Fungal biodiversity in aquatic habitats

Fungal biodiversity in freshwater, brackish and marine habitats was estimated based on reports in the literature. The taxonomic groups treated were those with species commonly found on submerged substrates in aquatic habitats: Ascomycetes (exclusive of yeasts), Basidiomycetes, Chytridiomycetes, and the non-fungal Saprolegniales in the Class Oomycetes. Based on presence/absence data for a large number and variety of aquatic habitats, about 3,000 fungal species and 138 saprolegnialean species have been reported from aquatic habitats. The greatest number of taxa comprise the Ascomycetes, including mitosporic taxa, and Chytridiomycetes. Taxa of Basidiomycetes are, for the most part, excluded from aquatic habitats. The greatest biodiversity for all groups occurs in temperate areas, followed by Asian tropical areas. This pattern may be an artifact of the location of most of the sampling effort. The least sampled geographic areas include Africa, Australia, China, South America and boreal and tropical regions worldwide. Some species overlap occurs among terrestrial and freshwater taxa but little species overlap occurs among freshwater and marine taxa. We predict that many species remain to be discovered in aquatic habitats given the few taxonomic specialists studying these fungi, the few substrate types studied intensively, and the vast geographical area not yet sampled.     

Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill

Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.     

Biodiversity and Enzyme Activity of Marine Fungi with 28 New Records from the Tropical Coastal Ecosystems in Vietnam

The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.     

Phylogenetic diversity of culturable fungi associated with the Hawaiian Sponges Suberites zeteki and Gelliodes fibrosa

Sponges are well documented to harbor large amounts of microbes. Both culture-dependent and molecular approaches have revealed remarkable bacterial diversity in marine sponges. Fungi are commonly isolated from marine sponges, yet no reports on phylogenetic diversity of sponge-inhabiting fungi exist. In this report, we investigated the phylogenetic diversity of culturable fungi from the Hawaiian alien marine sponges Suberites zeteki and Gelliodes fibrosa. A total of 44 independent isolates were recovered from these two sponge species, representing 7 orders and 22 genera of Ascomycota. The majority (58%) of fungal isolates from S. zeteki resided in the Pleosporales group, while the predominant isolates (52%) from G. fibrosa were members of the Hypocreales group. Though differing in fungal species composition and structure, culturable communities of these two sponges displayed similar phylogenetic diversity. At the genus level, only two genera Penicillium and Trichoderma in the Eurotiales and Hypocreales orders, respectively, were present in both sponge species. The other genera of the fungal isolates were associated with either S. zeteki or G. fibrosa. Some of these fungal genera had been isolated from sponges collected in other marine habitats, but more than half of these genera were identified for the first time in these two marine sponges. Overall, the diversity of culturable fungal communities from these two sponge species is much higher than that observed in studies of marine sponges from other areas. This is the first report of phylogenetic diversity of marine sponge-associated fungi and adds one more dimension to our current understanding of the phylogenetic diversity of sponge-symbiotic microbes.     

Species Richness and Adaptation of Marine Fungi from Deep-Subseafloor Sediments

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.     

Filamentous fungi of the submarine soils of the Sakhalin Gulf (Sea of Okhotsk)

This study examines the biodiversity of submarine-soil filamentous fungi in Sakhalin Gulf for the first time. A total of 82 species of fungi belonging to 35 genera were isolated and identified. Of these, representatives of Anamorphic fungi were predominant. All species identified were facultative marine fungi, except one, Acremonium fuci, which was known until now only from marine habitats. The qualitative and quantitative structure of submarine-soil fungal assemblages of the eastern part (Amur River plume) and the western part (continental shelf) of Sakhalin Gulf was studied.     

Microbial diversity in tropical marine sediments assessed using culture-dependent and culture-independent techniques

The microbial communities associated with marine sediments are critical for ecosystem function yet remain poorly characterized. While culture-independent (CI) techniques capture the broadest perspective on community composition, culture-dependent (CD) methods can select for low abundance taxa that are missed using CI approaches. This study aimed to assess microbial diversity in tropical marine sediments at five shallow-water sites in Belize using both CD and CI techniques. The CD methods captured approximately 3% of the >800 genera detected across all sites using the CI approach. Additionally, 39 genera were only detected in culture, revealing rare taxa that were missed with the CI approach. Significantly different communities were detected across sites, with rare taxa playing an important role in distinguishing among communities. This study provides important baseline data describing shallow-water sediment microbial communities, evidence that standard cultivation techniques may be more effective than previously recognized, and the first steps towards identifying new taxa that are amenable to agar plate cultivation.     

