Species delineation based on bacterial genomes is an essential part of the research of prokaryotes. In silico genome-to-genome comparison methods are computationally demanding, but much less tedious and error prone than the wet-lab methods. In this paper, we present a novel method for the delineation of bacterial genomes based on genomic signal processing. The proposed method uses numerical representations of whole bacterial genomes, phase signal and cumulated phase signal, from which four parameters are derived for each genome. The parameters characterize a genome and their calculation is independent of the other genomes comprising a delineation dataset. The delineation itself is processed as a calculation of the parameters' average similarity. The method was statistically verified on 1826 bacterial genomes. A similarity threshold of 96% was set based on the receiver operating characteristic curve that featured sensitivity of 99.78% and specificity of 97.25%. Additionally, comparative analysis on another 33 bacterial genomes was conducted using standard delineation tools as these tools were not able to process the dataset of 1826 genomes using desktop computer. The proposed method achieved comparable or better delineation results in comparison with the standard tools. Besides the excellent delineation results, another great advantage of the method is its small computational demands, which enables the delineation of thousands of genomes on a desktop computer. The calculation of the parameters takes tens of minutes for thousands of genomes. Moreover, they can be calculated in advance by creating a database, meaning the delineation itself is then completed in a matter of seconds.

• Klíčová slova
• Bacterial genome, Comparative genomics, Genomic signal processing, Numerical representation, Species delineation,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Species delineation is particularly challenging in taxa with substantial intra-specific variation. In systematic studies of fishes, meristics and linear measurements that describe shape are often used to delineate species. Yet, little is known about the taxonomic value of these two types of morphological characteristics. Here, we used Tropheus (Teleostei, Cichlidae) from the southern subbasin of Lake Tanganyika to test which of these types of characters best matched genetic lineages that could represent species in this group of stenotypic rock-dwelling cichlids. We further investigated intra-population variation in morphology. By linking this to a proxy of a population's age, we could assess the evolutionary stability of different kinds of morphological markers. RESULTS: Morphological data was collected from 570 specimens originating from 86 localities. An AFLP approach revealed the presence of five lineages in the southern subbasin: T. moorii, T. brichardi, T. sp. 'maculatus', T. sp. 'Mpimbwe' and T. sp. 'red', which we consider to represent distinct species. Although both types of morphological data supported this classification, a comparison of PST-values that describe inter-population morphological differentiation, revealed a better correspondence between the taxon delineation based on AFLP data and the patterns revealed by an analysis of meristics than between the AFLP-based taxon delineation and the patterns revealed by an analysis of shape. However, classifying southern populations of Tropheus was inherently difficult as they contained a large amount of clinal variation, both in genetic and in morphological data, and both within and among species. A scenario is put forward to explain the current-day distribution of the species and colour varieties and the observed clinal variation across the subbasin's shoreline. Additionally, we observed that variation in shape was larger in populations from shallow shores whereas populations from steep shores were more variable in meristics. This difference is explained in terms of the different timescales at which small and large scale lake level fluctuations affected populations of littoral cichlids at steep and shallow shores. CONCLUSIONS: Our results showed meristics to be more evolutionary stable, and of higher taxonomic value for species delimitation in Tropheus, than linear measurements that describe shape. These results should be taken into account when interpreting morphological differences between populations of highly stenotypic species, such as littoral cichlids from the Great East African Lakes.

• Klíčová slova
• AFLP, Africa, Body shape, Clinal variation, Evolution, Meristics, Morphology, PST, Population differentiation, Species delimitation,
• Publikační typ
• časopisecké články MeSH

This study aimed to define the taxonomic position and structure of a novel, taxonomically unique group of 26 Acinetobacter strains, provisionally designated Taxon 24 (T24). The strains were recovered from soil and freshwater ecosystems (n = 21) or animals (n = 5) in Czechia, Scotland, Germany, the Netherlands and Turkey between 1993 and 2015. They were non-glucose-acidifying, nonhemolytic, nonproteolytic, growing at 32 °C and on acetate and ethanol as single carbon sources, but not on 4-hydroxybenzoate and mostly not at 37 °C. Their whole-genome sequences were 3.0-3.7 Mb in size, with GC contents of 39.8-41.3%. Based on core genome phylogenetic analysis, the 26 strains formed a distinct clade within the genus Acinetobacter, with strongly supported subclades termed T24A (n = 11), T24B (n = 8), T24C (n = 2), T24D (n = 3) and T24E (n = 2). The internal genomic ANIb values for these subclades were >94.8%, while the ANIb values between them were <92.5%. The results of MALDI-TOF MS-based analyses agreed with this classification. The five subclades differed from each other in the results of one to six carbon source assimilation tests. Given the genomic and phenotypic distinctness, internal coherence, numbers of available strains and geographically diverse origin of T24A and T24B, we propose the names Acinetobacter terrae sp. nov. and Acinetobacter terrestris sp. nov. for these two taxa, respectively. The type strains are ANC 4282v (= CCM 8986T = CCUG 73811T = CNCTC 8082T) and ANC 4471T (= CCM 8985T = CCUG 73812T = CNCTC 8093T), respectively. We conclude that these two species together with the other T24 strains represent a widely dispersed Acinetobacter clade primarily associated with terrestrial ecosystems.

