Does selection favour the maintenance of porous species boundaries?

The endpoint of speciation has been viewed as complete isolation and the absence of gene flow between species. If the influx of genes from another species is maladaptive because species have different adaptations and genetic backgrounds, selection should favour the closing of species boundaries and zero gene flow, a process known as reinforcement. Recently, numerous cases of gene flow between species have been identified, many of which involved adaptive introgression of beneficial alleles. These cases could reflect transient states on the way to closed species boundaries or the result of declining strength or efficacy of selection for reinforcement as the level of gene flow approaches zero. An alternative hypothesis, however, is that selection favours porous species boundaries that allow beneficial alleles to cross, especially in changing environments. This perspective evaluates the conditions that would be needed for selection to favour porous species boundaries and the evidence for them. A contrast is made between hybridization in sexual eukaryotes and gene transfer via homologous recombination in bacteria. Current evidence is inconclusive on whether non-zero gene flow is favoured by selection. Studies are needed that quantify selection gradients on rates of gene flow and test for evolution towards intermediate values, especially experiments that manipulate conditions and track evolution for multiple generations. Estimation of gene flow networks for more clades and regional assemblages using emerging genome data will also allow the evolutionary determinants of interspecific gene flow to be better understood.

Physiological adaptation to irradiance in duckweeds is species and accession specific and depends on light habitat niche

Duckweeds span 36 species of free-floating aquatic organisms with body sizes ranging from 2 mm to 10 mm, where each plant body plan is reduced to a largely leaf-like structure. As an emerging crop, their fast growth rates offer potential for cultivation in closed systems. We describe a novel UK collection derived from low light (dLL) or high light (dHL) habitats, profiled for growth, photosynthesis, and photoprotection (non-photochemical quenching, NPQ) responses. Twenty-three accessions of three Lemna species and one Spirodela polyrhiza were grown under relatively low light (LL: 100 μmol m-2 s-1) and high light (HL: 350 μmol m-2 s-1) intensities. We observed broad within- and between-species level variation in photosynthesis acclimation. Duckweeds grown under HL exhibited a lower growth rate, biomass, chlorophyll, and quantum yield of photosynthesis. In HL compared with LL, carotenoid de-epoxidation state and NPQ were higher, whilst PSII efficiency (φPSII) and Chl a:b ratios were unchanged. The dLL plants showed relatively stronger acclimation to HL compared with dHL plants, especially Lemna japonica accessions. These achieved faster growth in HL with concurrent higher carotenoid levels and NPQ, and less degradation of chlorophyll. We conclude that these data support local adaptation to the light environment in duckweed affecting acclimation in controlled conditions.

Association between gut microbiota and onset of type 2 diabetes mellitus: a two-sample Mendelian randomization study

Aim

Mendelian randomization (MR) analysis has been used in the exploration of the role of gut microbiota (GM) in type 2 diabetes mellitus (T2DM); however, it was limited to the genus level. This study herein aims to investigate the relationship of GM, especially at the species level, with T2DM in order to provide some evidence for further exploration of more specific GM taxa and pathway abundance in T2DM.

Methods

This two-sample MR study was based on the summary statistics of GM from the available genome-wide association study (GWAS) meta-analysis conducted by the MiBioGen consortium as well as the Dutch Microbiome Project (DMP), whereas the summary statistics of T2DM were obtained from the FinnGen consortium released data. Inverse variance weighted (IVW), MR-Egger, strength test (F), and weighted median methods were used to examine the causal association between GM and the onset of T2DM. Cochran's Q statistics was employed to quantify the heterogeneity of instrumental variables. Bonferroni's correction was conducted to correct the bias of multiple testing. We also performed reverse causality analysis.

Results

The corrected IVW estimates suggested the increased relative abundance of family Oxalobacteraceae (OR = 1.0704) and genus Oxalobacter (OR = 1.0874), respectively, were associated with higher odds of T2DM, while that of species faecis (OR = 0.9460) had a negative relationship with T2DM. The relationships of class Betaproteobacteria, family Lactobacillaceae, species finegoldii, and species longum with T2DM were also significant according to the IVW results (all P < 0.05).

Conclusions

GM had a potential causal association with T2DM, especially species faecis, finegoldii, and longum. Further studies are still needed to clarify certain results that are contradictory with previous findings.

Species Distribution, Typical Clinical Features and Risk Factors for Poor Prognosis of Super-Elderly Patients with Bloodstream Infection in China

Objective

Bloodstream infection (BSI) is characterized by high mortality, especially among these increasing super-elderly patients (≥85 years), and this study was conducted to understand the species distribution, typical clinical features and risk factors for poor prognosis of super-elderly patients with BSI.

Methods

Based on previous work, this retrospective study was performed by reviewing an ongoing prospective medical database in a comprehensive tertiary center in China, and all super-elderly patients with BSI in the past 6 years were enrolled in this study.

Results

Out of 5944 adult-patients with BSI, there were totally 431 super-elderly patients (≥85 years old) enrolled in this study and age ≥90 years accounted for 31.1% (134/431). Among these 431 super-elderly patients with BSI, 40 patients (9.3%) were diagnosed with BSI and the remained 401 super-elderly patients (90.7%) were defined as hospital-acquired BSI. The typical feature of these super-elderly patients with BSI was the high proportion of patients with various comorbidities, such as cardiovascular disease (83.8%), ischemic cerebrovascular disease (63.3%) and pulmonary infection (61.0%). The other typical feature was that most (60.1%) of these patients had been hospitalized for long time (≥28 days) prior to the onset of BSI, and most patients had received various invasive treatments, such as indwelling central venous catheter (53.1%) and indwelling urinary catheter (47.1%). Unfortunately, due to these adverse features above, both the 7-day short-term mortality (13.2%, 57/431) and the 30-day long-term mortality (24.8%, 107/431) were high. The multivariate analysis showed that both chronic liver failure (OR 7.9, 95% CI 2.3-27.8, P=0.001) and indwelling urinary catheter (OR 2.3, 95% CI 1.1-4.7, P=0.023) were independent risk factors for 7-day short-term mortality, but not for 30-day long-term mortality. In addition, the microbiology results showed that the most common species were associated with nosocomial infection or self-opportunistic infection, such as Staphylococcus hominis (18.3%), Staphylococcus epidermidis (11.8%), Escherichia coli (9.7%), Klebsiella pneumoniae (9.3%) and Candida albicans (8.6%, fungi).

Conclusion

Super-elderly patients with BSI had typical features, regardless of the pathogenic species distribution and their drug resistance, or clinical features and their risk factors for poor prognosis. These typical features deserved attention and could be used for the prevention and treatment of BSI among super-elderly patients.

A review of CRISPR-Cas and PCR-based methods for the detection of animal species in the food chain-current challenges and future prospects

Regular testing and systematic investigation play a vital role to ensure product safety. Until now, the existing food authentication techniques have been based on proteins, lipids, and nucleic acid-based assays. Among various deoxyribonucleic acid (DNA)-based methods, the recently developed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) based bio-sensing is an innovative and fast-expanding technology. The CRISPR/Cas-9 is known as Clustered Regularly Interspaced Short Palindromic Repeats due to the flexibility and simplicity of the CRISPR/Cas9 site-specific editing tool has been applied in many biological research areas such as Gene therapy, cell line development, discovering mechanisms of disease, and drug discovery. Nowadays, the CRISPR-Cas system has also been introduced into food authentication via detecting DNA barcodes of poultry and livestock both in processed and unprocessed food samples. This review documents various DNA based approaches, in an accessible format. Future CRISPR technologies are forecast while challenges are outlined.

Lacticaseibacillus pabuli sp. nov., isolated from fermented cattle feed

Strain BSF-3MT is a Gram-stain-positive, non-flagellated, facultative anaerobic and rod-shaped bacterium that was isolated from fermented feed collected at a cattle farm in the Daejeon region of the Republic of Korea. It was studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strain was primarily identified as a member of the genus Lacticaseibacillus. Strain BSF-3MT contained a chromosome of 2.5 Mbp and a plasmid of 33.4 kbp. The G+C content of genomic DNA was 51.3 mol%. Strain BSF-3MT had the highest ortho-average nucleotide identity value of 73.7 % with Lacticaseibacillus songhuajiangensis 7-19T, its closest relative in the phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree based on up-to-date bacterial core genes. Based on the results of a polyphasic taxonomic study, strain BSF-3MT represents a novel species in the genus Lacticaseibacillus, for which the name Lacticaseibacillus pabuli sp. nov. is proposed. The type strain is BSF-3MT (=KACC 23028T=NBRC 116014T).

The scent of roses, a bouquet of fragrance diversity

Roses have been domesticated since antiquity for their therapeutic, cosmetic, and ornamental properties. Their floral fragrance has great economic value, which has influenced the production of rose varieties. The production of rose water and essential oil is one of the most lucrative activities, supplying bioactive molecules to the cosmetic, pharmaceutical, and therapeutic industries. In recent years, major advances in molecular genetics, genomic, and biochemical tools have paved the way for the identification of molecules that make up the specific fragrance of various rose cultivars. The aim of this review is to highlight current knowledge on metabolite profiles, and more specifically on fragrance compounds, as well as the specificities and differences between rose species and cultivars belonging to different rose sections and how they contribute to modern roses fragrance.

