Fungal diversity in sediments of the eastern tropical Pacific oxygen minimum zone revealed by metabarcoding

Abstract

Oxygen minimum zones (OMZ) represent ~8% of the ocean, with the Pacific as the largest and top expanding area. These regions influence marine ecosystems, promoting anaerobic microbial communities. Nevertheless, only a fraction of microbial diversity has been studied, with fungi being the less explored component. So, herein we analyzed fungal diversity patterns in surface and subsurface sediments along a bathymetric transect using metabarcoding of the ITS1 region in the OMZ of the Mexican Pacific off Mazatlán. We identified 353 amplicon sequence variants (ASV), within the Ascomycota, Basidiomycota, and Rozellomycota. Spatial patterns evidenced higher alpha diversity in nearshore and subsurface subsamples, probably due to temporal fluctuations in organic matter inputs. Small-scale heterogeneity characterized the community with the majority of ASV (269 ASV) occurring in a single subsample, hinting at the influence of local biogeochemical conditions. This baseline data evidenced a remarkable fungal diversity presenting high variation along a bathymetric and vertical transects.

Fig 1. Sampling stations along a transect off the coast of the Port of Mazatlán (cyan = S1, purple = S2, blue = S3, dark blue = S4).

The stations nomenclature is indicated in Table 1. Map was generated with the R package ggplot2 v. 3.4.0 [47].

Fig 2. Relative abundance of fungal phyla and classes across subsamples.

Stacked bar plots depicted the fungal relative abundances at the phylum (A) and class (C) level of the identified taxa across subsamples. Clustered heatmaps showed the fungal richness (horizontal lines in each subsample), and their relative abundance (white-red coded lines) at the phylum (B) and class (D) level across subsamples. The subsamples nomenclature is indicated in Table 1.

Fig 3. Relative abundance of Fungi spp. across subsamples.

Clustered heatmap showed the richness of fungi that were taxonomically assigned solely at the kingdom level as Fungi spp. (horizontal lines in each subsample) and their relative abundance (white-red coded lines) across subsamples. The subsamples nomenclature is indicated in Table 1.

Fig 4. Alpha diversity estimates of fungal ASV in sediment subsamples.

Bar plots depicting the richness of ASV at the species level (A), Shannon index (B), and evenness (C). The error bars indicate the standard deviation of richness and the Shannon index. The color of each bar corresponds to its station (cyan = S1, purple = S2, blue = S3, dark blue = S4). The subsamples nomenclature is indicated in Table 1.

Fig 5. Beta diversity estimates of fungal ASV in sediment subsamples.

Dendrogram based on Bray-Curtis (A) and Jaccard (B) metrics indicating dissimilarities of fungal communities across sediment subsamples, where height (y-axis) indicates distance given the dissimilarity metrics. The color of each subsample corresponds to its station (cyan = S1, purple = S2, blue = S3, dark blue = S4). Circles represent surface subsamples and triangles represent subsurface subsamples. The subsamples nomenclature is indicated in Table 1.

Fig 6. Constrained Correspondence Analysis plots of fungal ASV associated with environmental variables.

The variables were measured at the bottom of the water column (A) and in the sediments (B) along the bathymetric transect. The percent of the variation in the fungal community explained by each axis is indicated in parentheses after the axis label. DO, dissolved oxygen; OC, organic carbon. Fungal ASV are indicated as gray triangles. The subsamples nomenclature is indicated in Table 1.

Fig 7. Upset plot and Venn diagrams.

Upset plot representing unique (cyan = S1, purple = S2, blue = S3, dark blue = S4; station nomenclature in Table 1) and common (highlighted in red) fungal ASV occurrence across all subsamples stacked in the x-axis (A). Dots below a bar depict the occurrence of the ASV for each subsample. Vertical line figures the ASV common to several subsamples. The number of ASV per subsample represents the richness of each one. Besides, Venn diagrams exhibited the unique and common ASV among surface sediment subsamples (B), subsurface subsamples (C), and at different sediment depths at each station (D).

Fig 8. Assigned functional guilds.

Stacked bar plot showing the relative proportion (y-axis) of the fungal trophic modes (shown in red in the pie chart) in sediments across subsamples in the eastern tropical Pacific oxygen minimum zone (x-axis). The subsamples nomenclature is indicated in Table 1.