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Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Panzer K, Yilmaz P, Weiß M, Reich L, Richter M, Wiese J, Schmaljohann R, Labes A, Imhoff JF, Glöckner FO, Reich M - PLoS ONE (2015)

Bottom Line: Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure.Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.

View Article: PubMed Central - PubMed

Affiliation: University of Bremen, Molecular Ecology, FB2, Leobener Str. 2, 28359, Bremen, Germany; Jacobs University Bremen gGmbH, Department of Life Sciences and Chemistry, Campusring 1, 28759, Bremen, Germany.

ABSTRACT
Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.

No MeSH data available.


Phylogenetic signal analyses of aquatic fungal taxa present in different habitats.Net Relatedness Index and Nearest Taxa Index demonstrate clustering or overdispersion of fungal taxa in a habitat over the whole pool of phylogeny or within particular terminal clades, respectively. Comparison of observed data against randomly generated samples, number of generations = 9999.
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pone.0134377.g005: Phylogenetic signal analyses of aquatic fungal taxa present in different habitats.Net Relatedness Index and Nearest Taxa Index demonstrate clustering or overdispersion of fungal taxa in a habitat over the whole pool of phylogeny or within particular terminal clades, respectively. Comparison of observed data against randomly generated samples, number of generations = 9999.

Mentions: Freshwater fungal community structure differed significantly from all other habitat communities (Fig 3). This is similar to what has been observed for marine and freshwater microorganisms, which usually group in distinct marine and freshwater phylogenetic clusters [67]. Nearly 70% of all OTUs0.01 clustered in basal fungal lineages (Fig 4) and most of them belonged to the Chytridiomycota, which is known to be dominant in most freshwater samples [68,69]. Chytridiomycota play various roles as parasites [41] or in decomposing processes [5]. The other 30% of OTUs0.01 clustered equally in Asco- and Basidiomycota. We observed a tendency of taxonomic overdispersion in the freshwater habitat, mainly caused by these two phyla (Figs 5 and 6). Compared to other habitats, fungal assemblages of freshwater showed the highest diversity on the phylum level (Fig 4, subsampled data). The total amount of fungal sequences assigned to freshwater habitats clustered in several different fungal classes and subclasses (Fig 2). In contrast to other systems, freshwater systems are rich in carbon sources and structures, due to high terrestrial carbon input. Furthermore, freshwater systems are dynamic systems due to their physical nature, which degrade, sequester or translocate carbon [70]. In the pelagic zone of freshwater ecosystems, decreased amounts of soil organic carbon (C) associated with nutrient release from soil-microorganisms greatly influences the C dynamics, as well as the nutrient balance [71,72]. Fungi play essential roles in these freshwater nutrient processes [73]. As Chytridiomycota lack the ability to degrade cellulose [74], pre-processing of substrates by Ascomycota and Basidiomycota is essential to allow the colonization and use as a feeding source by other organisms [73,75]. Although several freshwater Ascomycota species have been intensively studied, about 70% of them were only reported once [62], explaining the tendency of overdispersion of higher fungi in our dataset.


Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Panzer K, Yilmaz P, Weiß M, Reich L, Richter M, Wiese J, Schmaljohann R, Labes A, Imhoff JF, Glöckner FO, Reich M - PLoS ONE (2015)

Phylogenetic signal analyses of aquatic fungal taxa present in different habitats.Net Relatedness Index and Nearest Taxa Index demonstrate clustering or overdispersion of fungal taxa in a habitat over the whole pool of phylogeny or within particular terminal clades, respectively. Comparison of observed data against randomly generated samples, number of generations = 9999.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520555&req=5

pone.0134377.g005: Phylogenetic signal analyses of aquatic fungal taxa present in different habitats.Net Relatedness Index and Nearest Taxa Index demonstrate clustering or overdispersion of fungal taxa in a habitat over the whole pool of phylogeny or within particular terminal clades, respectively. Comparison of observed data against randomly generated samples, number of generations = 9999.
Mentions: Freshwater fungal community structure differed significantly from all other habitat communities (Fig 3). This is similar to what has been observed for marine and freshwater microorganisms, which usually group in distinct marine and freshwater phylogenetic clusters [67]. Nearly 70% of all OTUs0.01 clustered in basal fungal lineages (Fig 4) and most of them belonged to the Chytridiomycota, which is known to be dominant in most freshwater samples [68,69]. Chytridiomycota play various roles as parasites [41] or in decomposing processes [5]. The other 30% of OTUs0.01 clustered equally in Asco- and Basidiomycota. We observed a tendency of taxonomic overdispersion in the freshwater habitat, mainly caused by these two phyla (Figs 5 and 6). Compared to other habitats, fungal assemblages of freshwater showed the highest diversity on the phylum level (Fig 4, subsampled data). The total amount of fungal sequences assigned to freshwater habitats clustered in several different fungal classes and subclasses (Fig 2). In contrast to other systems, freshwater systems are rich in carbon sources and structures, due to high terrestrial carbon input. Furthermore, freshwater systems are dynamic systems due to their physical nature, which degrade, sequester or translocate carbon [70]. In the pelagic zone of freshwater ecosystems, decreased amounts of soil organic carbon (C) associated with nutrient release from soil-microorganisms greatly influences the C dynamics, as well as the nutrient balance [71,72]. Fungi play essential roles in these freshwater nutrient processes [73]. As Chytridiomycota lack the ability to degrade cellulose [74], pre-processing of substrates by Ascomycota and Basidiomycota is essential to allow the colonization and use as a feeding source by other organisms [73,75]. Although several freshwater Ascomycota species have been intensively studied, about 70% of them were only reported once [62], explaining the tendency of overdispersion of higher fungi in our dataset.

Bottom Line: Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure.Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.

View Article: PubMed Central - PubMed

Affiliation: University of Bremen, Molecular Ecology, FB2, Leobener Str. 2, 28359, Bremen, Germany; Jacobs University Bremen gGmbH, Department of Life Sciences and Chemistry, Campusring 1, 28759, Bremen, Germany.

ABSTRACT
Molecular diversity surveys have demonstrated that aquatic fungi are highly diverse, and that they play fundamental ecological roles in aquatic systems. Unfortunately, comparative studies of aquatic fungal communities are few and far between, due to the scarcity of adequate datasets. We combined all publicly available fungal 18S ribosomal RNA (rRNA) gene sequences with new sequence data from a marine fungi culture collection. We further enriched this dataset by adding validated contextual data. Specifically, we included data on the habitat type of the samples assigning fungal taxa to ten different habitat categories. This dataset has been created with the intention to serve as a valuable reference dataset for aquatic fungi including a phylogenetic reference tree. The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.The combined data enabled us to infer fungal community patterns in aquatic systems. Pairwise habitat comparisons showed significant phylogenetic differences, indicating that habitat strongly affects fungal community structure. Fungal taxonomic composition differed considerably even on phylum and class level. Freshwater fungal assemblage was most different from all other habitat types and was dominated by basal fungal lineages. For most communities, phylogenetic signals indicated clustering of sequences suggesting that environmental factors were the main drivers of fungal community structure, rather than species competition. Thus, the diversification process of aquatic fungi must be highly clade specific in some cases.

No MeSH data available.