Soil Metabarcoding Offers a New Tool for the Investigation and Hunting of Truffles in Northern Thailand

Truffles (Tuber spp.) are well-known as edible ectomycorrhizal mushrooms, and some species are one of the most expensive foods in the world. During the fruiting process, truffles produce hypogeous ascocarps; a trained pig or dog is needed to locate the ascocarps under the ground. Truffles in northern Thailand have been recorded in association with Betulaalnoides and Carpinus poilanei. In this study, we investigated the soil mycobiota diversity of soil samples from both of these truffle host plants in native forests using environmental DNA metabarcoding to target the internal transcribed spacer 1 (ITS1) region of the rDNA gene for the purposes of investigation of truffle diversity and locating truffles during the non-fruiting phase. In this study, a total of 38 soil samples were collected from different locations. Of these, truffles had been found at three of these locations. Subsequently, a total of 1341 putative taxonomic units (OTUs) were obtained. The overall fungal community was dominated by phylum-level sequences assigned to Ascomycota (57.63%), Basidiomycota (37.26%), Blastocladiomycota (0.007%), Chytridiomycota (0.21%), Glomeromycota (0.01%), Kickxellomycota (0.01%), Mortierellomycota (2.08%), Mucoromycota (0.24%), Rozellomycota (0.01%), Zoopagomycota (0.003%), and unidentified (2.54%). The results revealed that six OTUs were determined to be representative and belonged to the genus Tuber. OTU162, OTU187, OTU447, and OTU530 belonged to T. thailandicum, T. lannaense, T. bomiense, and T. magnatum, whereas OTU105 and OTU720 were acknowledged as unrecognized Tuber species. From 38 locations, OTUs of truffles were found in 33 locations (including three previously known truffle locations). Thus, 30 collection sites were considered new locations for T. thailandicum, T. bomiense, and other unrecognized Tuber species. Interestingly, at 16 new locations, mature ascocarps of truffles that were undergoing the fruiting phase were located underground. All 16 truffle samples were identified as T. thailandicum based on morphological characteristics and molecular phylogenetic analysis. However, ascocarps of other truffle species were not found at the new OTUs representative locations. The knowledge gained from this study can be used to lead researchers to a better understanding of the occurrence of truffles using soil mycobiota diversity investigation. The outcomes of this study will be particularly beneficial with respect to the search and hunt for truffles without the need for trained animals. In addition, the findings of this study will be useful for the management and conservation of truffle habitats in northern Thailand.

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Biodiversity assessments in the 21st century: the potential of insect traps to complement environmental samples for estimating eukaryotic and prokaryotic diversity using high-throughput DNA metabarcoding

Genome ◽

10.1139/gen-2018-0096 ◽

2019 ◽

Vol 62 (3) ◽

pp. 147-159 ◽

Cited By ~ 10

Author(s):

Camila D. Ritter ◽

Sibylle Häggqvist ◽

Dave Karlsson ◽

Ilari E. Sääksjärvi ◽

A. Muthama Muasya ◽

...

Keyword(s):

Species Identification ◽

Environmental Dna ◽

Cost Effective ◽

Taxonomic Composition ◽

Soil Samples ◽

Morphological Studies ◽

Prokaryotic Diversity ◽

Dna Metabarcoding ◽

Morphological Species ◽

Ecosystem Interactions

The rapid loss of biodiversity, coupled with difficulties in species identification, call for innovative approaches to assess biodiversity. Insects make up a substantial proportion of extant diversity and play fundamental roles in any given ecosystem. To complement morphological species identification, new techniques such as metabarcoding make it possible to quantify insect diversity and insect–ecosystem interactions through DNA sequencing. Here we examine the potential of bulk insect samples (i.e., containing many non-sorted specimens) to assess prokaryote and eukaryote biodiversity and to complement the taxonomic coverage of soil samples. We sampled 25 sites on three continents and in various ecosystems, collecting insects with SLAM traps (Brazil) and Malaise traps (South Africa and Sweden). We then compared our diversity estimates with the results obtained with biodiversity data from soil samples from the same localities. We found a largely different taxonomic composition between the soil and insect samples, testifying to the potential of bulk insect samples to complement soil samples. Finally, we found that non-destructive DNA extraction protocols, which preserve insect specimens for morphological studies, constitute a promising choice for cost-effective biodiversity assessments. We propose that the sampling and sequencing of insect samples should become a standard complement for biodiversity studies based on environmental DNA.

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A new species and four new records of Amanita (Amanitaceae; Basidiomycota) from Northern Thailand

Phytotaxa ◽

10.11646/phytotaxa.286.4.1 ◽

2016 ◽

Vol 286 (4) ◽

pp. 211 ◽

Cited By ~ 7

Author(s):

BENJARONG THONGBAI ◽

RODHAM E. TULLOSS ◽

STEVEN L. MILLER ◽

KEVIN D. HYDE ◽

JIE CHEN ◽

...

Keyword(s):

New Records ◽

Phylogenetic Analyses ◽

Morphological Characteristics ◽

Molecular Data ◽

Similar Species ◽

Northern Thailand ◽

Molecular Phylogenetic ◽

Biodiversity Study ◽

Morphological And Molecular Data ◽

A New Species

Mushrooms belonging to the genus Amanita were collected during a fungal biodiversity study in northern Thailand in 2012–2014. Morphological characteristics and molecular phylogenetic analyses were used to identify the mushrooms to species. Amanita castanea is described as new to science and compared with phenetically and phylogenetically similar species. It is assignable to Amanita stirps Citrina within Amanita series Mappae. Four other species, A. concentrica, A. rimosa, A. cf. rubromarginata and A. zangii are first reports for Thailand; detailed morphological and molecular data are provided for the Thai material.

