Explore the vast range of titles available.

Bjerkandera adusta is a species of common white rot polyporoid fungi found worldwide. Despite playing an important role in deadwood decay, the species strains are used in bioremediation due to its ability to degrade polycyclic hydrocarbons and some of them are important etiological agents of chronic coughs and are associated with lung inflammations. In our experiments, diversity within the species was investigated using molecular approaches and we found that sequence diversity seen at ITS sequence level is not due to cryptic speciation but to intragenomic variability of ITS sequences in this species.

Delimitation of species and the search for a proper threshold for defining phylogenetic species in fungi are under discussion. In this study, morphological and molecular data are correlated to delimit species of Tulasnella, the most important mycobionts of Orchidaceae, which suffer from poor taxonomy. Resupinate basidiomata of Tulasnella species were collected in Ecuador and Germany, and 11 specimens (seven from Ecuador, four from Germany) were assigned to traditional species concepts by use of morphological keys. The specimens were compared by micro-anatomical examination with 75 specimens of Tulasnella borrowed from fungaria to obtain better insights on variation of characters. Sequences of the ITS region (127) were obtained after cloning from the fresh basidiomata and from pure cultures. Proportional variability of ITS sequences was analyzed within and among the cultures and the specimens designated to different morphospecies. Results suggested an intragenomic variation of less than 2%, an intraspecific variation of up to 4% and an interspecific divergence of more than 9% in Tulasnella. Cryptic species in Tulasnella, mostly from Ecuador, were revealed by phylogenetic analyses with 4% intraspecific divergence as a minimum threshold for delimiting species. Conventional diagnostic morphological characters appeared insufficient for species characterization. Arguments are presented for molecular delimitation of the established species Tulasnella albida, T. asymmetrica, T. eichleriana, T. cf. pinicola, T. tomaculum and T. violea.

Despite the full attention of malacologists to the study of Corbicula clams, stimulated mainly due to their high invasive potential and unique breeding system, studies based on an integrative taxonomic approach to identify various invasive lineages of this genus in European Russia are still limited. Our fieldwork was conducted in the Don, Volga, and Caspian Sea basins. In total, four distinct morphotypes belonging to the European forms R, Rlc, S, and “Int” of Corbicula clams were distinguished. According to our molecular genetic data, two Corbicula lineages, relevant to the nominal species Corbicula fluminea and C. fluminalis, can be defined. We observed a discrepancy between mtDNA haplotypes and morphological features for all individuals that were sampled from the Don and Kura Rivers. Identified mismatch may be due to the androgenetic reproduction of Corbicula that leads to cytonuclear inconsistencies. The 28S rRNA polymorphism in C. fluminea and C. fluminalis from studied localities was recorded. This occurrence is perhaps due to hybridization events between forms R, S, and Rlc. The biogeographic origins of Corbicula invasive lineages are discussed. Corbicula fluminalis (FW17, form S) has been detected for first time in the native range, namely in Azerbaijan, Tajikistan, Turkey, and Myanmar. We assume that the invasion of C. fluminalis into reservoirs and watercourses of the Caspian Sea basin (Republic of Dagestan and Stavropol Krai of Russia) was from Western Asia and Transcaucasia, and the introduction of C. fluminea to the Don and Volga River basins was from unspecified European countries.

Increases in human activity and climate change are factors that are expected to augment the number and impact of alien species in the northern regions. In the present paper, we report the discovery of a population of Asian Corbicula clams in the North of Russia near the Arctic frontier (64°N, 40°E), which is the most northern record of these invaders in the world. This population contains two distinct lineages that are living in sympatry in a man-made channel of the Arkhangelsk thermal power plant. The first lineage belongs to the morphotype Rlc by shell morphology but reveals the FW5 mtDNA haplotype (COI and 16S rRNA genes), which was typically recorded in the morphotype R. The second lineage reveals the shell morphological pattern of the morphotype R but has the FW17 mtDNA haplotype, which usually occurs in specimens of the morphotype S. Both forms that were identified, based on conchological and anatomical features and differences in mtDNA haplotypes, reveal the same 28S rDNA sequences but show intragenomic nDNA variability with two different variants of the 28S rDNA gene within each individual (allelic sequence heterogeneity). The discrepancy between mtDNA data and shell morphology could be explained by the well-known mechanism that is associated with androgenesis together with “egg parasitism” (mitochondrial genome-capture) in invasive Corbicula clams. The intragenomic 28S rDNA variability may be due to a hybridization event which can join different alleles from the two diploid (or polyploid) parental taxa to an allopolyploid descendant. We found that the lineages that rarely occur in European populations are exclusively established in a population near the Arctic frontier. Moreover, specimens belonging to the R-morphotype with the FW17 mtDNA haplotype that has sporadic occurrences in central Europe is prevalent (> 90% of a total sample) in a mollusk assemblage at the studied site in northern Russia. Additionally, we show that the life span of Corbicula clams in high latitudes may be longer than 1 year. Isolated Corbicula populations in artificially heated or geothermal reservoirs may therefore be primary sources for a broad invasion to seasonal waterbodies of the high-latitude regions in the future as climate warming progresses.