Responses of peritubular macrophages and the testis transcriptome profiles of peripubertal and adult rodents exposed to an acute dose of MEHP

Exposure of rodents to mono-(2-ethylhexyl) phthalate (MEHP) is known to disrupt the blood-testis barrier and cause testicular germ cell apoptosis. Peritubular macrophages (PTMφ) are a newly identified type of testicular macrophage that aggregates near the spermatogonial stem cell niche. We have previously reported that MEHP exposure increased the numbers of PTMφs by 6-fold within the testis of peripubertal rats. The underlying mechanism(s) accounting for this change in PTMφs and its biological significance is unknown. This study investigates if MEHP-induced alterations in PTMφs occur in rodents (PND 75 adult rats and PND 26 peripubertal mice) that are known to be less sensitive to MEHP-induced testicular toxicity. Results show that adult rats have a 2-fold higher basal level of PTMφ numbers than species-matched peripubertal animals, but there was no significant increase in PTMφ numbers after MEHP exposure. Peripubertal mice have a 5-fold higher basal level of PTMφ compared with peripubertal rats but did not exhibit increases in number after MEHP exposure. Further, the interrogation of the testis transcriptome was profiled from both the MEHP-responsive peripubertal rats and the less sensitive rodents via 3' Tag sequencing. Significant changes in gene expression were observed in peripubertal rats after MEHP exposure. However, adult rats showed lesser changes in gene expression, and peripubertal mice showed only minor changes. Collectively, the data show that PTMφ numbers are associated with the sensitivity of rodents to MEHP in an age- and species-dependent manner.

Taxonomy, ecology, and relevance to food safety of the genus Listeria with a particular consideration of new Listeria species described between 2010 and 2022

Since 2010, the genus Listeria has had the addition of 22 new species that more than tripled the number of species identified until 2010. Sixteen of these 22 new species are distantly related to the type species, Listeria monocytogenes, and several of these present phenotypes that distinguish them from classical Listeria species (L. monocytogenes, Listeria innocua, Listeria ivanovii, Listeria seeligeri, Listeria welshimeri, and Listeria grayi). These 22 newly described species also show that Listeria is more genetically diverse than previously estimated. While future studies and surveys are needed to clarify the distribution of these species, at least some of these species may not be widely spread, while other species may be frequently found spread to human-related settings (e.g., farms and processing facilities), and others may be adapted to specific environmental habitats. Here, we review the taxonomic, phylogenetic, and ecological characteristics of these new Listeria species identified since 2010 and re-iterate the suggestion of re-classification of some species into three new genera: Murraya, Mesolisteria, and Paenilisteria. We also provide a review of current detection issues and the relevance to food safety related to the identification of these new species. For example, several new non-pathogenic species could be misidentified as the pathogen L. monocytogenes, based on methods that do not target L. monocytogenes-specific virulence genes/factors, leading to unnecessary product recalls. Moreover, eight species in the proposed new genus Mesolisteria are not good indicators of environmental conditions that could allow L. monocytogenes to grow since Mesolisteria species are unable to grow at low temperatures.

Distribution and insecticide resistance profile of the major malaria vector Anopheles funestus group across the African continent

There has been significant progress in malaria control in the last 2 decades, with a decline in mortality and morbidity. However, these gains are jeopardised by insecticide resistance, which negatively impacts the core interventions, such as insecticide-treated nets (ITN) and indoor residual spraying (IRS). While most malaria control and research efforts are still focused on Anopheles gambiae complex mosquitoes, Anopheles funestus remains an important vector in many countries and, in some cases, contributes to most of the local transmission. As countries move towards malaria elimination, it is important to ensure that all dominant vector species, including An. funestus, an important vector in some countries, are targeted. The objective of this review is to compile and discuss information related to A. funestus populations' resistance to insecticides and the mechanisms involved across Africa, emphasising the sibling species and their resistance profiles in relation to malaria elimination goals. Data on insecticide resistance in An. funestus malaria vectors in Africa were extracted from published studies. Online bibliographic databases, including Google Scholar and PubMed, were used to search for relevant studies. Articles published between 2000 and May 2023 reporting resistance of An. funestus to insecticides and associated mechanisms were included. Those reporting only bionomics were excluded. Spatial variation in species distribution and resistance to insecticides was recorded from 174 articles that met the selection criteria. It was found that An. funestus was increasingly resistant to the four classes of insecticides recommended by the World Health Organisation for malaria vector control; however, this varied by country. Insecticide resistance appears to reduce the effectiveness of vector control methods, particularly IRS and ITN. Biochemical resistance due to detoxification enzymes (P450s and glutathione-S-transferases [GSTs]) in An. funestus was widely recorded. However, An. funestus in Africa remains susceptible to other insecticide classes, such as organophosphates and neonicotinoids. This review highlights the increasing insecticide resistance of An. funestus mosquitoes, which are important malaria vectors in Africa, posing a significant challenge to malaria control efforts. While An. funestus has shown resistance to the recommended insecticide classes, notably pyrethroids and, in some cases, organochlorides and carbamates, it remains susceptible to other classes of insecticides such as organophosphates and neonicotinoids, providing potential alternative options for vector control strategies. The study underscores the need for targeted interventions that consider the population structure and geographical distribution of An. funestus, including its sibling species and their insecticide resistance profiles, to effectively achieve malaria elimination goals.

Ancient tree genomes for old questions

Most foundational work on the evolution and migration of plant species relies on genomic data from contemporary samples. Ancient plant samples can give us access to allele sequences and distributions on the landscape dating back to the mid Holocene or earlier (Gugerli et al., 2005). Nuclear DNA from ancient wood, however, has been mostly inaccessible until now. In a From the Cover article in this issue of Molecular Ecology, Wagner et al. (2023) present the first resequenced nuclear genomes from ancient oak wood, including two samples dated to the 15th century and one that dates to more than 3500 years ago. These ancient tree genomes open the possibility for investigating species adaptation, migration, divergence, and hybridisation in the deep past. They pave the way for what we hope will be a new era in the use of paleogenomics to study Holocene tree histories.

Identification of Bletilla striata and related decoction pieces: a data fusion method combining electronic nose, electronic tongue, electronic eye, and high-performance liquid chromatography data

Introduction: We here describe a new method for distinguishing authentic Bletilla striata from similar decoctions (namely, Gastrodia elata, Polygonatum odoratum, and Bletilla ochracea schltr). Methods: Preliminary identification and analysis of four types of decoction pieces were conducted following the Chinese Pharmacopoeia and local standards. Intelligent sensory data were then collected using an electronic nose, an electronic tongue, and an electronic eye, and chromatography data were obtained via high-performance liquid chromatography (HPLC). Partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), and back propagation neural network (BP-NN) models were built using each set of single-source data for authenticity identification (binary classification of B. striata vs. other samples) and for species determination (multi-class sample identification). Features were extracted from all datasets using an unsupervised approach [principal component analysis (PCA)] and a supervised approach (PLS-DA). Mid-level data fusion was then used to combine features from the four datasets and the effects of feature extraction methods on model performance were compared. Results and Discussion: Gas chromatography-ion mobility spectrometry (GC-IMS) showed significant differences in the types and abundances of volatile organic compounds between the four sample types. In authenticity determination, the PLS-DA and SVM models based on fused latent variables (LVs) performed the best, with 100% accuracy in both the calibration and validation sets. In species identification, the PLS-DA model built with fused principal components (PCs) or fused LVs had the best performance, with 100% accuracy in the calibration set and just one misclassification in the validation set. In the PLS-DA and SVM authenticity identification models, fused LVs performed better than fused PCs. Model analysis was used to identify PCs that strongly contributed to accurate sample classification, and a PC factor loading matrix was used to assess the correlation between PCs and the original variables. This study serves as a reference for future efforts to accurately evaluate the quality of Chinese medicine decoction pieces, promoting medicinal formulation safety.

When Do Traits Tell More Than Species about a Metacommunity? A Synthesis across Ecosystems and Scales

AbstractLinking species traits with the variation in species assemblages across habitats has often proved useful for developing a more mechanistic understanding of species distributions in metacommunities. However, summarizing the rich tapestry of a species in all of its nuance with a few key ecological traits can also lead to an abstraction that provides less predictability than when using taxonomy alone. As a further complication, taxonomic and functional diversities can be inequitably compared, either by integrating taxonomic-level information into the calculation of how functional aspects of communities vary or by detecting spurious trait-environment relationships. To remedy this, we here synthesize analyses of 80 datasets on different taxa, ecosystems, and spatial scales that include information on abundance or presence/absence of species across sites with variable environmental conditions and the species' traits. By developing analyses that treat functional and taxonomic diversity equitably, we ask when functional diversity helps to explain metacommunity structure. We found that patterns of functional diversity explained metacommunity structure and response to environmental variation in only 25% of the datasets using a multitrait approach but up to 59% using a single-trait approach. Nevertheless, an average of only 19% (interquartile range = 0%-29%) of the traits showed a significant signal across environmental gradients. Species-level traits, as typically collected and analyzed through functional diversity patterns, often do not bring predictive advantages over what the taxonomic information already holds. While our assessment of a limited advantage of using traits to explain variation in species assemblages was largely true across ecosystems, traits played a more useful role in explaining variation when many traits were used and when trait constructs were more related to species' status, life history, and mobility. We propose future research directions to make trait-based approaches and data more helpful for inference in metacommunity ecology.