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Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding

10.22541/au.159309876.62184178/v2 ◽

2021 ◽

Author(s):

Sabrina Shirazi ◽

Rachel Meyer ◽

Beth Shapiro

Keyword(s):

Environmental Dna ◽

Data Interpretation ◽

Soil Samples ◽

Data Sets ◽

Average Depth ◽

Rare Taxa ◽

Β Diversity ◽

Large Numbers ◽

Dna Metabarcoding ◽

Methodological Approaches

Environmental DNA (eDNA) metabarcoding is a common tool for measuring and cataloguing biodiversity, yet standard methodological approaches to generate metabarcoding data sets have yet to emerge, in part due to challenges understanding the biological and technical biases that affect eDNA profiles. Here, we explore how two experimental choices – depth of sequencing of PCR amplicon libraries and the number of PCR replicates – influence estimates of α and β diversity. We extracted DNA from six soil samples from three ecologically distinct locations, performed 24 PCR replicates from each using two common metabarcodes, and sequenced each to an average depth of 83,898 reads. We found PCR replicates are consistent in composition and relative abundance of abundant taxa, allowing differentiation of samples and sites. However, rare taxa were unique to one or a few replicates, suggesting that even large numbers of experimental replicates may be insufficient to catalogue biodiversity fully. We recommend that to differentiate sites, separately sequencing only a minimum of two PCR replicates to a depth that allows 1,000 reads identified to taxa, is sufficient to differentiate sites. We also conclude that metabarcoding is impractical for exhaustive taxonomic inventory and, because rare taxa are not amplified consistently, taxonomic tallies that rely on consensus among replicates artificially lower richness estimates. These findings provide new considerations for eDNA experimental design and data interpretation.

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COMPARATIVE STUDY BETWEEN FISH COLLECTION BY NATIONAL CENSUS ON RIVER ENVIRONMENT AND ENVIRONMENTAL DNA METABARCODING

Journal of Japan Society of Civil Engineers Ser B1 (Hydraulic Engineering) ◽

10.2208/jscejhe.74.5_i_415 ◽

2018 ◽

Vol 74 (5) ◽

pp. I_415-I_420 ◽

Cited By ~ 1

Author(s):

Yoshihisa AKAMATSU ◽

Takayoshi TSUZUKI ◽

Ryota YOKOYAMA ◽

Yayoi FUNAHASHI ◽

Munehiro OHTA ◽

...

Keyword(s):

Comparative Study ◽

Environmental Dna ◽

Dna Metabarcoding ◽

Fish Collection

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Environmental DNA for functional diversity

10.1093/oso/9780198767220.003.0010 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pierre Taberlet ◽

Aurélie Bonin ◽

Lucie Zinger ◽

Eric Coissac

Keyword(s):

Functional Groups ◽

Functional Diversity ◽

Environmental Dna ◽

Soil Organisms ◽

Meaningful Information ◽

Dna Metabarcoding ◽

Pros And Cons ◽

Target Community

Chapter 10 “Environmental DNA for functional diversity” discusses the potential of environmental DNA to assess functional diversity. It first focuses on DNA metabarcoding and discusses the extent to which this approach can be used and/or optimized to retrieve meaningful information on the functions of the target community. This knowledge usually involves coarsely defined functional groups (e.g., woody, leguminous, graminoid plants; shredders or decomposer soil organisms; pathogenicity or decomposition role of certain microorganisms). Chapter 10 then introduces metagenomics and metatranscriptomics approaches, their advantages, but also the challenges and solutions to appropriately sampling, sequencing these complex DNA/RNA populations. Chapter 10 finally presents several strategies and software to analyze metagenomes/metatranscriptomes, and discusses their pros and cons.

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Environmental DNA

10.1093/oso/9780198767220.001.0001 ◽

2018 ◽

Cited By ~ 137

Author(s):

Pierre Taberlet ◽

Aurélie Bonin ◽

Lucie Zinger ◽

Eric Coissac

Keyword(s):

Graduate Students ◽

Feeding Habits ◽

Environmental Dna ◽

Research Field ◽

Background Information ◽

Ecological Processes ◽

Biodiversity Research ◽

Dna Metabarcoding ◽

Standard Information

Environmental DNA (eDNA), i.e. DNA released in the environment by any living form, represents a formidable opportunity to gather high-throughput and standard information on the distribution or feeding habits of species. It has therefore great potential for applications in ecology and biodiversity management. However, this research field is fast-moving, involves different areas of expertise and currently lacks standard approaches, which calls for an up-to-date and comprehensive synthesis. Environmental DNA for biodiversity research and monitoring covers current methods based on eDNA, with a particular focus on “eDNA metabarcoding”. Intended for scientists and managers, it provides the background information to allow the design of sound experiments. It revisits all steps necessary to produce high-quality metabarcoding data such as sampling, metabarcode design, optimization of PCR and sequencing protocols, as well as analysis of large sequencing datasets. All these different steps are presented by discussing the potential and current challenges of eDNA-based approaches to infer parameters on biodiversity or ecological processes. The last chapters of this book review how DNA metabarcoding has been used so far to unravel novel patterns of diversity in space and time, to detect particular species, and to answer new ecological questions in various ecosystems and for various organisms. Environmental DNA for biodiversity research and monitoring constitutes an essential reading for all graduate students, researchers and practitioners who do not have a strong background in molecular genetics and who are willing to use eDNA approaches in ecology and biomonitoring.

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