Assignment Of Species Research Articles

Molecular Data and Karyotype Revealed Two Distinct Species of Domesticated Water Buffaloes in the Philippines

The six species of the genus Bubalus include the lowland and mountain anoa, Asian wild buffalo, tamaraw, swamp buffalo, and riverine buffalo. Few studies were conducted on the matrilineal phylogeny and genetic diversity of Bubalus species. In addition, there is controversy regarding the identity of the two domesticated water buffaloes in the Philippines – the introduced riverine and the native swamp buffalo. Thus, this study aimed to determine the genetic distance and phylogenetic relationship of Bubalus species using the mitochondrial cytochrome b (cytb) variation and to re-evaluate the taxonomic species designation of Bubalus bubalis. A total of499 Philippine cytb sequences from this study (n = 179), as well as other Asian countries (n = 319)and Syncerus caffer (n = 1), from NCBI were included in the analysis. The highest interspecies genetic distance (d) (0.040) was between the tamaraw and lowland anoa, whereas the lowest genetic distance (0.020) was between mountain and lowland anoa. Moreover, the phylogenetic tree indicated 52 haplotypes that delineated three groups, including lowland anoa, mountain anoa, and tamaraw with two domesticated buffaloes. The latter group further separated into three species – tamaraw, riverine, and swamp buffaloes. The analyses of genetic distance,phylogeny, and median-joining network structure based on cytb confirmed that the swamp buffaloes from Occidental Mindoro and South Cotabato, Philippines belong to maternal lineage B. Karyotype analysis consistently confirms that riverine buffaloes possess 50 chromosomes, whereas swamp buffaloes have 48 chromosomes, aligning with previous findings. Moreover, the swamp and riverine buffaloes appear to be distinct species, with the swamp buffalo having a closer affinity to the tamaraw than to the riverine buffalo. We, therefore, propose to revive the species assignment of the Bubalus kerabau Fitzinger, 1860 as a distinct species to the swamp buffalo. Furthermore, a common maternal ancestry was confirmed between the tamaraw and two domesticated buffaloes – the swamp and riverine. Research findings provided valuable information on understanding and monitoring the matrilineal genetic diversity of the genus Bubalus toward conservation and management.

Performance of DNA barcodes for informing the subspecies controversy in North American populations of Callophrys gryneus (Hübner, [1819]) (Lepidoptera: Lycaenidae)

Abstract Analysis of genetic divergence in published mitochondrial DNA barcodes from ‘juniper’ and ‘cedar’ hairstreaks, Callophrys gryneus (Hübner) and Callophrys muiri (Hy. Edwards), together with a comparison of phenotypic differences in populations from North America, have been used to address the long-standing controversy regarding subspecies and species assignments in this confusing group of hairstreaks. The most recent view holds that C. gryneus is a single polytypic species comprising 11 nominal subspecies and that C. muiri from California is a valid species. An alternative view subdivides C. gryneus into three nominal species, C. gryneus (s.s.), Callophrys siva and Callophrys nelsoni, each with several named subspecies, and retains C. muiri as a full species. Haplotype networks, phylogenetic analysis and analysis of molecular variance of barcodes provided evidence supporting the subspecies scenario. However, barcodes from closely related congeners of C. gryneus (s.l.) revealed pairwise genetic divergences that would also support elevating three subspecies (C. g. castalis, C. g. siva and C. g. nelsoni) to full species. The barcode data also raise the question of whether C. muiri warrants full species status. Larval host plant preference as a possible driver of genetic differentiation in western populations of this group is also discussed briefly.

Automatic Assignment of Molecular Ion Species to Elemental Formulas in Gas Chromatography/Methane Chemical Ionization Accurate Mass Spectrometry.