Taxonomic marker gene analysis allows uncovering taxonomic profiles of microbial communities at low cost, making it omnipresent in microbiome research. There is an ever‐expanding set of tools to extract further biological information from this kind of data. In this perspective, we enunciate several concerns regarding the biological validity of predicting functional potential from taxonomic profiles, especially when they are generated by short‐read sequencing. The taxonomic resolution of marker genes, intragenomic variability of marker genes, and the compositional nature of microbiome data are discussed. Combining actual measurements of microbiome functions with predicted functional potentials is proposed as a powerful approach to better understand microbiome functioning. In this context, the significance of predicted functional potentials for generating and testing hypotheses is highlighted. We argue that functions of microbiomes predicted from microbiome DNA read count data generated by short‐read amplicon sequencing should not serve as the only basis to draw biological inferences. We raise concerns regarding the biological validity of predicting functional potential from microbiome taxonomic profiles generated by short‐read amplicon sequencing. We reason that predicted functional potential profiles can be improved by employing long‐read sequencing technologies, which in combination with independent measurements of actual functions can constitute a powerful approach to understanding microbiome functioning. Highlights Concerns regarding the biological validity of predicting functional potential from taxonomic profiles of microbiome data sets are enunciated. Taxonomic resolution of marker genes, intragenomic variability of marker genes, and the compositional nature of microbiome data are discussed. Combining measurements of actual functions and predicted functional potential profiles is a powerful approach to understanding microbial functioning.

Ribosomal RNA in fungi is encoded by a series of genes and spacers included in a large operon present in 100 tandem repeats, normally in a single locus. The multigene nature of this locus was somehow masked by Sanger sequencing, which produces a single sequence reporting the prevalent nucleotide of each site. The introduction of next generation sequencing led to deeper knowledge of the individual sequences (reads) and therefore of the variants between the same DNA sequences located in different tandem repeats. In this framework, NGS sequencing of the rDNA region was used to elucidate the extent of intra- and inter-genomic variation at both the strain and species level. Specifically, the use of an innovative NGS technique allowed the high-throughput high-depth sequencing of the ITS1-LSU D1/D2 amplicons of 252 strains belonging to four opportunistic yeast species of the genus Candida. Results showed the presence of a large extent of variability among strains and species. These variants were differently distributed throughout the analyzed regions with a higher concentration within the Internally Transcribed Spacer (ITS) region, suggesting that concerted evolution was not able to totally homogenize these sequences. Both the internal variability and the SNPs between strain can be used for a deep typing of the strains and to study their ecology.

The teleomorphic basidiomycetous yeast Xanthophyllomyces dendrorhous is important as a commercial source of astaxanthin, which is a component of feeds for mariculture. Phaffia rhodozyma is the anamorphic state of Xanthophyllomyces; however, there are conflicting reports in the literature concerning the presence of a sexual cycle in P. rhodozyma. The current study attempted to explain this enigma. Strains were obtained from the Phaff Yeast Culture Collection (University of California, Davis) and other sources in the northern hemisphere. Molecular sequences of three nuclear rDNA regions were examined: the internal transcribed spacers (ITS), intergenic spacer (IGS1) and the D1D2 region at the 5' end of the 26S gene. Different levels of genetic variability were observed in the three regions. The D1D2 differentiated major groups of strains, while an increased variability in the ITS suggested that the ITS region could be employed as an ecological marker. The greatest variability was in the IGS1 region, where strains can be defined by the presence and location of indels. Intragenomic sequence heterogeneity in the ITS and IGS1 regions led to the hypothesis that the type strain of P. rhodozyma (CBS 5905T, UCD 67-210T) was derived as a mating-deficient basidiospore from the parent teleomorphic strain CBS 9090.