• Klíčová slova
• Carbon source assimilation, Core genome phylogeny, MALDI-TOF MS, Whole genome sequence,
• MeSH
• Acinetobacter * klasifikace   MeSH
• bakteriální geny MeSH
• DNA bakterií genetika   MeSH
• ekosystém MeSH
• fylogeneze * MeSH
• hybridizace nukleových kyselin MeSH
• půdní mikrobiologie MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• sladká voda mikrobiologie   MeSH
• techniky typizace bakterií MeSH
• zastoupení bazí MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH
• Německo MeSH
• Nizozemsko MeSH
• Skotsko MeSH
• Turecko MeSH
• Názvy látek
• DNA bakterií MeSH
• RNA ribozomální 16S MeSH

The genus Ceratostomella has a long history of taxonomic confusion. While species with evanescent asci have been transferred to the Microascales and Ophiostomatales, the taxonomic status of species with persistent asci has not been completely resolved. In previous studies using DNA sequence data, cultures and morphology, several Ceratostomella spp. were allocated in 13 genera in the Eurotiomycetes and Sordariomycetes. In our study, the systematics of the remaining Ceratostomella spp. with persistent asci is revisited with new collection data, cultures and phylogeny based on novel DNA sequences from six nuclear loci. Bayesian inference and Maximum Likelihood analyses support the monophyly of several wood-inhabiting species formerly classified in Ceratostomella and other unknown morphologically similar taxa and their division into four genera, i.e. Lentomitella, Spadicoides, Torrentispora and the newly described Calyptosphaeria. This robust clade represents the order Xenospadicoidales in the Sordariomycetidae. Comparative analysis of the ITS2 secondary structure revealed a genetic variation among Lentomitella isolates; 11 species were recognised, of which five are newly introduced and two are new combinations. Other taxonomic novelties include four new species and eight new combinations in Calyptosphaeria, Spadicoides, and Torrentispora. Molecular data suggest that Spadicoides is polyphyletic. The core of the genus is positioned in the Xenospadicoidales; Spadicoides s. str. is experimentally linked with sexual morphs for the first time. Based on DNA sequence data, the monotypic genera Xenospadicoides and Pseudodiplococcium are reduced to synonymy under Spadicoides, while Fusoidispora and Pseudoannulatascus are synonymised with Torrentispora. Members of the Xenospadicoidales inhabit decaying wood in terrestrial and freshwater environments and share a few morphological characters such as the absence of stromatic tissue, ascomata with a cylindrical or rostrate neck, similar anatomies of the ascomatal walls, thin-walled unitunicate asci with a non-amyloid apical annulus, disintegrating paraphyses, usually ellipsoidal to fusiform ascospores and holoblastic-denticulate or tretic conidiogenesis. Revised Ceratostomella spp. with persistent asci are listed and the taxonomic status of each species is re-evaluated based on revision of the holotype and other representative material, published details and available phylogenetic data.

• Klíčová slova
• C. tenebrosa Réblová & A.N. Mill., C. tropica (Huhndorf et al.) Réblová & A.N. Mill., Calyptosphaeria Réblová & A.N. Mill, Calyptosphaeria collapsa Réblová & A.N. Mill., Calyptosphaeria subdenudata (Peck) Réblová & A.N. Mill., Ceratostomella, Conidiogenesis, Holoblastic-denticulate, L. investita (Schw.) Réblová, L. obscura Réblová, L. striatella Réblová, L. sulcata Réblová, L. tenuirostris Réblová, Lentomitella conoidea (Feltg.) Réblová, Lentomitella magna Réblová, Molecular systematics, New taxa, Phaeoisaria-like, S. hyalostoma (Munk) Réblová, Selenosporella-like, Spadicoides fuscolutea (Rehm) Réblová, Spadicoides iberica (Hern.-Restr. et al.) Réblová & A.N. Mill., T. biatriispora (K.D. Hyde) Réblová & A.N. Mill., T. dubia (Sacc.) Réblová & A.N. Mill, T. novae-zelandiae Réblová & A.N. Mill, Taxonomy, Torrentispora aquatica (Vijaykr. et al.) Réblová & A.N. Mill., Torrentispora calembola Réblová & A.N. Mill., Tretic, Xenospadicoidales,
• Publikační typ
• časopisecké články MeSH