Gas chromatography-mass spectrometry (GC-MS) usually employs hard electron ionization, leading to extensive fragmentations that are suitable to identify compounds based on library matches. However, such spectra are less useful to structurally characterize unknown compounds that are absent from libraries, due to the lack of readily recognizable molecular ion species. We tested methane chemical ionization on 369 trimethylsilylated (TMS) derivatized metabolites using a quadrupole time-of-flight detector (QTOF). We developed an algorithm to automatically detect molecular ion species and tested SIRIUS software on how accurate the determination of molecular formulas was. The automatic workflow correctly recognized 289 (84%) of all 345 detected derivatized standards. Specifically, strong [M - CH3]+ fragments were observed in 290 of 345 derivatized chemicals, which enabled the automatic recognition of molecular adduct patterns. Using Sirius software, correct elemental formulas were retrieved in 87% of cases within the top three hits. When investigating the cases for which the automatic pattern analysis failed, we found that several metabolites showed a previously unknown [M + TMS]+ adduct formed by rearrangement. Methane chemical ionization with GC-QTOF mass spectrometry is a suitable avenue to identify molecular formulas for abundant unknown peaks.

Is there hybridization between 2 species of the same genus in sympatry?-The genetic relationships between Anoplophora glabripennis, Anoplophora chinensis, and putative hybrids.

Anoplophora glabripennis (Asian longhorn beetle, ALB) and Anoplophora chinensis (Citrus longhorn beetle, CLB) are native forest pests in China; they have become important international quarantine pests. They are found using the same Salix aureo-pendula host tree of Cixi, Zhejiang province, China. On this host tree, we collected additional beetles that appeared to be morphologically intermediate between ALB and CLB. By using a stereoscope, we observed that there were several bumps on the base of the elytra, which was inconsistent with ALB, which typically has a smooth elytral base, but was more like CLB, which has numerous short tubercles on the elytral base. Given their sympatry and intermediate morphology, we hypothesized that these may represent ALB×CLB hybrids. We studied the genomic profiles for 46 samples (ALB, CLB, and putative hybrids) using genotyping-by-sequencing (GBS) providing a reduced representation of the entire genome. Employing principal component analyses on the 163 GBS-derived single nucleotide polymorphism data, we found putative hybrids tightly clustered with ALB, but genetically distinct from the CLB individuals. Therefore, our initial hybrid hypothesis was not supported by genomic data. Further, while mating experiments between adult ALB and CLB were successful in 4 separate years (2017, 2018, 2020, and 2021), and oviposition behavior was observed, no progeny was produced. Having employed population genomic analysis and biological hybridization experiments, we conclude that the putative hybrids represent newly discovered morphological variants within ALB. Our approach further confirmed the advantage of genome-wide information for Anoplophora species assignment in certain ambiguous classification cases.

Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022.

BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee. We report a comprehensive diagnostic approach that identified Vittaforma corneae as the aetiology, serving as proof of concept for using real-time metagenomics for outbreak investigation.MethodsCorneal scraping samples from a clinical case were subjected to standard microbiological testing. Samples were tested by calcofluor white staining and metagenomic short-read sequencing. We analysed the metagenome for taxonomical assignment and isolation of metagenome-assembled genome (MAG). Targets for a novel PCR were identified, and the assay was applied to clinical and environmental samples and confirmed by long-read metagenomic sequencing.ResultsFluorescent microscopy was suggestive of microsporidiosis. The most abundant species (96.5%) on metagenomics analysis was V. corneae. Annotation of the MAG confirmed the species assignment. A unique PCR target in the microsporidian rRNA gene was identified and validated against the clinical sample. The assay and metagenomic sequencing confirmed V. corneae in an environmental sludge sample collected at the exposure site.ConclusionsThe real-time utilisation of metagenomics allowed species detection and development of diagnostic tools, which aided in outbreak source tracking and can be applied for future cases. Metagenomics allows a fully culture-independent investigation and is an important modality for public health microbiology.

Intrinsic and extrinsic drivers of shape variation in the albatross compound bill.

