Table 1.
Fungi isolated from the seagrass, Zostera marina.
Fig 1.
Microbes isolated from the seagrass, Zostera marina.
An example of the morphological diversity of microbial isolates (bacteria, fungi and oomycota) associated with the seagrass, Z. marina. Depicted plates were arbitrarily chosen to depict the morphological diversity of the isolates cultured in this study. Putative taxonomy of isolates shown: (a) Penicillium sp. CLE73, (b) Cladosporium sp. CLE116, (c) Colletotrichum sp. CLE5, (d) Hypocreales sp. CLE105, (e) unidentified microorganism, (f) Penicillium sp. CLE130, (g) Penicillium sp. CLE68, (h) Halophytophthora sp. CLE94, (i) Pleosporales sp CLE57, (j) unidentified microorganism, (k) Pleosporales sp. CLE102, (l) Penicillium sp. CLE26, (m) Cladosporium sp. CLE118, (n) Ramularia sp. CLE122, (o) Pseudoalteromonas sp. CLE126, (p) Talaromyces sp. CLE92, (q) Colletotrichum sp. CLE4, (r) Talaromyces sp. CLE82, (s) unidentified microorganism, (t) Acrostalagmus sp. CLE7, (u) Ramularia sp. CLE1, (v) Pleosporales sp. CLE56, (w) Penicillium sp. CLE77, (x) Ramularia sp. CLE112, (y) Penicillium sp. CLE106, (z) unidentified microorganism, (aa) Streptomyces sp. CLE117, (ab) Penicillium sp. CLE114, (ac) Cladosporium sp. CLE127, and (ad) Penicillium sp. CLE110. Unidentified microorganisms were unable to be identified using molecular methods (i.e. a PCR product was not successfully generated).
Fig 2.
Distribution of counts of fungal isolates across isolation sources.
A histogram representing the number of fungal isolates grouped by order and colored by isolation source (leaf, rhizome, root, seawater or sediment). The numbers included on each bar represent the count of isolates obtained from that particular isolation source.
Table 2.
Bacteria isolated from the seagrass, Zostera marina.
Table 3.
Oomycota isolated from the seagrass, Zostera marina.
Fig 3.
Phylogenetic placement of seagrass fungal isolates in the Basidiomycota and Mucoromycota.
A molecular phylogeny of 28S rRNA genes for isolates in the Basidiomycota and Mucoromycota was constructed using Bayesian inference. This alignment was generated using MAFFT (v. 7.402) on the CIPRES Science Gateway web server, trimmed using trimAl (v.1.2) and a phylogenetic tree was inferred on the trimmed alignment with a GTR + I + G model using MrBayes (v. 3.2.2) [75–77, 81]. Displayed at each node as a circle in the tree are the Bayesian posterior probabilities (e.g. a black circle represents probabilities greater or equal to 90%, a grey circle represents probabilities greater or equal to 70%, a white circle represents probabilities less than 70%). The names of fungi isolated from Z. marina are shown in green, fungi isolated from other seagrass species are shown in black, and all other fungi are shown in grey. For visualization purposes, selected clades have been collapsed and the number of sequences within that clade is indicated. Collapsed clades are shown in green if the majority of sequences in the clade are from isolates associated with Z. marina, black if the majority of isolates are from other seagrass species, and grey otherwise. Clade names that are followed by an asterisk contain sequences from multiple sources. An expanded version of this phylogeny can be found in S7 Fig. The GenBank accession numbers of the sequences used to build this phylogeny can be found in Tables 1 and S2–S4.
Fig 4.
Phylogenetic placement of seagrass fungal isolates in the Eurotiomycetes.