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities

Endospores of thermophilic bacteria are found in cold and temperate sediments where they persist in a dormant state. As inactive endospores that cannot grow at the low ambient temperatures, they are akin to tracer particles in cold sediments, unaffected by factors normally governing microbial biogeography (e.g., selection, drift, mutation). This makes thermophilic endospores ideal model organisms for studying microbial biogeography since their spatial distribution can be directly related to their dispersal history. To assess dispersal histories of estuarine bacteria, thermophilic endospores were enriched from sediments along a freshwater‐to‐marine transect of the River Tyne in high temperature incubations (50°C). Dispersal histories for 75 different taxa indicated that the majority of estuarine endospores were of terrestrial origin; most closely related to bacteria from warm habitats associated with industrial activity. A subset of the taxa detected were marine derived, with close relatives from hot deep marine biosphere habitats. These patterns are consistent with the sources of sediment in the River Tyne being predominantly terrestrial in origin. The results point to microbial communities in estuarine and marine sediments being structured by bi‐directional currents, terrestrial run‐off and industrial effluent as vectors of passive dispersal and immigration.     

Coastal marine habitats harbor novel early-diverging fungal diversity

Despite nearly a century of study, the diversity of marine fungi remains poorly understood. Historical surveys utilizing microscopy or culture-dependent methods suggest that marine fungi are relatively species-poor, predominantly Dikarya, and localized to coastal habitats. However, the use of high-throughput sequencing technologies to characterize microbial communities has challenged traditional concepts of fungal diversity by revealing novel phylotypes from both terrestrial and aquatic habitats. Here, I used ion semiconductor sequencing (Ion Torrent) of the ribosomal large subunit (LSU/28S) to explore fungal diversity from water and sediment samples collected from four habitats in coastal North Carolina. The dominant taxa observed were Ascomycota and Chytridiomycota, though all fungal phyla were represented. Diversity was highest in sand flats and wetland sediments, though benthic sediments harbored the highest proportion of novel sequences. Most sequences assigned to early-diverging fungal groups could not be assigned beyond phylum with statistical support, suggesting they belong to unknown lineages.     

Mycorrhizal specificity, preference, and plasticity of six slipper orchids from South Western China

Mycorrhizal fungi of six endangered species, Paphiopedilum micranthum, Paphiopedilum armeniacum, Paphiopedilum dianthum, Cypripedium flavum, Cypripedium guttatum, and Cypripedium tibeticum, from two closely related genera in the Orchidaceae from Southwestern China, were characterized using the nuclear internal transcribed spacer (ITS) and part of the large subunit gene of mitochondrial rDNA (mtLSU) sequences. The most frequently detected fungi belonged to the Tulasnellaceae. These fungi were represented by 25 ITS sequence types and clustered into seven major clades in the phylogenetic analysis of 5.8S sequences. Species of Paphiopedilum and Cypripedium shared no fungal ITS sequence types in common, but their fungal taxa sometimes occurred in the same major clade of the 5.8S phylogenetic tree. Although it had several associated fungal ITS sequence types in a studied plot, each orchid species had in general only a single dominant type. The fungal sequence type spectra of different species of Paphiopedilum from similar habitats sometimes overlapped; however, the dominant sequence types differed among the species and so did the sequence-type spectra within Cypripedium. Orchids of P. micranthum and P. armeniacum transplanted from the field and grown in two greenhouses had a greater number of mycorrhizal associations than those sampled directly from the field. Root specimens from P. micranthum taken from the greenhouses were preferably associated with mycobionts of the Tulasnella calospora complex, while those from the field had mycorrhizal associations of other tulasnelloid taxa. Such plasticity in mycorrhizal associations makes ex situ conservation or even propagation by means of mycorrhization of axenically grown seedlings possible.     

Patterns in the benthic communities on the shelf of the sub-Antarctic Prince Edward Islands

Summary Benthic communities at the sub-Antarctic Prince Edward Islands were sampled qualitatively with an epi-benthic sled at 57 stations over a five year period. Additional information on these communities was obtained from replicate underwater photographs. In total, 546 macrofaunal species were found. Despite the extreme isolation and geological youth of the islands, there seems to have been a diverse colonisation. A cluster-analysis based on species abundance aggregated most stations into 8 groups. Each of these groups had a unique depth and substratum combination. Thourella variabilis (Octocoralea), and Cabarea darwinii (Bryozoa) characterised deep rocky assemblages and Serpula vermicularis, Lanice conchilega (Polychaeta) and Magellania kerguelenensis (Brachiopoda) characterised soft substrata. Indicator species separating each of the 8 clusters are given. Trends in percentage cover and densities of major taxa with respect to depth and substratum, as shown by photographs, are described. Deep, rocky substrata were dominated by Porifera, Bryozoa and Cnidaria, while soft-substrata were dominated by Polychaeta, Bivalvia and Brachiopoda. Errant forms consisted predominantly of Echinodermata, with Crustacea being important in shallower habitats. Filter-feeders dominated the benthos of the islands in all habitats.     

