Species richness and adaptation of marine fungi from deep-subseafloor sediments

Abstract

The fungal kingdom is replete with unique adaptive capacities that allow fungi to colonize a wide variety of habitats, ranging from marine habitats to freshwater and terrestrial habitats. The diversity, importance, and ecological roles of marine fungi have recently been highlighted in deep-subsurface sediments using molecular methods. Fungi in the deep-marine subsurface may be specifically adapted to life in the deep biosphere, but this can be demonstrated only using culture-based analyses. In this study, we investigated culturable fungal communities from a record-depth sediment core sampled from the Canterbury Basin (New Zealand) with the aim to reveal endemic or ubiquist adapted isolates playing a significant ecological role(s). About 200 filamentous fungi (68%) and yeasts (32%) were isolated. Fungal isolates were affiliated with the phyla Ascomycota and Basidiomycota, including 21 genera. Screening for genes involved in secondary metabolite synthesis also revealed their bioactive compound synthesis potential. Our results provide evidence that deep-subsurface fungal communities are able to survive, adapt, grow, and interact with other microbial communities and highlight that the deep-sediment habitat is another ecological niche for fungi.

FIG 1

Species richness along the core. Shannon diversity indices allow the identification of the relative complexity of fungal communities at different depths.

FIG 2

Phylogenetic tree of deep-sea fungal isolates (red) and 454 pyrotags (gray) obtained by analysis of SSU rRNA genes. The tree topology is based on maximum likelihood criteria and a ClustalW (version 1.83) alignment. Bootstrap values greater than 50% are shown at the nodes. Phylogenetic data of Ciobanu et al. (15) were integrated as 454 pyrotags. Mucor luteus (GenBank accession number FJ605511), which belongs to the phylum Glomeromycota, was used as an outgroup. Dark and light gray boxes, Basidiomycota and Ascomycota, respectively. OTU, operational taxonomic unit.

FIG 3

Phylogenetic tree of deep-sea yeast isolates (red) obtained by analysis of the D1/D2 domain of the 26S rRNA gene. The topology is based on the maximum likelihood method and a ClustalW (version 1.83) alignment. Bootstrap values greater than 50% are shown at the nodes. Mucor flavus (GenBank accession number EU071390), which belongs to the phylum Zygomycota, was used as an outgroup. Clusters highlighted with an asterisk were also retrieved in molecular analysis data sets (15, 19).

FIG 4

Physiological analysis of filamentous fungi (A) and yeast (B) isolates. Growth was measured at different temperatures (25°C, 30°C, and 35°C) and different sea salt concentrations (0, 1.5, 3, and 4.5%), and the general growth trend is shown as 3-part bars representing minimum, medium, and maximum growth. Blank cells indicate that the results were not determined. Red, green, and blue dots represent, respectively, nonhalophilic, halotolerant, and halophilic fungal isolates.

FIG 5

Presence/absence of genes encoding type I and III PKSs, NRPSs, PKS-NRPS hybrids, and TPS in filamentous fungi. Filamentous fungal MSP-PCR fingerprints coupled with type I PKS gene (light blue), type III PKS gene (pink), NRPS gene (light green), PKS-NRPS hybrid gene (dark blue), and TPS gene (dark green) occurrences are presented using an aligned multivalue bar chart (short bar, only one gene; long bar, several genes). This figure was generated using Interactive Tree of Life (version 2) (59).

FIG 6

Presence/absence of genes coding type I and III PKSs, NRPSs, PKS-NRPS hybrids, and TPS in yeasts. Yeast MSP-PCR fingerprints coupled with type I PKS gene (light blue), type III PKS gene (pink), NRPS gene (light green), PKS-NRPS hybrid gene (dark blue), and TPS gene (dark green) occurrences are presented using an aligned multivalue bar chart (short bar, only one gene; long bar, several genes). This figure was generated using the Interactive Tree of Life (version 2) (59).