Vladimir Vujanovic

Bio: Vladimir Vujanovic is an academic researcher from University of Saskatchewan. The author has contributed to research in topics: Fusarium & Zearalenone. The author has an hindex of 22, co-authored 72 publications receiving 1520 citations. Previous affiliations of Vladimir Vujanovic include Agriculture and Agri-Food Canada & Université de Montréal.

Preserving accuracy in GenBank

Abstract: GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for

Fungicide: Modes of Action and Possible Impact on Nontarget Microorganisms

Abstract: Fungicides have been used widely in order to control fungal diseases and increase crop production. However, the effects of fungicides on microorganisms other than fungi remain unclear. The modes of action of fungicides were never well classified and presented, making difficult to estimate their possible nontarget effects. In this paper, the action modes and effects of fungicides targeting cell membrane components, protein synthesis, signal transduction, respiration, cell mitosis, and nucleic acid synthesis were classified, and their effects on nontarget microorganisms were reviewed. Modes of action and potential non-target effects on soil microorganisms should be considered in the selection of fungicide in order to protect the biological functions of soil and optimize the benefits derived from fungicide use in agricultural systems.

Preserving accuracy in GenBank

Abstract: GenBank, the public repository for nucleotide and protein sequences, is a critical resource for molecular biology, evolutionary biology, and ecology. While some attention has been drawn to sequence errors ([1][1]), common annotation errors also reduce the value of this database. In fact, for

Chickpea genotypes shape the soil microbiome and affect the establishment of the subsequent durum wheat crop in the semiarid North American Great Plains

Abstract: Accumulating evidence supports the feasibility of creating biotic soil environments that promote root health using selected plant genotypes. Five years of field experimentation conducted in the semiarid grasslands of North America revealed genotypic variation in the influence of chickpea on the composition of the soil microbial community and on the establishment of the subsequent crop. A 2-year experiment documented the effects of four chickpea cultivars on the arable soil microbiome using cultural methods, the cloning and sequencing of soil-extracted DNA, and fatty acid methyl ester profiling. Cultivar CDC Frontier was characterized by low bacterial biomass, whereas Amit and CDC Anna selected similarly structured bacterial communities but contrasting soil fungal communities. Amit and CDC Anna became colonized by arbuscular mycorrhizal (AM) fungi to the same extent, but the arable soil planted with CDC Anna hosted the highest level of culturable fungal diversity, whereas the soil planted with Amit hosted the lowest. The highest diversity of culturable fungi and the richness of AM fungal ribotypes (11) were also associated with CDC Anna. Amit was preferentially associated with the antagonist species Penicillium canescens. Higher durum wheat stand density was found after CDC Anna than after Amit, indicating that microbial diversity is an important feature of productive soils. The influence of chickpea genotype on the arable soil microbiome and on the establishment of the subsequent durum wheat crop was related to the soil water reserve at depths of 30–120 cm and was eliminated when the chickpea crops experienced drought. Genetic variation in the influence of chickpea on the soil microbiome suggests the possibility of selecting genotypes to engineer beneficial soil biotic environments. Inadequate levels of soil water could limit the success of this strategy, however, in rainfed cropping systems of the semiarid grasslands of North America.

Towards a unified paradigm for sequence-based identification of fungi

Abstract: The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

Abstract: Summary • Soil fungi play a major role in ecological and biogeochemical processes in forests. Little is known, however, about the structure and richness of different fungal communities and the distribution of functional ecological groups (pathogens, saprobes and symbionts). • Here, we assessed the fungal diversity in six different forest soils using tagencoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer1 (ITS-1). No less than 166 350 ITS reads were obtained from all samples. In each forest soil sample (4 g), approximately 30 000 reads were recovered, corresponding to around 1000 molecular operational taxonomic units. • Most operational taxonomic units (81%) belonged to the Dikarya subkingdom (Ascomycota and Basidiomycota). Richness, abundance and taxonomic analyses identified the Agaricomycetes as the dominant fungal class. The ITS-1 sequences (73%) analysed corresponded to only 26 taxa. The most abundant operational taxonomic units showed the highest sequence similarity to Ceratobasidium sp., Cryptococcus podzolicus, Lactarius sp. and Scleroderma sp. • This study validates the effectiveness of high-throughput 454 sequencing technology for the survey of soil fungal diversity. The large proportion of unidentified sequences, however, calls for curated sequence databases. The use of pyrosequencing on soil samples will accelerate the study of the spatiotemporal dynamics of fungal communities in forest ecosystems.

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

Abstract: • Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.