Identifying wood-inhabiting fungi with 454 sequencing – what is the probability that BLAST gives the correct species?

Ovaskainen, Otso; Nokso-Koivisto, Jussi; Hottola, Jenni; Rajala, Tiina; Pennanen, Taina; Ali-Kovero, Heini; Miettinen, Otto; Oinonen, Petri; Auvinen, Petri; Paulín, Lars; Larsson, Karl‐Henrik; Mäkipää, Raisa

doi:10.1016/j.funeco.2010.01.001

Cited by 100 publications

(81 citation statements)

References 41 publications

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“…All of the European high-throughput sequencing based studies on WIF conducted to date focused on deadwood of either gymnosperm tree species, Picea abies, in a single biome, the boreal forest zone of Northern Europe (Kubartova et al 2012;Ovaskainen et al 2010Ovaskainen et al , 2013 or two angiosperm tree species, Fagus sylvatica and Quercus robur in temperate forests (Hiscox et al 2015;van der Wal et al 2015). Therefore, our information on community dynamics of WIF in deadwood of different tree species in the same forest ecosystem at different locations is still limited.…”

Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

et al. 2015

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Fungi play vital roles in the decomposition of deadwood due to their secretion of various enzymes that break down plant cell-wall complexes. The compositions of woodinhabiting fungal (WIF) communities change over the course of the decomposition process as the remaining mass of wood decreases and both abiotic and biotic conditions of the wood significantly change. It is currently not resolved which substrate-related factors govern these changes in WIF communities and whether such changes influence the deadwood decomposition rate. Here we report a study on fungal richness and community structure in deadwood of Norway spruce and European beech in temperate forest ecosystems using 454 pyrosequencing. Our aims were to disentangle the factors that correspond to WIF community composition and to investigate the links between fungal richness, taxonomically-resolved fungal identity, and microbial-mediated ecosystem functions and processes by analyzing physico-chemical wood properties, lignin-modifying enzyme activities and wood decomposition rates. Unlike fungal richness, we found significant differences in community structure between deadwood of different tree species. The composition of WIF communities was related to the physico-chemical properties of the deadwood substrates. Decomposition rates and the activities of ligninmodifying enzymes were controlled by the succession of the fungal communities and competition scenarios rather than fungal OTU richness. Our results provide further insights into links between fungal community structure and microbialmediated ecosystem functions and processes.

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Section: Electronic Supplementary Materialsmentioning

confidence: 99%

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

et al. 2015

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“…Such simple queries permit the user to examine and establish whether the expected species are present among the available ITS sequences in the database. Ross et al (2008) and Ovaskainen et al (2010) provide interesting statistics on the performance of BLAST under varying conditions, including incomplete database coverage.…”

Section: Guideline 4 Sequences Can Be Broken In Other Puzzling Waysmentioning

confidence: 99%

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson¹,

Tedersoo²,

Abarenkov³

et al. 2012

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Larsson K-H, Larsson E, Kõljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-63. doi: 10.3897/mycokeys.4.3606 Abstract Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contribut- Nilsson et al. / MycoKeys 4: 37-63 (2012) 38 ing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

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“…Peres-Neto et al (2001) modeled the presence-absence of each species first individually as a function of environmental variables, and then used the resulting models to construct randomized species distributions. As the simulated data were generated independently for each species, the simulated communities corresponded to an environmentally constrained null hypothesis.…”

Section: Introductionmentioning

confidence: 99%

“…As the simulated data were generated independently for each species, the simulated communities corresponded to an environmentally constrained null hypothesis. In this paper we combine the two above-mentioned steps of Peres-Neto et al (2001) by constructing a multivariate logistic regression model for the entire species community. Using a multivariate approach for community modeling is conceptually appealing, as the data are clearly of multivariate nature: for each sampling unit, there is a vector of zeros and ones describing which particular species were absent and which were present in that sampling unit.…”

Section: Introductionmentioning

confidence: 99%

Modeling species co‐occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

Ovaskainen

Hottola

Siitonen

2010

Ecology

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241

176

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Abstract. Signals of species interactions can be inferred from survey data by asking if some species occur more or less often together than what would be expected by random, or more generally, if any structural aspect of the community deviates from that expected from a set of independent species. However, a positive (or negative) association between two species does not necessarily signify a direct or indirect interaction, as it can result simply from the species having similar (or dissimilar) habitat requirements. We show how these two factors can be separated by multivariate logistic regression, with the regression part accounting for species-specific habitat requirements, and a correlation matrix for the positive or negative residual associations. We parameterize the model using Bayesian inference with data on 22 species of wood-decaying fungi acquired in 14 dissimilar forest sites. Our analyses reveal that some of the species commonly found to occur together in the same logs are likely to do so merely by similar habitat requirements, whereas other species combinations are systematically either over-or underrepresented also or only after accounting for the habitat requirements. We use our results to derive hypotheses on species interactions that can be tested in future experimental work.

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Identifying wood-inhabiting fungi with 454 sequencing – what is the probability that BLAST gives the correct species?

Cited by 100 publications

References 41 publications

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Modeling species co‐occurrence by multivariate logistic regression generates new hypotheses on fungal interactions

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