2013
DOI: 10.4172/2165-8056.1000110
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Assessment of Fungal Diversity in the Environment using Metagenomics:a Decade in Review

Abstract: Fungi are ubiquitous inhabitants of soil and aquatic environments, and they establish and maintain either parasitic or symbiotic relationships with animals and plants. They are major players in nutrient cycling, especially in organic matter decomposition, and they are major sources of biologically active substances. However, their full metabolic potential is yet to be unveiled, and fungal enzymes could be of great use in myriad of applications from industrial processes to natural products. The global number of… Show more

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Cited by 37 publications
(24 citation statements)
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References 185 publications
(211 reference statements)
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“…The most widely used marker gene for amplicon sequencing is the small subunit ribosomal RNA (16S) locus, that is both a taxonomically and phylogenetically informative marker for both bacteria and archaea [10,11]. Other markers such as the small subunit 18S, the large subunit (LSU: 23S/25S/28S) and the highly variable spacers ITS1 and ITS2 of the internal transcribed spacer (ITS) region have also been used, in particular for fungi, higher plants, insects and microalgae [12][13][14].…”
Section: Amplicon Sequencingmentioning
confidence: 99%
See 1 more Smart Citation
“…The most widely used marker gene for amplicon sequencing is the small subunit ribosomal RNA (16S) locus, that is both a taxonomically and phylogenetically informative marker for both bacteria and archaea [10,11]. Other markers such as the small subunit 18S, the large subunit (LSU: 23S/25S/28S) and the highly variable spacers ITS1 and ITS2 of the internal transcribed spacer (ITS) region have also been used, in particular for fungi, higher plants, insects and microalgae [12][13][14].…”
Section: Amplicon Sequencingmentioning
confidence: 99%
“…Analysis of other communities, such as for example fungi, are often done by ad-hoc methods or by hijacking software tools designed for bacteria (see e.g. [12,14]). …”
Section: Binningmentioning
confidence: 99%
“…Thus, enrichment of isolation media with fungal culture filtrates could offer interesting opportunities to enhance isolation success. Such symbioses might also, at least partially explain the descrepency in numbers of fungi isolated from various substrates and those known to be present as shown in contemporary metagenomic studies (Fierer et al 2007;Kemler et al 2013;Cuadros-Orellana et al 2013). …”
Section: Discussionmentioning
confidence: 92%
“…Metagenomics are culture-independent methods for the study of microbial diversity, based on next generation sequencing (NGS) and allowing characterization of fungi in complex environmental systems, using specific molecular markers for identification 15 . Abundant metagenomic data are available in public databases such as Sequence Read Archive (SRA 16 ), Rast Server (MG-RAST 17 ), and EBI metagenomics (EMG 18 ).…”
Section: Introductionmentioning
confidence: 99%