Reporting the biodiversity impacts of greenhouse gas emissions

There are increasing demands for organisations and governments to report their biodiversity impacts, yet there are limited methods to account for the consequences of emitting greenhouse gases on global biodiversity. We use published evidence to derive a conversion factor of approximately 2.3 × 10-7 species expected to be committed to extinction per tCO2 e emitted. We demonstrate how this conversion factor can be used to account for emissions-related biodiversity impacts of organisations and nations.

Comparison between indicine and taurine cattle DNA methylation reveals epigenetic variation associated to differences in morphological adaptive traits

Indicine and taurine subspecies present distinct morphological traits as a consequence of environmental adaptation and artificial selection. Although the two subspecies have been characterized and compared at genome-wide level and at specific loci, their epigenetic diversity has not yet been explored. In this work, Reduced Representation Bisulphite Sequencing (RRBS) profiling of the taurine Angus (A) and indicine Nellore (N) cattle breeds was applied to identify methylation differences between the two subspecies. Genotyping by sequencing (GBS) of the same animals was performed to detect single nucleotide polymorphisms (SNPs) at cytosines in CpG dinucleotides and remove them from the differential methylation analysis. A total of 660,845 methylated cytosines were identified within the CpG context (CpGs) across the 10 animals sequenced (5 N and 5 A). A total of 25,765 of these were differentially methylated (DMCs). Most DMCs clustered in CpG stretches nearby genes involved in cellular and anatomical structure morphogenesis. Also, sequences flanking DMC were enriched in SNPs compared to all other CpGs, either methylated or unmethylated in the two subspecies. Our data suggest a contribution of epigenetics to the regulation and divergence of anatomical morphogenesis in the two subspecies relevant for cattle evolution and sub-species differentiation and adaptation.

Successional theories

Succession is a fundamental concept in ecology because it indicates how species populations, communities, and ecosystems change over time on new substrate or after a disturbance. A mechanistic understanding of succession is needed to predict how ecosystems will respond to land-use change and to design effective ecosystem restoration strategies. Yet, despite a century of conceptual advances a comprehensive successional theory is lacking. Here we provide an overview of 19 successional theories ('models') and their key points, group them based on conceptual similarity, explain conceptual development in successional ideas and provide suggestions how to move forward. Four groups of models can be recognised. The first group (patch & plants) focuses on plants at the patch level and consists of three subgroups that originated in the early 20th century. One subgroup focuses on the processes (dispersal, establishment, and performance) that operate sequentially during succession. Another subgroup emphasises individualistic species responses during succession, and how this is driven by species traits. A last subgroup focuses on how vegetation structure and underlying demographic processes change during succession. A second group of models (ecosystems) provides a more holistic view of succession by considering the ecosystem, its biota, interactions, diversity, and ecosystem structure and processes. The third group (landscape) considers a larger spatial scale and includes the effect of the surrounding landscape matrix on succession as the distance to neighbouring vegetation patches determines the potential for seed dispersal, and the quality of the neighbouring patches determines the abundance and composition of seed sources and biotic dispersal vectors. A fourth group (socio-ecological systems) includes the human component by focusing on socio-ecological systems where management practices have long-lasting legacies on successional pathways and where regrowing vegetations deliver a range of ecosystem services to local and global stakeholders. The four groups of models differ in spatial scale (patch, landscape) or organisational level (plant species, ecosystem, socio-ecological system), increase in scale and scope, and reflect the increasingly broader perspective on succession over time. They coincide approximately with four periods that reflect the prevailing view of succession of that time, although all views still coexist. The four successional views are: succession of plants (from 1910 onwards) where succession was seen through the lens of species replacement; succession of communities and ecosystems (from 1965 onwards) when there was a more holistic view of succession; succession in landscapes (from 2000 onwards) when it was realised that the structure and composition of landscapes strongly impact successional pathways, and increased remote-sensing technology allowed for a better quantification of the landscape context; and succession with people (from 2015 onwards) when it was realised that people and societal drivers have strong effects on successional pathways, that ecosystem processes and services are important for human well-being, and that restoration is most successful when it is done by and for local people. Our review suggests that the hierarchical successional framework of Pickett is the best starting point to move forward as this framework already includes several factors, and because it is flexible, enabling application to different systems. The framework focuses mainly on species replacement and could be improved by focusing on succession occurring at different hierarchical scales (population, community, ecosystem, socio-ecological system), and by integrating it with more recent developments and other successional models: by considering different spatial scales (landscape, region), temporal scales (ecosystem processes occurring over centuries, and evolution), and by taking the effects of the surrounding landscape (landscape integrity and composition, the disperser community) and societal factors (previous and current land-use intensity) into account. Such a new, comprehensive framework could be tested using a combination of empirical research, experiments, process-based modelling and novel tools. Applying the framework to seres across broadscale environmental and disturbance gradients allows a better insight into what successional processes matter and under what conditions.

Green Synthesis and Characterization of Xanthium strumarium-Mediated Titanium Dioxide Nanoparticles

Background Green synthesis of nanoparticles is a growing trend. The annual plant Xanthium strumarium L. (X. strumarium) belongs to the Asteraceae family. The herb has traditionally been used to treat a variety of ailments, including leucoderma, dangerous insect bites, epilepsy, salivation, allergic rhinitis, sinusitis, etc. Inorganic, biocompatible, and non-toxic titanium is a substance employed in the pharmaceutical and biomedical industries as well as in fields like bone tissue engineering. The aim of the study is to characterize titanium dioxide nanoparticles (TiO₂NPs), which were synthesized from X.strumarium. Also, this study aims to assess the cytotoxic properties of the synthesized leaf extract and the TiO₂NPs. Materials and methods In this study, the biosynthesis of TiO₂NPs was made from X. strumarium leaf extract. The characterization of the green-synthesized TiO₂NPs was done using the spectral analysis of an ultraviolet (UV)-visible spectrophotometer, scanning electron microscopy (SEM), and Fourier Transform Infrared Spectroscopy (FTIR). The advantage of using TiO₂NPs is that they possess antimicrobial, antibacterial, chemical stability, and catalytic properties. The leaf extract and the biosynthesized nanoparticles were tested against human fibroblast cell lines for biocompatibility using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay.  Results SEM investigation showed that TiO₂NPs were crystalline in nature. FTIR confirms the presence of alkyne and amine functional groups, and the pointed vertices in the X-ray diffraction (XRD) pattern show the crystalline nature of TiO2NPs. The study found that the cell viability of TiO₂NPs was 110%. Conclusion TiO₂NPs were synthesized from X. strumarium leaf extract and characterized using SEM, FTIR, and XRD. The TiO₂NPs were found to be crystalline in nature with various functional groups. MTT assay shows that the synthesized nanoparticles are promising biocompatible agents that can be used in future research in the medical field.

The impact of electroacupuncture on anxiety-like behavior and gut microbiome in a mouse model of chronic restraint stress

Introduction

Electroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.

Methods

To address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.

Results

Our findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.

Discussion

In summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA's anti-anxiety effects and the gut microbiota.

Antioxidant Activity of Beef, Pork and Chicken Burgers before and after Cooking and after In Vitro Intestinal Digestion

The aim of the present work was to evaluate and compare in vitro the antioxidant activity of raw, cooked and cooked-digested pork, beef and chicken burgers. The cooking process influenced the antioxidant capacity of the meat by decreasing the values of ABTS, FRAP and the content of free thiols. Conversely, a positive effect was observed after in vitro gastrointestinal digestion which increased the biological activity of the meat, characterised by greater antioxidant activity. The type of meat influenced the chemical composition and biological capacity of the burgers. In fact, both before and after the cooking process, beef burgers showed higher thiol content and, consequently, a higher oxidative stability of proteins than chicken and pork burgers. In vitro gastrointestinal digestion also improved the nutraceutical quality of beef burgers, which showed higher ABTS values and thiol content than pork burgers, which showed higher FRAP values. This work aims to support the potential of meat constituents as a natural antioxidant component that is essential to counteract the oxidative stress responsible for imbalances in the human organism and several cardiovascular diseases.

