The chloroplast genome of Amorphophallus allenii, a rare species endemic to limestone habitats, was sequenced to resolve phylogenetic uncertainties within the genus. Using PacBio HiFi sequencing, we performed a de novo assembly and obtained a complete circular genome of 170,657 bp, featuring a typical quadripartite structure. The genome encodes 126 genes, including 81 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Maximum likelihood phylogenetic analyses based on whole plastome, coding sequence, and protein alignments robustly support the placement of A. allenii within the Continental Asia I clade, with A. muelleri identified as its closest relative. This study provides a reliable genomic resource that clarifies the species’ phylogenetic position and establishes a foundation for investigating evolutionary diversification and biogeographic patterns in the genus Amorphophallus.

This narrative review aims to aggregate all reports of nosocomial transmission of rare yeast species, to provide an overview of global trends, causative species, clinical characteristics and preventive measures. A comprehensive literature search of multiple databases was conducted, to identify all reported nosocomial transmission events involving rare yeast species. The five most common yeasts, Candida albicans, Nakaseomyces glabratus, Candida parapsilosis, Candida tropicalis and Pichia kudriavzevii, in addition to Candida auris were excluded. A total of 76 reports were retrieved since 1984, caused by 28 different species. Wickerhamoyces anomalus was the most common agent, followed by Magnusiomyces, Trichosporon and species of the Candida haemulonii complex. Since the early 2000s, a clear increase was noted both in the number of outbreak reports and range of associated species, largely due to improved diagnostics. Most species were resistant to one or multiple antifungals and although environmental sampling was often performed, virtually all efforts yielded negative results. Once noted, strict hand hygiene practices and proper cleaning and disinfection of medical equipment has shown in curbing nosocomial spread. As hospital outbreak events are increasingly reported, accurate species identification and epidemiological surveillance should be in place for rapid detection. An enhanced focus on infection control measures was often sufficient to prevent new cases. Importantly, high-resolution genotyping is needed to confirm clonal transmission, which is often not conducted.

PmPPO-mediated drought adaptation mechanism in Prunus mira Koehne: Interaction with PmRad23d and regulation of ROS homeostasis.

Multi-omics analysis elucidates sesquiterpenoid compounds and identifies IrTPS3 as a key multifunctional terpene synthase in roots and rhizomes of Inula racemosa.

Understanding how soil types influence functional traits and growth performance is essential for effective plant cultivation and management. Ardisia gigantifolia (A. gigantifolia) is a rare traditional medicinal plant in China; however, the mechanisms underlying its growth responses remain poorly understood. This study utilized a pot experiment to investigate the effects of different soil types (humus, loam, and sand) on the functional traits and growth performance of one-year-old A. gigantifolia cuttings and to characterize the interrelationships among these factors. Compared to sand, humus soil significantly increased the height, as well as root and stem biomass of A. gigantifolia cuttings. In humus, the specific leaf area, leaf water content, root average diameter, root volume, stem length, and stem average diameter were significantly higher, whereas leaf dry matter content and the tissue density of leaves, roots, and stems were lower. Additionally, loam significantly improved the photosynthetic and pigment traits of the cuttings. Results from RDA and PLS-SEM demonstrated that the growth performance of A. gigantifolia cuttings is primarily and directly governed by root, stem, and leaf morphological traits, which also mediate soil-driven regulation. Root morphological traits, in particular, showed the greatest direct and indirect impacts, highlighting them as key potential indicators for predicting the performance of A. gigantifolia cuttings. This study demonstrates that the growth performance and functional traits of A. gigantifolia cuttings are modulated by soil properties, while organ morphological traits serve as reliable predictors of plant growth performance. Our findings provide a scientific foundation for the conservation of wild A. gigantifolia resources and the advancement of its sustainable industrial development.

