Fungal Diversity In Deep-sea Sediments Research Articles

Fungi Present in Antarctic Deep-Sea Sediments Assessed Using DNA Metabarcoding.

We assessed fungal diversity in deep-sea sediments obtained from different depths in the Southern Ocean using the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA bymetabarcoding through high-throughput sequencing (HTS). We detected 655,991 DNA reads representing 263 fungal amplicon sequence variants (ASVs), dominated by Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Chytridiomycota and Rozellomycota, confirming that deep-sea sediments can represent a hotspot of fungal diversity in Antarctica. The community diversity detected included 17 dominant fungal ASVs, 62 intermediate and 213 rare. The dominant fungi included taxa of Mortierella, Penicillium, Cladosporium, Pseudogymnoascus, Phaeosphaeria and Torula. Despite the extreme conditions of the Southern Ocean benthos, the total fungal community detected in these marine sediments displayed high indices of diversity and richness, and moderate dominance, which varied between the different depths sampled. The highest diversity indices were obtained in sediments from 550m and 250m depths. Only 49 ASVs (18.63%) were detected at all the depths sampled, while 16 ASVs were detected only in the deepest sediment sampled at 1463m. Based on sequence identities, the fungal community included some globally distributed taxa, primarily recorded otherwise from terrestrial environments, suggesting transport from these to deep marine sediments. The assigned taxa included symbionts, decomposers and plant-, animal- and human-pathogenic fungi, suggesting that deep-sea sediments host a complex fungal diversity, although metabarcoding does not itself confirm that living or viable organisms are present.

Fungal diversity in deep-sea sediments from Magellan seamounts environment of the western Pacific revealed by high-throughput Illumina sequencing.

There are lots of seamounts globally whose primary production is disproportionally greater than the surrounding areas. Compared to other deep-sea environments, however, the seamounts environment is relatively less explored for fungal diversity. In the present study, we explored the fungal community structure in deep-sea sediments from four different stations of the Magellan seamounts environment by using high-throughput sequencing of the ITS1 region. A total of 1,897,618 ITS1 sequences were obtained. Among these sequences, fungal ITS1 sequences could be clustered into 1,662 OTUs. The majority of these sequences belonged to Ascomycota. In the genera level, the most abundant genus was Mortierella (4.79%), which was reported as a common fungal genus in soil and marine sediments, followed by Umbelopsis (3.80%), Cladosporium (2.98%), Saccharomycopsis (2.53%), Aspergillus (2.42%), Hortaea (2.36%), Saitozyma (2.20%), Trichoderma (2.12%), Penicillium (2.11%), Russula (1.86%), and Verticillium (1.40%). Most of these recovered genera belong to Ascomycota. The Bray-Curtis analysis showed that there was 37 to 85% dissimilarity of fungal communities between each two sediment samples. The Principal coordinates analysis clearly showed variations in the fungal community among different sediment samples. These results suggested that there was a difference in fungal community structures not only among four different sampling stations but also for different layers at the same station. The depth and geographical distance significantly affect the fungal community, and the effect of depth and geographical distance on the structure of the fungal community in the Magellan seamounts is basically same. Most of the fungi were more or less related to plants, these plant parasitic/symbiotic/endophytic fungi constitute a unique type of seamounts environmental fungal ecology, different from other marine ecosystems.

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N2O ex situ in the presence of nitrite. No fungus was found to produce N2O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.

Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions

ABSTRACT Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge

Deep-sea hydrothermal sediment is known to support remarkably diverse microbial consortia. In deep sea environments, fungal communities remain less studied despite their known taxonomic and functional diversity. High-throughput sequencing methods have augmented our capacity to assess eukaryotic diversity and their functions in microbial ecology. Here we provide the first description of the fungal community diversity found in deep sea sediments collected at the Southwest Indian Ridge (SWIR) using culture-dependent and high-throughput sequencing approaches. A total of 138 fungal isolates were cultured from seven different sediment samples using various nutrient media, and these isolates were identified to 14 fungal taxa, including 11 Ascomycota taxa (7 genera) and 3 Basidiomycota taxa (2 genera) based on internal transcribed spacers (ITS1, ITS2 and 5.8S) of rDNA. Using illumina HiSeq sequencing, a total of 757,467 fungal ITS2 tags were recovered from the samples and clustered into 723 operational taxonomic units (OTUs) belonging to 79 taxa (Ascomycota and Basidiomycota contributed to 99% of all samples) based on 97% sequence similarity. Results from both approaches suggest that there is a high fungal diversity in the deep-sea sediments collected in the SWIR and fungal communities were shown to be slightly different by location, although all were collected from adjacent sites at the SWIR. This study provides baseline data of the fungal diversity and biogeography, and a glimpse to the microbial ecology associated with the deep-sea sediments of the hydrothermal vent system of the Southwest Indian Ridge.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidium diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.

