Introduction

The Southern Ocean contributes 30% of global ocean area, surrounding the Antarctic continent [1,2]. It is characterized by extreme conditions for life, including chronically low temperature, salinity, pH variability and low nutrient availability, stressors that have strongly influenced the life that inhabits its ecosystems. Even today, the Southern Ocean is a unique region where microbial studies are still in their infancy [3], even though its varied substrates and habitats have the potential to support diverse microbial life [2].

The deep-sea benthos is one of the least known microbial environments on the planet. Its microbial ecosystems include bacteria, archaea [4] and fungi [5,6,7]. Fungi in marine ecosystems include saprophytic, pathogenic and symbiotic taxa, which are found from shallow coastal to deep-sea environments [8,9]. Fungi are among the most ecologically successful eukaryotic groups and have been detected at 10,897 m depth in the Mariana trench [10]. However, despite their ecological importance, few studies have addressed the presence of fungi in deep-sea sediments [11,12,13,14]. Knowledge of fungal diversity and ecology in the marine ecosystems of Antarctica is generally poor and particularly so in the deep sea [15]. Gonçalves et al. [16] highlighted that Antarctic deep-sea sediments represent important habitats that are suitable for the exploration of fungal life under extreme conditions.

Fungal taxa already reported from Antarctic marine sediments include primarily members of the phyla Ascomycota, Basidiomycota and Mucoromycota [15]. However, in studies of microbial diversity, difficulties in isolation and successful culturing mean that molecular studies involving non-culturing approaches can potentially reveal previously unrecognized fungal diversity [2]. In the current study, we assessed the fungal diversity, richness, abundance and distribution in marine sediments obtained from the Southern Ocean at depths between 153 and 1463 m using DNA metabarcoding through high-throughput sequencing (HTS).

Materials and Methods

Marine Sediment Sampling

Four deep-sea sediment samples (one per site) were collected from different locations around the South Shetland Islands and Drake Passage (Fig. 1) during the austral summers of the years 2014/2015 and 2015/2016. Samples were collected at depths of 153 m, 250 m, 550 m and 1463 m, using a gravity corer. Sections of 10 cm length (approximately 500 g of sediment) from the base of each core were selected, sealed, placed in sterile Whirl-pack (Nasco, Ft. Atkinson, WI) bags and frozen at − 20 °C until processing in the laboratory at the Federal University of Minas Gerais, Brazil. There, the sampled core was gradually thawed at 4 °C for 24 h before carrying out DNA extraction. Three subsamples of the central parts of each core were obtained under aseptic conditions and processed, to increase the fungal DNA yield.

Fig. 1
figure 1

Locations where deep-sea sediments were sampled in the Southern Ocean. (a) Antarctic Continent with the South Shetland Islands archipelago north-west of the Antarctic Peninsula indicated within the red rectangle, (b) Drake Passage (59°00′090″ S; 62°45′270″ W) where the 1463 m depth, KGI (King George Island) where the 550 m (62°11′258″ S; 58°00′383″ W), and MB (Maxwell Bay, King George Island) where the 250 m (62°14′667″ S; 58°56′035″ W) and 153 m (62°14′632″ S; 58°57′135″ W) samples were collected. Maps created from Antarctic Digital Database Viewer (SCAR)

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DNA Extraction and Sequence Identification

Total DNA of the three replicate subsamples from each core was extracted using the QIAGEN Power Soil Kit, following the manufacturer’s instructions. Extracted DNA was used as a template for generating PCR amplicons. The internal transcribed spacer 2 region (ITS2) of the nuclear ribosomal DNA was used as a DNA barcode for molecular species identification [17,18]. PCR amplicons were generated using the universal primers ITS3 and ITS4 [19]. Library construction and DNA amplification were performed using the Library kit Herculase II Fusion DNA Polymerase Nextera XT Index Kit V2, following Illumina 16S Metagenomic Sequencing Library Preparation Part #15044223 Rev. B protocol. Paired-end sequencing (2 × 300 bp) was performed on a MiSeq System (Illumina) by Macrogen Inc. (South Korea).