The description and delineation of trematode species is a major ongoing task. Across the field there has been, and currently still is, great variation in the standard of this work and in the sophistication of the proposal of taxonomic hypotheses. Although most species are relatively unambiguously distinct from their congeners, many are either morphologically very similar, including the major and rapidly growing component of cryptic species, or are highly variable morphologically despite little to no molecular variation for standard DNA markers. Here we review challenges in species delineation in the context provided to us by the historical literature, and the use of morphological, geographical, host, and molecular data. We observe that there are potential challenges associated with all these information sources. As a result, we encourage careful proposal of taxonomic hypotheses with consideration for underlying species concepts and frank acknowledgement of weaknesses or conflict in the data. It seems clear that there is no single source of data that provides a wholly reliable answer to our taxonomic challenges but that nuanced consideration of information from multiple sources (the 'integrated approach') provides the best possibility of developing hypotheses that will stand the test of time.

• Klíčová slova
• cryptic species, hypotheses, species concept, synonymy, taxonomy,
• MeSH
• fylogeneze MeSH
• infekce červy třídy Trematoda parazitologie   MeSH
• klasifikace * metody   MeSH
• Trematoda * klasifikace   genetika   anatomie a histologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

The removal efficiency of heavy metal ions (cadmium(II), Cd(II); cobalt(II), Co(II); nickel(II), Ni(II); copper(II), Cu(II)) by potassium ferrate(VI) (K2FeO4, Fe(VI)) was studied as a function of added amount of Fe(VI) (or Fe) and varying pH. At pH = 6.6, the effective removal of Co(II), Ni(II), and Cu(II) from water was observed at a low Fe-to-heavy metal ion ratio (Fe/M(II) = 2:1) while a removal efficiency of 70% was seen for Cd(II) ions at a high Fe/Cd(II) weight ratio of 15:1. The role of ionic radius and metal valence state was explored by conducting similar removal experiments using Al(III) ions. The unique combination of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), in-field Mössbauer spectroscopy, and magnetization measurements enabled the delineation of several distinct mechanisms for the Fe(VI)-prompted removal of metal ions. Under a Fe/M weight ratio of 5:1, Co(II), Ni(II), and Cu(II) were removed by the formation of MFe2O4 spinel phase and partially through their structural incorporation into octahedral positions of γ-Fe2O3 (maghemite) nanoparticles. In comparison, smaller sized Al(III) ions got incorporated easily into the tetrahedral positions of γ-Fe2O3 nanoparticles. In contrast, Cd(II) ions either did not form the spinel ferrite structure or were not incorporated into the lattic of iron(III) oxide phase due to the distinct electronic structure and ionic radius. Environmentally friendly removal of heavy metal ions at a much smaller dosage of Fe than those of commonly applied iron-containing coagulants and the formation of ferrimagnetic species preventing metal ions leaching back into the environment and allowing their magnetic separation are highlighted.

• MeSH
• chemické látky znečišťující vodu chemie   izolace a purifikace   MeSH
• čištění vody metody   MeSH
• difrakce rentgenového záření MeSH
• fotoelektronová spektroskopie MeSH
• kationty chemie   MeSH
• koncentrace vodíkových iontů MeSH
• magnetické nanočástice chemie   MeSH
• sloučeniny draslíku chemie   MeSH
• sloučeniny železa chemie   MeSH
• spektroskopie Mossbauerova MeSH
• těžké kovy chemie   izolace a purifikace   MeSH
• voda MeSH
• železité sloučeniny chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chemické látky znečišťující vodu MeSH
• ferric oxide MeSH Prohlížeč
• kationty MeSH
• magnetické nanočástice MeSH
• potassium ferrate MeSH Prohlížeč
• sloučeniny draslíku MeSH
• sloučeniny železa MeSH
• těžké kovy MeSH
• voda MeSH
• železité sloučeniny MeSH

