Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities

Samson, R.A.; Rajput, Vinay; Shah, Manan; Yadav, Rakeshkumar; Sarode, Priyanka; Dastager, Syed G.; Dharne, Mahesh; Khairnar, Krishna

doi:10.1016/j.chemosphere.2020.126507

Cited by 18 publications

(9 citation statements)

References 25 publications

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“…The number of metagenome projects investigating the presence and activity of fungal communities in environmental samples has been rapidly increasing [118]. These studies of the mycobiome have been focused on samples from diverse sources such as water (e.g., Brumfield et al [119]), air (e.g., Calderón-Ezquerro et al [120], soil/sediments (e.g., Samson et al [121]), plants (e.g., Nguyen et al [122], Yang et al [123]) and humans (e.g., Hall et al [124], Hanger et al [125]). The number of complete fungal genomes and fungal environmental DNA/RNA sequences in public databases has grown considerably, reaching more than a billion reads just considering the ITS region [126].…”

Section: Culture-independent Methodsmentioning

confidence: 99%

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Wijayawardene

Bahram

Sánchez-Castro

et al. 2021

JoF

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Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual–asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.

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Section: Culture-independent Methodsmentioning

confidence: 99%

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Wijayawardene

Bahram

Sánchez-Castro

et al. 2021

JoF

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“…For the tissue of aquatic organisms, biomass concentration will be unnecessary [32,34,59]. Genetic material from biomass-rich sediment samples (0.2 to 1 g) and sludge samples (0.5 mL) can also be extracted directly [45,51,60,61,75], or after centrifugation of small to medium slurry volumes (2 to 50 mL) with collection of the pellets [52,62,69]. Zooplanktonic biomass can be harvested with meshes having 200 µm openings [36], while the biomass of algae [74] and cyanobacteria [48] can be isolated by medium to large volume centrifugation (0.05 to 1 L).…”

Section: Biomass Collection and Concentrationmentioning

confidence: 99%

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

Werner

Acharya

Blackburn

et al. 2022

Water

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In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% savings in upfront costs as compared to conventional platforms, the MinION put sequencing capacity into the hands of many researchers and enabled novel applications with diverse remits, including in countries without universal access to safe water and sanitation. However, to realize the MinION’s fabled portability, all the auxiliary equipment items for biomass concentration, genetic material extraction, cleanup, quantification, and sequencing library preparation also need to be lightweight and affordable. Only a few studies demonstrated fully portable workflows by using the MinION onboard a diving vessel, an oceanographic research ship, and at sewage treatment works. Lower nanopore sequencing read accuracy as compared to alternative platforms currently hinders MinION applications beyond research, and inclusion of positive and negative controls should become standard practice. ONT’s EPI2ME platform is a major step towards user-friendly bioinformatics. However, no consensus has yet emerged regarding the most appropriate bioinformatic pipeline, which hinders intercomparison of study results. Processing, storing, and interpreting large data sets remains a major challenge for ubiquitous genetics and democratizing sequencing applications.

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“…Fungi make up a significant component of the benthic microbial biomass in freshwater ecosystems, and play a pivotal role in decomposing organic matter in river habitats (Pascoal and Cassio 2004;Zhang et al 2013). In general, representatives of Ascomycota account for the largest number of species recovered from water systems (Kelley et al 2001;Liu et al 2015;Khomich et al 2017;Sutcliffe et al 2018;Samson et al 2020), their asexual forms with stauro-or scolecoconidia (aquatic hyphomycetes) being the most representative fungal group in freshwater environments (Pascoal et al 2005;Jones and Pang 2012). Although common Ascomycota like Penicillium species are not considered aquatic fungi, they are one of the most common genera identified from freshwater (Pitt 1979;Hageskal et al 2006;Sonjak et al 2006;Samson et al 2010;Heo et al 2019;Pangging et al 2019) and recently were also reported in marine environments (Kirichuk et al 2017;Gonçalves et al 2019;Grossart et al 2019).…”

Section: Introductionmentioning

confidence: 99%

New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain

Torres-Garcia¹,

Gené²,

García³

2022

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Penicillium species are common fungi found worldwide from diverse substrates, including soil, plant debris, food products and air. Their diversity in aquatic environments is still underexplored. With the aim to explore the fungal diversity in Spanish freshwater sediments, numerous Penicillium strains were isolated using various culture-dependent techniques. A preliminary sequence analysis of the β-tubulin (tub2) gene marker allowed us to identify several interesting species of Penicillium, which were later characterized phylogenetically with the barcodes recommended for species delimitation in the genus. Based on the multi-locus phylogeny of the internal transcribed spacer region (ITS) of the ribosomal DNA, and partial fragments of tub2, calmodulin (cmdA), and the RNA polymerase II largest subunit (rpb2) genes, in combination with phenotypic analyses, five novel species are described. These are P. ausonanum in section Lanata-Divaricata, P. guarroi in sect. Gracilenta, P. irregulare in sect. Canescentia, P. sicoris in sect. Paradoxa and P. submersum in sect. Robsamsonia. The study of several isolates from samples collected in different locations resulted in the reinstatement of P. vaccaeorum into section Citrina. Finally, P. heteromorphum (sect. Exilicaulis) and P. tardochrysogenum (sect. Chrysogena) are reported, previously only known from Antarctica and China, respectively.

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Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities

Cited by 18 publications

References 25 publications

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain

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Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities

Cited by 18 publications

References 25 publications

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

﻿New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain

Contact Info

Product

Resources

About

New and interesting species of Penicillium (Eurotiomycetes, Aspergillaceae) in freshwater sediments from Spain