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A special issue of Journal of Fungi (ISSN 2309-608X). This special issue belongs to the section "Environmental and Ecological Interactions of Fungi".

Deadline for manuscript submissions: closed (20 December 2021) | Viewed by 46705

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Dr. Federico Baltar

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Department of Functional & Evolutionary Ecology, Universitat Wien, Vienna, Austria
Interests: marine microbial ecology; biological oceanography; fungal oceanography; marine biogeochemistry
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Microbes are the central players in the ecology and biogeochemistry of marine systems. Yet, most of the research on microbial ecology in oceans has been performed on prokaryotes and eukaryotic phytoplankton, and fungi have been essentially neglected in open-ocean studies. One of the main reasons why the ecology of fungi in pelagic oceanic environments has been overlooked thus far is probably the preconception that fungi are outcompeted by prokaryotes when living in a resource-limited liquid environment like the ocean. Most of the available studies on marine fungi are based on the isolation and identification of fungi from different surfaces (e.g., submerged wood, sediments, macrophytes), mostly in coastal benthic environments. However, recent evidence suggests that fungi are also present in the oceanic water column, most likely mainly associated to particles, with the genomic potential to significantly contribute to marine biogeochemical cycles. Still, we lack even basic information on the ecology of the oceanic mycobiome, precluding us from determining the ecological role of this enigmatic kingdom in our oceans. The aim of this Special Issue is to focus on the ecology of marine fungi. Topics include, but are not limited to, fungal abundance, distribution, activity, and phylogenetic and/or functional diversity in coastal to open ocean environments, including seawater column and sediments, derived both from laboratory and field studies. Manuscripts summarizing recent advances in the topic or introducing novel experimental approaches are also welcome.

Dr. Federico Baltar
Guest Editor

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Keywords

marine fungi
coastal waters
open-ocean water column
marine sediment
fungal abundance
fungal physiology
fungal activity
fungal genetics
fungal phylogenetic diversity
fungal functional diversity

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Published Papers (11 papers)

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Research

Jump to: Review

17 pages, 2022 KiB

Open AccessArticle

Extracellular Enzymatic Activities of Oceanic Pelagic Fungal Strains and the Influence of Temperature

by Katherine Salazar Alekseyeva, Gerhard J. Herndl and Federico Baltar

J. Fungi 2022, 8(6), 571; https://doi.org/10.3390/jof8060571 - 26 May 2022

Cited by 7 | Viewed by 3406

Abstract

Although terrestrial and aquatic fungi are well-known decomposers of organic matter, the role of marine fungi remains largely unknown. Recent studies based on omics suggest that marine fungi potentially play a major role in elemental cycles. However, there is very limited information on the diversity of extracellular enzymatic activities performed by pelagic fungi in the ocean and how these might be affected by community composition and/or critical environmental parameters such as temperature. In order to obtain information on the potential metabolic activity of marine fungi, extracellular enzymatic activities (EEA) were investigated. Five marine fungal species belonging to the most abundant pelagic phyla (Ascomycota and Basidiomycota) were grown at 5 °C and 20 °C, and fluorogenic enzymatic assays were performed using six substrate analogues for the hydrolysis of carbohydrates (β-glucosidase, β-xylosidase, and N-acetyl-β-D-glucosaminidase), amino acids (leucine aminopeptidase), and of organic phosphorus (alkaline phosphatase) and sulfur compounds (sulfatase). Remarkably, all fungal strains were capable of hydrolyzing all the offered substrates. However, the hydrolysis rate (V_max) and half-saturation constant (K_m) varied among the fungal strains depending on the enzyme type. Temperature had a strong impact on the EEAs, resulting in Q₁₀ values of up to 6.1 and was species and substrate dependent. The observed impact of temperature on fungal EEA suggests that warming of the global ocean might alter the contribution of pelagic fungi in marine biogeochemical cycles. Full article

(This article belongs to the Special Issue Marine Fungus)

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14 pages, 3199 KiB

Open AccessArticle

Local Environmental Conditions Promote High Turnover Diversity of Benthic Deep-Sea Fungi in the Ross Sea (Antarctica)

by Giulio Barone, Cinzia Corinaldesi, Eugenio Rastelli, Michael Tangherlini, Stefano Varrella, Roberto Danovaro and Antonio Dell’Anno