In this study, we assessed the phylogenetic relationships among members of Ceratostomella and the morphologically similar genus Xylomelasma, currently classified within the Sordariomycetes. Our phylogenetic analyses, utilising three and five gene markers, revealed that species from these two genera are congeneric, supporting the transfer of Xylomelasma to Ceratostomella. Consequently, we propose two new combinations: C.sordida comb. nov. and C.novae-zelandiae comb. nov. In addition, we identified two cryptic species within the C.sordida species complex, which are described as C.crypta sp. nov. and C.melanospora sp. nov. Traditional micromorphological characters have proven insufficient for differentiating these new species; however, they are clearly distinguishable by molecular data, particularly using the internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) of the nuclear rRNA cistron, and genes encoding the second largest subunit of RNA polymerase II (rpb2), and translation elongation factor 1-α (tef1-α) as primary and secondary barcodes. This study provides new insights into the morphological characteristics of Ceratostomella, identifying the ascogenous system as an important diagnostic trait at the generic level, which distinguishes Ceratostomella from morphologically similar fungi. Ceratostomella is currently recognised with eight species. We also investigated the relationship between Ceratostomella and the closely related Barbatosphaeria. The lack of statistical support in the Maximum likelihood analysis is discussed and the inclusion of Ceratostomella in Barbatosphaeriaceae is not supported. Ceratostomella is accepted as a genus incertae sedis, while Barbatosphaeriaceae remains a monotypic family. The global diversity of Ceratostomella is inferred from metabarcoding data and published field observations. Biogeographic analysis indicates that members of Ceratostomella are widespread, found in soil and decaying wood, as well as in air, dust, roots, shoots, and water across temperate, subtropical and tropical regions in both the Northern and Southern Hemispheres. We are concurrently publishing whole-genome analyses of three ex-type strains of Ceratostomella, i.e. C.crypta, C.melanospora and C.sordida. This effort aims to establish a new standard for high-quality taxonomic studies, which, in accordance with current trends, should incorporate whole-genome sequencing data for future research and application. Our findings underscore the importance of integrating morphological, biogeographic and molecular data for accurate species delineation and highlight the complexity within the genus Ceratostomella.

• Klíčová slova
• Ascogenous hyphae, Sordariomycetes, biogeography, cryptic species, molecular systematics, saprobes, two new species,
• Publikační typ
• časopisecké články MeSH

Since the last revision in 2015, the taxonomy of section Flavipedes evolved rapidly along with the availability of new species delimitation techniques. This study aims to re-evaluate the species boundaries of section Flavipedes members using modern delimitation methods applied to an extended set of strains (n = 90) collected from various environments. The analysis used DNA sequences of three house-keeping genes (benA, CaM, RPB2) and consisted of two steps: application of several single-locus (GMYC, bGMYC, PTP, bPTP) and multi-locus (STACEY) species delimitation methods to sort the isolates into putative species, which were subsequently validated using DELINEATE software that was applied for the first time in fungal taxonomy. As a result, four new species are introduced, i.e. A. alboluteus, A. alboviridis, A. inusitatus and A. lanuginosus, and A. capensis is synonymized with A. iizukae. Phenotypic analyses were performed for the new species and their relatives, and the results showed that the growth parameters at different temperatures and colonies characteristics were useful for differentiation of these taxa. The revised section harbors 18 species, most of them are known from soil. However, the most common species from the section are ecologically diverse, occurring in the indoor environment (six species), clinical samples (five species), food and feed (four species), droppings (four species) and other less common substrates/environments. Due to the occurrence of section Flavipedes species in the clinical material/hospital environment, we also evaluated the susceptibility of 67 strains to six antifungals (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, terbinafine) using the reference EUCAST method. These results showed some potentially clinically relevant differences in susceptibility between species. For example, MICs higher than those observed for A. fumigatus wild-type were found for both triazoles and amphotericin B for A. ardalensis, A. iizukae, and A. spelaeus whereas A. lanuginosus, A. luppiae, A. movilensis, A. neoflavipes, A. olivimuriae and A. suttoniae were comparable to or more susceptible as A. fumigatus. Finally, terbinafine was in vitro active against all species except A. alboviridis.

