User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences

Vasar, Martti; Davison, John; Neuenkamp, Lena; Sepp, Siim‐Kaarel; Young, J. Peter W.; Moora, Mari; Öpik, Maarja

doi:10.1111/1755-0998.13340

Cited by 42 publications

(23 citation statements)

References 79 publications

(142 reference statements)

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“…The 18S rRNA gene animal data were analysed using the gDAT pipeline (Vasar et al., 2021). Demultiplexed paired‐end reads were analysed in the following way: barcode and primer sequences were matched, allowing one mismatch for both pairs.…”

Section: Methodsmentioning

confidence: 99%

“…ITS PacBio CCS reads (minPasses = 3, MinAccuracy = 0.9) were generated using SMRT Link v.6.0.0.47841. Subsequent quality filtering was performed using pipeCraft v.1.0 (Anslan et al, 2017) The 18S rRNA gene animal data were analysed using the gDAT pipeline (Vasar et al, 2021). Demultiplexed paired-end reads were analysed in the following way: barcode and primer sequences were matched, allowing one mismatch for both pairs.…”

Section: Eukaryotesmentioning

confidence: 99%

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Global soil microbiomes: A new frontline of biome‐ecology research

Vasar

Davison

Sepp

et al. 2022

Global Ecol Biogeogr

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2,845

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Aim Organisms on our planet form spatially congruent and functionally distinct communities, which at large geographical scales are called “biomes”. Understanding their pattern and function is vital for sustainable use and protection of biodiversity. Current global terrestrial biome classifications are based primarily on climate characteristics and functional aspects of plant community assembly. These and other existing biome schemes do not take account of soil organisms, including highly diverse and functionally important microbial groups. We aimed to define large‐scale structure in the diversity of soil microbes (soil microbiomes), pinpoint the environmental drivers shaping it and identify resemblance and mismatch with existing terrestrial biome schemes. Location Global. Time period Current. Major taxa studied Soil eukaryotes and prokaryotes. Methods We collected soil samples from natural environments world‐wide, incorporating most known terrestrial biomes. We used high‐throughput sequencing to characterize soil biotic communities and k‐means clustering to define soil microbiomes describing the diversity of microbial eukaryotic and prokaryotic groups. We used climatic data and soil variables measured in the field to identify the environmental variables shaping soil microbiome structure. Results We recorded strong correlations among fungal, bacterial, archaeal, plant and animal communities, defined a system of global soil microbiomes (producing seven biome types for microbial eukaryotes and six biome types for prokaryotes) and showed that these are typically structured by pH alongside temperature. None of the soil microbiomes are directly paralleled by any current terrestrial biome scheme, with mismatch most substantial for prokaryotes and for microbial eukaryotes in cold climates; nor do they consistently distinguish grassland and forest ecosystems. Main conclusions Existing terrestrial biome classifications represent a limited surrogate for the large‐scale diversity patterns of microbial soil organisms. We show that empirically defined soil microbiomes are attainable using metabarcoding and statistical clustering approaches and suggest that they can have wide application in theoretical and applied biodiversity research.

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Section: Methodsmentioning

confidence: 99%

Section: Eukaryotesmentioning

confidence: 99%

Global soil microbiomes: A new frontline of biome‐ecology research

Vasar

Davison

Sepp

et al. 2022

Global Ecol Biogeogr

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2,845

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“…Bioinformatic data analysis and processing was conducted using the graphical downstream analysis tool (gDAT) for analysing rDNA sequences (Vasar et al, 2021). Raw reads (2X×X2,412,166 reads in total) were demultiplexed and cleaned using a series of bioinformatic steps (see Vasar et al, 2017Vasar et al, , 2021. In short, reads were demultiplexed by checking double barcodes, allowing one mismatch for both reads.…”

Section: Root Chemistrymentioning

confidence: 99%

Belowground plant responses to root herbivory depend on the composition and structure of their root-colonising arbuscular mycorrhizal fungi