Albatross are the largest seabirds on Earth and have a suite of adaptations for their pelagic lifestyle. Rather than having a bill made of a single piece of keratin, Procellariiformes have a compound rhamphotheca, made of several joined plates. Drivers of the shape of the albatross bill have not been explored. Here we use three-dimensional scans of 61 upper bills from 12 species of albatross to understand whether intrinsic (species assignment & size) or extrinsic (diet) factors predict bill shape. Diet is a significant predictor of bill shape with coarse dietary categories providing higher R2 values than dietary proportion data. We also find that of the intrinsic factors, species assignment accounts for ten times more of the variation than size (72% versus 6.8%) and that there is a common allometric vector of shape change between all species. When considering species averages in a phylogenetic framework, there are significant Blomberg's K results for both shape and size (K = 0.29 & 1.10) with the first axis of variation having a much higher K value (K = 1.9), reflecting the split in shape at the root of the tree. The influence of size on bill shape is limited, with species assignment and diet predicting far more of the variation. The results show that both intrinsic and extrinsic factors are needed to understand morphological evolution.

DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity

AbstractDespite the increasing popularity of DNA metabarcoding in the assessment of aquatic ecosystems using fish eDNA or ichthyoplankton, challenges have hampered its broader application in the Neotropical freshwaters. Using five mock communities composed of fish species from two Neotropical River basins, we evaluated the influence of DNA concentration and choice of mitochondrial 12S molecular markers (MiFish, NeoFish, and Teleo) on species detection and relative read abundance (RRA) using DNA metabarcoding. Of the three 12S markers analyzed, only MiFish detected all species from all mock communities. The performance of a taxonomy‐free approach using ASV/MOTUs was not as precise as assigning DNA reads to species using a curated 12S library that includes approximately 100 fish species since more than one ASV/MOTU was observed for the same specimen. Thus, here we showcase the importance of a custom reference database to allow precise assignment of Neotropical fish species in metabarcoding studies and that the RRA is dependent on community composition, marker, and DNA concentration. We highlight the importance of controlled experiments using known species communities before large investments are made in assessing biodiversity using non‐invasive methods that apply DNA metabarcoding.

The largest record of the minute beaver Euroxenomys minutus (Mammalia, Castoridae) from the early Late Miocene hominid locality Hammerschmiede (Bavaria, Southern Germany) and palaeoecological considerations

ABSTRACT In this study, we describe the dental remains of a very minute beaver from the early Late Miocene locality Hammerschmiede (MN 7/8) located at the Northern Alpine Foreland Basin (Southern Germany, Bavaria). The finds represent the so far most comprehensive (>1.000 dental specimens) collection of the trogontheriine castorid Euroxenomys minutus. Metrically and morphologically, the large data set demonstrates an extensive intraspecific variability of this beaver from Hammerschmiede that covers most finds of other European localities and confirms previous species assignments. The subspecies Euroxenomys minutus rhenanus from Dorn-Dürkheim (Germany), clearly isolates from this range of variation and can thus be validated. The performed age-frequency distributions for Euroxenomys minutus from the local stratigraphic levels HAM 5 (rivulet) and HAM 4 (river) correspond roughly and also resemble Euroxenomys from the swamp deposit Rudabánya (Hungary). Since previous mortality studies on the also occurring larger beaver Steneofiber depereti from Hammerschmiede demonstrated dominance of behavioural or internal factors, this cross-ecosystem similarity in mortality for the small beaver species is likely explained by external factors, such as predation. Supported by a taphonomic bone analysis, a multitude of predators are finally considered to prey on Euroxenomys minutus and indicate a predatory bone assemblage.

A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.

