scholarly journals DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Otávio Henrique Bezerra Pinto ◽  
Tina Šantl-Temkiv ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Rank Order ◽  
Mesh Size ◽  
Diversity Indices ◽  
South Shetland Islands ◽  
Livingston Island ◽  
Dna Metabarcoding ◽  
Air Sample ◽  
Total Dna

AbstractWe assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

scholarly journals Fungi in the Antarctic cryosphere: using DNA metabarcoding to reveal fungal diversity in glacial ice from the Antarctic Peninsula region

2021 ◽  
Author(s):  
Graciéle de Menezes ◽  
Paulo Câmara ◽  
Otávio Pinto ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Antarctic Peninsula ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
South Shetland Islands ◽  
Glacial Ice ◽  
North West ◽  
The North ◽  
Animal Pathogens ◽  
Dna Metabarcoding ◽  
The Antarctic

Abstract We assessed fungal diversity present in glacial of the Antarctic Peninsula using DNA metabarcoding through high throughput sequencing (HTS). We detected a total of 353,879 fungal DNA reads, representing 94 genera and 184 taxa, in glacial ice fragments obtained from seven sites in the north-west Antarctic Peninsula and South Shetland Islands. The phylum Ascomycota dominated the sequence diversity, followed by Basidiomycota and Mortierellomycota. Penicillium sp., Cladosporium sp., Penicillium atrovenetum, Epicoccum nigrum, Pseudogymnoascus sp. 1, Pseudogymnoascus sp. 2, Phaeosphaeriaceae sp. and Xylaria grammica were the most dominant taxa, respectively. However, the majority of the fungal diversity comprised taxa of rare and intermediate relative abundance, predominately known mesophilic fungi. High indices of diversity and richness were calculated, along with moderate index of dominance, which varied among the different sampling sites. Only 26 (14%) of the total fungal taxa detected were present at all sampling sites. The identified diversity was dominated by saprophytic taxa, followed by known plant and animal pathogens and a low number of symbiotic fungi. Our data suggest that Antarctic glacial ice may represent a hotspot of previously unreported fungal diversity; however, further studies are required to integrate HTS and culture approaches to confirm viability of the taxa detected.

scholarly journals Characterization of fungal microbial diversity in healthy and diarrheal Tibetan piglets

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qinghui Kong ◽  
Suozhu Liu ◽  
Aoyun Li ◽  
Yaping Wang ◽  
Lihong Zhang ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Dynamic Balance ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Republic Of China ◽  
Tibet Autonomous Region ◽  
The Tibet Autonomous Region

Abstract Background Diarrhea is an important ailment limiting the production of the Tibetan pig industry. Dynamic balance of the intestinal microbiota is important for the physiology of the animal. The objective of this work was to study fungal diversity in the feces of early weaning Tibetan piglets in different health conditions. Results In the present study, we performed high-throughput sequencing to characterize the fungal microbial diversity in healthy, diarrheal and treated Tibetan piglets at the Tibet Autonomous Region of the People’s Republic of China. The four alpha diversity indices (Chao1, ACE, Shannon and Simpson) revealed no significant differences in the richness across the different groups (P > 0.05). In all samples, the predominant fungal phyla were Ascomycota, Basidiomycota and Rozellomycota. Moreover, the healthy piglets showed a higher abundance of Ascomycota than the treated ones with a decreased level of Basidiomycota. One phylum (Rozellomycota) showed higher abundance in the diarrheal piglets than in the treated. At genus level, compared with that to the healthy group, the proportion of Derxomyces and Lecanicillium decreased, whereas that of Cortinarius and Kazachstania increased in the diarrheal group. The relative abundances of Derxomyces, Phyllozyma and Hydnum were higher in treated piglets than in the diarrheal ones. Conclusions A decreased relative abundance of beneficial fungi (e.g. Derxomyces and Lecanicillium) may cause diarrhea in the early-weaned Tibetan piglets. Addition of probiotics into the feed may prevent diarrhea at this stage. This study presented the fungal diversity in healthy, diarrheal and treated early-weaned Tibetan piglets.