Wilson

Frew

2022

Preprint

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There is growing interest in managing arbuscular mycorrhizal (AM) fungi in agriculture to support plant production. These fungi can support crop growth and nutrient uptake, but also affect plant-herbivore interactions. However, our knowledge of how native AM fungal diversity and community composition influence these interactions is limited, while our understanding of this in relation to root-herbivory is lacking altogether. To begin to address these knowledge gaps, plants were grown with no AM fungi or were inoculated with native fungal communities sourced from either a crop field (field community), a sclerophyll forest (forest community), or a crop field in fallow (fallow community). We then explored how the composition and structure (species richness and relative abundance) of root-colonising AM fungal communities was associated with the growth and belowground nutrient responses of a major crop (Sorghum bicolor) to attack from a root-feeding insect (Dermolepida albohirtum). DNA metabarcoding revealed plant associated with three distinct root-colonising AM fungal communities. Fungal taxon richness in roots was highest in the field community and lowest in the fallow community. Both the field and fallow communities were dominated by the putatively ruderal genera Glomus and Claroideoglomus, while the forest-derived community contained greater proportions of Paraglomus and Ambispora. In response to root herbivory, plants without AM fungi and plants colonised by the forest community exhibited root biomass losses of 61% and 44%, respectively. Similarly, these two groups also had reductions of 59% and 65% in their phosphorus content, respectively, when subjected to the root herbivore. In contrast, plants associating with communities harbouring greater proportions of Glomus and Claroideoglomus (the field and fallow communities) did not exhibit reductions in root biomass or nutrient content. Our results show that plant responses to root-herbivory vary with root-colonising AM fungal community composition and structure. In a community context, our findings suggest that stronger associations with the genera Claroideoglomus and Glomus may potentially support crop tolerance-associated responses belowground. There is an urgent need for more exploration of how natural assemblages of AM fungi differentially mediate plant-herbivore interactions if we are to effectively manage soil fungi in sustainable agricultural systems.

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“…Paired-end Illumina reads were cleaned using gDAT pipeline (Vasar et al 2021). In short, reads were demultiplexed into samples using an 8-bp barcode allowing one mismatch for both forward and reverse reads.…”

Section: Bioinformaticsmentioning

confidence: 99%

Hedgerows increase diversity and modifies composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes

Fradejas

León

Vasar

et al. 2022

Preprint

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Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities in four farmland sites located in Central Spain, where 120 samples in total were collected to assess soil physical and chemical properties and analyse AM fungal metabarcode data. We compared the richness (number of AM fungal taxa), abundance (number of sequences), taxonomic, functional, and phylogenetic diversity, and composition of AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard) and an herbaceous (barley) crop. Our results showed positive effects of hedgerows on most diversity metrics. Many AM fungal taxa were shared among the three farmland habitat types. Planting hedgerows increased AM fungal richness (F2,112 = 23.21, P < 0.01) and alpha diversity (F2,112= 11.62, P < 0.01), especially in herbaceous crops. Hedgerows and woody crops harboured more AM fungal sequences than herbaceous crops (F2,112 = 15.10, P < 0.01). Hedgerows exhibited higher proportions of AM fungi with non-ruderal life-history strategies (F2,112 = 11.08, P < 0.01). AM fungi communities were more similar in hedgerows and woody crops (F2,112 = 3.93, P < 0.01) than in hedgerows and herbaceous crops due to lack of tillage in hedgerows and woody crops. Unexpectedly, planting hedgerows reduced phylogenetic diversity, which might be related to random processes shaping communities in crops. Overall, the observed results hint that planting hedgerows contributes to restoring belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.

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User‐friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences

Cited by 42 publications

References 79 publications

Global soil microbiomes: A new frontline of biome‐ecology research

Global soil microbiomes: A new frontline of biome‐ecology research

Belowground plant responses to root herbivory depend on the composition and structure of their root-colonising arbuscular mycorrhizal fungi

Hedgerows increase diversity and modifies composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes

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