A molecular phylogeny of 28S rRNA genes for isolates in the Eurotiomycetes was constructed using Bayesian inference. This alignment was generated using MAFFT (v. 7.402) on the CIPRES Science Gateway web server, trimmed using trimAl (v.1.2) and a phylogenetic tree was inferred on the trimmed alignment with a GTR + I + G model using MrBayes (v. 3.2.2) [75–77, 81]. Displayed at each node as a circle in the tree are the Bayesian posterior probabilities (e.g. a black circle represents probabilities greater or equal to 90%, a grey circle represents probabilities greater or equal to 70%, a white circle represents probabilities less than 70%). The names of fungi isolated from Z. marina are shown in green, fungi isolated from other seagrass species are shown in black, and all other fungi are shown in grey. For visualization purposes, selected clades have been collapsed and the number of sequences within that clade is indicated. Collapsed clades are shown in green if the majority of sequences in the clade are from isolates associated with Z. marina, black if the majority of isolates are from other seagrass species, and grey otherwise. Clade names that are followed by an asterisk contain sequences from multiple sources. An expanded version of this phylogeny can be found in S8 Fig. The GenBank accession numbers of the sequences used to build this phylogeny can be found in Tables 1 and S2–S4.
Fig 5.
Phylogenetic placement of seagrass fungal isolates in the Sordariomycetes.
A molecular phylogeny of 28S rRNA genes for isolates in the Sordariomycetes was constructed using Bayesian inference. This alignment was generated using MAFFT (v. 7.402) on the CIPRES Science Gateway web server, trimmed using trimAl (v.1.2) and a phylogenetic tree was inferred on the trimmed alignment with a GTR + I + G model using MrBayes (v. 3.2.2) [75–77, 81]. Displayed at each node as a circle in the tree are the Bayesian posterior probabilities (e.g. a black circle represents probabilities greater or equal to 90%, a grey circle represents probabilities greater or equal to 70%, a white circle represents probabilities less than 70%). The names of fungi isolated from Z. marina are shown in green, fungi isolated from other seagrass species are shown in black, and all other fungi are shown in grey. For visualization purposes, selected clades have been collapsed and the number of sequences within that clade is indicated. Collapsed clades are shown in green if the majority of sequences in the clade are from isolates associated with Z. marina, black if the majority of isolates are from other seagrass species, and grey otherwise. Clade names that are followed by an asterisk contain sequences from multiple sources. An expanded version of this phylogeny can be found in S9 Fig. The GenBank accession numbers of the sequences used to build this phylogeny can be found in Tables 1 and S2–S4.
Fig 6.
Phylogenetic placement of seagrass fungal isolates in the Dothideomycetes.
A molecular phylogeny of 28S rRNA genes for isolates in the Dothideomycetes was constructed using Bayesian inference. This alignment was generated using MAFFT (v. 7.402) on the CIPRES Science Gateway web server, trimmed using trimAl (v.1.2) and a phylogenetic tree was inferred on the trimmed alignment with a GTR + I + G model using MrBayes (v. 3.2.2) [75–77, 81]. Displayed at each node as a circle in the tree are the Bayesian posterior probabilities (e.g. a black circle represents probabilities greater or equal to 90%, a grey circle represents probabilities greater or equal to 70%, a white circle represents probabilities less than 70%). The names of fungi isolated from Z. marina are shown in green, fungi isolated from other seagrass species are shown in black, and all other fungi are shown in grey. For visualization purposes, selected clades have been collapsed and the number of sequences within that clade is indicated. Collapsed clades are shown in green if the majority of sequences in the clade are from isolates associated with Z. marina, black if the majority of isolates are from other seagrass species, and grey otherwise. Clade names that are followed by an asterisk contain sequences from multiple sources. An expanded version of this phylogeny can be found in S10 Fig. The GenBank accession numbers of the sequences used to build this phylogeny can be found in Tables 1 and S2–S4.
Fig 7.
Comparison of the detection of a fungal genus across methods.
A heatmap representing a comparison of the detection of the presence / absence of fungal genera isolated in this study (using a culture-dependent method) and fungal genera identified in high throughput sequencing data from Ettinger & Eisen [43] (using a culture-independent method). For each fungal genera, we visualize if it was not detected (light grey), detected using only the culture-dependent method (medium grey), detected using only the culture-independent method (dark grey) or detected by both methods (black) for each sample type / isolation source (leaf, root, rhizome, sediment).