Despite the rapid development of molecular techniques relevant for natural product research, culture isolates remain the primary source from which natural products chemists discover and obtain new ...molecules from microbial sources. Techniques for obtaining and identifying microbial isolates (such as filamentous fungi) are thus of crucial importance for a successful natural products' discovery program. This review is presented as a "best-practices guide" to the collection and isolation of marine fungi for natural products research. Many of these practices are proven techniques used by mycologists for the isolation of a broad diversity of fungi, while others, such as the construction of marine baiting stations and the collection and processing of sea foam using dilution to extinction plating techniques, are methodological adaptations for specialized use in marine/aquatic environments. To this day, marine fungi,
, remain one of the few underexplored resources of natural products. Cultivability is one of the main limitations hindering the discovery of natural products from marine fungi. Through encouraged collaboration with marine mycologists and the sharing of historically proven mycological practices for the isolation of marine fungi, our goal is to provide natural products chemists with the necessary tools to explore this resource in-depth and discover new and potentially novel natural products.
An online resource for marine fungi Jones, E. B. Gareth; Pang, Ka-Lai; Abdel-Wahab, Mohamed A. ...
Fungal diversity,
05/2019, Letnik:
96, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Index Fungorum, Species Fungorum and MycoBank are the key fungal nomenclature and taxonomic databases that can be sourced to find taxonomic details concerning fungi, while DNA sequence data can be ...sourced from the NCBI, EBI and UNITE databases. Nomenclature and ecological data on freshwater fungi can be accessed on
http://fungi.life.illinois.edu/
, while
http://www.marinespecies.org/provides
a comprehensive list of names of marine organisms, including information on their synonymy. Previous websites however have little information on marine fungi and their ecology, beside articles that deal with marine fungi, especially those published in the nineteenth and early twentieth centuries may not be accessible to those working in third world countries. To address this problem, a new website
www.marinefungi.org
was set up and is introduced in this paper. This website provides a search facility to genera of marine fungi, full species descriptions, key to species and illustrations, an up to date classification of all recorded marine fungi which includes all fungal groups (Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota and fungus-like organisms e.g. Thraustochytriales), and listing recent publications. Currently, 1257 species are listed in the marine fungi website (
www.marinefungi.org
), in 539 genera, 74 orders, 168 families, 20 classes and five phyla, with new taxa continuing to be described. The website has curators with specialist mycological expertise who help to provide update data on the classification of marine fungi. This article also reviews knowledge of marine fungi covering a wide range of topics: their higher classification, ecology and world distribution, role in energy transfer in the oceans, origin and new chemical structures. An updated classification of marine fungi is also included. We would like to invite all mycologists to contribute to this innovative website.
Knowledge about the presence and ecological significance of bacteria and archaea in the deep-sea environments has been well recognized, but the eukaryotic microorganisms, such as fungi, have rarely ...been reported. The present study investigated the composition and abundance of fungal community in the deep-sea sediments of the Pacific Ocean. In this study, a total of 1,947 internal transcribed spacer (ITS) regions of fungal rRNA gene clones were recovered from five sediment samples at the Pacific Ocean (water depths ranging from 5,017 to 6,986 m) using three different PCR primer sets. There were 16, 17, and 15 different operational taxonomic units (OTUs) identified from fungal-universal, Ascomycota-, and Basidiomycota-specific clone libraries, respectively. Majority of the recovered sequences belonged to diverse phylotypes of Ascomycota (25 phylotypes) and Basidiomycota (18 phylotypes). The multiple primer approach totally recovered 27 phylotypes which showed low similarities (≤97 %) with available fungal sequences in the GenBank, suggesting possible new fungal taxa occurring in the deep-sea environments or belonging to taxa not represented in the GenBank. Our results also recovered high fungal LSU rRNA gene copy numbers (3.52 × 10⁶to 5.23 × 10⁷copies/g wet sediment) from the Pacific Ocean sediment samples, suggesting that the fungi might be involved in important ecological functions in the deep-sea environments.