Erosional exhumation of carbonate rock facilitates dispersal-mediated allopatric speciation in freshwater fishes

A fundamental goal of evolutionary biology is to understand the mechanisms that generate and maintain biodiversity. Discovery and delimitation of species represent essential prerequisites for such investigations. We investigate a freshwater fish species complex comprising Etheostoma bellator and the endangered E. chermocki, which is endemic to the Black Warrior River system in Alabama, USA, a global hotspot of temperate freshwater biodiversity. Phylogenomic analyses delimit five geographically disjunct species masquerading as E. bellator. Three of these new species exhibit microendemic distributions comparable to that of E. chermocki raising the possibility that they also require protection. The species of the complex are found in streams flowing over carbonate rock and they are separated by waterways flowing over siliciclastic rock, a geographic pattern dictated by the underlying stratigraphy and structural geology. Over time, rivers have eroded downward through layers of siliciclastic rocks in the basin, gradually exposing underlying carbonate rock, the substrate of suitable habitat today. Our results suggest that episodic dispersal to patches of suitable habitat set the stage for allopatric speciation in the species complex. Our study suggests that the presence of heterogeneous rock can facilitate dispersal-mediated allopatric speciation in freshwater organisms in the absence of external tectonic or climatic perturbations.

Differences of clinical characteristics and outcome in proven invasive Trichosporon infections caused by asahii and non-asahii species

BACKGROUND

Trichosporon is an emerging yeast that causes invasive infections in immunocompromised patients experiencing prolonged hospitalisation, indwelling venous catheters and neutropenia.

METHODS

This retrospective observational cohort study analysed invasive Trichosporon infections (ITIs) occurring between January 2005 and December 2022 at three tertiary hospitals and compared the clinical characteristics and prognostic factors of ITIs caused by Trichosporon asahii and non-T. asahii spp. After evaluating 1067 clinical isolates, we identified 46 patients with proven ITIs, defined as cases in which Trichosporon was isolated from blood, cerebrospinal fluid, or sterile tissues.

RESULTS

The patients were separated into T. asahii and non-T. asahii groups containing 25 and 21 patients, respectively, all of which except one were immunocompromised. During this period, both the number of clinical isolates and patients with ITIs (mainly T. asahii) increased; whereas, cases involving non-T. asahii spp. decreased. Compared with the non-T. asahii group, the T. asahii group had more patients with multiple catheters (84% vs. 33%, p = .001) and those receiving renal replacement therapy (48% vs. 14%, p = .005). The all-cause 28-day mortality rate after ITI in the T. asahii group (44%) was significantly higher than in the non-T. asahii group (10%, Log-rank p = .014). The multivariate Cox regression model revealed that T. asahii (reference, non-T. asahii spp.; aHR = 4.3; 95% CI = 1.2-15.2, p = .024) and neutropenia for 5 days or more (aHR = 2.2, 95% CI = 1.5-3.6, p = .035) were independent factors in the 28-day mortality after ITI.

CONCLUSION

The proven ITIs due to T. asahii produced more unfavourable outcomes compared with ITIs caused by non-T. asahii spp.

Predominance of Acinetobacter pseudolwoffii among Acinetobacter species in domestic animals in the Czech Republic

The aim of this study was to map the spectrum of microorganisms belonging to the genus Acinetobacter in domestic animals with a specific focus on the prevalence of Acinetobacter pseudolwoffii. Additionally, the susceptibility of isolates to antimicrobial agents was determined. In the period from January 1, 2014, to August 31, 2015, a total of 9 544 samples originating from gross lesions and pathological processes of animals exhibiting clinical symptoms of the disease were examined across 41 districts in the Czech Republic. The examinations were carried out using culture methods involving meat-peptone blood agar and Endo agar under aerobic conditions at a temperature of 37 ± 1 °C for 18-24 hours. Isolates were confirmed using molecular phenotypic method MALDI-TOF MS with the MBT Compass Library Revision L 2020 covering 3 239 species/entries (9 607 MSP) from Bruker Daltonics company. Out of the 108 isolates (prevalence 1.13%), 14 species of Acinetobacter spp. were identified, with 5 isolates remaining unclassified as species. A. pseudolwoffii was the predominant species isolated in 25 cases (prevalence 0.26%). Antimicrobial susceptibility was determined for 12 antimicrobials by the disc diffusion method, with A. pseudolwoffii isolates exhibiting the lowest susceptibility to ceftazidime (32%) and co-trimoxazole (60%).

Addition of Five Novel Fungal Flora to the Xylariomycetidae (Sordariomycetes, Ascomycota) in Northern Thailand

The deviation of conventional fungal niches is an important factor in the implications of hidden fungal diversity and global fungal numbers. The Xylariomycetidae (Sordariomycetes, Ascomycota), which is also referred to as xylarialean taxa, has a wide range of species that demonstrate a high degree of variation in their stromatic characteristics, showing either conspicuous or inconspicuous forms. In this study, samples were collected while focusing on temporal and spatial parameters and substrate characteristics. Based on internal transcribed spacer (ITS), 28S large subunit rDNA (LSU), RNA polymerase II second largest subunit (RPB2), and β-tubulin (TUB2) multigene phylogeny and morphology, five new species are introduced as Muscodor brunneascosporus, M. lamphunensis (Xylariaceae), Nigropunctata hydei, N. saccata (Incertae sedis), and Xenoanthostomella parvispora (Gyrotrichaceae). Plant substrates in the early stages of decay and attached to the host were feasible sample niches, with an emphasis on the collection of inconspicuous, hidden xylarialean species. The appearance of inconspicuous saprobic xylarialean forms during the rainy season may be linked to the change in nutritional mode, from endophytic mode during the dry season to saprobic in the wet. Therefore, it would be fascinating to concentrate future research on how seasonal fluctuations affect nutritional mode shifts, especially in northern Thailand, which would provide the optimal spatial characteristics. In order to establish a comprehensive linkage between endophytic and saprobic modes, it is imperative to have a substantial representation of endophytic isolate sequences resembling inconspicuous xylariaceous fungi within publicly accessible databases.

Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8

MXRA8 is a receptor for chikungunya (CHIKV) and other arthritogenic alphaviruses with mammalian hosts. However, mammalian MXRA8 does not bind to alphaviruses that infect humans and have avian reservoirs. Here, we show that avian, but not mammalian, MXRA8 can act as a receptor for Sindbis, western equine encephalitis (WEEV), and related alphaviruses with avian reservoirs. Structural analysis of duck MXRA8 complexed with WEEV reveals an inverted binding mode compared with mammalian MXRA8 bound to CHIKV. Whereas both domains of mammalian MXRA8 bind CHIKV E1 and E2, only domain 1 of avian MXRA8 engages WEEV E1, and no appreciable contacts are made with WEEV E2. Using these results, we generated a chimeric avian-mammalian MXRA8 decoy-receptor that neutralizes infection of multiple alphaviruses from distinct antigenic groups in vitro and in vivo. Thus, different alphaviruses can bind MXRA8 encoded by different vertebrate classes with distinct engagement modes, which enables development of broad-spectrum inhibitors.

Contribution to the Knowledge of Gastrointestinal Nematodes in Roe Deer (Capreolus capreolus) from the Province of León, Spain: An Epidemiological and Molecular Study

A study of gastrointestinal nematodes in roe deer was carried out in the regional hunting reserves of Riaño and Mampodre, Province of León, Spain, to provide information on their prevalence and intensity of infection in relation to the sampling areas, age of the animals, and body weight. Through a regulated necropsy of the animals, all of them harbored gastrointestinal nematodes in their digestive tract, with a mean intensity of parasitism of 638 ± 646.1 nematodes/infected animal. Eleven genera were found and 18 species of gastrointestinal nematodes were identified, three of them polymorphic: Trichostrongylus axei, Trichostrongylus vitrinus, Trichostrongylus capricola, Trichostrongylus colubriformis, Haemonchus contortus, Spiculopteragia spiculoptera/Spiculopteragia mathevossiani, Ostertagia leptospicularis/Ostertagia kolchida, Ostertagia (Grosspiculopteragia) occidentalis, Teladorsagia circumcincta/Teladorsagia trifurcate, Marshallagia marshalli, Nematodirus europaeus, Cooperia oncophora, Capillaria bovis, Oesophagostomum venulosum, and Trichuris ovis. All of them have already been cited in roe deer in Europe, but Marshallagia marshalli, Capillaria bovis, and Ostertagia (Grosspiculopteragia) occidentalis are reported for the first time in Spain in this host. The abomasum was the intestinal section, where the prevalence (98.9%) and mean intensity (x¯ = 370.7 ± 374.4 worms/roe deer; range 3-1762) were significantly higher, but no statistically significant differences were found when comparing the sampling areas and age of animals. The animals with lower body weight had a higher parasite load than those in better physical condition, finding, in this case, statistically significant differences (p = 0.0020). Seven genera and 14 species were identified. In the small intestine, 88% of the animals examined presented gastrointestinal nematodes, with an average intensity of x¯ = 131.7 ± 225.6 parasites/infected animal, ranging between 4-1254 worms. No statistically significant differences were found when the three parameters studied were compared. Four genera and seven species were identified. In the large intestine/cecum, 78.3% of the examined roe deer presented adult worms, with an average intensity of 6.3 ± 5.5 worms/infected animal; range 1-26 worms. Only statistically significant differences were observed when considering the mean intensity of parasitism and the sampling area (p = 0.0093). Two genera and two species were identified. Several of the species found in the study were studied molecularly, and with the sequences obtained compared with those deposited in GenBank, phylogenetic trees were prepared to determine their taxonomic status. Using coprological techniques, the existing correlation in the shedding of gastrointestinal nematode eggs in roe deer was investigated with that of semi-extensive sheep farms in the same study area to verify the existence of cross-transmission of these parasites between wild and domestic animals. The high values found in the studied parameters show that northern Spain is an area of high-intensity infection for roe deer.