DNA barcoding approaches provide powerful tools for characterizing fungal diversity. However, DNA barcoding is limited by poor representation of species-level diversity in fungal sequence databases. Can the development of custom, regionally focused DNA reference libraries improve species-level identification rates for lichen-forming fungi? To explore this question, we created a regional ITS database for lichen-forming fungi (LFF) in the Intermountain West of the United States. The custom database comprised over 4800 sequences and represented over 600 formally described and provisional species. Lichen communities were sampled at 11 sites throughout the Intermountain West, and LFF diversity was characterized using high-throughput ITS2 amplicon sequencing. We compared the species-level identification success rates from our bulk community samples using our regional ITS database and the widely used UNITE database. The custom regional database resulted in significantly higher species-level assignments (72.3%) of candidate species than the UNITE database (28.3-34.2%). Within each site, identification of candidate species ranged from 72.3-82.1% using the custom database; and 31.5-55.4% using the UNITE database. These results highlight that developing regional databases may accelerate a wide range of LFF research by improving our ability to characterize species-level diversity using DNA barcoding.

Detection of multiple fish species in the diet of the invasive round goby reveals new trophic interactions in the Baltic Sea

The mesopredatory round goby (Neogobius melanostomus) is an important fish invader in fresh and brackish waters of the northern hemisphere. Trophic interactions of invasive species can generate ecological impacts across the food web in invaded ecosystems. Here we investigated major diet components, spatiotemporal variation in diet and the effect of round goby densities on diet composition in two geographically distinct round goby populations in the Baltic Sea. The round goby is a generalist feeder but previous diet studies, based on visual prey identification, have likely over-emphasized the importance of hard-shelled, invertebrate prey in round goby diet, as shells degrade and evacuate slowly relative to soft-bodied prey that break down rapidly in the stomach. We therefore, in addition to visual stomach content analysis, used DNA metabarcoding, which is less biased towards hard body structures of prey and can be used for species assignment of highly degraded prey. The results demonstrated that round goby diet composition varied between areas and years. Visual stomach content analysis indicated that blue mussel was the main prey in the southern area, whereas hydrobiid gastropods were the major diet component in the northern area. Metabarcoding revealed that several fish species, likely the egg or larval stages of e.g. stickleback, cod and herring, were also part of the round goby diet. Analyses suggested that round goby feeding on fishes was positively associated with round goby densities. Our study shows that round goby, in addition to benthic invertebrates, preys on several fish species of ecological and commercial importance. Thus, there is potential for predator-prey reversal and negative effects of the invasive round goby on large, predatory fishes.

Structural, harmonic force field and vibrational studies of cholinesterase inhibitor tacrine used for treatment of Alzheimer's disease

Different structures of free base (FB), two cationic forms (CA) and three hydrochloride forms (HCl) of cholinesterase inhibitor tacrine used for treatment of Alzheimer ’s disease was evaluated using hybrid B3LYP calculations in order to perform their complete vibrational assignments using the scaled harmonic force fields. Structures of anhydrous form of tacrine have been optimized in gas phase and in aqueous solution. The structure of form III HCl is in agreement with the experimental determined by X-ray diffraction while the predicted IR, Raman, 1H– 13C NMR and UV spectra show good correlations with the corresponding experimental ones. Energy values show that the three forms of HCl can exist in both media because these energetic values decrease from 35.15 kJ/mol in gas phase to 5.51 kJ/mol in solution. For the most stable species of tacrine, the following stability order using natural bond orbital (NBO) studies was found: form I HCl > form III HCl > form I CA > FB. CA presents the higher solvation energy value, as reported for hydrochloride species of alkaloids and antihypertensive agents. The structural parameters of form III of HCl present better concordance and corresponds to that experimental observed in the solid phase. Higher topological properties of form III together with the strong N2–H26⋯Cl31 interaction could justify the presence of this form in the solid phase and in solution and the higher stabilities in both media. The gap values support the higher reactivity of form III while FB is the less reactive species in both media. Complete vibrational assignments for FB, CA and HCl species together with the corresponding scaled force constants are reported.