J. Fungi 2022, 8(1), 65; https://doi.org/10.3390/jof8010065 - 8 Jan 2022

Cited by 5 | Viewed by 2709

Abstract

Fungi are a ubiquitous component of marine systems, but their quantitative relevance, biodiversity and ecological role in benthic deep-sea ecosystems remain largely unexplored. In this study, we investigated fungal abundance, diversity and assemblage composition in two benthic deep-sea sites of the Ross Sea (Southern Ocean, Antarctica), characterized by different environmental conditions (i.e., temperature, salinity, trophic availability). Our results indicate that fungal abundance (estimated as the number of 18S rDNA copies g⁻¹) varied by almost one order of magnitude between the two benthic sites, consistently with changes in sediment characteristics and trophic availability. The highest fungal richness (in terms of Amplicon Sequence Variants−ASVs) was encountered in the sediments characterized by the highest organic matter content, indicating potential control of trophic availability on fungal diversity. The composition of fungal assemblages was highly diverse between sites and within each site (similarity less than 10%), suggesting that differences in environmental and ecological characteristics occurring even at a small spatial scale can promote high turnover diversity. Overall, this study provides new insights on the factors influencing the abundance and diversity of benthic deep-sea fungi inhabiting the Ross Sea, and also paves the way for a better understanding of the potential responses of benthic deep-sea fungi inhabiting Antarctic ecosystems in light of current and future climate changes. Full article

(This article belongs to the Special Issue Marine Fungus)

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23 pages, 2690 KiB

Open AccessArticle

Genome and Metabolome MS-Based Mining of a Marine Strain of Aspergillus affinis

by Micael F. M. Gonçalves, Sandra Hilário, Marta Tacão, Yves Van de Peer, Artur Alves and Ana C. Esteves

J. Fungi 2021, 7(12), 1091; https://doi.org/10.3390/jof7121091 - 18 Dec 2021

Cited by 10 | Viewed by 4687

Abstract

Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ochratoxin A (OTA)). Given their relevance, it is important to analyze the genetic and metabolic diversity of the species of this section. We sequenced the genome of Aspergillus affinis CMG 70, isolated from sea water, and compared it with the genomes of species from section Circumdati, including A. affinis’s strain type. The A. affinis genome was characterized considering secondary metabolites biosynthetic gene clusters (BGCs), carbohydrate-active enzymes (CAZymes), and transporters. To uncover the biosynthetic potential of A. affinis CMG 70, an untargeted metabolomics (LC-MS/MS) approach was used. Cultivating the fungus in the presence and absence of sea salt showed that A. affinis CMG 70 metabolite profiles are salt dependent. Analyses of the methanolic crude extract revealed the presence of both unknown and well-known Aspergillus compounds, such as ochratoxin A, anti-viral (e.g., 3,5-Di-tert-butyl-4-hydroxybenzoic acid and epigallocatechin), anti-bacterial (e.g., 3-Hydroxybenzyl alcohol, l-pyroglutamic acid, lecanoric acid), antifungal (e.g., lpyroglutamic acid, 9,12,13-Trihydroxyoctadec-10-enoic acid, hydroxyferulic acid), and chemotherapeutic (e.g., daunomycinone, mitoxantrone) related metabolites. Comparative analysis of 17 genomes from 16 Aspergillus species revealed abundant CAZymes (568 per species), secondary metabolite BGCs (73 per species), and transporters (1359 per species). Some BGCs are highly conserved in this section (e.g., pyranonigrin E and UNII-YC2Q1O94PT (ACR toxin I)), while others are incomplete or completely lost among species (e.g., bikaverin and chaetoglobosins were found exclusively in series Sclerotiorum, while asperlactone seemed completely lost). The results of this study, including genome analysis and metabolome characterization, emphasize the molecular diversity of A. affinis CMG 70, as well as of other species in the section Circumdati. Full article

(This article belongs to the Special Issue Marine Fungus)

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14 pages, 2624 KiB

Open AccessArticle

Insights on Lulworthiales Inhabiting the Mediterranean Sea and Description of Three Novel Species of the Genus Paralulworthia

by Anna Poli, Valeria Prigione, Elena Bovio, Iolanda Perugini and Giovanna Cristina Varese