Raw fastq files were filtered using BBDuk version 38.34 (BBMap – Bushnell B. – sourceforge.net/projects/bbmap/) to remove Illumina adapters, known Illumina artifacts, and the PhiX Control v3 Library. Quality read filtering was carried out using Sickle version 1.33 -q 30 -l 50 [20], to trim 3′ or 5′ ends with low Phred quality score, and sequences shorter than 50 bp were also discarded. The remaining sequences were imported to QIIME2 version 2019.10 (https://qiime2.org/) for bioinformatics analyses [21]. The qiime2-dada2 plugin is a complete pipeline that was used for filtering, dereplication, turning paired-end fastq files into merged, and removing chimeras [22]. Taxonomic assignments were determined for amplicon sequence variants (ASVs) using the qiime2-feature-classifie [23] classify-sklearn against the UNITE ITS database version 8.2 [24] (filtered by fungi) and trained with Naive Bayes classifier with confidence threshold of 98.5%. Fungal classification followed Kirk et al. [25], Tedersoo et al. [26], MycoBank (http://www.mycobank.org) and the Index Fungorum (http://www.indexfungorum.org).

Statistical Analyses

To quantify ASV diversity, richness and dominance, we used the following ecological indices: (i) Fisher’s α (diversity), (ii) Margalef’s (richness) and (iii) Simpson’s (dominance). The numbers of reads of the ASVs were used to quantify the fungal taxa present in the deep-sea sediments, where fungal ASVs with > 6000 reads were considered as dominant, ASVs with < 6000 and > 1000 reads as intermediate, and ASVs with < 1000 reads as minor (rare) components of the diversity present. All of the results were obtained with 95% confidence, and bootstrap values were calculated from 1000 iterations. Taxon accumulation curves were obtained using the Mao Tao index. All diversity indices and Mao Tao accumulation curve calculations were performed using PAST, version 1.90 [27]. Venn diagrams were prepared as described by Bardou et al. [28] to compare the sequence assemblages present in the deep-sea sediment samples. Functional assignments of fungal ASVs at species and generic levels were prepared using FunGuild [29], which can be accessed at http://www.funguild.org/.

Results

Fungal Taxonomy

Overall we detected 655,991 DNA reads in the sediment samples obtained from Maxwell Bay at 153 m (221,608) and 250 m (253,568), Bransfield Strait at 500 m (129,370) and Drake Passage at 1463 m (51,445) depths. The reads were classified into 263 fungal ASVs, with 126 detected at 153 m, 149 at 250 m, 135 at 550 m and 101 at 1453 m depths (Suppl. Table 1). The fungal community was dominated, in rank order, by the taxa of the phyla Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota (Fig. 2). Of the total DNA reads, 182,257 (27.78%) could only be assigned as Fungi sp. and may represent currently unknown taxa or taxa not included in the UNITE database. Similarly, 46 ASVs could only be identified to higher taxonomic levels (phylum, class, order, family) and may represent new taxa and/or new records for Antarctica. The fungal community included 17 dominant fungal ASVs, 62 intermediate ASVs and 213 minority ASVs.

Fig. 2
figure 2

Numbers of DNA reads at phylum level of fungal amplicon sequence variants (ASVs) detected in deep-sea sediments from the Southern Ocean

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The dominant fungi, in rank order, included the taxa Fungi sp., Mortierella sp., Penicillium sp., Cladosporium sp., Agaricomycetes sp., Mortierella parvispora, Leotiomycetes sp., Pseudogymnoascus sp., Pseudogymnoascus appendiculatus, Didymosphaeriaceae sp., Penicillium herquei, Phaeosphaeria sp., Cladosporium halotolerans, Mortierella turficola, Pseudogymnoascus roseus, Diaporthales sp. and Torula hollandica.

Fungal Diversity

The Mao Tao rarefaction curves of the fungal assemblages detected in the sediment samples from the different depths reached asymptote (Fig. 3), indicating that the data provided a good description of the diversity present. Despite the extreme conditions of the Southern Ocean, the total fungal communities detected displayed high indices of diversity (Fisher’s α) and richness (Margalef), and moderate dominance (Simpson), with some variation among the depths sampled (Table 1). The highest values of diversity and richness were obtained at 250 m and 550 m depths, followed by 150 m and 1463 m depths. Of the 263 fungal ASVs detected in total, only 49 (18.63%) were detected at all four depths, with these including taxa from different genera (Fig. 4). Functional ecological assignments of the ASVs detected at generic level are shown in Suppl. Table 2.