Novel species discrimination method elucidates colony growth form variation between the New Zealand soft corals Kotatea aurantiaca and Kotatea lobata

In New Zealand, Kotatea aurantiaca and Kotatea lobata are two common, endemic, co-occurring, and morphologically similar soft coral species that currently cannot be distinguished without microscopic examination of sclerites and of which little is known regarding any aspect of their ecology or biology. The aim of the present study is to ascertain if, and in what ways, their colony growth forms differ, and to test the taxonomic value of macroscopic morphological character measurements using statistical discrimination analyses. A binary logistic regression model is developed whereby macroscopic characters of colony morphology can be used to assign specimens to either species with ~ 90% accuracy. Species assignment accuracy is greatest when ratios formed from morphological measurements are used rather than direct measurements. Here, these ratios are used for the first time to account for the appearance-altering habit among soft corals of hydrostatically expanding and contracting their coelenteron with seawater. Relationships between colony morphology and depth are also examined, and it is suggested that phenotypic plasticity detected in K. lobata, causing it to resemble K. aurantiaca more closely at greater depths, may contribute to their morphological overlap. It is anticipated that this discrimination technique will facilitate future research on the ecology and biology of these species and will be replicated on other sets of morphologically similar soft corals for which species discrimination has been problematic.

DNA Barcoding of Cardinalfish (Apogonidae) in Gilimanuk Bay, Bali, Indonesia

Highlight Research Eight species of cardinalfish in Gilimanuk Bay were delineated using the barcoding method. This study provides the first nucleotide sequence for Ostorhinchus hartzfeldii in GenBank online database. The phylogenetic tree showed that each sample resided in a distinct cluster, indicating that the barcoding method efficiently differentiated at the species level. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. Abstract The Apogonidae is estimated to consist of nearly 300 fish species, most of which inhabit coral reef areas. The lack of distinctive body markings and overlapping species distribution makes species assignment challenging. Therefore, this study aimed to delineate species and establish barcoding reference databases of Apogonidae in Gilimanuk Bay (Bali, Indonesia) using the Cytochrome Oxidase I (COI) gene of the mitochondrial DNA. A total of 22 fish tissue samples were extracted with 10% Chelex solution. BLAST analysis was performed and genetic differentiation between species was calculated. The phylogenetic tree was constructed using the Maximum Likelihood method and tree visualization was generated using iTOL V5. The morphology and genetic identification results based on the mitochondrial COI gene revealed eight species of seven genera, and one species was new to GenBank online database. This study was the first-ever addition of COI sequence for Ostorhinchus hartzfeldii into the GenBank database. The average K2P genetic distance within species and K2P distance between genera within the family were 0.60% and 19.10%, respectively. The mean genetic distance between genera within the family was 31.8-fold higher than the mean genetic distance within species. The phylogenetic tree showed that each sample resided in a distinct cluster, which indicates that DNA barcoding is a reliable and effective approach for species delimitation in Apogonidae fishes.

Aspergillus welwitschiae; an otomycosis predominant agent, new epidemiological and antifungal susceptibility data from Iran