J. Fungi 2021, 7(11), 940; https://doi.org/10.3390/jof7110940 - 6 Nov 2021

Cited by 7 | Viewed by 2713

Abstract

The order Lulworthiales, with its sole family Lulworthiaceae, consists of strictly marine genera found on a wide range of substrates such as seagrasses, seaweeds, and seafoam. Twenty-one unidentified Lulworthiales were isolated in previous surveys aimed at broadening our understanding of the biodiversity hosted in the Mediterranean Sea. Here, these organisms, mostly found in association with Posidonia oceanica and with submerged woods, were examined using thorough multi-locus phylogenetic analyses and morphological observations. Maximum-likelihood and Bayesian phylogeny based on nrITS, nrSSU, nrLSU, and four protein-coding genes led to the introduction of three novel species of the genus Paralulworthia: P. candida, P. elbensis, and P. mediterranea. Once again, the marine environment is a confirmed huge reservoir of novel fungal lineages with an under-investigated biotechnological potential waiting to be explored. Full article

(This article belongs to the Special Issue Marine Fungus)

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10 pages, 2365 KiB

Open AccessCommunication

Autofluorescence Is a Common Trait in Different Oceanic Fungi

by Eva Breyer, Markus Böhm, Magdalena Reitbauer, Chie Amano, Marilena Heitger and Federico Baltar

J. Fungi 2021, 7(9), 709; https://doi.org/10.3390/jof7090709 - 29 Aug 2021

Cited by 7 | Viewed by 2818

Abstract

Natural autofluorescence is a widespread phenomenon observed in different types of tissues and organisms. Depending on the origin of the autofluorescence, its intensity can provide insights on the physiological state of an organism. Fungal autofluorescence has been reported in terrestrial and human-derived fungal samples. Yet, despite the recently reported ubiquitous presence and importance of marine fungi in the ocean, the autofluorescence of pelagic fungi has never been examined. Here, we investigated the existence and intensity of autofluorescence in five different pelagic fungal isolates. Preliminary experiments of fungal autofluorescence at different growth stages and nutrient conditions were conducted, reflecting contrasting physiological states of the fungi. In addition, we analysed the effect of natural autofluorescence on co-staining with DAPI. We found that all the marine pelagic fungi that were studied exhibited autofluorescence. The intensity of fungal autofluorescence changed depending on the species and the excitation wavelength used. Furthermore, fungal autofluorescence varied depending on the growth stage and on the concentration of available nutrients. Collectively, our results indicate that marine fungi can be auto-fluorescent, although its intensity depends on the species and growth condition. Hence, oceanic fungal autofluorescence should be considered in future studies when fungal samples are stained with fluorescent probes (i.e., fluorescence in situ hybridization) since this could lead to misinterpretation of results. Full article

(This article belongs to the Special Issue Marine Fungus)

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12 pages, 2156 KiB

Open AccessArticle

Adapting an Ergosterol Extraction Method with Marine Yeasts for the Quantification of Oceanic Fungal Biomass

by Katherine Salazar Alekseyeva, Barbara Mähnert, Franz Berthiller, Eva Breyer, Gerhard J. Herndl and Federico Baltar

J. Fungi 2021, 7(9), 690; https://doi.org/10.3390/jof7090690 - 26 Aug 2021

Cited by 10 | Viewed by 4556

Abstract

Ergosterol has traditionally been used as a proxy to estimate fungal biomass as it is almost exclusively found in fungal lipid membranes. Ergosterol determination has been mostly used for fungal samples from terrestrial, freshwater, salt marsh- and mangrove-dominated environments or to describe fungal degradation of plant matter. In the open ocean, however, the expected concentrations of ergosterol are orders of magnitude lower than in terrestrial or macrophyte-dominated coastal systems. Consequently, the fungal biomass in the open ocean remains largely unknown. Recent evidence based on microscopy and -omics techniques suggests, however, that fungi contribute substantially to the microbial biomass in the oceanic water column, highlighting the need to accurately determine fungal biomass in the open ocean. We performed ergosterol extractions of an oceanic fungal isolate (Rhodotorula sphaerocarpa) with biomass concentrations varying over nine orders of magnitude. While after the initial chloroform-methanol extraction ~87% of the ergosterol was recovered, a second extraction recovered an additional ~10%. Testing this extraction method on samples collected from the open Atlantic Ocean, we successfully determined ergosterol concentrations as low as 0.12 pM. Thus, this highly sensitive method is well suited for measuring fungal biomass from open ocean waters, including deep-sea environments. Full article