scholarly journals Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia

2020 ◽  
Vol 96 (9) ◽  
Author(s):  
Vaso Taleski ◽  
Ivica Dimkić ◽  
Blazo Boev ◽  
Ivan Boev ◽  
Sanja Živković ◽  
...  
Keyword(s):  
Inductively Coupled Plasma ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Optical Emission ◽  
Diversity Indices ◽  
Emission Spectrometry ◽  
High Concentration ◽  
Bacterial Phyla ◽  
The Republic

ABSTRACT The Allchar mineral mine is one of the oldest arsenic–antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp. and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

scholarly journals DNA metabarcoding uncovers fungal diversity in soils of protected and non-protected areas on Deception Island, Antarctica

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Luiz Henrique Rosa ◽  
Thamar Holanda da Silva ◽  
Mayara Baptistucci Ogaki ◽  
Otávio Henrique Bezerra Pinto ◽  
Michael Stech ◽  
...  
Keyword(s):  
Fungal Diversity ◽  
South Shetland Islands ◽  
Anthropogenic Influences ◽  
Deception Island ◽  
Shetland Islands ◽  
Dna Metabarcoding ◽  
Symbiotic Fungi ◽  
Soil Fungal Diversity ◽  
Long Term Studies

AbstractWe assessed soil fungal diversity at two sites on Deception Island, South Shetland Islands, Antarctica using DNA metabarcoding analysis. The first site was a relatively undisturbed area, and the second was much more heavily impacted by research and tourism. We detected 346 fungal amplicon sequence variants dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Chytridiomycota. We also detected taxa belonging to the rare phyla Mucoromycota and Rozellomycota, which have been difficult to detect in Antarctica by traditional isolation methods. Cladosporium sp., Pseudogymnoascus roseus, Leotiomycetes sp. 2, Penicillium sp., Mortierella sp. 1, Mortierella sp. 2, Pseudogymnoascus appendiculatus and Pseudogymnoascus sp. were the most dominant fungi. In addition, 440,153 of the total of 1,214,875 reads detected could be classified only at the level of Fungi. In both sampling areas the DNA of opportunistic, phytopathogenic and symbiotic fungi were detected, which might have been introduced by human activities, transported by birds or wind, and/or represent resident fungi not previously reported from Antarctica. Further long-term studies are required to elucidate how biological colonization in the island may be affected by climatic changes and/or other anthropogenic influences.

scholarly journals In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols

2021 ◽  
Vol 7 (2) ◽  
pp. 99
Author(s):  
Hamza Mbareche ◽  
Marc Veillette ◽  
Guillaume J. Bilodeau
Keyword(s):  
In Silico ◽  
Fungal Diversity ◽  
High Throughput Sequencing ◽  
In Silico Analysis ◽  
Its Region ◽  
Internal Transcribed Spacers ◽  
Sequence Length ◽  
Universal Method ◽  
Continuous Work ◽  
Its1 And Its2

This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

scholarly journals The Fecal Bacterial Microbiota in Horses with Equine Recurrent Uveitis

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 745
Author(s):  
Michelle Martin de Bustamante ◽  
Diego Gomez ◽  
Jennifer MacNicol ◽  
Ralph Hamor ◽  
Caryn Plummer
Keyword(s):  
Beta Diversity ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Linear Discriminant ◽  
Alpha And Beta Diversity ◽  
Bacterial Microbiota ◽  
Healthy Control ◽  
Equine Recurrent Uveitis