BackgroundBlack aspergilli (section Nigri) are predominate etiologic agents of otomycosis, however, there is controversy in the exact differentiation of species. For several decades Aspergillus niger is considered the main otomycosis etiologic agent. Recently calmodulin gene has been accepted as a more suitable gene for the accurate assignment of Aspergillus species. Therefore, it is found that A. welwitschiae and A. tubingensis are the main otomycosis agents based on calmodulin gene sequencing. AimsThe objective of the study was to isolate and identify black aspergilli from otomycosis using the calmodulin gene and their susceptibility was evaluated against several antifungals. Methods134 clinically confirmed patients with otomycosis were sampled and specimens were cultured on Sabouraud dextrose agar (SDA) at ambient temperature. Black aspergilli were screened based on colony morphology on SDA and microscopy features and then subjected to sequencing using calmodulin primers. Moreover, antifungal susceptibility for isolates was applied based on CLSI M38 3rd edition. Results132 (98.5%) of patients had positive cultures for different species of molds or yeasts. Most of the patients (30.3%) ranged from 31 to 40 years, and 56.1% of them were female. Aspergillus section Nigri was the most prevalent fungal pathogen and of 86 isolates, 60.5% isolates were identified as A. welwitschiae, A. tubingensis, 31 (36.0%), A. niger (sensu stricto), 2 (2.3%), and A. neoniger 1 (1.2%). According to the maximum likelihood method, all isolates of A. tubingensis and one isolate of A. neoniger were included in the A. tubingensis clade. On the other hand, the clade of A. niger/A. welwitschiae contains, all isolates of A. welwitschiae, two A. niger (sensu stricto) isolates, and 36 isolates from other countries. Aspergillus welwitschiae was more sensitive to luliconazole, voriconazole, and amphotericin B compared to A. tubingensis. 78.8% of A. welwitschiae strains were classified as non-wild type to nystatin compared to 35.5% of A. tubingensis. Moreover, 3.2% of A. tubingensis strains were non-wild type against amphotericin B. The isolates of A. tubingensis were more sensitive to itraconazole than A. welwitschiae. ConclusionsIt is concluded that in contrast, to the previous study A. welwitschiae from section Nigri is the most causative agent of otomycosis followed by A. tubingensis. In addition, the isolates of A. welwitschiae were more sensitive to luliconazole, voriconazole, and amphotericin B compared to A. tubingensis. Whereas, the isolates of A. tubingensis were more sensitive to itraconazole than A. welwitschiae. On the other hand, 78.8% and 35.5% of A. welwitschiae and A. tubingensis strains were classified as a non-wild type against nystatin. Also, 3.2% of A. tubingensis strains were non-wild type against amphotericin B. All A. welwitschiae were included in the A. niger/A. welwitschiae clade, associated with different clinical and environmental species from different countries.

Understanding surface structures of In2O3 catalysts during CO2 hydrogenation reaction using time-resolved IR, XPS with in situ treatment, and DFT calculations

The In2O3 catalyst has been shown to have a high activity for CO2 hydrogenation to methanol. For this high pressure process, reliable spectral assignment of surface species formed by interaction with CO2, H2O, and other major reaction ingredients, is the key step to achieve mechanistic understanding. In this study, in situ IR and XPS are performed to investigate the O1s binding energies of the adsorbates induced by CO2 and H2O treatments along with density functional theory (DFT) simulations to further correlate the calibrated assignments with surface structures. Time resolved IR indicates that carbonates formation induced by CO2 exposure replaces the original hydroxyl on In2O3, and XPS further reveals that these two oxygen species have very similar binding energies (532.0 ± 0.2 eV). Computational results using the In2O3(110) and (111) slab models give good agreement with the XPS experiments, further suggesting that the amount of oxygen vacancy concentration does not induce new lattice oxygen O1s binding energy, but resulting in a slight shift to a higher binding energy instead. Our results provide useful structure information for the In2O3 catalyst surface and shed light for further investigations into its kinetic behavior under methanol synthesis condition.

A new species of the genus Ceriodaphnia Dana, 1853 (Cladocera: Daphnidae) from Eastern Siberia (Russia) that combines morphological features of two species groups.

Taxa of the genus Ceriodaphnia Dana, 1853 (Cladocera: Daphniidae) are ubiquitous in temperate and tropical lakes, and the taxonomy of the genus is confused. Moreover, present keys are often regional and insufficient for the taxonomic assignment of species at a global scale. This communication is aimed at improving our understanding of the C. dubia s.l. species group. We redescribe C. dubia s.l. from Northern Eurasia and describe a new species from Central Yakutia (Eastern Siberia, Russia). In contrast to typical members of the C. dubia group, C. nikolaii sp.nov. has the postabdomen of the parthenogenetic female with preanal margin slightly or strongly projecting and angulated. Moreover, adult males have a pronounced preanal angle and sensory seta of antenna I which is shorter than the longest easthetasc. Our finding challenges current definitions of species groups in Ceriodaphnia. Indeed, a postabdomen shape with a strongly projected preanal angle is characterstic of another group of this genus, namely the C. laticaudata-group. We found a taxon that combines the diagnostic morphological characters of two species groups. Further development of the genus taxonomy must be accompanied by redescriptions of all well-accepted and dubious taxa from their type localities and revisions of populations from other localities of the world.

