Does host plant richness explain diversity of ectomycorrhizal fungi? Re‐evaluation of Gao <i>et al</i>. (2013) data sets reveals sampling effects

Tedersoo, Leho; Bahram, Mohammad; Dickie, Ian A.

doi:10.1111/mec.12660

Cited by 49 publications

(55 citation statements)

References 25 publications

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“…Our previous study (Miyamoto et al, 2014) demonstrated that intensive sampling (many samples from each community) is effective for recording a relatively large number of fungal taxa in a community and for identifying species overlaps among study sites. Consistent sampling across study sites also helps to remove the variations imposed by methodological discrepancies found in many meta-analyses (Nakagawa and Santos, 2012;Tedersoo et al, 2014). A detailed examination of species overlaps among communities improves the chances of detecting distribution patterns, community structures and the underlying mechanisms of organisms (Leibold and Mikkelson, 2002;Presley et al, 2010;Thébault, 2013).…”

Section: Introductionmentioning

confidence: 99%

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

et al. 2015

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Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the regional scale. Soil cores were collected from various forest types along an elevation gradient in southwestern Japan. Fungal species were identified by the internal transcribed spacer regions of the rDNA using direct sequencing. The occurrence of fungal species in this study was compared with a previous study conducted on a mountain separated by B550 km. In total, we recorded 454 EM fungi from 330 of 350 soil cores. Forty-seven fungal species (B20% of the total excluding singletons) were shared between two mountains, mostly between similar forest types on both mountains. Variation partitioning in redundancy analysis revealed that climate explained the largest variance in EM fungal composition. The similarity of forest tree composition, which is usually determined by climatic conditions, was positively correlated with the similarity of the EM fungal composition. However, the lack of large host effects implied that communities of forest trees and EM fungi may be determined independently by climate. Our data provide important insights that host plants and mutualistic fungi may respond to climate change idiosyncratically, potentially altering carbon and nutrient cycles in relation to the plant-fungus associations.

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Section: Introductionmentioning

confidence: 99%

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

et al. 2015

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“…Sequence chimeras are common when pooled DNA s are co-amplified by a PCR process (Edgar et al 2011;Judo et al 1998;Jumpponen 2007;Meyerhans et al 1990;Odelberg et al 1995;Qiu et al 2001a;Smyth et al 2010;Tedersoo et al 2014;Wang and Wang 1997). There has been speculation that chimeras may be the result of incomplete extension of PCR products which subsequently act as primers for the next amplification cycle and, in fact, there seems to be a reduction in chimeric PCR products when extension times are increased (Meyerhans et al 1990;Qiu et al 2001a;Smyth et al 2010; Thompson et al 2002) or by optomizing the PCR protocol (Qiu et al 2001b;Wang and Wang 1997).…”

Section: Introductionmentioning

confidence: 99%

Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

Hughes¹,

Morris²,

Reboredo-Segovia³

2015

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Gymnopus dichrous exists in the southern Appalachians (USA) as two distinct entities with essentially identical nuclear ribosomal ITS1 sequences but differing ITS2 and LSU sequences (for convenience, called G. dichrous I and II). F 1 ITS heterozygotes between the two are routinely collected from nature. Cloning of ITS PCR products from F 1 heterozygotes produced sequences of both parental haplotypes but also numerous chimeric sequences (21.9%). The location of template switching was non-random leading to recovery of the same chimera several times and the chimeric region varied from 45bp to 300bp. By comparison, single-basidiospore isolates from heterozygote F 1 fruitbodies showed no recombinant haplotypes within the ITS + LSU span and clones derived from P 1 homozygotes were identical to the P 1 parent. Thus, chimeric sequences are likely an artifact of the PCR-cloning process and not a consequence of natural recombination events found in nature, nor are they due to hidden existing variation within the ribosomal repeat. Chimeras and PCR-induced mutations are common in cloned PCR products and may result in incorrect sequence information in public databases.

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“…Many of the pioneering ecological studies failed to separate sampling effect from the diversity effect per se, which requires optimizing the experimental design (Huston, 1997;Wardle, 1999;Tedersoo et al, 2014a). Sampling effect can be eliminated or accounted for by (i) comparing species performance in monocultures and polycultures (Wardle, 1999) or (ii) by using model selection or variation partitioning, incorporating component species as dummy variables (Healy et al, 2008;Wagg et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

et al. 2015

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Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

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Does host plant richness explain diversity of ectomycorrhizal fungi? Re‐evaluation of Gao et al. (2013) data sets reveals sampling effects

Cited by 49 publications

References 25 publications

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

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