Marine fungal communities in water and surface sediment of a sea cucumber farming system: Habitat-differentiated distribution and nutrients driving succession

Fungal Ecology

Volumn 14, Issue , 2015, Pages 87-98

  Guo, Xiaohong ^a,b   Zhang, Qianqian ^a   Zhang, Xiaoli ^a   Zhang, Jiasong ^c   Gong, Jun ^a  

^a YANTAI INSTITUTE OF COASTAL ZONE RESEARCH   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SOUTH CHINA SEA FISHERIES RESEARCH INSTITUTE   (China)

Author keywords

18S rDNA; Mariculture; Microbial diversity; Nutrient; Zoosporic fungi

Indexed keywords

ASCOMYCOTA; BASIDIOMYCOTA; CHYTRIDIOMYCOTA; FUNGI; HOLOTHUROIDEA;

EID: 84923845548     PISSN: 17545048     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.funeco.2014.12.001     Document Type: Article

References (58)

1. Amend A.S., Barshis D.J., Oliver T.A. Coral-associated marine fungi form novel lineages and heterogeneous assemblages. The ISME Journal 2012, 6:1291-1301.
2. Anderson I.C., Campbell C.D., Prosser J.I. Potential bias of fungal 18S rDNA and internal transcribed spacer polymerase chain reaction primers for estimating fungal biodiversity in soil. Environmental Microbiology 2003, 5:36-47.
3. Arfi Y., Marchand C., Wartel M., Record E. Fungal diversity in anoxic-sulfidic sediments in a mangrove soil. Fungal Ecology 2012, 5:282-285.
4. Bent S.J., Forney L.J. The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity. The ISME Journal 2008, 2:689-695.
5. Borneman J., Hartin R.J. PCR primers that amplify fungal rRNA genes from environmental samples. Applied and Environmental Microbiology 2000, 66:4356-4360.
6. Clarke K.R., Gorley R.N. PRIMER 6 User Manual/Tutorial 2006, PRIMER-E Ltd, Plymouth.
7. Conley D.J., Malone T.C. Annual cycle of dissolved silicate in Chesapeake Bay: implications for the production and fate of phytoplankton biomass. Marine Ecology Progress Series 1992, 81:121-128.
8. Dong J., Shi F., Li H., Zhang X., Hu X., Gong J. SSU rDNA sequence diversity and seasonally differentiated distribution of nanoplanktonic ciliates in neritic Bohai and Yellow Seas as revealed by T-RFLP. PLoS One 2014, 9:e102640.
9. Egge J.K., Aksnes D.L. Silicate as regulating nutrient in phytoplankton competition. Marine Ecology Progress Series 1992, 83:281-289.
10. Felsenstein J. PHYLIP-phylogeny Inference package (Version 3.2). Cladistics 1989, 17:164-166.
11. Gao Z., Li B., Zheng C., Wang G. Molecular detection of fungal communities in the Hawaiian marine sponges Suberites zeteki and Mycale armata. Applied and Environmental Microbiology 2008, 74:6091-6101.
12. Gao Z., Johnson Z.I., Wang G. Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters. The ISME Journal 2010, 4:111-120.
13. Gleason F.H., Crawford J.W., Neuhauser S., Henderson L.E., Lilje O. Resource seeking strategies of zoosporic true fungi in heterogeneous soil habitats at the microscale level. Soil Biology and Biochemistry 2012, 45:79-88.
14. Gleason F.H., Carney L.T., Lilje O., Glockling S.L. Ecological potentials of species of Rozella (Cryptomycota). Fungal Ecology 2012, 5:651-656.
15. Gleason F.H., Kagami M., Lefevre E., Sime-Ngando T. The ecology of chytrids in aquatic ecosystems: roles in food web dynamics. Fungal Biology Reviews 2008, 22:17-25.
16. Gleason F.H., Küpper F.C., Amon J.P., Picard K., Gachon S.M.M., Marano A.V., Sime-Ngando T., Lilje O. Zoosporic true fungi in marine ecosystems: a review. Marine and Freshwater Research 2011, 62:383-393.
17. Gleason F.H., Chambouvet A., Sullivan B.K., Lilje O., Rowley J.J.L. Multiple zoosporic parasites pose a significant threat to amphibian populations. Fungal Ecology 2014, 11:181-192. 10.1016/j.funeco.2014.04.001.
18. Guindon S., Delsuc F., Dufayard J.F., Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods in Molecular Biology 2009, 537:113-137.
19. Guo X., Gong J. Differential effects of abiotic factors and host plant traits on diversity and community composition of root-colonizing arbuscular mycorrhizal fungi in a salt-stressed ecosystem. Mycorrhiza 2014, 24:79-94.
20. Huber T., Faulkner G., Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 2004, 20:2317-2319.
21. Humber R.A. Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi. Mycotaxon 2012, 120:477-492.
22. Hyde K.D. Fungi in Marine Environments, Fungal Diversity Research Series no. 7 2002, (Hong Kong).
23. Jebaraj C.S., Raghukumar C., Behnke A., Stoeck T. Fungal diversity in oxygen-depleted regions of the Arabian Sea revealed by targeted environmental sequencing combined with cultivation. FEMS Microbiology Ecology 2010, 71:399-412.
24. Jebaraj C.S., Raghukumar C. Nitrate reduction by fungi in marine oxygen-depleted laboratory microcosms. Botanica Marina 2010, 53:469-474.
25. Jobard M., Rasconi S., Sime-Ngando T. Diversity and functions of microscopic fungi: a missing component in pelagic food webs. Aquatic Sciences 2010, 72:255-268.
26. Jones E.B.G., Sakayaroj J., Suetrong S., Somrithipol S., Pang K.L. Classification of marine Ascomycota, anamorphic taxa and Basidiomycota. Fungal Diversity 2009, 35:1-187.