Understanding the responses of soil microbial communities to environmental change, as well as their contributions to ecosystem functioning under disturbed conditions, is of fundamental importance. Yet, the relative roles of rare and abundant microbes in sustaining soil functions under environmental changes remain poorly understood, particularly in agricultural ecosystems. Here, we sampled soils from 50 agricultural fields across eastern China to examine the response patterns of rare and abundant sub-communities, encompassing multitrophic soil organisms, including bacteria, fungi, and protists, to climate warming, dry-wet cycles, and nutrient enrichment, and assessed their relative contributions to ecosystem multifunctionality. We found that, unlike abundant taxa, rare species diversity significantly decreased with dry-wet cycles but increased with nutrient addition. In addition, the community resistance of abundant species was significantly higher than that of rare species under all of treatments. Co-occurrence network analysis showed that species associations increased under environmental changes in both abundant and rare sub-communities, while the shift was more pronounced in rare species. Notably, rare species emerged as the main drivers of ecosystem function, with their contributions becoming more pronounced under environmental changes. Collectively, these results highlight the pivotal role of rare species in supporting and enhancing agricultural ecosystem functioning under global change scenarios.

The brown alga Dictyota dolabellana is a rare species that was described based on morphological and natural product analyses from a population found in 2004 at Itaparica Island in Bahia, Brazil. However, it has not been found anywhere since then. The original crude acetonic extract was analyzed by 1H and 13C NMR and showed as the major secondary metabolite, the dolabellane diterpene (1S*, 2E, 4S*, 7S*, 8R*, 11S*, 12R*)-4- hydroxy-7,8-epoxy-2-dolabellene, which is the chemotaxonomic marker of this species. Two additional new diterpenes for this species were obtained: (1S*, 2E, 4S*,7R*, 8E, 11S*, 12R*)-4,7- hydroxy-2,8-dolabelladiene and (1R*, 4S*, 7R*, 8E, 11S*,12R*)-4,7-hydroxy-8-dolabellene. All three structures were assigned by 1D and 2D NMR spectral data. Biological tests carried out with those three diterpenes revealed that diterpenes 1 and 2 inhibited the replication of herpes simplex virus type 1 (HSV-1) in a dose-dependent manner. Supplementary data showed that diterpene 1 has no inhibitory activity against the reverse transcriptase enzyme of human immunodeficiency virus type 1 (HIV-1 RT). Finally, the antiviral and cytotoxic activities of dolabellanes of Dictyota spp depend on both the functionality of the molecule and the position of the hydroxyl groups and double bonds. This study may enhance the interest in D. dolabellana for its biotechnological applications, such as antiviral products and assist in its chemotaxonomy.

Iris kuschakewiczii B.Fedtsch. is a rare ornamental plant endemic to the Northern Tien Shan mountains. The analysis of the species' distribution range is important given the declining habitat area. This study employed MaxEnt to project the distribution of I. kuschakewiczii under current and three future climate change scenarios (SSP126, SSP245, SSP585) for two time periods (the 2050s and the 2090s). Prediction models showed high validity (AUC = 0.997), strong accuracy, and reliability. Moreover, key environmental variables affecting the distribution of I. kuschakewiczii were identified. It included Weight and Percentage of Sand (70%), Temperature Seasonality (~ 2300), and Elevation (700-1300m above the sea level). Highly suitable distribution areas were mainly found in the Chu-Ili Mountains (Southeastern Kazakhstan). The analysis showed that only 26.7% of the total highly suitable area is protected by reserves and nature parks, underlying the need for conservation. The recently founded Kurty Valley Important Plant Area in Kazakhstan provides a strong foundation for the scientific conservation of I. kuschakewiczii and other rare and endangered plants. This research provides insights into the potential dynamics of habitat distribution for the endangered I. kuschakewiczii and offers a basis for strengthening cooperative international conservation and sustainable management strategies in the face of climate change.

Introduction Aconitum pendulum is a rare medicinal plant endemic to the Qinghai-Tibet Plateau and a key indicator species for alpine ecosystems. It possesses both medicinal and ecological value. However, its wild populations are on the verge of decline due to overharvesting and low reproductive capacity, and the species is highly sensitive to climate change. Methods In this research, the kuenm package was employed to optimize the maximum entropy model, so as to predict the distribution of A. pendulum in China under both current and future climate scenarios. From a total of 103 environmental variables, 11 key factors influencing the distribution of A. pendulum were selected through correlation analysis and variable contribution rate evaluation. Based on 188 valid distribution sites of A. pendulum , an analysis was conducted on its potential habitat distribution in China under current and future climatic conditions. Results The results demonstrate that under the current climate, the total area of suitable habitats for A. pendulum is 2.08×10 6 km 2 , accounting for 21.56% of China’s land area, and these habitats are mainly distributed in the southwest, northwest, and central regions of the country. Altitude, september solar radiation, and temperature seasonality were identified as the main factors affecting the distribution of A. pendulum . Under future climate change scenarios, the overall area of suitable habitats for A. pendulum exhibits a decreasing trend. Under the low-emission scenario, the area of unsuitable areas shows slight fluctuations, while the low-, medium-, and high-suitable distribution areas within the suitable zones remain balanced. Under the high-emission scenario, the edge areas of unsuitable areas shrink rapidly, whereas the high-suitable areas expand slightly. The centroid migration of the suitable habitats did not deviate from the core region located on the eastern edge of the Qinghai-Tibet Plateau, indicating that A. pendulum still has adaptive potential under climate change. Discussion This study highlights the significant impacts of altitude, September solar radiation, and temperature seasonality on the distribution of A. pendulum , and provides a scientific basis for the protection, planting planning, and sustainable development of A. pendulum .

