1995) Thraustochytrid and fungalcomponent of marine detritus. III. Field studies on decomposition of leaves of the mangrove Rhizophora apiculata Blume. Aquat Microb Ecol 9:117–125CrossRefGoogle Scholar
  114. Raghukumar C, Raghukumar S, Sheelu G, Gupta SM, Nath BN, Rao BR (2004) Buried in time: culturable fungi in a deep-sea sediment core from the Chagos Trench. Indian Ocean. Deep-Sea Res Pt I 51:1759–1768CrossRefGoogle Scholar
  115. Rama T, Norden J, Davey ML, Mathiassen GH (2014) Fungiahoy! Diversity on marine wooden substrata in the high North. Fungal Ecol 8:46–58CrossRefGoogle Scholar
  116. Ramaiah N (2006) A review on fungal diseases of algae, marine fishes, shrimps and corals. Ind J Mar Sci 35:380–387Google Scholar
  117. Rampadaruth S,Bandhoa K, Puchooa D, Jeewon R, Bal S (2018) Metatranscriptomics analysis of mangroves habitats around Mauritius. World J Microbiol Biotechnol 34:59.  https://doi.org/10.1007/s11274-018-2442-7
  118. Ravindran J, Raghukumar C, Raghukumar S (2001) Fungi in Porites lutea: association withhealthy and diseased corals. Dis Aquat Org 47:219–228PubMedCrossRefGoogle Scholar
  119. Rédou V, Ciobanu MC, Pachiadaki MG, Edgcomb V, Alain K, Barbier G, Burgaud G (2014) In-depth analyses of deep subsurface sediments using 454 pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths. FEMS Microbiol 90:908–921CrossRefGoogle Scholar
  120. Rédou V, Navarri M, Meslet-Cladiere L, Barbier G, Bergaud G (2015) Species richness and adaptation of marine fungi from deep-sub seafloor sediments. Appl Environ Microbiol 81:3571–3583PubMedPubMedCentralCrossRefGoogle Scholar
  121. Reich M, Labes A (2017) How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry. Mar Genomics 36:57–75PubMedCrossRefGoogle Scholar
  122. Richards TA, Jones MDM, Leonard G, Bass D (2012) Marine fungi: their ecology and molecular diversity. Annu Rev Mar Sci 4:495–522CrossRefGoogle Scholar
  123. Richards TA, Leonard G, Mahé F, del Campo J, Romac S, Jones MDM, Maguire F, Dunthorn M, De Vargas C, Massana R, Chambouvet A (2015) Molecular diversity and distribution of marine fungi across 130 European environmental samples. Proc R Soc Lond [Biol] 282:20152243.  https://doi.org/10.1098/rspb.2015.2243CrossRefGoogle Scholar
  124. Sarma VV, Hyde KD (2001) A review on frequently occurring fungi in mangroves. Fungal Divers 8:1–34Google Scholar
  125. Sarma VV, Vittal BPR (1998–1999) Ecological studies on mangrove fungi from east coast of India. Observations on seasonal occurrence. Kavaka 26&27:105–120Google Scholar
  126. Sarma VV, Vittal BPR (2000) Biodiversity of mangrove fungi on different substrata of Rhizophora apiculata and Avicennia spp. from Godavari and Krishna deltas, east coast of India. In Hyde KD, Ho WH, Pointing SB (eds) Aquatic mycology across the millennium. Fungal Divers 5:23–41Google Scholar
  127. Sarma VV, Vittal BPR (2001) Biodiversity of fungi on selected mangrove plants in the Godavari and Krishna deltas, east coast of India. Fungal Divers 6:113–129Google Scholar
  128. Sarma VV, Vittal BPR (2002) A preliminary study on vertical distribution of manglicolous fungi on prop roots of Rhizophora apiculata Blume at Krishna delta, east coast of India. Kavaka 30:21–29Google Scholar
  129. Sarma VV, Hyde KD, Vittal BPR (2001) Frequency of occurrence of mangrove fungi from the East coast of India. Hydrobiologia 455:41–53CrossRefGoogle Scholar
  130. Schmidt JP, Shearer CA (2003) A checklist of mangrove–associated fungi, their geography and known host plants. Mycotaxon 80:423–477Google Scholar
  131. Schmidt JP, Shearer CA (2004) Geographical and host distribution of lignicolous mangrove microfungi. Bot Mar 47:496–500Google Scholar
  132. Senanayake IC, Crous PW, Groenewald JZ, SSN M, Jeewon R, AJL P, Bhat JD, Perera RH, Li QR, Li WJ, Tangthirasunun N, Norphanphoun C, Karunarathna SC, Camporesi E, Manawasighe I, Al-Sadi AM, Hyde KD (2017) Families of Diaporthales based on morphological and phylogenetic evidence. Stud Mycol 86:217–296PubMedPubMedCentralCrossRefGoogle Scholar
