Biochemical and Molecular Methods for the Study of Marine Fungi

Fell, Jack W.; Newell, Steven Y.

doi:10.1007/978-94-011-4928-0_12

Cited by 23 publications

(21 citation statements)

References 97 publications

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“…Several lines of evidence suggest the existence of 'marine fungal phylotypes' (Gao et al, 2008;Wang et al, 2008a;Li and Wang, 2009), but marine fungi are still considered Functional ecology of marine mycoplankton Z Gao et al as an ecologically, but not taxonomically, defined group (Kohlmeyer and Volkmann-Kohlmeyer, 2003). Marine fungi primarily include the Ascomycetes, the Basidiomycetes, and the Chytridiomycetes (Kohlmeyer and Volkmann-Kohlmeyer, 2003;Fell and Newell, 1998;Pang and Mitchell, 2005). In addition, the Oomycetes and Labyrinthulomycetes, formerly known as pseudofungi or fungal-like organisms were originally classified as fungi and have now been reclassified under the new Kingdom of Straminipila (Raghukumar, 2004;Wang and Johnson, 2009).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, the Oomycetes and Labyrinthulomycetes, formerly known as pseudofungi or fungal-like organisms were originally classified as fungi and have now been reclassified under the new Kingdom of Straminipila (Raghukumar, 2004;Wang and Johnson, 2009). As they are still commonly studied by marine mycologists and mycoplankton ecologists (Fell and Newell, 1998;Raghukumar, 2004), marine mycoplankton can be broadly defined to include marine filamentous fungi, yeasts and fungal-like protists in water column (Wang and Johnson, 2009). Results of this study revealed two phyla of marine fungi in the Hawaiian coastal water, with basidiomycetes as the dominant phylotypes (Table 1 and Figure 4).…”

Section: Discussionmentioning

confidence: 99%

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Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

2009

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Microbial community diversity and composition have critical biogeochemical roles in the functioning of marine ecosystems. Large populations of planktonic fungi exist in coastal ocean waters, yet their diversity and role in carbon and nutrient cycling remain largely unknown. Lack of information on critical functional microbial groups limits our understanding of their ecological roles in coastal oceans and hence our understanding of its functioning in the ocean's carbon and nutrient cycles. To address this gap, this study applied the molecular approach denaturing gradient gel electrophoresis (DGGE) coupled with clone library construction to investigate mycoplankton communities in Hawaiian coastal waters. Mycoplankton communities displayed distinct lateral and vertical variations in diversity and composition. Compared with the open ocean, surface (o100 m) near-shore waters had the greatest diversity and species richness of mycoplankton, whereas no differences were found among stations at depths below 150 m. Vertical diversity profiles in the coastal waters suggested that diversity and species richness were positively correlated to phytoplankton biomass in the coastal waters, but not in offshore waters. A total of 46 species were identified and belonging to two phyla Basidiomycota and Ascomycota, with the basidiomycetes as the dominant group (n ¼ 42). The majority (n ¼ 27) of the basidiomycetes are novel phylotypes showing less than 98% identity in the 18S rRNA gene with any sequence in GenBank. This study provides insight into mycoplankton ecology and is the first molecular analysis of planktonic fungi in the oceans. The ISME Journal (

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

2009

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“…Bärlocher 1992), and in the marine environment (e.g. Fell & Newell 1998). Therefore, they presumably also colonize micro-and macroaggregates in these ecosystems rich in macrophyte-derived organic matter.…”

Section: Fungimentioning

confidence: 99%

Microbial ecology of organic aggregates in aquatic ecosystems

Simon¹,

Grossart²,

Schweitzer³

et al. 2002

Aquat. Microb. Ecol.

926

858

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Macroscopic organic aggregates, which are > 500 µm and known as marine and lake snow, are important components in the turnover, decomposition and sinking flux of both organic and inorganic matter and elements in aquatic ecosystems. They are composed of various organic and inorganic materials depending largely on the given system and environmental conditions. The systems include the pelagic limnetic, the neritic and oceanic marine region, as well as shallow turbid environments, e.g. rivers, the littoral zone of lakes, estuaries and tidally affected coastal areas with intense turbulence and a high load of suspended matter. Aggregate abundance and size vary greatly among these systems. Macroaggregates are heavily colonized by bacteria and other heterotrophic microbes and greatly enriched in organic and inorganic nutrients as compared to the surrounding water. During the last 15 yr, many studies have been carried out to examine various aspects of the formation of aggregates, their microbial colonization and decomposition, nutrient recycling and their significance for the sinking flux. They have been identified as hot-spots of the microbial decomposition of organic matter. Further, microaggregates, which are < 5 to 500 µm in size and stained by different dyes, such as transparent exopolymer particles (TEP) and Coomassie blue-stained particles, have been discovered and shown also to be important in the formation and decomposition of macroaggregates. In this review we give an overview of the present state of the microbial ecology of macro-and microaggregates, including the mentioned points but highlighting in particular the recent findings on the bacterial colonization of aggregates using molecular tools, their microbial decomposition and mineralization, and the significance of protozoans and metazoans for the colonization and decomposition of macroaggregates. Today it is evident that not only the aggregates but also their surroundings are sites and hot-spots of microbial processes, with the plume of solutes leaking out of the aggregates and greatly extending the volume of the intense decomposition processes. This microheterogeneity has important implications for the spatial and temporal dynamics of the organic-matter field in aquatic ecosystems and for our understanding of how heterotrophic organisms are involved in the decomposition of organic matter. The significance of aggregate-associated microbial processes as key processes and also for the overall decomposition and flux of organic mattervaries greatly among the various systems, and is greatly affected by the total amount of suspended particulate matter. A conclusion from the presented studies and results is that the significance of bacteria for the formation and decomposition of aggregates appears to be much greater than previously estimated. For a better understanding of the functioning of aquatic ecosystems it is of great importance to include aggregate-associated processes in ecosystem modeling approaches.