A high diversity of fungi was discovered on various substrates collected at the marine shallow-water Kueishan Island Hydrothermal Vent Field, Taiwan, using culture and metabarcoding methods but ...whether these fungi can grow and play an active role in such an extreme environment is unknown. We investigated the combined effects of different salinity, temperature and pH on growth of ten fungi (in the genera Aspergillus, Penicillium, Fodinomyces, Microascus, Trichoderma, Verticillium) isolated from the sediment and the vent crab Xenograpsus testudinatus. The growth responses of the tested fungi could be referred to three groups: (1) wide pH, salinity and temperature ranges, (2) salinity-dependent and temperature-sensitive, and (3) temperature-tolerant. Aspergillus terreus NTOU4989 was the only fungus which showed growth at 45 °C, pH 3 and 30 ‰ salinity, and might be active near the vents. We also carried out a transcriptome analysis to understand the molecular adaptations of A. terreus NTOU4989 under these extreme conditions. Data revealed that stress-related genes were differentially expressed at high temperature (45 °C); for instance, mannitol biosynthetic genes were up-regulated while glutathione S-transferase and amino acid oxidase genes down-regulated in response to high temperature. On the other hand, hydrogen ion transmembrane transport genes and phenylalanine ammonia lyase were up-regulated while pH-response transcription factor was down-regulated at pH 3, a relative acidic environment. However, genes related to salt tolerance, such as glycerol lipid metabolism and mitogen-activated protein kinase, were up-regulated in both conditions, possibly related to maintaining water homeostasis. The results of this study revealed the genetic evidence of adaptation in A. terreus NTOU4989 to changes of environmental conditions.
Sordariomycetes
is one of the largest classes of
Ascomycota
and is characterised by perithecial ascomata and inoperculate unitunicate asci. The class includes many important plant pathogens, as well ...as endophytes, saprobes, epiphytes, and fungicolous, lichenized or lichenicolous taxa. The class includes freshwater, marine and terrestrial taxa and has a worldwide distribution. This paper provides an updated outline of the
Sordariomycetes
and a backbone tree incorporating asexual and sexual genera in the class. Based on phylogeny and morphology we introduced three subclasses;
Diaporthomycetidae, Lulworthiomycetidae
and
Meliolomycetidae
and five orders;
Amplistromatales
,
Annulatascales
,
Falcocladiales
,
Jobellisiales
and
Togniniales
. The outline is based on literature to the end of 2014 and the backbone tree published in this paper. Notes for 397 taxa with information, such as new family and genera novelties, novel molecular data published since the Outline of Ascomycota 2009, and new links between sexual and asexual genera and thus synonymies, are provided. The Sordariomycetes now comprises six subclasses, 28 orders, 90 families and 1344 genera. In addition a list of 829 genera with uncertain placement in
Sordariomycetes
is also provided.
The hadal zone is among the least studied habitats on the planet, and the composition, distribution and variations of the biological communities in the hadal zone are poorly understood. Recent ...explorations of the ocean trenches have revealed distinctive metabolic and functional microbial communities in the hadal biosphere. Compared to bacteria and archaea, fungal community in hadal trenches is poorly documented. In this study, we present, for the first time, results of a comparative survey of the sediment-associated fungal communities at the Yap Trench by using high-throughput sequencing and culture-based techniques. The fungal diversity obtained from these techniques were different, with 11.1% of the fungal genera shared between both techniques. Through ITS2 (internal transcribed spacer 2 of the rDNA) metabarcode sequencing from 42 sediment samples, 890 fungal operational taxonomic units (OTUs) were found based on clustering at a 97% sequence similarity cutoff level. Of these OTUs, 98 OTUs belonged to Ascomycota, 52 OTUs to Basidiomycota, 1 OTU to Chytridiomycota, 4 OTUs to Mortierellomycota, 19 OTUs to Mucoromycota and 2 OTUs to Rozellomycota, whereas 714 OTUs could not be assigned to any fungal phylum. The Ascomycota and the Basidiomycota comprised 49.74% and 5.84% of the total sequences, respectively t. Eurotiomycetes was identified as the most dominant fungal class. The culture-based technique also revealed Eurotiomycetes as the most abundant class, but some classes, such as Endogonomycetes and Umbelopsidomycetes, were not detected by the culture-based technique. Altogether, our findings provide valuable information for the understanding of fungal distribution and potential ecological roles of fungi in deep-sea hadal trenches.
•A comparative survey of the sediment-associated fungal communities at the Yap Trench by using high-throughput sequencing and culture-based techniques.•A total of 321,593 fungal ITS2 sequences clustered into 890 operational taxonomic units (OTUs) with 97% sequence similarity and 40 genera were recovered from these sediments, and functional analysis of fungal communities, saprotrophic fungi are the dominant forms in deep-sea sediment of the Yap Trench.•Four fungal classes: Archaeorhizomycetes (phylum Ascomycota), Agaricostilbomycetes (phylum Basidiomycota), Endogonomycetes and Umbelopsidomycetes (phylum Mucoromycota) are firstly reported in the deep-sea environments.