Plant-based dietary index in relation to gut microbiota in Arab women

Plant-based foods may influence gut microbiota profiles and contribute to overall human health. However, not all plant-based diets are nutritionally equivalent. We aimed to assess the association between a plant-based dietary index (PDI), specifically unhealthy PDI and healthy PDI (hPDI), and gut microbial composition and diversity in young women in Saudi Arabia. This observational study included 92 healthy women aged 18 to 25 years. Dietary and anthropometric data were collected. Fecal samples were analyzed using a novel whole-genome shotgun sequencing technique. Alpha and beta diversities measured the richness and composition of the gastrointestinal system. Relationships were examined with Pearson correlation, linear regression, and Wilcoxon Rank-Sum tests. Participants with higher PDI had higher levels of Bacteroides_u_s than those with lower PDI. hPDI was positively correlated with Bifidobacterium pseudocatenulatum, Bifidobacterium longum, Oscillibacter, and Lactobacillus acidophilus and inversely correlated with Clostridioides difficile (P < .05). Unhealthy plant-based dietary index was inversely correlated with B pseudocatenulatum, B longum, and L acidophilus and positively correlated with C difficile (P < .05) and other species of interest. In conclusion, hPDI scores were significantly associated with microbiota species linked with favorable health outcomes, independent of body mass index and gut microbial richness and composition in Arab women. Future studies should investigate the modulating effect of plant-based diets on the species identified in the current study.

Terrestrial nematodes from the Maritime Antarctic

Background

Soil nematodes are one of the most important terrestrial faunal groups in Antarctica, as they are a major component of soil micro-food webs. Despite their crucial role in soil processes, knowledge of their species diversity and distribution is still incomplete. Taxonomic studies of Antarctic nematodes are fragmented, which prevents assessment of the degree of endemicity and distribution of the species, as well as other aspects of biogeography.

New information

The present study is focused on the nematode fauna of one of the three Antarctic sub-regions, the Maritime Antarctic and summarises all findings published up to April 2023. A species list that includes 44 species, belonging to 21 genera, 16 families and eight orders is provided. A review of the literature on terrestrial nematodes inhabiting the Maritime Antarctic showed that the sites are unevenly studied. Three islands (Signy, King George and Livingston Islands) revealed highest species richness, probably due to the highest rates of research effort. Most species and four genera (Antarctenchus, Pararhyssocolpus, Amblydorylaimus and Enchodeloides) are endemic, proving that nematode fauna of the Maritime Antarctic is autochthonous and unique. Several groups of islands/sites have been revealed, based on their nematode fauna. The study showed that species with a limited distribution prevailed, while only two species (Plectusantarcticus and Coomansusgerlachei) have been found in more than 50% of the sites. Based on the literature data, details on species localities, microhabitat distribution, plant associations and availability of DNA sequences are provided.

Species variations in the gut microbiota of captive snub-nosed monkeys

Introduction

Snub-nosed monkeys are species in danger of extinction due to habitat fragmentation and human activities. Captivity has been suggested as an Auxiliary Conservation Area (ASA) strategy. However, little is known about the adaptation of different species of snub-nosed monkeys to captive environments.

Methods

This study compared the gut microbiota between Rhinopithecus bieti, R. brelichi, and R. roxellana under identical captive conditions to provide insights for improving captive conservation strategies.

Results

The results showed that these three Rhinopithecus species shared 80.94% of their Operational Taxonomic Unit (OTU), indicating high similarity in gut microbiota composition. The predominant phyla were Firmicutes and Bacteroidetes for all three Rhinopithecus species, but differences were observed in diversity, characteristic bacterial communities, and predicted function. Significant enrichment of cellulolytic families, including Ruminococcaceae, Clostridiales vadinBB60 group, Christensenellaceae, and Erysipelotrichaceae, and pathways involved in propionate and butyrate metabolism in the gut of R. bieti suggested that it may have a superior dietary fiber utilization capacity. In contrast, Bacteroidetes, Ruminoccaceae, and Trichospiraceae were more abundant in R. brelichi and R. roxellana, and were associated with saccharide and glycan metabolic pathways. Moreover, R. brelichi and R. roxellana also had higher similarity in microbiota composition and predicted function.

Discussion

In conclusion, the results demonstrate that host species are associated with the composition and function of the gut microbiota in snub-nosed monkeys. Thus, host species should be considered when formulating nutritional strategies and disease surveillance in captive snub-nosed monkeys.

Future climate change effects on US forest composition may offset benefits of reduced atmospheric deposition of N and S

Climate change and atmospheric deposition of nitrogen (N) and sulfur (S) are important drivers of forest demography. Here we apply previously derived growth and survival responses for 94 tree species, representing >90% of the contiguous US forest basal area, to project how changes in mean annual temperature, precipitation, and N and S deposition from 20 different future scenarios may affect forest composition to 2100. We find that under the low climate change scenario (RCP 4.5), reductions in aboveground tree biomass from higher temperatures are roughly offset by increases in aboveground tree biomass from reductions in N and S deposition. However, under the higher climate change scenario (RCP 8.5) the decreases from climate change overwhelm increases from reductions in N and S deposition. These broad trends underlie wide variation among species. We found averaged across temperature scenarios the relative abundance of 60 species were projected to decrease more than 5% and 20 species were projected to increase more than 5%; and reductions of N and S deposition led to a decrease for 13 species and an increase for 40 species. This suggests large shifts in the composition of US forests in the future. Negative climate effects were mostly from elevated temperature and were not offset by scenarios with wetter conditions. We found that by 2100 an estimated 1 billion trees under the RCP 4.5 scenario and 20 billion trees under the RCP 8.5 scenario may be pushed outside the temperature record upon which these relationships were derived. These results may not fully capture future changes in forest composition as several other factors were not included. Overall efforts to reduce atmospheric deposition of N and S will likely be insufficient to overcome climate change impacts on forest demography across much of the United States unless we adhere to the low climate change scenario.

Why is there no service to support taxonomy?

Increasing complexity and specialisation of modern sciences has led to increasingly collaborative publications, as well as the involvement of commercial services. Modern integrative taxonomy likewise depends on many lines of evidence and is increasingly complex, but the trend of collaboration lags and various attempts at 'turbo taxonomy' have been unsatisfactory. We are developing a taxonomic service in the Senckenberg Ocean Species Alliance to provide fundamental data for new species descriptions. This will also function as a hub to connect a global network of taxonomists, assembling an alliance of scientists working on potential new species to tackle both the extinction and inclusion crises we face today. The current rate of new species descriptions is simply too slow; the discipline is often dismissed as old fashioned, and there is a crisis level need for taxonomic descriptions to come to grips with the scale of Anthropocene biodiversity loss. Here, we envision how the process of describing and naming species would benefit from a service supporting the acquisition of descriptive data. Also see the video abstract here: https://youtu.be/E8q3KJor_F8.

nov

Five Hymenobacter strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus Hymenobacter. Digital DNA-DNA hybridization values and average nucleotide identities values for species delineation (70 and 95-96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus Hymenobacter for which we propose the names, Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov., with strains 5116 S-3T (=KACC 21925T=JCM 35216T), 5116 S-27T (=KACC 21926T=JCM 35217T), 5413 J-13T (=KACC 21928T=JCM 35219T), 5516 S-25T (=KACC 21931T=JCM 35222T) and 5420 S-77T (=KACC 21932T=JCM 35223T) as the type strains, respectively.

Development and Degeneration of the Intervertebral Disc-Insights from Across Species

Back pain caused by intervertebral disc (IVD) degeneration has a major socio-economic impact in humans, yet historically has received minimal attention in species other than humans, mice and dogs. However, a general growing interest in this unique organ prompted the expansion of IVD research in rats, rabbits, cats, horses, monkeys, and cows, further illuminating the complex nature of the organ in both healthy and degenerative states. Application of recent biotechnological advancements, including single cell RNA sequencing and complex data analysis methods has begun to explain the shifting inflammatory signaling, variation in cellular subpopulations, differential gene expression, mechanical loading, and metabolic stresses which contribute to age and stress related degeneration of the IVD. This increase in IVD research across species introduces a need for chronicling IVD advancements and tissue biomarkers both within and between species. Here we provide a comprehensive review of recent single cell RNA sequencing data alongside existing case reports and histo/morphological data to highlight the cellular complexity and metabolic challenges of this unique organ that is of structural importance for all vertebrates.