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“…Mar Ecol Prog Ser 399: [53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] 2010 require these fatty acids for their growth and reproduction but possess a limited or no ability to synthesize them (Kanazawa et al 1979a,b, Lubzens et al 1985, Nichols & Nichols 2008, Labyrinthulomycetes present in the water column might play an important role in the marine food web by serving as sources of these fatty acids for the zooplankton (Fell & Newell 1998, Kimura et al 1999, Raghukumar 2002.…”

Section: Resale or Republication Not Permitted Without Written Consenmentioning

confidence: 99%

“…11 & 12). The importance of Labyrinthulomycetes (thraustochytrids) in the marine food web, as sources of the omega-3 polyunsaturated fatty acid (PUFA) 'docosahexaenoic acid' (DHA) to zooplankton, has been stressed by many (Fell & Newell 1998, Kimura et al 1999, Raghukumar 2002. Although there have been several reports of zooplankton feeding on Labyrinthulomycetes in the laboratory as well as in aquaculture (Brown 2002, Alonzo et al 2005, Bergé & Barnathan 2005, there are few reports of actual feeding of zooplankton on these protists in nature.…”

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confidence: 99%

Association of the stramenopilan protists, the aplanochytrids, with zooplankton of the equatorial Indian Ocean

Damare¹,

Raghukumar²

2010

Mar. Ecol. Prog. Ser.

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Thraustochytrids and aplanochytrids, belonging to the Labyrinthulomycetes of the Kingdom Stramenopila, have been frequently reported to occur as parasites or symbionts in a number of coastal invertebrates. Given the fact that these protists are widespread in coastal and oceanic waters, it is possible that they are also associated with pelagic zooplankton. This study examines their occurrence in zooplankton from equatorial waters of the Indian Ocean. A total of 171 of 2100 individual specimens of zooplankton yielded Labyrinthulomycetes in culture, the colony morphology and/or life cycles of which corresponded to aplanochytrids. Small-subunit ribosomal DNA (SSU rDNA) sequence analysis of 8 of the isolates placed them in a distinct clade among aplanochytrids, but closest to Aplanochytrium yorkensis or A. kerguelensis. The 8 isolates were further segregated into 2 clusters, corresponding to isolates obtained from 2 different seasons. Biotinylated probes for 2 isolates of A. kerguelensis from the 2 different seasons were developed based on internal transcribed spacer (ITS) sequences. In situ hybridization (ISH) of zooplankton using the probes with streptavidin-alkaline phosphatase showed that aplanochytrid cells fed to copepods were grazed and could subsequently be detected in the animals. ISH on natural samples of zooplankton yielded a positive but diffuse reaction in copepods, while cells resembling aplanochytrids were detected within chaetognaths. ISH using streptavidin-peroxidase conjugate lent further support for their presence within chaetognaths. This study suggests the predominant occurrence of A. kerguelensis in association with mesozooplankton of the equatorial Indian Ocean, particularly with chaetognaths. Further studies are suggested to determine whether genetically distinct populations of A. kerguelensis are associated with chaetognaths in oceanic waters and if such an association is parasitic, mutualistic or commensalistic.KEY WORDS: Stramenopila · Labyrinthulomycetes · Aplanochytrids · Zooplankton · Internal transcribed spacer · In situ hybridization · Biotinylated probes Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 399: [53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68] 2010 require these fatty acids for their growth and reproduction but possess a limited or no ability to synthesize them (Kanazawa et al. 1979a,b, Lubzens et al. 1985, Nichols & Nichols 2008, Labyrinthulomycetes present in the water column might play an important role in the marine food web by serving as sources of these fatty acids for the zooplankton (Fell & Newell 1998, Kimura et al. 1999, Raghukumar 2002.Thraustochytrids and aplanochytrids are known to be associated with invertebrates in a variety of ways. observed thraustochytrids in the faecal pellets of salps. They were found to be endolithic in mollusk shell fragments, especially mussel shells and clam shells (Porter & Lingle 1992), and were isolated from oyster tissue (Perkins 1973) and surface mucus...

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Biochemical and Molecular Methods for the Study of Marine Fungi

Cited by 23 publications

References 97 publications

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

Molecular characterization of the spatial diversity and novel lineages of mycoplankton in Hawaiian coastal waters

Microbial ecology of organic aggregates in aquatic ecosystems

Association of the stramenopilan protists, the aplanochytrids, with zooplankton of the equatorial Indian Ocean

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