  133. Senanayake IC, Jeewon R, Chomnunti P, Wanasinghe D, Norphanphoun C, Karunarathna A, Pem D, Perera RH, Camporesi E, McKenzie EHC, Hyde KD, Karunarathna SD (2018a) Taxonomic circumscription of Diaporthales based on multigene phylogeny and morphology. Fungal Divers 93:241.  https://doi.org/10.1007/s13225-018-0410-zCrossRefGoogle Scholar
  134. Senanayake IC, Jeewon R, Camporesi E, Hyde KD, Zeng Y-J, Tian S-L, Xie N (2018b) Sulcispora supratumida sp. nov. (Phaeosphaeriaceae, Pleosporales) on Anthoxanthum odoratum from Italy. Myco Keys 38:35–46CrossRefGoogle Scholar
  135. Shields JD, Overstreet RM (2007) Diseases, parasites, and other symbionts. Chapter 8. In Kennedy, VS, Cronin LE (eds) The blue crab, Callinectes sapidus. Maryland Sea Grant, College Park, pp 299–417Google Scholar
  136. Simonato F, Campanaro S, Lauro FM, Vezzi A, D’Angelo M, Vitulo N, Valle G, Barlett DH (2006) Piezophilic adaptation: a genomic point of view. J Biotechnol 126:11–25PubMedCrossRefGoogle Scholar
  137. Singh P, Raghukumar C, Verma P, Shouche Y (2010) Phylogenetic diversity of culturablefungi from the deep-sea sediments of the Central Indian Basin and theirgrowth characteristics. Fungal Divers 40:89–102CrossRefGoogle Scholar
  138. Singh P, Raghukumar C, Verma P, Shouche Y (2011) Fungal community analysis inthe deep-sea sediments of the Central Indian Basin by culture-independent approach. Microb Ecol 61:507–517PubMedCrossRefGoogle Scholar
  139. Singh P, Raghukumar C, Meena RM, Verma P, Shouche Y (2012) Fungal diversityin deep-sea sediments revealed by culture-dependent and culture-independent approaches. Fungal Ecol 5:543–553CrossRefGoogle Scholar
  140. Sridhar KR, Maria GL (2006) Fungal diversity on mangrove woody litter Rhizophora mucronata (Rhizophoraceae). Ind J Mar Sci 35:318–325Google Scholar
  141. Stief P, Fuchs-Ocklenburg S, Kamp A, Manohar CS, Houbraken J, Boekhout T, de Beer D, Stoeck T (2014) Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea. BMC Microbiol 14:35PubMedPubMedCentralCrossRefGoogle Scholar
  142. Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS (2006) A multiple PCR-primer approachto access the microeukaryotic diversity in environmental samples. Protist 157:31–43PubMedCrossRefGoogle Scholar
  143. Stoeck T, Bass D, Nebel M, Christen R, Jones MDM, Briner H-W, Richards TA (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Mol Ecol 19(1):21–31.  https://doi.org/10.1111/j.1365-294X.2009.04480CrossRefPubMedGoogle Scholar
  144. Suetrong S, Schoch CL, Spatafora JW, Kohlmeyer J, Volkmann-Kohlmeyer B, Sakayaroj J, Phongpaichit S, Tanaka K, Hirayama K, Jones EBG (2009) Molecular systematics of the marine Dothideomycetes. Stud Mycol 64:155–173PubMedPubMedCentralCrossRefGoogle Scholar
  145. Swe A, Jeewon R, Hyde KD (2008a) Nematode-trapping fungi from mangrove habitats. Cryptogam Mycol 29:333–354Google Scholar
  146. Swe A, Jeewon R, Pointing SB, Hyde KD (2008b) Taxonomy and phylogeny of Arthrobotrys mangrovispora, a new marine nematode-trapping fungal species. Bot Mar 51:331–338Google Scholar
  147. Swe A, Jeewon R, Pointing SB, Hyde KD (2009) Diversity and abundance of nematode-trapping fungi from decaying litter in terrestrial, freshwater and mangrove habitats. Biodivers Conserv 18:1695–1714CrossRefGoogle Scholar
  148. Takishita K, Miyake H, Kawato M, Maruyama T (2005) Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine caldera floor based on the small-subunit rDNA phylogeny. Extremophiles 9:185–196PubMedCrossRefGoogle Scholar
  149. Takishita K, Tsuchiya M, Reimer JD, Maruyama T (2006) Molecular evidence demonstrating the basidiomycetousfungus Cryptococcus curvatus is the dominant microbial eukaryote in sediment at the Kuroshima Knollmethane seep. Extremophiles 10:165–169PubMedCrossRefGoogle Scholar
  150. Takishita K, Yubuki N, Kakizoe N, Inagaki Y, Maruyama T (2007) Diversity of microbial eukaryotes in sediment at a deep-sea methane cold seep: surveys of ribosomal DNA libraries from raw sediment samples and two enrichment cultures. Extremophiles 11:563–576PubMedCrossRefGoogle Scholar
