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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.


Schematic diagram of the phylogenetic tree using 18S rRNA gene sequences from aquatic fungi.Sequence data were collected from the SILVA dataset and the KSMP-Kiel culture collection. Thickness of taxonomic triangles is proportional to the sequence amount of each taxonomic groups. Piecharts beside triangles show group-specific sequence assignments to the habitat types.
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pone.0134377.g002: Schematic diagram of the phylogenetic tree using 18S rRNA gene sequences from aquatic fungi.Sequence data were collected from the SILVA dataset and the KSMP-Kiel culture collection. Thickness of taxonomic triangles is proportional to the sequence amount of each taxonomic groups. Piecharts beside triangles show group-specific sequence assignments to the habitat types.

Mentions: Our dataset is the first comprehensive in-depth survey of published nearly full-length 18S rRNA gene sequence data on aquatic-derived fungi (S1 Fig) and contains 1,784 fungal sequences [26]. Consistent with literature [58,62], Ascomycota was the largest group (Fig 2). The three main classes of Ascomycota—Eurotiomycetes, Dothideomycetes and Sordariomycetes (Fig 2)—are well known and dominant marine fungal lineages [63]. Interestingly, a high proportion of Basidiomycota sequences were also found in our dataset, with the majority being yeast fungi (Fig 2, S1 Fig). Recent studies on isolated Basidiomycota reported less than 100 species isolated from aquatic sources [62,64], but molecular data suggest that Basidiomycota diversity must be much higher in aquatic environments [9,17]. Chytridiomycota formed the third largest sequence group in our dataset. Furthermore, seven additional phyla/subphyla of basal fungal lineages were discovered. Of those, the recently described Cryptomycota [65] formed the largest sequence group (Fig 2; S2 Table). However, a reliable statement about the proportion of these seven groups cannot be made. Partly due to PCR primer bias, sequences associated with basal fungal lineages are often not detected in molecular surveys [11]. For instance, Cryptomycota normally accounts for only 0.02–4.5% of total sequence reads [66], and additionally, it is generally difficult to map these sequences to reference clades.


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)

Schematic diagram of the phylogenetic tree using 18S rRNA gene sequences from aquatic fungi.Sequence data were collected from the SILVA dataset and the KSMP-Kiel culture collection. Thickness of taxonomic triangles is proportional to the sequence amount of each taxonomic groups. Piecharts beside triangles show group-specific sequence assignments to the habitat types.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134377.g002: Schematic diagram of the phylogenetic tree using 18S rRNA gene sequences from aquatic fungi.Sequence data were collected from the SILVA dataset and the KSMP-Kiel culture collection. Thickness of taxonomic triangles is proportional to the sequence amount of each taxonomic groups. Piecharts beside triangles show group-specific sequence assignments to the habitat types.
Mentions: Our dataset is the first comprehensive in-depth survey of published nearly full-length 18S rRNA gene sequence data on aquatic-derived fungi (S1 Fig) and contains 1,784 fungal sequences [26]. Consistent with literature [58,62], Ascomycota was the largest group (Fig 2). The three main classes of Ascomycota—Eurotiomycetes, Dothideomycetes and Sordariomycetes (Fig 2)—are well known and dominant marine fungal lineages [63]. Interestingly, a high proportion of Basidiomycota sequences were also found in our dataset, with the majority being yeast fungi (Fig 2, S1 Fig). Recent studies on isolated Basidiomycota reported less than 100 species isolated from aquatic sources [62,64], but molecular data suggest that Basidiomycota diversity must be much higher in aquatic environments [9,17]. Chytridiomycota formed the third largest sequence group in our dataset. Furthermore, seven additional phyla/subphyla of basal fungal lineages were discovered. Of those, the recently described Cryptomycota [65] formed the largest sequence group (Fig 2; S2 Table). However, a reliable statement about the proportion of these seven groups cannot be made. Partly due to PCR primer bias, sequences associated with basal fungal lineages are often not detected in molecular surveys [11]. For instance, Cryptomycota normally accounts for only 0.02–4.5% of total sequence reads [66], and additionally, it is generally difficult to map these sequences to reference clades.

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.