Fungi in the sea fan <Emphasis Type="Italic">Gorgonia ventalina</Emphasis>: diversity and sampling strategies

Fungal communities from gorgonians have been poorly documented and most studies of these communities have lacked defined sampling strategies. The objectives of this study were: (1) to estimate fungal diversity in Gorgonia ventalina; (2) to compare two sampling and tissue processing strategies: tissue fragments of different sizes vs. homogenized tissue. A total of seven genera and fourteen species of fungi were isolated on culture medium and identified by sequencing the nrITS. All but one species were new reports. In both treatments Aspergillus and Penicillium were the most common genera isolated. Most species isolated from fragments were not observed from homogenized tissue and vice versa. Reducing the size fragment increased significantly the number of species isolated per fragment. To better estimate fungal diversity in sea fans a strategy is proposed that combines sampling of small tissue fragments with homogenized tissue, since each technique yielded fungal species not detected by the other.     

Potentially pathogenic and biocontrol Ascomycota associated with green wall structures of basket willow (<Emphasis Type="Italic">Salix viminalis</Emphasis> L.) revealed by phenotypic characters and ITS phylogeny

Ascomycota are among the fungi that cause serious willow diseases in all natural habitats worldwide. This study was conducted to determine if basket willow used in green wall structures (GWS) built of willow stems were infected by potentially important fungal diseases or their antagonists in urban areas of eastern Canada. In total, 13 different phenotypic genera belonging to eight families of ascomycetous fungi were isolated and identified according to their sexual and/or asexual forms. Venturia pathogenic species complex were represented by three different anamorphs: Fusicladium, Fusicladium-Cladosporium, and Pollaccia as anamorph. They were responsible for the highest incidence value on leaves (IF > 15%). Cryptodiaporthe, Drepanopeziza, and Glomerella dominated on bark (IF > 5%). A significantly higher incidence value of fungal communities was found on first year than on second year GWS. The correspondence analysis using χ² distance showed that communities of potentially pathogenic species are closely related to diseased plants, while healthy plants often contain biocontrol species such as Cladobotryum mycoparasite on healthy bark and Alternaria sp. antagonist on healthy leaves. The phylogenetic positions of the different fungal taxa and their relationship have been revealed by use of PCR amplified internal transcriber spacer (ITS) region of rDNA.     

Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false‐positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along‐shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat‐specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.     

Community Assembly of Biological Soil Crusts of Different Successional Stages in a Temperate Sand Ecosystem, as Assessed by Direct Determination and Enrichment Techniques

In temperate regions, biological soil crusts (BSCs: complex communities of cyanobacteria, eukaryotic algae, bryophytes, and lichens) are not well investigated regarding community structure and diversity. Furthermore, studies on succession are rare. For that reason, the community assembly of crusts representing two successional stages (initial, 5 years old; and stable, >20 years old) were analyzed in an inland sand ecosystem in Germany in a plot-based approach (2 × 18 plots, each 20 × 20 cm). Two different methods were used to record the cyanobacteria and eukaryotic algae in these communities comprehensively: determination directly out of the soil and enrichment culture techniques. Additionally, lichens, bryophytes, and phanerogams were determined. We examine four hypotheses: (1) A combination of direct determination and enrichment culture technique is necessary to detect cyanobacteria and eukaryotic algae comprehensively. In total, 45 species of cyanobacteria and eukaryotic algae were detected in the study area with both techniques, including 26 eukaryotic algae and 19 cyanobacteria species. With both determination techniques, 22 identical taxa were detected (11 eukaryotic algae and 11 cyanobacteria). Thirteen taxa were only found by direct determination, and ten taxa were only found in enrichment cultures. Hence, the hypothesis is supported. Additionally, five lichen species (three genera), five bryophyte species (five genera), and 24 vascular plant species occurred. (2) There is a clear difference between the floristic structure of initial and stable crusts. The different successional stages are clearly separated by detrended correspondence analysis, showing a distinct structure of the community assembly in each stage. In the initial crusts, Klebsormidium flaccidum, Klebsormidium cf. klebsii, and Stichococcus bacillaris were important indicator species, whereas the stable crusts are especially characterized by Tortella inclinata. (3) The biodiversity of BSC taxa and vascular plant species increases from initial to stable BSCs. There are significantly higher genera and species numbers of cyanobacteria and eukaryotic algae in initial BSCs. Stable BSCs are characterized by significantly higher species numbers of bryophytes and vascular plant species. The results show that, in the investigated temperate region, the often-assumed increase of biodiversity in the course of succession is clearly taxa-dependent. Both successional stages of BSCs are diversity “hot spots” with about 29 species of all taxa per 20 × 20 cm plot. (4) Nitrogen and chlorophyll a concentrations increase in the course of succession. The chlorophyll a content of the crusts (cyanobacteria, eukaryotic algae, bryophyte protonemata) is highly variable across the studied samples, with no significant differences between initial and stable BSCs; nor were ecologically significant differences in soil nutrient contents observed. According to our results, we cannot confirm this hypothesis; the age difference between our two stages is probably not big enough to show such an increase. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Ecology and diversity of Cortinarius species (Agaricales,Basidiomycota) associated with Quercus ilex L. in the Mediterranean area of Liguria (North-western Italy)