  151. Tsui CKM, Berbee M, Jeewon R, Hyde KD (2006) Molecular phylogeny of Dictyosporium and allied genera inferred from ribosomal DNA. Fungal Divers 21:157–166Google Scholar
  152. Vega Thurber R, Willner-Hall D, Rodriguez-Mueller B, Desnues C, Edwards RA, Angly F, Dinsdale E, Kelly L, Rohwer F (2009) Metagenomic analysis of stressed coralholobionts. Environ Microbiol 8:2148–2163CrossRefGoogle Scholar
  153. Vijaykrishna D, Mostert L, JeewonR HKD, Crous PW (2004) Pleurostomosphora, an anamorph of Pleurostoma (Calosphaeriales), a new anamorph genus morphologically similar to Phialophora. Stud Mycol 50:387–398Google Scholar
  154. Vinit K, Cheewangkoon R, Thambugala KM, Jones EBG, Jeewon R, Doilom M, Brahmanage RS, Hyde KD (2018a) Rhytidhysteron mangrovei, (Hysteriaceae) a new species from mangroves in Phetchaburi Province, Thailand. Phytotaxa. (in press)Google Scholar
  155. Vinit K, Doilom M, Wanasinghe DN, Bhat DJ, Brahmanage RS, Jeewon R, Xiao Y, Hyde KD (2018b) Phylogenetic placement of Akanthomyces muscarius, a new endophyte record from Nypa fruticans in Thailand. Curr Res Environ Appl Mycol J 8(3):404–417CrossRefGoogle Scholar
  156. Volkmann-Kohlmeyer B, Kohlmeyer J (1993) Biogeographic observations on Pacificmarine fungi. Mycologia 85:337–346CrossRefGoogle Scholar
  157. Wanasinghe DN, Phukhamsakda C, Hyde KD, Jeewon R, Lee HB, Jones EBG, Tibpromma S, Tennakoon DS, Dissanayake AJ, Jayasiri SC, Gafforov Y, Camporesi E, Bulgakov TS, Ekanayake AH, Perera RH, Samarakoon MC, Goonasekara ID, Mapook A, Li WJ, Senanayake IC, Li JF, Norphanphoun C, Doilom M, Bahkali AH, Xu JC, Mortimer PE, Tibell L, Savic ST, Karunarathna SC (2018) Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae. Fungal Divers 89:1–236CrossRefGoogle Scholar
  158. Webster J, Weber WS (2007) Introduction to fungi. Cambridge University Press, Cambridge, p 841CrossRefGoogle Scholar
  159. Wegley L, Edwards R, Rodriguez-Brito B, Liu H, Rohwer F (2007) Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environ Microbiol 9:2707–2719PubMedCrossRefGoogle Scholar
  160. Xu D, Jiao N, Ren R and Warren A (2017). Distribution and diversity of microbial eukaryotes in bathypelagic waters of the South China Sea. J. Eukaryot. Microbiol. 64: 370–382.  https://doi.org/10.1111/jeu.12372PubMedCrossRefGoogle Scholar
  161. Yarden O (2014) Fungal association with sessile marine invertebrates. Front Microbiol 5:228.  https://doi.org/10.3389/fmicb.2014.00228CrossRefPubMedPubMedCentralGoogle Scholar
  162. Yarden O, Ainsworth TD, Roff G, Leggat W, Fine M, Hoegh-Guldberg O (2007) Increased prevalence ofubiquitous ascomycetes in an acropoid coral (Acropora formosa) exhibiting symptoms of brown band syndromeand skeletal eroding band disease. Appl Environ Microbiol 73:2755–2757PubMedPubMedCentralCrossRefGoogle Scholar
  163. Zhang Y, Jeewon R, Fournier J, Hyde KD (2008) Multi-gene phylogeny and morphotaxonomy of Amniculicola lignicola: novel freshwater fungus from France and its relationships to the Pleosporales. Fungal Biol 112:1186–1194Google Scholar
  164. Zhang XY, Tang GL, Xu XY, Nong XH, Qi SH (2014) Insights into deep-seasediment fungal communities from the East Indian Ocean using targetedenvironmental sequencing combined with traditional cultivation. PLoS One 9(10):e109118.  https://doi.org/10.1371/journal.pone.0109118CrossRefPubMedPubMedCentralGoogle Scholar
  165. Zhao RL, JeewonR GE, Desjardin D, Soytong K, Hyde KD (2007) Ribosomal DNA phylogenies of Cyathus: Is current morphotaxonomic classification robust? Mycologia 99:385–395PubMedCrossRefGoogle Scholar
  166. Zhuo R, Ma L, Fan F, Gong Y, Wan X, Jiang M, Zhang X, Yang Y (2011) Decolorization of different dyes by a newlyisolated white-rot fungi strain Ganoderma sp.En3 and cloning and functional analysis of its laccase gene. J Hazard Mater 192:855–873PubMedCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • V. Venkateswara Sarma
    • 1
  • Rajesh Jeewon
    • 2
  1. 1.Department of BiotechnologyPondicherry UniversityKalapetIndia
  2. 2.Department of Health Sciences, Faculty of ScienceUniversity of MauritiusReduitMauritius

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