(This article belongs to the Special Issue Marine Fungus)

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16 pages, 2715 KiB

Open AccessArticle

The Culturable Mycobiome of Mesophotic Agelas oroides: Constituents and Changes Following Sponge Transplantation to Shallow Water

by Eyal Ben-Dor Cohen, Micha Ilan and Oded Yarden

J. Fungi 2021, 7(7), 567; https://doi.org/10.3390/jof7070567 - 16 Jul 2021

Cited by 4 | Viewed by 2477

Abstract

Marine sponges harbor a diverse array of microorganisms and the composition of the microbial community has been suggested to be linked to holo-biont health. Most of the attention concerning sponge mycobiomes has been given to sponges present in shallow depths. Here, we describe the presence of 146 culturable mycobiome taxa isolated from mesophotic niche (100 m depth)-inhabiting samples of Agelas oroides, in the Mediterranean Sea. We identify some potential in vitro interactions between several A. oroides-associated fungi and show that sponge meso-hyl extract, but not its predominantly collagen-rich part, is sufficient to support hyphal growth. We demonstrate that changes in the diversity of culturable mycobiome constituents occur following sponge transplantation from its original mesophotic habitat to shallow (10 m) waters, where historically (60 years ago) this species was found. We conclude that among the 30 fungal genera identified as associated with A. oroides, Aspergillus, Penicillium and Trichoderma constitute the core mycobiome of A. oroides, and that they persist even when the sponge is transplanted to a suboptimal environment, indicative of the presence of constant, as well as dynamic, components of the sponge mycobiome. Other genera seemed more depth-related and appeared or disappeared upon host’s transfer from 100 to 10 m. Full article

(This article belongs to the Special Issue Marine Fungus)

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14 pages, 3097 KiB

Open AccessArticle

Mold and Yeast-Like Fungi in the Seaside Air of the Gulf of Gdańsk (Southern Baltic) after an Emergency Disposal of Raw Sewage

by Małgorzata Michalska, Monika Kurpas, Katarzyna Zorena, Piotr Wąż and Roman Marks

J. Fungi 2021, 7(3), 219; https://doi.org/10.3390/jof7030219 - 17 Mar 2021

Cited by 9 | Viewed by 3543

Abstract

The aim of this study was to determine the correlation between the meteorological factors and the number of molds and yeast-like fungi in the air in the five coastal towns in the years 2014–2017, and in 2018, after emergency disposal of raw sewage to the Gdańsk Gulf. In the years 2014–2018, a total number of 88 air samples were collected in duplicate in the five coastal towns of Hel, Puck, Gdynia, Sopot, and Gdańsk-Brzeźno. After the application of the (PCA) analysis, this demonstrated that the first principal component (PC1) had a positive correlation with the water temperature, wind speed, air temperature, and relative humidity. The second principal component (PC2) had a positive correlation with the relative humidity, wind speed, wind direction, and air temperature. In 2018, potentially pathogenic mold and yeast-like fungi (Candida albicans, Stachybotrys chartarum complex, Aspergillus section Fumigati) were detected in the seaside air. While the detected species were not observed in the years 2014–2017. We suggest that it is advisable to inform residents about the potential health risk in the event of raw sewage disposal into the water. Moreover, in wastewater treatment plants, tighter measures, including wastewater disinfection, should be introduced. Full article

(This article belongs to the Special Issue Marine Fungus)