All records of rodents (Mammalia, Rodentia) and hares (Mammalia, Lagomorpha) in Georgia from 1855 through to 2022

Background

In Georgia, there are 40 species from 21 genera and nine families of rodents, along with one species from a single genus and a family of hares. The dataset, which includes 3146 records, provides information regarding the presence of these species within 1559 locations. Of the total of 3146 records, 285 records from 281 locations belong to hares, while 2864 records from 1394 locations are associated with rodents. The dataset incorporates data sourced from various institutions, including the Collection of the Institute of Zoology of Ilia State University, the Georgian National Museum, the Collection of the Zoological Institute of Russian Academy of Sciences, the Zoological Museum of Moscow State University, as well as data extracted from literature and our own field data. The method for establishing the dataset included data compilation from all the above-mentioned sources. The dataset includes records from 1855 through to 2022.

New information

In this publication, out of 3146 records, 14.9% are our new unpublished data. The unpublished data were collected from 2004 through to 2022. In total, 26% of all records are literature data, 50% are museum data and 24% are data collected by us. The dataset includes data obtained from literature sources, museum collections and the field observations. It includes occurrences of species found in the same locality, but within different years, resulting in separate records for each location. The dataset provided has the potential to significantly contribute to our understanding of the distribution of rodents and hares in Georgia.

Looking back on biodiversity change: lessons for the road ahead

Estimating biodiversity change across the planet in the context of widespread human modification is a critical challenge. Here, we review how biodiversity has changed in recent decades across scales and taxonomic groups, focusing on four diversity metrics: species richness, temporal turnover, spatial beta-diversity and abundance. At local scales, change across all metrics includes many examples of both increases and declines and tends to be centred around zero, but with higher prevalence of declining trends in beta-diversity (increasing similarity in composition across space or biotic homogenization) and abundance. The exception to this pattern is temporal turnover, with changes in species composition through time observed in most local assemblages. Less is known about change at regional scales, although several studies suggest that increases in richness are more prevalent than declines. Change at the global scale is the hardest to estimate accurately, but most studies suggest extinction rates are probably outpacing speciation rates, although both are elevated. Recognizing this variability is essential to accurately portray how biodiversity change is unfolding, and highlights how much remains unknown about the magnitude and direction of multiple biodiversity metrics at different scales. Reducing these blind spots is essential to allow appropriate management actions to be deployed. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.

The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation

Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely 'Candidatus Phytoplasma aurantifolia' and 'Ca. Phytoplasma australasia'. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.

Spatial and Temporal Variability in Prevalence Rates of Members of the Borrelia burgdorferi Species Complex in Ixodes ricinus Ticks in Urban, Agricultural and Sylvatic Habitats in Slovakia

Lyme borreliosis (LB) is the most prevalent tick-borne human infection in Europe, with increasing incidence during the latest decades. Abundant populations of Ixodes ricinus, the main vector of the causative agent, spirochetes from the Borrelia burgdorferi sensu lato (Bbsl) complex, have been observed in urban and suburban areas of Europe, in general, and Slovakia, particularly. Understanding the spread of infectious diseases is crucial for implementing effective control measures. Global changes affect contact rates of humans and animals with Borrelia-infected ticks and increase the risk of contracting LB. The aim of this study was to investigate spatial and temporal variation in prevalence of Bbsl and diversity of its species in questing I. ricinus from three sites representing urban/suburban, natural and agricultural habitat types in Slovakia. Ixodes ricinus nymphs and adults were collected by dragging the vegetation in green areas of Bratislava town (urban/suburban habitat), in the Small Carpathians Mountains (natural habitat) (south-western Slovakia) and in an agricultural habitat at Rozhanovce in eastern Slovakia. Borrelia presence in ticks was detected by PCR and Bbsl species were identified by restriction fragment length polymorphism (RFLP). Borrelia burgdorferi s.l. species in coinfected ticks were identified by reverse line blot. Significant spatial and temporal variability in prevalence of infected ticks was revealed in the explored habitats. The lowest total prevalence was detected in the urban/suburban habitat, whereas higher prevalence was found in the natural and agricultural habitat. Six Bbsl species were detected by RFLP in each habitat type -B. burgdorferi sensu stricto (s.s.), B. afzelii, B. garinii, B. valaisiana, B. lusitaniae and B. spielmanii. Coinfections accounted for 3% of the total infections, whereby B. kurtenbachii was identified by RLB and sequencing in mixed infection with B. burgdorferi s.s, B. garinii and B. valaisiana. This finding represents the first record of B. kurtenbachii in questing I. ricinus in Slovakia and Europe. Variations in the proportion of Bbsl species were found between nymphs and adults, between years and between habitat types. Spatial variations in prevalence patterns and proportion of Bbsl species were also confirmed between locations within a relatively short distance in the urban habitat. Habitat-related and spatial variations in Borrelia prevalence and distribution of Bbsl species are probably associated with the local environmental conditions and vertebrate host spectrum. Due to the presence of Borrelia species pathogenic to humans, all explored sites can be ranked as areas with high epidemiological risk.

Assessment of Phenolic Acid Content and Antioxidant Properties of the Pulp of Five Pumpkin Species Cultivated in Southeastern Poland

Antioxidant properties and phenolic acid content in the pulp of five pumpkin species were evaluated. The following species cultivated in Poland were included: Cucurbita maxima 'Bambino', Cucurbita pepo 'Kamo Kamo', Cucurbita moschata 'Butternut', Cucurbita ficifolia 'Chilacayote Squash', and Cucurbita argyrosperma 'Chinese Alphabet'. The content of polyphenolic compounds was determined by ultra-high performance liquid chromatography coupled with HPLC, while the total content of phenols and flavonoids and antioxidant properties were determined by spectrophotometric methods. Ten phenolic compounds (protocatechuic acid, p-hydroxybenzoic acid, catechin, chlorogenic acid, caffeic acid, p-coumaric acid, syringic acid, ferulic acid, salicylic acid, kaempferol) were identified. Phenolic acids were the most abundant compounds; the amount of syringic acid was found to be the highest, ranging from 0.44 (C. ficifolia) to 6.61 mg∙100 g^-1 FW (C. moschata). Moreover, two flavonoids were detected: catechin and kaempferol. They were found at their highest level of content in C. moschata pulp (catechins: 0.31 mg∙100 g^-1 FW; kaempferol: 0.06 mg∙100 g^-1 FW), with the lowest amount detected in C. ficifolia (catechins: 0.15 mg∙100 g^-1 FW; kaempferol below the limit of detection). Analysis of antioxidant potential showed significant differences depending on the species and the test used. The DPPH radical scavenging activity of C. maxima was 1.03 times higher than C. ficiofilia pulp and 11.60 times higher than C. pepo. In the case of the FRAP assay, the multiplicity of FRAP radical activity in C. maxima pulp was 4.65 times higher than C. Pepo pulp and only 1.08 times higher compared to C. ficifolia pulp. The study findings show the high health-promoting value of pumpkin pulp; however, the content of phenolic acids and antioxidant properties are species dependent.

Parvularcula maris sp. nov., an algicidal bacterium isolated from seawater

A taxonomic study was carried out on strain BGMRC 0090^T, which was isolated from seawater. The isolate was a Gram-negative, aerobic, flagellated, rod-shaped bacterium with algicidal activity. Optimal growth was observed at 30 °C, pH 6.0 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BGMRC 0090^T belonged to the genus Parvularcula, with highest sequence similarity to Parvularcula lutaonensis CC-MMS-1^T (98.4 %). Average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values between strain BGMRC 0090^T and five strains of the genus Parvularcula with publicly available genomes were below 84.0, 69.2 and 21.4 %, respectively. The genome of strain BGMRC 0090^T was 3.2 Mb with 64.8 mol% DNA G+C content and encoded 2905 predicted proteins, three rRNA, 42 tRNA and four ncRNA genes. Some algicidal biosynthesis-associated genes were detected in the genome. Strain BGMRC 0090^T contained Q-10 as the major quinone. The predominant fatty acids were identified as summed feature 8 (C_18 : 1ω7c/ω6c) and C_16 : 0. Based on the polyphasic evidence presented in this paper, strain BGMRC 0090^T is concluded to represent a novel species of the genus Parvularcula, for which the name Parvularcula maris sp. nov. is proposed. The type strain is BGMRC 0090^T (= KCTC 92591^T=MCCC 1K08100^T).

Inhibitory Activities of Samples on Tyrosinases Were Affected by Enzyme Species and Sample Addition Methods

The inhibition of tyrosinase (TYR) activity is an effective measure to inhibit melanin synthesis. At present, there are many methods with discrepant details that study the TYR inhibitory activity of samples. Under the same experimental conditions, this paper systematically studies whether enzyme species and sample addition methods are the key factors that determine the TYR inhibitory activity of samples. TYRs extracted from B16F10 cells, apple and mushroom, called BTYR, ATYR and MTYR, respectively, were selected to implement this study. Results showed that TYR inhibitory activities of samples were obviously affected by the above two factors. It was necessary to select the appropriate enzyme according to the problems to be explained. It was speculated that indirectly inhibitory activity reflected the comprehensive effects of samples on TYR catalytic activity and intracellular TYR synthesis pathway, while directly inhibitory activity reflected the effects of samples on TYR catalytic activity. Additionally, kojic acid could be used as a positive control for both B16F10 cells and MTYR models. The TYR inhibitory activity of β-arbutin was complicated and fickle, while that of epigallocatechin gallate (EGCG) was universal and stable, which is to say, EGCG always inhibited TYR activity in a dose-dependent manner. In conclusion, the TYR inhibitory activities of samples were affected by enzyme species and sample addition methods. Compared with the unstable β-arbutin, EGCG was more valuable for clinical research.