• Klíčová slova
• Antifungal susceptibility testing, Aspergillus alboluteus F. Sklenar, Jurjević, Ezekiel, Houbraken & Hubka, Aspergillus alboviridis J.P.Z. Siqueira, Gené, F. Sklenar & Hubka, Aspergillus flavipes, Aspergillus inusitatus F. Sklenar, C. Silva Pereira, Houbraken & Hubka, Aspergillus lanuginosus F. Sklenar & Hubka, Clinical fungi, Indoor fungi, Multigene phylogeny, Soil-borne fungi, Species delimitation,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: The systematics of echinostomes within the so-called 'revolutum' group of the genus Echinostoma, which encompasses the type-species E. revolutum and a number of morphologically similar species, has long been controversial. Recent molecular studies indicate the existence of more species than previously considered valid, thus stressing the need for wider taxon sampling from natural host populations. This is especially true for Europe where morphological evidence indicates higher species diversity than previously thought, but where molecular data are virtually lacking. This gap in our knowledge was addressed in the present study through an integration of morphological and molecular approaches in the investigation of a dataset with larger taxonomic and geographical coverage. METHODS: More than 20,000 freshwater snails belonging to 16 species were collected during 1998-2012 from various localities in eight countries in Europe. Snail screening provided representative larval isolates for five species of the 'revolutum' group, identified by their morphology. Adult isolates for four species recovered from natural and experimental infections were also identified. Partial fragments of the mitochondrial nad1 and 28S rRNA genes were amplified for 74 and 16 isolates, respectively; these were analysed together with the sequences of Echinostoma spp. available on GenBank. RESULTS: Delineation of the European Echinostoma spp. was carried out based on molecular, morphological and ecological data. The large-scale screening revealed infections with five Echinostoma spp., including one new species: E. revolutum (sensu stricto), E. miyagawai, E. paraulum, E. bolschewense and Echinostoma n. sp. The newly-generated nad1 sequences from Europe fall into six distinct, well-supported, reciprocally monophyletic lineages corresponding to the species identifications based on morphology; this was corroborated by the 28S rDNA sequences. The analyses of the total nad1 dataset provided evidence for 12 monophyletic groups and five singletons, which represent seven described/named species and ten cryptic species-level lineages of Echinostoma. CONCLUSION: We conclude that nad1 should be the first choice for large-scale barcode-based identification of the species of the 'revolutum' group. Our study provides a comprehensive reference library for precisely identified isolates of the European species and highlights the importance of an integrative approach for species identification linking molecular, morphological and biological data.

• MeSH
• druhová specificita MeSH
• Echinostoma anatomie a histologie   klasifikace   genetika   MeSH
• fylogeneze MeSH
• haplotypy MeSH
• hlemýždi parazitologie   MeSH
• interakce hostitele a parazita MeSH
• sladká voda MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

Many ecological experiments are based on the extraction and downstream analyses of microorganisms from different environmental samples. Due to its high throughput, cost-effectiveness and rapid performance, Matrix Assisted Laser Desorption/Ionization Mass Spectrometry with Time-of-Flight detector (MALDI-TOF MS), which has been proposed as a promising tool for bacterial identification and classification, could be advantageously used for dereplication of recurrent bacterial isolates. In this study, we compared whole-cell MALDI-TOF MS-based analyses of 49 bacterial cultures to two well-established bacterial identification and classification methods based on nearly complete 16S rRNA gene sequence analyses: a phylotype-based approach, using a closest type strain assignment, and a sequence similarity-based approach involving a 98.65% sequence similarity threshold, which has been found to best delineate bacterial species. Culture classification using reference-based MALDI-TOF MS was comparable to that yielded by phylotype assignment up to the genus level. At the species level, agreement between 16S rRNA gene analysis and MALDI-TOF MS was found to be limited, potentially indicating that spectral reference databases need to be improved. We also evaluated the mass spectral similarity technique for species-level delineation which can be used independently of reference databases. We established optimal mass spectral similarity thresholds which group MALDI-TOF mass spectra of common environmental isolates analogically to phylotype- and sequence similarity-based approaches. When using a mass spectrum similarity approach, we recommend a mass range of 4-10 kDa for analysis, which is populated with stable mass signals and contains the majority of phylotype-determining peaks. We show that a cosine similarity (CS) threshold of 0.79 differentiate mass spectra analogously to 98.65% species-level delineation sequence similarity threshold, with corresponding precision and recall values of 0.70 and 0.73, respectively. When matched to species-level phylotype assignment, an optimal CS threshold of 0.92 was calculated, with associated precision and recall values of 0.83 and 0.64, respectively. Overall, our research indicates that a similarity-based MALDI-TOF MS approach can be routinely used for efficient dereplication of isolates for downstream analyses, with minimal loss of unique organisms. In addition, MALDI-TOF MS analysis has further improvement potential unlike 16S rRNA gene analysis, whose methodological limits have reached a plateau.

• Klíčová slova
• 16S rRNA gene, MALDI BioTyper, MALDI-TOF mass spectrometry (MS), bacterial identification, bacterial isolation, dereplication of isolates, species delineation,
• Publikační typ
• časopisecké články MeSH