The objective of this study was to describe and compare the fecal bacterial microbiota of horses with equine recurrent uveitis (ERU) and healthy horses using next-generation sequencing techniques. Fecal samples were collected from 15 client-owned horses previously diagnosed with ERU on complete ophthalmic examination. For each fecal sample obtained from a horse with ERU, a sample was collected from an environmentally matched healthy control with no evidence of ocular disease. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. The relative abundance of predominant taxa, and alpha and beta diversity indices were calculated and compared between groups. The phyla Firmicutes, Bacteroidetes, Verrucomicrobia, and Proteobacteria predominated in both ERU and control horses, accounting for greater than 60% of sequences. Based on linear discriminant analysis effect size (LEfSe), no taxa were found to be enriched in either group. No significant differences were observed in alpha and beta diversity indices between groups (p > 0.05 for all tests). Equine recurrent uveitis is not associated with alteration of the gastrointestinal bacterial microbiota when compared with healthy controls.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Fungi in the Antarctic Cryosphere: Using DNA Metabarcoding to Reveal Fungal Diversity in Glacial Ice from the Antarctic Peninsula Region

2021 ◽  
Author(s):  
Graciéle Cunha Alves de Menezes ◽  
Paulo E. A. S. Câmara ◽  
Otávio Henrique Bezerra Pinto ◽  
Peter Convey ◽  
Micheline Carvalho-Silva ◽  
...  
Keyword(s):  
Antarctic Peninsula ◽  
Fungal Diversity ◽  
Glacial Ice ◽  
Dna Metabarcoding ◽  
The Antarctic

scholarly journals Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas

2019 ◽  
Vol 8 (1) ◽  
pp. 63
Author(s):  
Huilong Ou ◽  
Mingyu Li ◽  
Shufei Wu ◽  
Linli Jia ◽  
Russell T. Hill ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Inorganic Phosphorus ◽  
Marine Sponges ◽  
Strongly Correlated ◽  
Mantel Tests ◽  
Low Concentrations ◽  
Enrichment Rate ◽  
Total Dna ◽  
Polyphosphate Accumulation ◽  
Sequence Similarities

Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP.

Lithostratigraphy of volcanic and sedimentary sequences in central Livingston Island, South Shetland Islands

1995 ◽  
Vol 7 (1) ◽  
pp. 99-113 ◽  
Author(s):  
J.L. Smellie ◽  
M. Liesa ◽  
J.A. Muñoz ◽  
F. Sàbat ◽  
R. Pallàs ◽  
...  
Keyword(s):  
Debris Flows ◽  
Lower Jurassic ◽  
South Shetland Islands ◽  
Polyphase Deformation ◽  
Magmatic Arc ◽  
Shetland Islands ◽  
Sedimentary Sequences ◽  
Early Mesozoic ◽  
Livingston Island ◽  
Volcaniclastic Rocks

Livingston Island contains several, distinctive sedimentary and volcanic sequences, which document the history and evolution of an important part of the South Shetland Islands magmatic arc. The turbiditic, late Palaeozoic–early Mesozoic Miers Bluff Formation (MBF) is divided into the Johnsons Dock and Napier Peak members, which may represent sedimentation in upper and lower mid-fan settings, respectively, prior to pre-late Jurassic polyphase deformation (dominated by open folding). The Moores Peak breccias are formed largely of coarse clasts reworked from the MBF. The breccias may be part of the MBF, a separate unit, or part of the Mount Bowles Formation. The structural position is similar to the terrigenous Lower Jurassic Botany Bay Group in the northern Antarctic Peninsula, but the precise stratigraphical relationships and age are unknown. The (?) Cretaceous Mount Bowles Formation is largely volcanic. Detritus in the volcaniclastic rocks was formed mainly during phreatomagmatic eruptions and redeposited by debris flows (lahars), whereas rare sandstone interbeds are arkosic and reflect a local provenance rooted in the MBF. The Pleistocene–Recent Inott Point Formation is dominated by multiple, basaltic tuff cone relicts in which distinctive vent and flank sequences are recognized. The geographical distribution of the Edinburgh Hill Formation is closely associated with faults, which may have been reactivated as dip-slip structures during Late Cenozoic extension (arc splitting).

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