Fig. 3
figure 3

Rarefaction curves of fungal amplicon sequence variants (ASVs) obtained from deep-sea sediments at 153 m, 250 m, 550 m and 1463 m depths. Red lines represent the rarefaction curves and blue lines represent 95% confidence limits

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Table 1 Ecological indices of the uncultured fungal DNA recovered from deep-sea sediment samples from the Southern Ocean
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Fig. 4
figure 4

Venn diagram showing the fungal amplicon sequence variants (ASVs) detected in the deep-sea sediment samples obtained from different depths in the Southern Ocean, highlighting those detected in all samples and in the deepest sediment sample (1463 m depth)

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Discussion

Fungal Taxonomy, Diversity, and Distribution

The main focus of our study was to detect and compare fungal DNA present in environmental samples obtained at different depths from four locations in the Southern Ocean. Few studies of fungal diversity in marine sediments of the Southern Ocean are available to date [2], with the majority of those based on traditional cultivation techniques which revealed the presence of relatively few taxa [15,16,30,31,32,33]. Lopez-Garcia et al. [34] used phylogenetic information from ribosomal RNA genes directly amplified from the environment to assess the biota present in the deep-sea environment, but they detected only one unidentified fungal taxon in the aphotic zone between 250 m and 3000 m depths south of the Antarctic Polar Front.

Many factors, including extraction, PCR and primer bias, can affect the number of reads obtained [35] and thus lead to misinterpretation of absolute abundance [36]. However, Giner et al. [37] concluded that such biases did not affect the proportionality between reads and cell abundance, implying that more reads are linked with higher abundance [38,39]. Therefore, for comparative purposes, we used the number of reads as a proxy for relative abundance. The data generated in the current study, using an up-to-date HTS approach, focused exclusively on the detection of fungal DNA in environmental samples, provide a striking contrast with the previous reports. Ogaki et al. [15] assessed the same samples to recover culturable fungi. Using different established culturing techniques (six culture media, incubations under normal atmospheric pressure, with three different inoculation methods and under aerobic and anaerobic conditions), Ogaki et al. [15] recovered only taxa of the genera Acremonium, Penicillium and Pseudogymnoascus. In contrast, our sequence data obtained using metabarcoding indicated the potential presence of a rich and diverse fungal community in marine sediments from all depths sampled, including multiple taxa not previously reported from Antarctica. The dominant fungal taxa detected in our study included representatives of genera often reported in different Antarctic environments, including Mortierella, Penicillium, Cladosporium, Pseudogymnoascus and Phaeosphaeria [40,41,42]. More unusual taxa such as the species Torula hollandica were included among the dominant group and as intermediate or rare taxa.

The genus Mortierella (Mortierellomycota) includes taxa commonly detected in Antarctica and abundant in association with plants [32,43,44,45], lichens [46], and also recovered from soil [47,48], freshwater lakes [49] and the thalli of marine macroalgae [50]. Representatives of Cladosporium and Penicillium included many cosmopolitan species and are often reported in Antarctic ecosystems. Cladosporium species are dominant in different soil types and in association with Antarctic plants [42]. Penicillium is widespread across Antarctica, occurring in many different ecosystems and habitats such as soils [48,51,52], permafrost [53,54], associated with marine macroalgae [50], snow [55], ice [56] and air [57]. Pseudogymnoascus species have been recorded from many different cold environments in Arctic, alpine, temperate and Antarctic regions [42,58,59,60]. They have been detected in soils [48,58,61,62], associated with plants [43,44,63], marine macroalgae [64,65], lichens [46] and in freshwater lakes [49]. Phaeosphaeria includes species known to be phytopathogenic and frequently recovered from tissues of Antarctic plants [41,63], lichens [66] and in soil [67]. Representatives of Phaeosphaeria have also been isolated from the Antarctic marine environment from thalli of the macroalga Adenocystis utricularis [64]. Torula (Torulaceae) includes species frequently found in association with plants, such as Torula hollandica that was originally isolated from a dead stem of Delphinium sp. in the Netherlands [68]; however, there are no reports of its presence in marine environments.