(Viannia) panamensis in Central-Western Venezuela

Transmission of cutaneous leishmaniasis in Venezuela reveals diverse and changing epidemiological landscapes, as well as a spectrum of clinical phenotypes presumed to be linked to a variety of Leishmania species. Central-western Venezuela constitutes one of the highest endemic epicenters in the country, yet updated molecular epidemiological information is still lacking. Therefore, in this study we aimed to characterize the landscape of circulating Leishmania species across central-western Venezuela through the last two decades, performed comparisons of haplotype and nucleotide diversity, and built a geospatial map of parasite species distribution. A total of 120 clinical samples were collected from patients across the cutaneous disease spectrum, retrieving parasitic DNA, and further characterizing by PCR and sequencing of the HSP70 gene fragment. This data was later collated with further genetic, geospatial and epidemiological analyses. A peculiar pattern of species occurrence including Leishmania (Leishmania) amazonensis (77.63% N=59), Leishmania (Leishmania) infantum (14.47% N=11), Leishmania (Viannia) panamensis (5.26% N=4) and Leishmania (Viannia) braziliensis (2.63% N=2) was revealed, also highlighting a very low genetic diversity amongst all analyzed sequences. Geographical distribution showed that most cases are widely distributed across the greater urban-sub urban area of the Irribaren municipality. L.(L.) amazonensis appears to be widely dispersed throughout Lara state. Statistical analyses failed to reveal significance for any comparisons, leading to conclude a lack of association between the infective Leishmania species and clinical phenotypes. To the best of our knowledge, this is an unprecedented study which addresses comprehensively the geographical distribution of Leishmania species in central-western Venezuela throughout the last two decades, and the first to incriminate L. (L.) infantum as an etiologic agent of cutaneous leishmaniasis in this region. Our findings support that Leishmania endemism in central-western Venezuela is caused mainly by L.(L.) amazonensis. Future studies are needed to unveil additional details on the ecological intricacies and transmission aspects of leishmaniasis (i.e. sampling phlebotomines and mammals) and to adopt adequate public health prevention and control strategies and mitigate disease impact in this endemic region.

Prevalence of bovine trypanosomiasis in Côte d'Ivoire: Systematic review and meta-analysis

Bovine trypanosomiasis is a parasitic disease caused by protozoans of the genus Trypanosoma. The disease cause economic losses in livestock production. In order to determine the status of research on this disease in Côte d'Ivoire, we used the systematic review method and meta-analysis. Three electronics databases, namely Google Scholar, PubMed and CrossRef were used to search for publications on trypanosomiasis prevalence that met our inclusion criteria. Twenty five articles were identified, 11 of which met the inclusion criteria. Bovine trypanosomiasis prevalence of 2.99% (95% confidence interval [CI]: 2.96% - 3.01%) to 25.28% (95% CI: 25.17% - 25.38%) were recorded between 1960 and 2021. The analyses showed that the most infected regions were the Bagoue 11.26% (95% CI: 11.25% - 11.27%), Bounkani 14.94% (95% CI: 14.93% - 14.95%), Gbeke 10.34% (95% CI: 10.33% - 10.35%), Marahoue 13.79% (95% CI: 13.78% - 13.80%), Poro 8.50% (95% CI: 8.49% - 8.51%), and Tchologo 11.83% (95% CI: 11.82% - 11.84%).The most sensitive diagnostic method used was the polymerase chain reaction (PCR). The species of trypanosomes diagnosed were Typanosoma vivax 4.99% (95% CI: 4.97% - 5.01%), T. congolense 1.51% (95% CI: 1.49% - 1.52%), and T. brucei 0.61% (95% CI: 0.59% - 0.62%). Despite some variation, the prevalence of bovine trypanosomiasis in Côte d'Ivoire caused mainly by T. vivax has increased in the years between 1977 and 2017. Efforts to control tsetse and other mechanical vectors should also be put in place to minimize its transmission.Contribution: The authors studied the prevalence of bovine trypanosomiasis using the systematic review method and MA in order to determine the status of research on this disease in Côte d'Ivoire.

Selenium Species and Fractions in the Rock-Soil-Plant Interface of Maize (Zea mays L.) Grown in a Natural Ultra-Rich Se Environment

Selenium (Se) enrichments or deficiency in maize (Zea mays L.), one of the world's most important staple foods and livestock feeds, can significantly affect many people's diets, as Se is essential though harmful in excess. In particular, Se-rich maize seems to have been one of the factors that led to an outbreak of selenosis in the 1980s in Naore Valley in Ziyang County, China. Thus, this region's geological and pedological enrichment offers some insight into the behavior of Se in naturally Se-rich crops. This study examined total Se and Se species in the grains, leaves, stalks, and roots of 11 maize plant samples, Se fractions of soils around the rhizosphere, and representative parent rock materials from Naore Valley. The results showed that total Se concentrations in the collected samples were observed in descending order of soil > leaf > root > grain > stalk. The predominant Se species detected in maize plants was SeMet. Inorganic Se forms, mainly Se(VI), decreased from root to grain, and were possibly assimilated into organic forms. Se(IV) was barely present. The natural increases of Se concentration in soils mainly affected leaf and root dry-weight biomasses of maize. In addition, Se distribution in soils markedly correlated with the weathered Se-rich bedrocks. The analyzed soils had lower Se bioavailability than rocks, with Se accumulated predominantly as recalcitrant residual Se. Thus, the maize plants grown in these natural Se-rich soils may uptake Se mainly from the oxidation and leaching of the remaining organic-sulfide-bound Se fractions. A viewpoint shift from natural Se-rich soils as menaces to possibilities for growing Se-rich agricultural products is also discussed in this study.

Trying to Understand the Complicated Taxonomy in Amaranthus (Amaranthaceae): Insights on Seeds Micromorphology

Amaranthus is a genus taxonomically complex because of its high morphological variability, which led to nomenclatural disorders, misapplication of names, and misidentifications. Floristic and taxonomic studies on this genus are still incomplete, and many questions remain open. Seed micromorphology has been shown to play an important role in the taxonomy of plants. Regarding Amaranthaceae and Amaranthus, investigations are rare, and they refer to one or a few species. With the primary aim to test if seed features are helpful in the taxonomy of Amaranthus, we here present a detailed SEM study on seed micromorphology in 25 Amaranthus taxa using morphometric methods. Seeds were collected from field surveys and herbarium specimens; 14 seed coat features (7 qualitative and 7 quantitative) were measured on 111 samples (up to 5 seeds per sample). The results obtained revealed that seeds micromorphology provides interesting new taxonomic data concerning some taxa (species and below ranks). In fact, we were able to distinguish a few seed types, including one or more taxa, i.e., blitum-type, crassipes-type, deflexus-type, tuberculatus-type, and viridis-type. On the other hand, seed features are not useful for other species, for example, those included in the deflexus-type (A. deflexus, A. vulgatissimus, A. cacciatoi, A. spinosus, A. dubius, and A. stadleyanus). A diagnostic key of the studied taxa is proposed. Subgenera cannot be distinguished using seed features, thus confirming the published molecular data. All these facts reveal, once again, the taxonomic complexity of the genus Amaranthus since, e.g., just a few seed types can be defined.

The Hybridization Barrier between Herbaceous Medicago sativa and Woody M. arborea Is Weakened by Reproductive Abnormalities in M. sativa Seed Parents

Historically, crosses between Medicago sativa (alfalfa) and M. arborea with alfalfa as the seed parent failed, as did crosses using M. arborea as the seed parent. Thus, a reproductive barrier kept the two species isolated until early in this century. The breakthrough came when alfalfa seed parents were identified in Wisconsin USA and Queensland AU that produced partial hybrids (hereafter hybrids). The hybrids were obtained by making large numbers of crosses on selected alfalfa parents. This was the first level of weakening the crossing barrier as reported in Plants in 2013. Further weakening of the barrier is reported herein whereby more hybrids were obtained with fewer crosses. This was accomplished by pedigree selection for new alfalfa seed parents and by using a product of the first hybrids called Alborea. New alfalfa seed parents were crossed with M. arborea, and Alborea parents were backcrossed to M. arborea. Hybrid plants were produced with fewer crosses in both cases. These hybrids, like the first hybrids, have mostly alfalfa traits but also have traits from M. arborea. It was theorized early on that the alfalfa component could be explained by 2n eggs in the alfalfa parents that were fertilized by normal n gametes from M. arborea. Evidence that the Wisconsin alfalfa and Alborea seed parents did in fact produce 2n eggs was reported in Plants in 2022. Moreover, they produced 2n eggs at approximately the same frequency that they produced hybrids. As reported herein, Alborea parents produced the highest frequency of hybrids and thus had the weakest barrier. Importantly, they also have the highest frequency of 2n eggs. It was determined that alfalfa and Alborea parents that produce 2n eggs and hybrids, also produce 2n pollen. In effect, an experiment was undertaken in reverse showing that 2n pollen could be used to screen for plants that produce hybrids. In the thousands of crosses made over the years, fertilization of normal n eggs in alfalfa parents always failed. Normal meiosis appears to be the main barrier to producing interspecific hybrids in our case. Fertilization of abnormal 2n eggs ensures sufficient alfalfa genetic material to continue embryogenesis. Evidently, the meiotic abnormality of 2n eggs is the major factor that weakens the crossing barrier.

MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis

Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.

Rare and declining bee species are key to consistent pollination of wildflowers and crops across large spatial scales

Biodiversity promotes ecosystem function (EF) in experiments, but it remains uncertain how biodiversity loss affects function in larger-scale natural ecosystems. In these natural ecosystems, rare and declining species are more likely to be lost, and function needs to be maintained across space and time. Here, we explore the importance of rare and declining bee species to the pollination of three wildflowers and three crops using large-scale (72 sites across 5000 km² ), multi-year datasets. Half of the sampled bee species (82/164) were rare or declining, but these species provided only ~15% of overall pollination. To determine the number of species important to EF, we used two methods of "scaling up," both of which have previously been used for biodiversity-function analysis. First, we summed bee species' contributions to pollination across space and time and then found the minimum set of species needed to provide a threshold level of function across all sites; according to this method, effectively no rare and declining bee species were important to pollination. Second, we account for the "insurance value" of biodiversity by finding the minimum set of bee species needed to simultaneously provide a threshold level of function at each site in each year. The second method leads to the conclusion that 25 rare and eight declining bee species (36% and 53% of all rare and declining bee species, respectively) are included in the minimum set. Our findings provide some of the strongest evidence yet that rare and declining species are key to meeting threshold levels of EF, thereby providing a more direct link between real-world biodiversity loss and EF.

Ecological and Geographical Structure of the Plant Cover of the East Asian Boreal-Nemoral Ecotone (the Lower Amur Region, Far East Russia)

The study of the biodiversity of vegetation cover in the context of its genesis and development is an important task. The results of these studies are the basis for the development of ecological, biogeographical, evolutionary, and sociological research, such as modelling the dynamic processes of natural ecosystems, understanding the consequences of natural and anthropogenic changes for biodiversity, solving problems of biodiversity conservation, etc. Of particular interest from this point of view is the biodiversity of ecotones, which can serve as a model for studying the factors of the genesis of the plant cover structure in a dynamic environment. In this paper, we analyze the taxonomic structure of the flora of vascular plants and the spatial structure of the plant cover in the East Asian boreal-nemoral ecotone (of the Lower Amur region). The botanical research was conducted through the application of traditional techniques for floristic and geobotanical studies. The material for this article was drawn from over 15,000 herbarium samples and 1400 floristic and geobotanical descriptions made between 1993 and 2021 in the Lower Amur region. The analyzed flora includes 2240 species from 760 genera and 158 families, which constitute 80% of the species composition of the Russian part of the Amur River basin. The native flora comprises 1801 species from 602 genera and 152 families. The species diversity and quantitative characteristics of the natural and adventive flora of vascular plants in the Lower Amur region are comparable to those of the southern limit of the distribution of taiga ecosystems in the Holarctic. The spectrum of the leading families and genera in terms of the number of species corresponds to the geographical position of the territory (the family spectrum is led by Asteraceae, Cyperaceae, Poaceae, Ranunculaceae, Rosaceae and Polygonaceae and in the generic spectrum, Carex, Artemisia, Salix, Viola, Saxifraga, Poa and Saussurea). The specificity of the flora is determined by a combination of elements in the boreal and sub-boreal flora of East Asia. Seven floristic complexes are defined for the Lower Amur region flora: forest (41.4% of the native flora), meadow (19.2%), mire (4.1%), mountain tundra (12.5%), rocky scree (8.9%), aquatic-semiaquatic (7.8%) and floodplain-estuarine shallow (6.2%). The regularity of some floristic complexes is defined by the landscape's ecological conditions, and the variety in the edaphic, orographic and climatic parameters within the region. The spatial structure of the plant cover of the boreal-nemoral ecotone is described.

Efficient Removal of Heavy Metals from Contaminated Sunflower Straw by an Acid-Assisted Hydrothermal Process

The removal of heavy metals is crucial to the utilization of contaminated biomass resources. In this study, we report an efficient process of hydrothermal conversion (HTC) of sunflower straw (Helianthus annuus L.) to remove heavy metals. The effect of different HTC temperatures and concentrations of HCl additives on heavy metal removal efficiency was investigated. The results revealed that increasing the temperature or concentration of HCl promoted the transfer of heavy metals from hydrochar to liquid products during HTC. The heavy metals removed to the liquid products included up to 99% of Zn and Cd, 94% of Cu, and 87% of Pb after hydrothermal conversion with a temperature of 200 °C and HCl 2%. The species of heavy metals in hydrochars converted from unstable to stable with an increase in temperature from 160 °C to 280 °C. The stable fractions of heavy metals in the acidic condition decreased as the acid concentration increased. This aligns well with the high transfer efficiency of heavy metals from the solid phase to the liquid phase under acidic conditions. The FTIR indicated that the carboxy and hydroxy groups decreased significantly as the temperature increased and the concentration of HCl increased, which promoted the degradation of sunflower straw. A scan electron microscope showed that the deepening of the destruction of the initial microstructure promotes the transfer of heavy metals from hydrochars to liquid phase products. This acid-assisted hydrothermal process is an efficient method to treat biomass containing heavy metals.

Changes in Fatty Acid Content in Solanum spp. Fruits during Ripening

This study aimed to determine the effects of the ripening stage and species on the contents of saturated (SFA), monounsaturated (MUFA), and polyunsaturated (PUFA) fatty acids in Solanum spp. fruits. A two-factor field experiment with four different Solanum spp. species (S. nigrum, S. melanocerasum, S. retroflexum, and S. villosum) and three ripening stages was conducted over two growing seasons (2020-2021). The fatty acid composition of the Solanum fruits was characterized using gas chromatography with a flame ionization detection. The results show that PUFAs are the dominant type of fatty acid in Solanum fruits, followed by MUFAs and SFAs. Overall, the highest PUFA contents were observed in S. nigrum fruits in the ripening stage I, and the highest MUFA and SFA contents were observed in S. melanocerasum fruits during ripening stages I and II, respectively.

Authenticity and species identification of Fritillariae cirrhosae: a data fusion method combining electronic nose, electronic tongue, electronic eye and near infrared spectroscopy

This paper focuses on determining the authenticity and identifying the species of Fritillariae cirrhosae using electronic nose, electronic tongue, and electronic eye sensors, near infrared and mid-level data fusion. 80 batches of Fritillariae cirrhosae and its counterfeits (including several batches of Fritillaria unibracteata Hsiao et K.C. Hsia, Fritillaria przewalskii Maxim, Fritillaria delavayi Franch and Fritillaria ussuriensis Maxim) were initially identified by Chinese medicine specialists and by criteria in the 2020 edition of Chinese Pharmacopoeia. After obtaining the information from several sensors we constructed single-source PLS-DA models for authenticity identification and single-source PCA-DA models for species identification. We selected variables of interest by VIP value and Wilk's lambda value, and we subsequently constructed the three-source fusion model of intelligent senses and the four-source fusion model of intelligent senses and near-infrared spectroscopy. We then explained and analyzed the four-source fusion models based on the sensitive substances detected by key sensors. The accuracies of single-source authenticity PLS-DA identification models based on electronic nose, electronic eye, electronic tongue sensors and near-infrared were respectively 96.25%, 91.25%, 97.50% and 97.50%. The accuracies of single-source PCA-DA species identification models were respectively 85%, 71.25%, 97.50% and 97.50%. After three-source data fusion, the accuracy of the authenticity identification of the PLS-DA identification model was 97.50% and the accuracy of the species identification of the PCA-DA model was 95%. After four-source data fusion, the accuracy of the authenticity of the PLS-DA identification model was 98.75% and the accuracy of the species identification of the PCA-DA model was 97.50%. In terms of authenticity identification, four-source data fusion can improve the performance of the model, while for the identification of the species the four-source data fusion failed to optimize the performance of the model. We conclude that electronic nose, electronic tongue, electronic eye data and near-infrared spectroscopy combined with data fusion and chemometrics methods can identify the authenticity and determine the species of Fritillariae cirrhosae. Our model explanation and analysis can help other researchers identify key quality factors for sample identification. This study aims to provide a reference method for the quality evaluation of Chinese herbs.