Martin Unterseher

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

Summary 1. The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and BLAST searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. 2. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 – as well as full-length ITS sequences – from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. 3. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. 4. ITSx paves the way for more sensitive BLAST searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.

Species abundance distributions and richness estimations in fungal metagenomics – lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log‐normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant‐associated fungal communities – phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log‐normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log‐normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data – a log‐normal model for the core group and a log‐series model for the satellite group. The prominent log‐series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

Dilution-to-extinction cultivation of leaf-inhabiting endophytic fungi in beech (Fagus sylvatica L.) ― Different cultivation techniques influence fungal biodiversity assessment

Two cultivation-based isolation techniques - the incubation of leaf fragments (fragment plating) and dilution-to-extinction culturing on malt extract agar - were compared for recovery of foliar endophytic fungi from Fagus sylvatica near Greifswald, north-east Germany. Morphological-anatomical characters of vegetative and sporulating cultures and ITS sequences were used to assign morphotypes and taxonomic information to the isolates. Data analysis included species-accumulation curves, richness estimators, multivariate statistics and null model testing. Fragment plating and extinction culturing were significantly complementary with regard to species composition, because around two-thirds of the 35 fungal taxa were isolated with only one of the two cultivation techniques. The difference in outcomes highlights the need for caution in assessing fungal biodiversity based upon single isolation techniques. The efficiency of cultivation-based studies of fungal endophytes was significantly increased with the combination of the two isolation methods and estimations of species richness, when compared with a 20-years old reference study, which needed three times more isolates with fragment plating to attain the same species richness. Intensified testing and optimisation of extinction culturing in endophyte research is advocated.

Improving ITS sequence data for identification of plant pathogenic fungi

SummaryPlant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results – a total of 31,954 changes – are incorporated in and made available through the UNITE database for molecular identification of fungi (http://unite.ut.ee), including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

Application of species richness estimators for the assessment of fungal diversity

Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Grays predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale.

Leaf-inhabiting endophytic fungi of European Beech (Fagus sylvatica L.) co-occur in leaf litter but are rare on decaying wood of the same host

Many microfungi are able to live in living plant tissues. In contrast to plant pathogens and parasites the so-called endophytic fungi do not cause obvious disease symptoms in their hosts. Nevertheless, they constitute an ubiquitous active component in direct and multitrophic interactions. The present study was conducted to assess the level of overlap of cultivable microfungi in living and decaying tissues of European Beech (Fagus sylvatica L.) from a forest stand in North-Eastern Germany. The focus lay on the hypothesized fall-spring relationship of leaf-inhabiting forest endophytes, which means that endophytes from autumn leaves persist as saprobes in litter or dead wood, sporulate and re-invade living leaves in spring. Fungal cultures were isolated from living leaves, leaf litter and dead wood still attached to the tree by dilution-to-extinction cultivation in the years 2007–2010. Analyses of species identity, species richness and species composition were based on microscopic identification and of sequencing the fungal DNA ‘barcode’ ITS (internal transcribed spacer). Species richness of litter-inhabiting microfungi equaled that of wood-inhabiting fungi and exceeded that of leaf endophytes. The most distinctive species assemblage was observed on wood, fungal species composition in living leaves and leaf litter were also significantly different from each other. On the other hand a considerable compositional and phylogenetic overlap between leaf and litter fungi was revealed with phylogenetics, cluster analysis and non-metric multidimensional scaling. The taxa accounting most to the similarity between living and decaying leaves belonged to Capnodiales, Xylariales, Diaporthales and Pleosporales. Finally, data from cultivated leaf-inhabiting beech endophytes were compared with a fungal 454 sequence data set from beech phyllosphere. This analysis allowed the partition of species lists into active fungal endophytes, fungal “epiphytes” and dormant fungal propagules.

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

Species richness and distribution patterns of leaf-inhabiting endophytic fungi in a temperate forest canopy

In 2005, researchers at the Leipzig Canopy Crane Research Facility collected living leaves of four temperate tree species at heights of between 15 and 33 m above the ground. Following surface sterilisation of the leaves, leaf-fragments were cultured on malt extract agar which allowed the growth of endophytic fungi into the surrounding medium. Isolated cultures were identified by morphology and sequence analysis of the D1/D2 region of the large subunit rDNA. Phylogenetic analysis established the taxonomic positions of the fungi. A total of 49 different taxa were identified, representing 20 families and ten orders. With the exception of one basidiomycetous yeast, all taxa belonged to filamentous ascomycetes. Species richness was highest on Tilia cordata and lowest on Quercus robur. Species-accumulation curves showed that the sampling effort was not sufficient to cover the majority of the likely species at the investigation site. Most endophytes proved to be ubiquitous within the canopy of the investigation site, but habitat preferences in terms of different tree species, different light regimes and season (sampling times) were obvious for some abundant endophytes. Apiognomonia errabunda and Aspergillus niger occurred predominantly on Q. robur, Diplodina acerina on Acer pseudoplatanus, one species of Phoma significantly prefered shaded leaves from the lower canopy layer whereas Sordaria fimicola prefered sun-exposed leaves from the upper tree crowns. Seasonal patterns were observed, for example, for A. errabunda, which was abundant in young leaves in the spring and almost completely absent in aged autumn-leaves, thus suggesting the accumulation of antifungal secondary plant metabolites during the growing season.

Species richness and ecological characterization of myxomycetes and myxomycete-like organisms in the canopy of a temperate deciduous forest

The ecological community of myxomycetes and myxomycete-like organisms (MMLO) in the canopy of living deciduous trees was studied in a riparian deciduous forest at Leipzig, Germany. A systematic survey carried out with a total of 146 moist chamber cultures resulted in 386 records of 37 taxa, with 32 myxomycetes, two myxobacteria, two protostelids and the fruit body forming ciliate Sorogena stoianovitchae, the latter recorded for the first time for Europe. With 94% of all cultures positive for MMLO, these organisms are present consistently in the investigated sections of white-rotten twigs attached to living trees at 10–30 m above the ground. Our sampling recovered a majority of the likely species, with 37 out of the 42–45 predicted according to a species-accumulation curve and two other estimators of species richness. Nonmetric multidimensional scaling revealed pH, water-holding capacity and stage of decay to explain most of the variation in species distribution. Arcyria cinerea and Perichaena depressa as the most common species occurred in 32% and 29% of all samples, respectively. Viewing the sampled twigs as habitat islands and a single spore as sufficient to establish a population, a simulation program assuming a random spore rain estimated an average of 0.4 and 0.35 spore hits per twig as necessary to explain the observed frequencies. This is matched by the potential productivity of the substrate. All fruit bodies from the cultured twigs would be able to create a spore rain of 86 (A. cinerea) or 40 (P. depressa) spore hits per twig when dispersed evenly over the plot. The terminal fall velocity of spores was measured, revealing that it took about 5 h for a spore to land (30 m) in still air and indicating high dispersal ability for canopy-inhabiting MMLO.