Some of these dominant fungi have previously been detected in Antarctic marine sediments. Using traditional culturing methods, Gonçalves et al. [16] recovered only Penicillium solitum from sediments sampled at 100 m, 500 m, 700 m and 1100 m depths. Ogaki et al. [15] recovered 31 cultured fungal isolates identified as taxa of Acremonium, Penicillium and Pseudogymnoascus from the same cores and depths sampled in the current study. However, the overall diversity recorded by Ogaki et al. [15] was low; at 153 m, only Pseudogymnoascus verrucosus was recorded; at 250 m only Penicillium allii-sativi; at 550 m Acremonium fusidioides, P. allii-sativi, P. chrysogenum, P. palitans and P. solitum; and at 1463 m only P. solitum. The HTS approach used here detected a considerably greater diversity of fungal taxa. The dominance of these genera in marine sediments at different depths also suggests that they are able to resist and survive the multiple extreme environmental stresses of the Southern Ocean. Our diversity results are consistent with the findings of Raghukumar et al. [69], who suggested that the majority of fungi detected in deep-sea sediments are similar to those present in the terrestrial environment, indicating the possibility of connectivity between these two environments, possibly mediated by either aerial dispersal or terrestrial runoff.

The DNA of an unexpectedly rich and diverse fungal community comprising intermediate and rare taxa was also detected in the deep-sea sediments examined and thus included unusual taxa for Antarctica, such as members of the genera Amyloxenasma, Articulospora, Arxiella, Byssocorticium, Calvatia, Clitopilus, Clonostachys, Crepidotus, Crocicreas, Emericellopsis, Hyphodiscus, Kotlabaea, Lasiodiplodia, Mycocentrospora, Mycoleptodiscus, Naganishia, Pseudopithomyces, Pyrenochaetopsis, Rhizoscyphus, Schizopora, Schwanniomyces, Setophoma, Tranzscheliella, Trechispora and Tulostoma. This diversity includes taxa distributed across terrestrial and marine environments globally and that perform multiple different ecological roles. These include decomposers, symbionts, plant, animal and human pathogens and Ingoldian fungi. Furthermore, included within the diversity detected was the DNA of taxa able to produce metabolites useful in biotechnological processes such as Beauveria amorpha [70], Clonostachys rosea [71] and Wickerhamomyces anomalus [72].

Ecological Profile

Antarctic fungi perform many different ecological roles including as saprophytes, mutualists, symbionts and/or parasites. However, perhaps the key ecological roles of Antarctic fungi are related to their capability to degrade organic matter at low temperature, releasing carbon, nitrogen and other elements to other organisms [73]. Among the fungal taxa detected in the deep-sea marine sediments examined here, saprophytes were the most common trophic guild, followed by plant and animal pathogens and symbionts. These results suggest that Antarctic deep-sea marine sediment habitat might host complex microbial ecosystems. However, as our study focused on fungal detection by quantifying the presence of DNA, further detailed studies will be necessary to elucidate the ecology of marine deep-sea fungi present in the Southern Ocean.

Conclusions

Compared with the few previous studies available based on traditional culturing methods [15,16,30,32,33], the metabarcoding approach applied here revealed that deep-sea sediments may represent a hotspot of fungal diversity in Antarctica, including possible new taxa of different hierarchical levels, new records or endemic species. The DNA detected included diverse fungal taxa, some with global distribution, with the dominant fungi similar to those present in terrestrial ecosystems. The diversity detected included fungal species with many different ecological roles suggesting that, despite the multiple extreme conditions characterizing the Southern Ocean, its deep-sea sediments may host a complex fungal community. However, detection of specific DNA sequences using metabarcoding does not confirm that living or viable organisms are present. Further studies are required to elucidate the taxonomy and ecological roles of the active fungi present, as well as to assess their metabolites and/or genes for potential use in biotechnological applications such as natural product discovery for use in medicine and agriculture.