In this study, a marine brown alga
-derived fungal strain,
SC29, was isolated and identified. Column chromatography of the extracts from liquid fermented products of the fungal strain was carried out ...and led to the isolation of six compounds. Their structures were elucidated by spectroscopic analysis and supported by single-crystal X-ray diffraction as four previously undescribed (
)-3-hydroxybutyric acid and glycolic acid derivatives, namely penisterines A (
) and C-E (
-
) and penisterine A methyl ether (
), isolated for the first time from natural resources, along with (
)-3-hydroxybutyric acid (
). Of these compounds identified, penisterine E (
) was a unique 6/6/6-tricyclic ether with an acetal and two hemiketal functionalities. All the isolates were subjected to in vitro anti-angiogenic assays using a human endothelial progenitor cell (EPCs) platform. Among these, penisterine D (
) inhibited EPC growth, migration, and tube formation without any cytotoxic effect. Further, in in vivo bioassays, the percentages of angiogenesis of compound
on
(
:EGFP) transgenic zebrafish were 54% and 37% as the treated concentration increased from 10.2 to 20.4 µg/mL, respectively, and the percentages of angiogenesis of compound
were 52% and 41% as the treated concentration increased from 8.6 to 17.2 µg/mL, respectively. The anti-angiogenic activity of penisterine D (
) makes it an attractive candidate for further preclinical investigation.
A high diversity of culturable foliar endophytic fungi is known from various mangrove plants, and the core taxa include species from
,
,
,
,
, among others. Since a small fraction of fungi is able to ...grow in culture, this study investigated the diversity of fungi associated with leaves of
var.
using both isolation and metabarcoding approaches. A total of 203 isolates were cultured from surface-sterilized leaves, representing 47 different fungal species: 30 species from the winter samples (104 isolates), and 26 species from the summer samples (99 isolates). Ascomycota was dominant in both types of leaf samples, while Basidiomycota was isolated only from the summer samples.
(10.58%, percentage of occurrence),
sp. 3 (7.69%) and
sp. (7.69%) were dominant in the winter samples;
(13.13%),
(10.10%) and
sp. 1 (9.09%) in the summer samples. Overall,
(6.90%),
(6.40%) and
sp. (6.40%) had the highest overall percentage of occurrence. In the metabarcoding analysis, a total of 111 operational taxonomic units (OTUs) were identified from 17 leaf samples: 96 OTUs from the winter and 70 OTUs from the summer samples. Sequences belonging to Ascomycota and Basidiomycota were detected in both samples but the former phylum was dominant over the latter. Based on read abundance, taxa having the highest percentage of occurrence included
sp. (3.46%),
(2.56%) and
(1.41%) in the winter leaves, and
sp. (10.72%),
sp. (7.90%),
(3.45%) and
(3.21%) in the summer leaves. These latter four species also had the highest overall percentage of occurrence. Combining the results from both methods, a high diversity of fungi (at least 110 species) was found associated with leaves of
var.
. Many of the fungi identified were plant pathogens and may eventually cause diseases in the host.
Background
Acanthus ilicifolius var. xiamenensis
(Acanthaceae) is an old world mangrove species and has long been used as a folk remedy for treating various ailments in traditional medicine. The ...nature source of
A. ilicifolius var. xiamenensis
is now in short supply because of the urban development and habitat destruction. To better utilize this resource, biodiversity and bioactivity of endophytic fungi isolated from
A. ilicifolius var. xiamenensis
were investigated.
Results
A total of 168 fungal isolates were cultured from leaves and stems of the mangrove plant collected in January (winter) and July (summer) 2014 at Kinmen County, Taiwan. Spent culture extract of 28 isolates were found to have bioactivities against one of the following pathogenic microorganisms: the bacteria
Bacillus subtilis
,
Staphylococcus aureus
(Gram-positive) and
Escherichia coli
(Gram-negative) and the fungi
Candida albicans
and
Cryptococcus neoformans
. These positive extracts were mostly active against the Gram-positive bacteria and
C. albicans
.
Corynespora cassiicola
NTOU4889 and
Xylaria
sp. NTOU4900 inhibited growth of all 3 test bacteria whereas
Phellinus noxius
NTOU4917 inhibited both test fungi. A further anti-inflammatory study of culture extracts of these 28 isolates revealed that extracts with a high iNOS inhibition caused a low viability of cells, and those with a low iNOS inhibition had a high cell viability. Three extracts showed low cytotoxicity (i.e. > 100% cell viability) and high iNOS inhibition (< 15% of NO production) of cells and they were
Phoma
sp. 2 NTOU4338,
Nodulisporium
sp. NTOU4868 and
Guignardia
sp. NTOU4871.
Conclusion
These results indicate that the endophytic fungi associated with
A. ilicifolius var. xiamenensis
can be a potential source of novel natural active substance.
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.
•The diversity of fungi in SWIR using a combined culture-dependent and culture-independent sequence-based approach.•A total of 723 OTUs belonging to 79 taxa were identified by Illumina sequencing.•The high percentage of uncharacterized fungi (34.83% at class level and 37.67% at genus level) suggests that there are unknown fungal taxa inhabiting in the deep-sea sediments.
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