27. Jones M.D.M., Forn I., Gadelha C., Egan M.J., Bass D., Massana R., Richards T.A. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 2011, 474:200-203.
28. Jones E.B.G., Pang K.L. Marine Fungi and Fungal-like Organisms 2012, Walter de Gruyter.
29. Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 2013, 30:772-780.
30. Küpper F.C., Müller D.G., Peters A.F., Kloareg B., Potin P. Oligoalginate recognition and oxidative burst play a key role in natural and induced resistance of sporophytes of Laminariales. Journal of Chemical Ecology 2002, 28:2057-2081.
31. Letcher P.M., Lopez S., Schmieder R., Lee P.A., Behnke C., Powell M.J., McBride R.C. Characterization of Amoeboaphelidium protococcarum, an algal parasite new to the Cryptomycota isolated from an outdoor algal pond used for the production of biofuel. PloS One 2013, 8:e56232.
32. Manohar C.S., Raghukumar C. Fungal diversity from various marine habitats deduced through culture-independent studies. FEMS Microbiology Letters 2013, 341:69-78.
33. Mohamed D.J., Martiny J.B.H. Patterns of fungal diversity and composition along a salinity gradient. The ISME Journal 2011, 5:379-388.
34. Mouton M., Postma F., Wilsenach J., Botha A. Diversity and characterization of culturable fungi from marine sediment collected from St. Helena Bay, South Africa. Microbial Ecology 2012, 64:311-319.
35. Moriarty D.J.W. The role of microorganisms in aquaculture ponds. Aquaculture 1997, 151:333-349.
36. Müller D.G., Küpper F.C., Küpper H. Infection experiments reveal broad host ranges of Eurychasma dicksonii (Oomycota) and Chytridium polysiphoniae (Chytridiomycota), two eukaryotic parasites in marine brown algae (Phaeophyceae). Phycological Research 1999, 47:217-223.
37. Nagahama T., Takahashi E., Nagano Y., Abdel-Wahab M.A., Miyazaki M. Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments. Environmental Microbiology 2011, 13:2359-2370.
38. Nemergut D.R., Townsend A.R., Sattin S.R., Freeman K.R., Fierer N., Neff J.C., William D., Bowman W.D., Christopher W., Schadt C.W., Michael N., Weintraub M.N., Schmidt S.K. The effects of chronic nitrogen fertilization on alpine tundra soil microbial communities: implications for carbon and nitrogen cycling. Environmental Microbiology 2008, 10:3093-3105.
39. Osono T., Takeda H. Fungal decomposition of Abies needle and Betula leaf litter. Mycologia 2006, 98:172-179.
40. Pang K.L., Mitchell J.I. Molecular approaches for assessing fungal diversity in marine substrata. Botanica Marina 2005, 48:332-347.
41. Pang K.L., Cheng J.S., Jones E.B.G. Marine Mangrove Fungi of Taiwan 2010, 131. National Taiwan Ocean University, Chilung.
42. Pedrós-Alió C. Marine microbial diversity: can it be determined?. Trends in Microbiology 2006, 14:257-263.
43. Pivkin M.V. Filamentous fungi associated with holothurians from the Sea of Japan, off the Primorye coast of Russia. The Biological Bulletin 2000, 198:101-109.
44. Posada D., Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
45. Raghukumar C. Marine fungal biotechnology: an ecological perspective. Fungal Diversity 2008, 31:19-35.
46. Raveendran K., Manimohan P. Marine Fungi of Kerala: A Preliminary Floristic and Ecological Study 2007, Malabar Natural History Society, Kerala.
47. Richards T.A., Jones M.D., Leonard G., Bass D. Marine fungi: their ecology and molecular diversity. Annual Review of Marine Science 2012, 4:495-522.
48. Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Applied and Environmental Microbiology 2005, 71:1501-1506.
49. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 2009, 75:7537-7541.
50. Smit E., Leeflang P., Glandorf B., Van Elsas J.D., Wernars K. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Applied and Environmental Microbiology 1999, 65:2614-2621.
51. Tamura K., Dudley J., Nei M., Kumar S. MEGA 4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 2007, 24:1596-1599.
52. ter Braak C.J.F., Smilauer P. CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Ordination, Version 4.5 2002, Microcomputer Power, Ithaca, New York, USA.
53. van der Wal A., Geydan T.D., Kuyper T.W., de Boer W. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes. FEMS Microbiology Reviews 2013, 37:477-494.
54. Velez P., González M.C., Rosique-Gil E., Cifuentes J., Reyes-Montes M.R., Capello-García S., Hanlin R.T. Community structure and diversity of marine ascomycetes from coastal beaches of the southern Gulf of Mexico. Fungal Ecology 2013, 6:513-521.
55. Wang G., Johnson Z.I. Impact of parasitic fungi on the diversity and functional ecology of marine phytoplankton. Marine Phytoplankton 2009, 211-228. Nova Science Publishers Inc., New York. W.T. Kersey, S.P. Munger (Eds.).
56. Wetz M.S., Wheeler P.A. Release of dissolved organic matter by coastal diatoms. Limnology and Oceanography 2007, 52:798-807.
57. Worrall J.J., Anagnost S.E., Zabel R.D. Comparison of wood decay among diverse lignicolous fungi. Mycologia 1997, 89:199-219.
58. Zuccaro A., Summerbell R.C., Gams W., Schroers H.F., Mitchell J.I. A new Acremonium species associated with Fucus spp., and its affinity with a phylogenetically distinct marine Emericellopsis clade. Studies in Mycology 2004, 50:283-297.