Automating pollinator identification using artificial intelligence and participatory science.

Carnivores frequently rely on scent and visual markings for intraspecific communication, delineating territorial boundaries, attracting mates and assessing competitors. However, studying such behaviours in rare and elusive species poses significant challenges. To enhance our understanding of the diel marking behaviours of common leopard (Panthera pardus), from November, 2019 to June, 2023, we conducted a comprehensive camera-trap survey in Luolong county of Tibet, China. Our monitoring encompassed 159 locations yielded 1,208 (excluded 700 unknown sex) individual leopard detections over 60,000 trap days, allowing us to quantify the frequency and temporal patterns of marking behaviours. Of these, 153 detections involved territorial marking in snowy conditions, while 355 occurred in snow-free environments. Female leopards in mixed forests and shrublands exhibited higher diurnal activity in snow-presence days. Male leopards engaged in a range of behaviours - including sniffing and rolling - primarily within mixed, coniferous and shrubland habitats. Male leopards engaged more frequently in behaviours such as sniffing, scraping, urine spraying, body rubbing, vocalizations, rolling and scat deposition with notable differences in scraping frequency compared to females. Female leopards displayed similar behaviours but at reduced levels particularly in scraping activities. The number of scrapes observed at camera-trap sites appears to be an indicator of leopard visitation rates suggesting its usefulness for optimizing monitoring efforts. Our findings contribute valuable insights into how environmental factors influence social communication strategies in leopards, enhance our understanding of male and female leopard territorial and making behaviours in various environments, and benefit for the conservation and monitoring of carnivore populations.

Currently, clinical bacteriology finds itself at the crossroads, as increasingly more advanced diagnostic techniques such as MALDI-TOF mass spectrometry or whole-genome sequencing (WGS) become available and popular. However, despite these technological innovations, this review highlights the significance and value of classic biochemical analyses, particularly those involving the DNase test, in the modern context. The classic DNase test continues to prove its reliability by demonstrating high sensitivity and specificity values ranging from 96% to 99% regarding the detection of Staphylococcus aureus. Although the use of contemporary technologies, e.g., MALDI-TOF, allows obtaining the diagnosis faster, these tools may fail to achieve the level of accuracy provided by traditional techniques, especially in case of rare species of bacteria or lack of data in the spectrum database. Additionally, modern automated devices such as VITEK 2 operate based on the same biochemical principles as the classic approaches; thus, their implementation represents further development of the latter. As for developing nations, classic biochemical analysis still represents the most cost-effective and sustainable method for conducting the diagnostics without requiring sophisticated equipment such as a spectrophotometer. Overall, this review reveals that the "tiered" strategy combining the approaches discussed above should represent the cornerstone of the diagnostics of the field.

Transposable elements (TEs) have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read based metagenomically assembled reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publicly available genomes to investigate the relationships between species traits (i.e., dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of TEs using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradicts previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of TEs in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater TE activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving TE proliferation in rare species' genomes, and if TE content is predictive of increased extinction risk.