Assessing a potential to improve data quality for accelerated identification of microorganisms derived from positive blood cultures

Diagnostics of blood-borne infections is still an urgent problem of modern medicine. The main causative agents of septic conditions are gram-positive microorganisms particularly Staphylococcus aureus, enterococci, etc., whereas clinical significance of isolated coagulase-negative staphylococci is ambiguous. Escherichia coli, Klebsiella pneumoniae and other enterobacteria, as well as Acinetobacter baumannii prevail among the gram-negative flora. Modern possibilities of accelerated identification of microorganisms derived from positive blood cultures based on mass-spectrometry consist of two approaches. Firstly, the manufacturers developed consumables for mass spectrometry are proposed, and secondly, there are domestic developments of accelerated sample preparation protocols developed by microbiological laboratories. The approaches used have a number of advantages and disadvantages, but to summarize, the use of the proposed methods in routine practice is quite limited. At the same time, the need to accelerate the issuing a microbiological conclusion related to nosology is great being associated with improved outcomes. In this regard, the aim of the study was to evaluate convergence and accuracy of results for accelerated identification of microorganisms derived from positive blood cultures in blood-borne infections. The study included 87 positive blood cultures, the identification of pathogens from them occurred in four ways: the classical microbiological analysis of blood for sterility, pathogen identification directly from the vial without isolating a pure culture, as well as two sample preparation methods based on ethylenediaminetetraacetic acid (EDTA) and potassium ethylenediaminetetraacetate disubstituted (EDTA-K2) as wash additives. It was found that gram-positive and gram-negative flora were isolated from the blood almost evenly often. When evaluating an influence of biomaterial used for mass spectrometry, it turned out that use of wash additives increases chances of successful identification of bacteria from a blood sample. The influence of tinctorial properties on the results of determining the species assignment of isolates was also evaluated. Identification of gram-positive flora is more accurate, since some pathogens were not identified without washing additives, and when using EDTA-K2 and the corresponding acid, assignment to the genus was obtained in the same samples. A similar pattern was also characteristic of gram-negative flora. At the same time, modern manufacturers of laboratory equipment and reagents allow to standardize sample preparation procedures in the protocols used. The effects of EDTA-K2, which allowing to use it as a washing component, are associated with the binding of calcium and magnesium ions in solution, which reduces the adhesion of bacterial cells to blood cells, thereby contributing to better mass spectrometry of microbial sediments with accelerated identification of microorganisms from positive blood cultures. Thus, use of the described additives can provide high quality, timely and adequate diagnostics of serious and life-threatening conditions such as blood-borne infections.

Integrative taxonomy using the plant core DNA barcodes in Sumatra's Burseraceae.

