Coming up short: Identifying substrate and geographic biases in fungal sequence databases

Khomich, Maryia; Cox, Filipa; Andrew, Carrie; Andersen, Tom; Kauserud, Håvard; Davey, Marie L.

doi:10.1016/j.funeco.2018.08.002

Cited by 12 publications

(11 citation statements)

References 33 publications

(36 reference statements)

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“…Compared to other terrestrial habitats, fewer genomic studies have been conducted in aquatic habitats. As a result, fewer ITS sequence records are available and new phylogenetic groups are expected to be found (Grossart et al 2019;Khomich et al 2018). Furthermore, for basal fungi living in an aquatic habitat, such as chytrids, more conservative regions such as large subunit (LSU) and small subunit (SSU) regions of rDNA are often used (Nilsson et al 2019).…”

Section: Methodological Limitationsmentioning

confidence: 99%

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka¹,

Sugiyama²,

Sato³

et al. 2019

MBMG

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Growing evidence has revealed high diversity and spatial heterogeneity of fungal communities in local habitats of terrestrial ecosystems. Recently, the analysis of environmental DNA has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. In the present study, we investigated fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding targeting the internal transcribed spacer 1 (ITS1) region of the rRNA gene cluster in habitats across different branches of rivers in forest landscapes. A total of 1,956 operational taxonomic units (OTUs) were detected. Of these, 770 were assigned as Ascomycota, 177 as Basidiomycota, and 38 as Chytridiomycota. The river water was found to contain functionally diverse OTUs of both aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, river branches. In addition, the assemblages were more similar between spatially closer branches. This spatial structuring was significantly associated with geographic distances but not with vegetation of the catchment area and the elevation at the sampling points. Our results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water.

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Section: Methodological Limitationsmentioning

confidence: 99%

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka¹,

Sugiyama²,

Sato³

et al. 2019

MBMG

View full text Add to dashboard Cite

show abstract

“…Compared to other terrestrial habitats, fewer genomic studies have been conducted in aquatic habitats. As a result, fewer ITS sequence records are available and new phylogenetic groups are expected to be found (Grossart et al, 2019; Khomich et al, 2018). Furthermore, for basal fungi living in an aquatic habitat, such as cystrids, more conservative regions such as large subunit (LSU) and small subunit (SSU) regions of rDNA are often used (Nilsson et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Matsuoka

Sugiyama

Sato

et al. 2019

Preprint

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24Growing evidence has revealed high diversity and spatial heterogeneity of fungal 25 communities including in local habitats in terrestrial ecosystems. These findings highlight 26 the considerable sampling effort, analysis time, and costs required for the investigation 27 of fungal diversity over large spatial scales. Recently, the analysis of environmental DNA 28 in river water has been undertaken to study the biodiversity of organisms, such as animals 29 and plants, in both aquatic and terrestrial habitats. However, previous studies have not 30 investigated the spatial structure of fungal DNA assemblages in river water. In the present 31 study, we investigate fungal DNA assemblages and their spatial structure using 32 environmental DNA metabarcoding in water across different branches of river over forest 33 landscapes. The river water was found to contain both phylogenetically and functionally 34 diverse fungal DNA, including aquatic and terrestrial fungi, such as plant decomposers 35 and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather 36 than between, branches. In addition, the assemblages were more similar between spatially 37 closer branches. These results imply that information on the terrestrial and aquatic fungal 38 compositions of watersheds, and therefore their spatial structure can be obtained by 39 investigating the fungal DNA assemblages in river water. 40 41 Keywords 42 environmental DNA, fungi, forest river, metabarcoding, spatial structure 43 44 45 Information on biodiversity composition is essential to understand the ecological 46 processes and functions of ecosystems. Understanding patterns of biodiversity is 47 fundamental for the maintenance of ecological processes during this era of environmental 48 change (Margules and Pressey, 2000; Pecl et al., 2017). The Kingdom Fungi boasts high 49 species diversity and undertakes unique functions in both terrestrial and aquatic 50 ecosystems via the decomposition of organic substrates and symbiotic or parasitic 51 interactions with other organisms, such as animals and plants (Peay et al., 2016; 52 Hawksworth and Lücking, 2017; Grossart et al., 2019). Recently, with the growing use 53 of DNA metabarcoding techniques, an increasing number of studies are investigating 54 fungal diversity on a variety of substrates in terrestrial and aquatic habitats (Duarte et al., 55 2015; Peay et al., 2016; Nilsson et al., 2019). However, as fungi show high local diversity 56 and spatial heterogeneity (Bahram et al., 2015, 2016), the investigation of fungal diversity 57 over large spatial scales, such as landscape (tens of km) and regional scales (hundreds to 58 thousands of km) requires a significant amount of sampling effort, time for analysis, and 59 costs. 60 Recently, the availability of environmental DNA in river water for biodiversity 61 exploration has been discussed in several studies (Deiner et al., 2016; Nakagawa et al. 62 2018). Deiner et al. (2016) suggest that river water can integrate DNA from the catchment 63 ...

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“…In the present study, approximately 40% of all OTUs could not be identified, which could be partly due to differences in barcoding regions, especially in the ancestral lineages. In addition, the environmental sequences often return unknown lineages of fungi, and some of the OTUs for which taxonomic and functional groups could not be estimated in the present study may be due in part to insufficient DNA and functional data in the database (Grossart et al, 2019;Khomich et al, 2018). Recently, long-read sequencing technology (e.g., Oxford Nanopore) has been used to decipher the SSU-ITS-LSU region to infer the phylogenetic position of OTUs with no closely related sequences registered in the database (e.g., Tedersoo et al, 2020).…”

Section: Technical Challengesmentioning

confidence: 92%

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

Matsuoka

Sugiyama

Shimono

et al. 2020

Preprint

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Investigation of the seasonal variation in the fungal community is essential for understanding biodiversity and its ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community compositions, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis, including both aquatic and terrestrial species, has been explored for its usefulness in biodiversity surveys. Examining eDNA may allow for the survey of the community over time with less disturbance to the ecosystem. In this study, we assessed whether seasonality of fungal communities can be detected with monitoring of eDNA in a flow-regulated stream in a restored forest. We conducted monthly water sampling in the stream over two years, and used DNA metabarcoding to estimate the taxonomic and functional groups of fungal eDNA in the water. The river water contained taxonomically and functionally diverse DNA from both aquatic and terrestrial fungi, such as plant decomposers, parasites, and mutualists. The DNA assemblages showed a distinct annual periodicity, meaning that the assemblages were similar to each other regardless of the year, in the same sampling season. These seasonal changes were partially explained by temperature alterations. Furthermore, the strength of the one-year periodicity may vary across functional groups. Our results suggest that forest streams act as a “natural trap” for fungal DNA and that studies of fungal DNA in stream water may provide information on the temporal variation of fungal communities inhabiting not only water but also the surrounding ecosystem.

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Coming up short: Identifying substrate and geographic biases in fungal sequence databases

Cited by 12 publications

References 33 publications

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Spatial structures of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

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