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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.


Number of aquatic fungal community studies and the different fungal marker genes targeted.For the summary all community studies containing fungal sequence information were counted, which targeted one of the following marker genes: ITS, LSU or SSU.
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pone.0134377.g001: Number of aquatic fungal community studies and the different fungal marker genes targeted.For the summary all community studies containing fungal sequence information were counted, which targeted one of the following marker genes: ITS, LSU or SSU.

Mentions: Most often, aquatic fungi are studied as part of eukaryotic or protistan communities [51–54], while molecular studies using fungal-specific primers are less common [48,55]. Therefore, the majority of sequence data on aquatic fungi is 18S rRNA gene sequences (Fig 1). The ITS regions perform poorly in inferring phylogenies [56] and thus, only 352 of the high-quality fungal ITS sequences derived from aquatic systems in the UNITE database [57] can be assigned to any taxonomic level (https://unite.ut.ee/, accessed January 2015). However, as the aquatic realm is a rich source of novel fungal species and groups [58,59], proper phylogenetic inference is needed to resolve their placement within the fungal tree of life. Thus, current aquatic fungal-specific studies use a double marker gene approach. They target the 18S rRNA gene and the ITS regions [48,60], which results in a deeper taxonomic resolution of the community [47].


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)

Number of aquatic fungal community studies and the different fungal marker genes targeted.For the summary all community studies containing fungal sequence information were counted, which targeted one of the following marker genes: ITS, LSU or SSU.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134377.g001: Number of aquatic fungal community studies and the different fungal marker genes targeted.For the summary all community studies containing fungal sequence information were counted, which targeted one of the following marker genes: ITS, LSU or SSU.
Mentions: Most often, aquatic fungi are studied as part of eukaryotic or protistan communities [51–54], while molecular studies using fungal-specific primers are less common [48,55]. Therefore, the majority of sequence data on aquatic fungi is 18S rRNA gene sequences (Fig 1). The ITS regions perform poorly in inferring phylogenies [56] and thus, only 352 of the high-quality fungal ITS sequences derived from aquatic systems in the UNITE database [57] can be assigned to any taxonomic level (https://unite.ut.ee/, accessed January 2015). However, as the aquatic realm is a rich source of novel fungal species and groups [58,59], proper phylogenetic inference is needed to resolve their placement within the fungal tree of life. Thus, current aquatic fungal-specific studies use a double marker gene approach. They target the 18S rRNA gene and the ITS regions [48,60], which results in a deeper taxonomic resolution of the community [47].

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.