Cortinarius is one of the most widespread macrofungal genera. Although Mediterranean basin is considered a biodiversity hotspot, very few studies have addressed the presence and importance of Cortinarius species in such area. Surveys were carried out in Liguria (NW Italy) in different habitats characterized by the presence of Quercus ilex. Altogether 67 taxa were observed: 49 of them are new records for Liguria while 23 represent new records for Italy. In addition, we report the distinguishing characters and ecological traits of the species which are also rare in Europe.     

Molecular phylogeny of neodalyellid flatworms (Rhabdocoela), including three new species from British Columbia

Rhabdocoel flatworms are abundant members of marine meiofaunal communities worldwide, contributing to a reservoir of biodiversity that thrives in sediments and on macroalgae. Yet, they are relatively understudied due to bias in meiofaunal collection techniques, time‐intensive identification and a lack of taxonomic expertise. Here, sampling of intertidal habitats in British Columbia, Canada, was undertaken to enhance our understanding of rhabdocoel diversity in this region. Six species of neodalyellid rhabdocoel were discovered and characterized with DNA sequence and morphological data: Pogaina paranygulgus, Anoplodium hymanae, Baicalellia pusilla n. comb., B. solaris n. sp., B. daftpunka n. sp. and Tamanawas kalipis n. g., n. sp. The latter three species are new to science. A phylogenetic analysis of neodalyellid rhabdocoels, inferred from 18S and 28S ribosomal RNA gene sequences of 39 taxa, provided further insight into their interrelationships, trait evolution and systematics, including the recognition of a new genus, Tamanawas, and the suppression of Canetellia and Coronopharynx.     

Diversity,ecology, and bioprospecting of culturable fungi in lakes impacted by anthropogenic activities in Maritime Antarctica

In this study, we accessed culturable fungal assemblages present in the sediments of three lakes potentially impacted anthropogenically in the Fildes Peninsula, King George Island, Antarctica and identified 63 taxa. Cladosporium sp. 2, Pseudeurotium hygrophilum, and Pseudogymnoascus verrucosus were recovered from the sampled sediments of all lakes. High concentrations of metals and the lowest fungal diversity indices were detected in the sediments of the Central Lake, which can be influenced by human activities due to their proximity to research stations to those of the other two lakes, which were far from the Antarctic stations. At least one type of biological activity was demonstrated by 40 fungal extracts. Among these, P. hygrophilum, P. verrucosus, Penicillium glabrum, and Penicillium solitum demonstrated strong trypanocidal, herbicidal, and antifungal activities. Our results suggest that an increase of the anthropogenic activities in the region might have affected the microbial diversity and composition. In addition, the fungal diversity in these lakes may be a useful model to study the effect of anthropogenic activities in Antarctica. We isolated a diverse group of fungal taxa from Antarctic lake sediments, which have the potential to produce novel compounds for the both the medical and agriculture sectors.

     

Quantitative and qualitative seasonal changes in the microbial community from the phyllosphere of sugar beet (Beta vulgaris)

Bacteria, yeasts and filamentous fungi colonizing immature, mature and senescing primary leaves of field grown Beta vulgaris (sugar beet) were analysed over a complete growing season. Greatest microbial numbers were detected on senescing primary leaves and these numbers increased over most of the season. The number of colonizers detected on mature leaves was found to be stable over most of the study.Filamentous fungi and yeasts were identified to the genus level and the communities found to have greatest diversity during the summer months. There was no consistent pattern of diversity according to leaf type. Two genera of filamentous fungi, Cladosporium and Alternaria and two yeast genera, Cryptococcus and Sporobolomyces were the most numerous fungal populations isolated. Only 8 filamentous fungi and 3 yeast genera were commonly isolated on PDA (potato dextrose agar).Bacterial strains (1236) were isolated on Tryptic Soy Broth (TSB) agar and identified to species, or in some cases sub-species level, by analysis of their fatty acid methyl ester (FAME) profiles. Isolated bacteria were grouped into 78 named and 37 unnamed species clusters. Greatest number of bacterial species were isolated from young plants and leaves, sampled during the autumn months. Bacterial community diversity was lowest in mid-summer and winter months. Pseudomonas was the most commonly isolated genus and Erwinia herbicola the most common species. P. aureofaciens was the only species isolated from soil that was also isolated from the phyllosphere of B. vulgaris throughout the season.