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15 pages, 1847 KiB

Open AccessArticle

Diversity and N₂O Production Potential of Fungi in an Oceanic Oxygen Minimum Zone

by Xuefeng Peng and David L. Valentine

J. Fungi 2021, 7(3), 218; https://doi.org/10.3390/jof7030218 - 17 Mar 2021

Cited by 20 | Viewed by 3617

Abstract

Fungi in terrestrial environments are known to play a key role in carbon and nitrogen biogeochemistry and exhibit high diversity. In contrast, the diversity and function of fungi in the ocean has remained underexplored and largely neglected. In the eastern tropical North Pacific oxygen minimum zone, we examined the fungal diversity by sequencing the internal transcribed spacer region 2 (ITS2) and mining a metagenome dataset collected from the same region. Additionally, we coupled ¹⁵N-tracer experiments with a selective inhibition method to determine the potential contribution of marine fungi to nitrous oxide (N₂O) production. Fungal communities evaluated by ITS2 sequencing were dominated by the phyla Basidiomycota and Ascomycota at most depths. However, the metagenome dataset showed that about one third of the fungal community belong to early-diverging phyla. Fungal N₂O production rates peaked at the oxic–anoxic interface of the water column, and when integrated from the oxycline to the top of the anoxic depths, fungi accounted for 18–22% of total N₂O production. Our findings highlight the limitation of ITS-based methods typically used to investigate terrestrial fungal diversity and indicate that fungi may play an active role in marine nitrogen cycling. Full article

(This article belongs to the Special Issue Marine Fungus)

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Review

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72 pages, 21366 KiB

Open AccessReview

Fungal Biodiversity in Salt Marsh Ecosystems

by Mark S. Calabon, E. B. Gareth Jones, Itthayakorn Promputtha and Kevin D. Hyde

J. Fungi 2021, 7(8), 648; https://doi.org/10.3390/jof7080648 - 9 Aug 2021

Cited by 31 | Viewed by 6957

Abstract

This review brings together the research efforts on salt marsh fungi, including their geographical distribution and host association. A total of 486 taxa associated with different hosts in salt marsh ecosystems are listed in this review. The taxa belong to three phyla wherein Ascomycota dominates the taxa from salt marsh ecosystems accounting for 95.27% (463 taxa). The Basidiomycota and Mucoromycota constitute 19 taxa and four taxa, respectively. Dothideomycetes has the highest number of taxa, which comprises 47.12% (229 taxa), followed by Sordariomycetes with 167 taxa (34.36%). Pleosporales is the largest order with 178 taxa recorded. Twenty-seven genera under 11 families of halophytes were reviewed for its fungal associates. Juncus roemerianus has been extensively studied for its associates with 162 documented taxa followed by Phragmites australis (137 taxa) and Spartina alterniflora (79 taxa). The highest number of salt marsh fungi have been recorded from Atlantic Ocean countries wherein the USA had the highest number of species recorded (232 taxa) followed by the UK (101 taxa), the Netherlands (74 taxa), and Argentina (51 taxa). China had the highest number of salt marsh fungi in the Pacific Ocean with 165 taxa reported, while in the Indian Ocean, India reported the highest taxa (16 taxa). Many salt marsh areas remain unexplored, especially those habitats in the Indian and Pacific Oceans areas that are hotspots of biodiversity and novel fungal taxa based on the exploration of various habitats. Full article

(This article belongs to the Special Issue Marine Fungus)

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24 pages, 926 KiB

Open AccessReview

Diversity, Ecological Role and Biotechnological Potential of Antarctic Marine Fungi

by Stefano Varrella, Giulio Barone, Michael Tangherlini, Eugenio Rastelli, Antonio Dell’Anno and Cinzia Corinaldesi

J. Fungi 2021, 7(5), 391; https://doi.org/10.3390/jof7050391 - 17 May 2021

Cited by 30 | Viewed by 6314

Abstract

The Antarctic Ocean is one of the most remote and inaccessible environments on our planet and hosts potentially high biodiversity, being largely unexplored and undescribed. Fungi have key functions and unique physiological and morphological adaptations even in extreme conditions, from shallow habitats to deep-sea sediments. Here, we summarized information on diversity, the ecological role, and biotechnological potential of marine fungi in the coldest biome on Earth. This review also discloses the importance of boosting research on Antarctic fungi as hidden treasures of biodiversity and bioactive molecules to better understand their role in marine ecosystem functioning and their applications in different biotechnological fields. Full article

(This article belongs to the Special Issue Marine Fungus)

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