DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Urbina, Héctor; Scofield, Douglas G.; Cafaro, Matías J.; Rosling, Anna

doi:10.1016/j.myc.2016.02.001

Cited by 24 publications

(21 citation statements)

References 38 publications

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“…The gITS7 primer included unique indexed tags for each sample to allow for multiplex sequencing. Amplication of the ITS2 region was performed using a real-time (quantitative) PCR instrument (CFX96 Touch, Bio-Rad Laboratories, Inc., USA) in order to observe the process of the reaction and stop it, while the majority of the samples were still in the loglinear amplification phase, as described by Urbina, Scofield, Cafaro, and Rosling (2016). The reaction mix was SSOAdvanced SYBR Green Master Mix (Bio-Rad Laboratories, Inc., USA) at 1× concentration, with 0.8 μM of each primer and approximately 600 pg of extracted DNA.…”

Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Vowles

Lindwall

Ekblad

et al. 2017

Ecology and Evolution

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Mycorrhizal associations are widespread in high‐latitude ecosystems and are potentially of great importance for global carbon dynamics. Although large herbivores play a key part in shaping subarctic plant communities, their impact on mycorrhizal dynamics is largely unknown. We measured extramatrical mycelial (EMM) biomass during one growing season in 16‐year‐old herbivore exclosures and unenclosed control plots (ambient), at three mountain birch forests and two shrub heath sites, in the Scandes forest‐tundra ecotone. We also used high‐throughput amplicon sequencing for taxonomic identification to investigate differences in fungal species composition. At the birch forest sites, EMM biomass was significantly higher in exclosures (1.36 ± 0.43 g C/m2) than in ambient conditions (0.66 ± 0.17 g C/m2) and was positively influenced by soil thawing degree‐days. At the shrub heath sites, there was no significant effect on EMM biomass (exclosures: 0.72 ± 0.09 g C/m2; ambient plots: 1.43 ± 0.94). However, EMM biomass was negatively related to Betula nana abundance, which was greater in exclosures, suggesting that grazing affected EMM biomass positively. We found no significant treatment effects on fungal diversity but the most abundant ectomycorrhizal lineage/cortinarius, showed a near‐significant positive effect of herbivore exclusion (p = .08), indicating that herbivory also affects fungal community composition. These results suggest that herbivory can influence fungal biomass in highly context‐dependent ways in subarctic ecosystems. Considering the importance of root‐associated fungi for ecosystem carbon balance, these findings could have far‐reaching implications.

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Section: Dna Extraction Amplification and Sequencingmentioning

confidence: 99%

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Vowles

Lindwall

Ekblad

et al. 2017

Ecology and Evolution

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“…None of the sequences (deposited in GenBank under accessions MH843963-MH844060) matched Archaeorhizomycetes . From the 36 composite soil sample, DNA was extracted using the (Xpedition™ Soil/Fecal DNA miniprep, Zymo Research Corporation, Irvine, California, USA) (Urbina et al 2016 ) (Method S2). Two different sequence datasets were generated from these samples: 1) a “phylogenetic” dataset of long amplicons using PacBio SMRT, and 2) an “ecological” dataset based on short read metabarcoding using IonTorrent.…”

Section: Methodsmentioning

confidence: 99%

Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi

et al. 2020

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Due to their submerged and cryptic lifestyle, the vast majority of fungal species are difficult to observe and describe morphologically, and many remain known to science only from sequences detected in environmental samples. The lack of practices to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here, we use environmental sequence data as taxonomical evidence and combine phylogenetic and ecological data to generate and test species hypotheses in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing from a well-studied Swedish pine forest podzol soil, we generate 68 distinct species hypotheses of Archaeorhizomycetes, of which two correspond to the only described species in the class. Nine of the species hypotheses represent 78% of the sequenced Archaeorhizomycetes community, and are supported by long read data that form the backbone for delimiting species hypothesis based on phylogenetic branch lengths. Soil fungal communities are shaped by environmental filtering and competitive exclusion so that closely related species are less likely to co-occur in a niche if adaptive traits are evolutionarily conserved. In soil profiles, distinct vertical horizons represent a testable niche dimension, and we found significantly differential distribution across samples for a well-supported pair of sister species hypotheses. Based on the combination of phylogenetic and ecological evidence, we identify two novel species for which we provide molecular diagnostics and propose names. While environmental sequences cannot be automatically translated to species, they can be used to generate phylogenetically distinct species hypotheses that can be further tested using sequences as ecological evidence. We conclude that in the case of abundantly and frequently observed species, environmental sequences can support species recognition in the absences of physical specimens, while rare taxa remain uncaptured at our sampling and sequencing intensity.

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“…A sequencing library was prepared by pooling 35 ng PCR products from each sample, loaded onto a 318 chip for PGM Ion Torrent sequencing technology (Life Technologies Corporation, Carlsbad, CA, US) and sequenced at the National Genomics Infrastructure (NGI Uppsala; SciLifeLab, Uppsala, Sweden). The current study was sequenced on the same IonTorrent chip as four other studies with samples from different ecosystems including forest soils across Puerto Rico (Urbina et al, 2016), mixed deciduous forest in Indiana, US (Rosling et al, 2016) and two un-published datasets from west Africa (Benin and Burkina Faso) and central Asia (India and Kyrgyzstan), as well as a negative and positive control on this IonTorrent chip. The 4,805,942 raw sequence reads were demultiplexed by the sequencing facility and provided as 96 fastq les.…”

Section: Soil Dna Extractionmentioning

confidence: 99%

Peeking into the black box – integrated taxonomy of Archaeorhizomycetes

Khan

Kluting

Tångrot

et al. 2020

Preprint

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Abstract Due to their submerged and cryptic lifestyle the vast majority of fungal species are difficult to observe and describe morphologically and many remains known to science only from sequences detected in environmental samples. The lack of rules to delimit and name most fungal species is a staggering limitation to communication and interpretation of ecology and evolution in kingdom Fungi. Here we use environmental sequence data as taxonomical evidence and take an integrated taxonomic approach by combining phylogenetic and ecological data to generate and test species hypothesis in the class Archaeorhizomycetes (Taphrinomycotina, Ascomycota). Based on environmental amplicon sequencing we recognize 68 distinct phylogenetic species hypotheses (PSHs) of Archaeorhizomycetes, including the two described species in the class, in a well-studied Swedish pine forest podzol soil. Nine of the species hypotheses, including the more abundant ones, are supported by long read data and represent 78% of the sequenced Archaeorhizomycetes community. Among well supported sister PSHs, significantly differential distribution in the soil profile provide additional ecological evidence supporting the identification of two novel species for which we provide molecular diagnostics and propose names. Our analysis indicates that frequent and abundant taxa can be phylogenetically resolved in environmental samples, while rare taxa remain un-captured at our sampling and sequencing intensity. While environmental sequences cannot be automatically translated to species hypothesis, they can be used to generate phylogenetic and ecological evidence supporting species recognition of abundant species without physical specimens.

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DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Cited by 24 publications

References 38 publications

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi

Peeking into the black box – integrated taxonomy of Archaeorhizomycetes

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