The high diversity and limited floral information in tropical forests often pose a challenge for species identification. However, over the past decade, DNA barcoding has been employed in tropical forests, including Sumatran forests, to enhance floristic surveys. This technique facilitates the discrimination of morphologically similar species and addresses the limitations of conventional species identification, which relies on short-lived reproductive structures. This study aimed to evaluate the efficiency of matK, rbcL, and the combination of both chloroplast markers for species identification in Burseraceae by employing genetic distance and species tree inference. In this study, we collected 197 specimens representing 20 species from five genera of Burseraceae. The highest percentage of specimens' identification (36%) at the species level was obtained using matK + rbcL, followed by matK (31%), and rbcL (7%). The matK dataset presented the highest interspecific divergence with a mean of 0.008. In addition, a lack of barcode gap was observed in both markers, suggesting potential limitations of the core barcodes for distinguishing Sumatran species within Burseraceae. The monophyly test confirmed five species as monophyletic using Bayesian species tree inferences for matK. Overall, our results demonstrate that matK outperforms rbcL in species identification of Burseraceae, whereas their combination did not enhance species delimitation. To improve the molecular species assignments of this family, future studies may consider including more DNA markers in conjuction with matK, and broadening the availability of reference sequences for species that have not yet been included in the databases. The outcomes of molecular species identification vary depending on the taxonomic group under investigation. Implementation of phylogenomics for species delimitation and diagnostic marker development is strongly recommended for tropical biodiversity assessments, especially for poorly studied clades.

Marine and freshwater centrohelid heliozoans (Haptista: Centroplasthelida) in Canada, including taxonomic revisions and descriptions of 22 new species and subspecies

Canadian coastal waters of the Pacific Ocean and the Atlantic Ocean as well as inland freshwater habitats in Ontario were sampled for centrohelid heliozoans (free-living heterotrophic single-celled organisms) over a period of nearly five decades. More than 60 species and subspecies were revealed, including 1 Triangulopteris, 1 Raphidocystis, 2 Pseudoraphidocystis, 3 Raineriophrys, 4 Pseudoraphidiophrys, 12 Choanocystis, 15 Pterocystis, and 25 Acanthocystis taxa. Of these, 22 were officially named and described as new to science based primarily on the morphology of the siliceous scales that cover the cell. New species were compared with images and/or descriptions of close “relatives” to validate their new species assignments. New data on five species of Acanthocystis and one species of Choanocystis required revisions of their descriptive taxonomy that in some cases resulted in the splitting off of separate species or subspecies. Very little can be concluded about global distribution of centrohelid heliozoans, owing to the paucity of records. For many of the taxa reported here, previous records consist of just one or two findings from other parts of the world. One example is Choanocystis antarctica Tikhonenkov and Mylnikov, 2011 that was previously known only from Antarctic seawater, but is reported here from an Ontario softwater lake.

Successional shifts in tree demographic strategies in wet and dry Neotropical forests

AbstractAimTropical forest succession and associated changes in community composition are driven by species demographic rates, but how demographic strategies shift during succession remains unclear. Our goal was to identify generalities in demographic trade‐offs and successional shifts in demographic strategies across Neotropical forests that cover a large rainfall gradient and to test whether the current conceptual model of tropical forest succession applies to wet and dry forests.LocationMexico and Central America.Time period1985–2018.Major taxa studiedTrees.MethodsWe used repeated forest inventory data from two wet and two dry forests to quantify demographic rates of 781 tree species. For each forest, we explored the main demographic trade‐offs and assigned tree species to five demographic groups by performing a weighted principal components analysis to account for differences in sample size. We aggregated the basal area and abundance across demographic groups to identify successional shifts in demographic strategies over the entire successional gradient from very young (<5 years) to old‐growth forests.ResultsAcross all forests, we found two demographic trade‐offs, namely the growth–survival trade‐off and the stature–recruitment trade‐off, enabling the data‐driven assignment of species to five demographic strategies. Fast species dominated early in succession and were then replaced by long‐lived pioneers in three forests. Intermediate and slow species increased in basal area over succession in all forests, but, in contrast to the current conceptual model, long‐lived pioneers continued to dominate until the old‐growth stage in all forests. The basal area of short‐lived breeders was low across all successional stages.Main conclusionsThe current conceptual model of Neotropical forest succession should be revised to incorporate the dominance of long‐lived pioneers in late‐successional and old‐growth forests. Moreover, the definition of consistent demographic strategies that show clear dominance shifts across succession substantially improves the mechanistic understanding and predictability of Neotropical forest succession.