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

Panzer, Katrin, Yilmaz, Pelin, Weiß, Michael, Reich, Lothar, Richter, Michael, Wiese, Jutta , Schmaljohann, Rolf, Labes, Antje, Imhoff, Johannes F. , Glöckner, Frank Oliver and Reich, Marlis (2015) Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data. Open Access PLoS ONE, 10 (7). e0134377. DOI 10.1371/journal.pone.0134377.

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Text (Subsections of the Maximum Likelihood tree of fungal 18S rRNA gene sequences. doi:10.1371/journal.pone.0134377.s001)
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Text (Information on sequences of the KSMP-Kiel culture collection used for this study. doi:10.1371/journal.pone.0134377.s003)
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Text (Phylogenetic distances between sub-communities of diverse habitat types. doi:10.1371/journal.pone.0134377.s002)
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Text (New taxonomic assignment of sequences of basal fungal lineages. doi:10.1371/journal.pone.0134377.s004)
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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.

Document Type: Article
Additional Information: Data Availability: Sequences from fungal strains obtained during this study were submitted to the GenBank database and were assigned to accession numbers KJ939309 – KJ939313 and KM096133 – KM096374, respectively. All data supporting this article can be accessed via the Dryad Digital Repository (http://dx.doi.org/10.5061/dryad.7fv64). The following files can be found: (i) a newick-formatted file of the phylogenetic tree, (ii) a file including all information on sequences used in this study and assignment of sequences to the diverse habitat categories, (iii) a list indicating which sequences cluster together at a 99% similarity level, and (iv) OTU count per habitat category.
Keywords: Habitats; Fungal genetics; Phylogenetics; Fungi; Fungal structure; Fresh water; Phylogenetic analysis; Ribosomal RNA
Research affiliation: OceanRep > The Future Ocean - Cluster of Excellence > FO-R05
OceanRep > GEOMAR > FB3 Marine Ecology > FB3-MI Marine Microbiology
OceanRep > The Future Ocean - Cluster of Excellence
Refereed: Yes
Open Access Journal?: Yes
DOI etc.: 10.1371/journal.pone.0134377
ISSN: 1932-6203
Related URLs:
Projects: Future Ocean
Date Deposited: 07 Sep 2015 09:08
Last Modified: 05 Apr 2017 12:25
URI: http://oceanrep.geomar.de/id/eprint/29516

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