ABSTRACTIdentifying key factors influencing the survival of animals, particularly rare and endangered species, is crucial to biodiversity conservation. In birds, hatching failure is pronounced in endangered species. Accurate assessment of egg development and the ability to distinguish nonviable eggs are essential prerequisites for evaluating the impact of factors that lead to hatching failure and applying appropriate conservation practices. The crested ibis (Nipponia nippon), a flagship endangered species, has a long history of captive breeding, which has contributed to population recovery. However, little is known about the specific process and characteristics of its egg development. In this study, we provided the first comprehensive description of normal egg development in the crested ibis, including both the changes observed in unfertilized eggs during incubation and embryonic development via candling (n = 98 eggs; total = 1422 candling images; mean ± SE = 14.52 ± 1.38 images per egg), and offered a practical reference for assessing fertilization status and embryo viability. In addition, we estimated the timing of embryo mortality and found that most deaths occurred during mid‐incubation (Day 7–15) (n = 12, 60.0%) and shortly before hatching (Day 23–29) (n = 7, 35.0%), highlighting these critical periods that require particular attention. This species‐specific documentation of egg development provides a valuable reference for accurately assessing embryonic progress, evaluating environmental effects on survival, and guiding adaptive management, benefiting both captive breeding programs and field conservation efforts.

Accurate identification and genotypic drug resistance prediction in mycobacteria are essential for early diagnosis and appropriate clinical management. Targeted next-generation sequencing (tNGS) detects multiple genetic targets and enables direct testing from primary specimens. We evaluated identification using the Deeplex Myc-TB assay for Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM) as well as MTBC drug-resistance prediction from 78 isolates and 102 sputum samples. DNA libraries were sequenced (Illumina MiSeq), and results were analyzed using defined acceptability criteria. Performance was compared against reference phenotypic and genotypic methods. Testing for MTBC was invalid in <2.5% of cases, but NTM testing was invalid more frequently, especially in sputum (>50%). Of the evaluable isolates/sputum, specificity was 100% for negative/nontarget organisms. Among isolates, sensitivity for organism identification was 92.7% (38/41) for MTBC, 100% (5/5) for rapidly growing mycobacteria (RGM), and 87.5% (14/16) for slowly growing mycobacteria (SGM). For sputum, sensitivity was 97.6% (41/42) for MTBC, 70% (7/10) for SGM, and 66% (2/3) for RGM. Categorical agreement of MTBC resistotypes against reference susceptibility methods was 91.9% (489/532) for isolates and 90.8% (472/520) for sputum, increasing to 96.8% (489/505) and 97.3% (472/485), respectively, when variants of unknown significance were excluded. Limit-of-detection studies confirmed published thresholds of 100-1,000 genomes/PCR in both isolates and sputum. Deeplex Myc-TB provides highly specific identification and reliable genotypic resistance profiling from isolates and sputum, especially for MTBC. While identification of rare NTM species and mixed infections remain challenging, tNGS demonstrates substantial promise for rapid mycobacterial diagnostics.IMPORTANCERapid and accurate diagnosis of mycobacterial infections is essential for initiating effective treatment, interrupting transmission, and improving patient outcomes. Traditional phenotypic methods for organism identification and antibiotic susceptibility testing are slow and may be unreliable for certain drugs. This study evaluates the Deeplex Myc-TB targeted next-generation sequencing assay to identify mycobacteria and resistance-associated mutations from the Mycobacterium tuberculosis complex (MTBC) for both isolates and clinical sputum. Our findings show strong correlation of MTBC identification and resistance markers compared with reference methods.

Rupirana cardosoi is an endemic and threathened anuran species from the Chapada Diamantina region (Bahia, Brazil), with limited information available on its natural history, particularly its feeding behavior and diet. Using the stomach-flushing technique, we analyzed the stomach contents of 55 individuals collected in the Chapada Diamantina National Park (PNCD). We describe the species’ diet and assess prey availability in the environment. Based on our findings, we classify R. cardosoi as an active forager and ant specialist, given its strong preference for ants compared to other prey categories available in the habitat. Consequently, we conducted a detailed identification of the Formicidae species consumed. The diet revealed a remarkable proportion of ants from species known to produce alkaloids and from species with aggressive defensive behaviors — typically a critical component in the diets of poisonous anurans or actively avoided by many frog species. Additionally, we documented the ant Anochetus horridus as a new occurrence for Bahia. Our findings highlight the value of anuran diet analysis for understanding the natural history of species, as it can provide insights into rare or novel arthropod species present in the environment through the examination of prey items.