Exploring fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing

The present study investigated the fungal diversity in four different deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS1). A total of 40,297 fungal ITS1 sequences clustered into 420 operational taxonomic units (OTUs) with 97% sequence similarity and 170 taxa were recovered from these sediments. Most ITS1 sequences (78%) belonged to the phylum Ascomycota, followed by Basidiomycota (17.3%), Zygomycota (1.5%) and Chytridiomycota (0.8%), and a small proportion (2.4%) belonged to unassigned fungal phyla. Compared with previous studies on fungal diversity of sediments from deep-sea environments by culture-dependent approach and clone library analysis, the present result suggested that Illumina sequencing had been dramatically accelerating the discovery of fungal community of deep-sea sediments. Furthermore, our results revealed that Sordariomycetes was the most diverse and abundant fungal class in this study, challenging the traditional view that the diversity of Sordariomycetes phylotypes was low in the deep-sea environments. In addition, more than 12 taxa accounted for 21.5% sequences were found to be rarely reported as deep-sea fungi, suggesting the deep-sea sediments from Okinawa Trough harbored a plethora of different fungal communities compared with other deep-sea environments. To our knowledge, this study is the first exploration of the fungal diversity in deep-sea sediments from Okinawa Trough using high-throughput Illumina sequencing.

Fungal diversity in deep-sea sediments revealed by culture-dependent and culture-independent approaches

Abstract Diversity of fungi from deep biosphere is recently gaining an increasing attention. We investigated fungal diversity in two sediment cores ∼40 cmbsf (cm below seafloor) at a depth of ∼5 000 m in the Central Indian Basin (CIB), by culture-dependent as well as culture-independent approaches. This resulted in recovering a total of 19 culturable fungi and 46 operational taxonomic units (OTUs) respectively. Two of the cultured fungi showed similarity to Hortaea werneckii and Aspergillus versicolor , and 11 OTUs from environmental libraries showed high divergence (86–97 %) from the existing sequences in the GenBank (NCBI database). Some of the fungi, such as Cerrena , Hortaea and Aspergillus sp., were recovered by culture-dependent as well as culture-independent approaches. Together, culture-dependent and culture-independent approaches detected a total of 12 distinct fungal genera and 42 OTUs respectively from two sediment cores indicating presence of a high fungal diversity in deep-sea sediments.

Assessment of fungal diversity in deep-sea sediments by multiple primer approach

Increasing evidence of the fungal diversity in deep-sea sediments has come from amplification of environmental DNA with fungal specific or eukaryote primer sets. In order to assess the fungal diversity in deep-sea sediments of the Central Indian Basin (CIB) at ~5,000m depth, we amplified sediment DNA with four different primer sets. These were fungal-specific primer pair ITS1F/ITS4 (internal transcribed spacers), universal 18S rDNA primers NS1/NS2, Euk18S-42F/Euk18S-1492R and Euk18S-555F/Euk18S-1269R. One environmental library was constructed with each of the primer pairs, and 48 clones were sequenced per library. These sequences resulted in 8 fungal Operational Taxonomic Units (OTUs) with ITS and 19 OTUs with 18S rDNA primer sets respectively by taking into account the 2% sequence divergence cut-off for species delineation. These OTUs belonged to 20 distinct fungal genera of the phyla Ascomycota and Basidiomycota. Seven sequences were found to be divergent by 79-97% from the known sequences of the existing database and may be novel. A majority of the sequences clustered with known sequences of the existing taxa. The phylogenetic affiliation of a few fungal sequences with known environmental sequences from marine and hypersaline habitat suggests their autochthonous nature or adaptation to marine habitat. The amplification of sequences belonging to Exobasidiomycetes and Cystobasidiomycetes from deep-sea is being reported for the first time in this study. Amplification of fungal sequences with eukaryotic as well as fungal specific primers indicates that among eukaryotes, fungi appear to be a dominant group in the sampling site of the CIB.

Fungal diversity in deep-sea sediments – the presence of novel fungal groups

Abstract We investigated the diversity of fungal communities in 10 different deep-sea sediment samples by PCR-mediated internal transcribed spacer (ITS) regions of rRNA gene clone analysis. Although some of the amplified sequences were identified as common terrestrial fungal species, the majority were novel sequences that were not closely related to previously identified fungal ITS sequences in public databases. Phylogenetic analysis also suggested the novel phylogenetic affiliation of a group of predominant deep-sea phylotypes within the phylum Ascomycota. These phylotypes may be distributed widely in global deep-sea sediments. Another novel phylotype was placed in deep branches within the phylum Chytridiomycota with Rozella spp. as the closest related organisms. This study revealed the possible existence of previously unknown fungal components in various depths and sites of deep-sea sedimentary habitats. It is suggested that deep-sea environments are habitats hosting previously unexplored fungi, which may provide key insights into the early evolution of fungi and their ecological and physiological significance.

Fungal Diversity in Deep-Sea Environments

Fungi are one of the most important components in ecosystems and they occupy a wide variety of environments by virtue of their highly versatile physiology function. Recently, the presence of fungi in one of the extreme environments, deep-sea, has started to be recognized. In this article, recent scientific findings through the investigation of fungal diversity in deep-sea sediments collected from several deep-sea environments, including water depths of 10,000 m and methane cold-seep sites were described. PCR-mediated analysis revealed the presence of diverse highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum of Chytridiomycota with Rozella spp. as the closest related organisms, which may provide key insights into the early evolution of fungi.