Meiofauna samples were collected using the multicorer during three FS POLARSTERN research expeditions to the Southern Ocean between 2013 and 2019. The samples yielded, among other representatives of the CopepodaHarpacticoida, 11 individuals of a previously unknown species of the Ancorabolidae Sars. The six males and five females could be assigned to the genus Breviconia Conroy-Dalton & Huys, within which they form a separate species. Breviconiaacuminatasp. nov. differs from the two already known species B.australis (George) from the Beagle Channel (Chile) and B.andrei Garlitska, George & Chertoprud from the Barents Sea (Russia) in the following autapomorphies: (i) the female antennule has only nine setae on the last segment instead of ten, (ii) the inner apical seta on P2enp2 is strongly shortened and only reaches half the length of the outer apical seta. In addition to the detailed description of the new species, a morphologically based comparison with the taxa Arthropsyllus Sars and Uptionyx Conroy-Dalton & Huys confirmed the monophyletic status of Breviconia. A key to the Breviconia species is also provided. Breviconiaacuminatasp. nov. has a very limited distribution range. To date, it has only been found on the continental shelf at the northernmost tip of the Antarctic Peninsula and on the continental slope in Bransfield Strait, at depths between 420 and 750 metres. The sediments at the stations where the new species was found were characterised by low bottom temperatures, a high silt and clay content (84–89%), and high pigment content, indicating a high food availability.

Most larvae of phytophagous insects have little mobility, so they must complete their development on those plants 'chosen' by their mothers, even if this does not always increase the performance of her offspring. Here, we tested the hypothesis that the defence strategy expressed by host plants and the frequency at which they are represented within populations can condition both the preference of the female and the performance of her offspring. Using the plant Datura stramonium and its specialist insect Lema daturaphila, we conducted an experiment in which the frequency of resistant and tolerant genotypes within cages was manipulated, and the initial density of herbivorous adults was controlled. Results provide conclusive evidence of negative frequency-dependent oviposition preference for tolerant plants and differential density-dependent effect between resistant and tolerant plants on larval survival. Female oviposition preference also changed larval density, which in turn fed back to influence larval survival. Moreover, we found that oviposition preference for rare tolerant plants resulted, indeed, in lower plant fitness. Thus, the evolution of phytophagous insects' oviposition preference can be shaped by the frequency in which different plant defensive strategies are represented within the population and can create evolutionary feedback on their host plants. This article is part of the theme issue 'Exploring negative frequency dependent selection across levels: from genetics to ecology and back again'.

Anthropogenic disturbances and climate warming threaten the rare paleoendemic species Tetracentron sinense. To identify the divers of its latitudinal adaptation, we integrated functional trait differentiation, environmental filtering, and phylogenetic conservatism. We measured 35 functional traits (leaf morphology, nutrient stoichiometry, stomatal traits, whole-plant architecture) across four natural populations spanning the species' latitudinal range: BMXS (Baima Snow Mountain), DFD (Dafengding), FP (Foping), LGS (Leigong Mountain). Using correlation analysis, principal component analysis, and phylogenetic community metrics, we found that T. sinense dominated all communities. Populations exhibited divergent strategies: DFD expanded leaf area for light capture under high rainfall and shaded conditions; FP increased height and crown width to compete for light; LGS enhanced nutrient-use efficiency under phosphorus limitation; BMXS promoted phosphorus uptake under nitrogen limitation (N/P < 14). Trait variation correlated significantly with elevation, solar radiation, and temperature. PCA explained 90.44% of total variance, and standardized effect size (SES) values for phylogenetic signals range from -2.031 to 1.973; Phylogenetic signals were stronger in co-occurring taxa than in T. sinense. T. sinense populations in BMXS and FP are structured by competitive exclusion, while those in LGS and DFD by habitat filtering. We conclude that T. sinense achieves latitudinal adaptation by overcoming phylogenetic niche conservatism through phenotypic plasticity. While leaf economic traits remain evolutionarily conserved and niches in glacial refugium are relatively stable, populations adjust trait syndromes via metabolic shifts and structural trade-offs in response to heterogeneous environmental filters. Identifying these adaptive strategies can guide seed sourcing for restoration efforts under climate change.

The irrational exploitation of medicinal plant contributes to their population decline and constitutes a threat to phytodiversity. Combretum micranthum G. Don, Entada africana Guill. &amp; Perr. and Carissa edulis (Forssk.) are highly exploited species in the South-West of Burkina Faso. Thus, this study aimed to evaluate the influence of land use types on the population structure of these species. Vegetation surveys were conducted in a classified forest, a protected village forest and agrosystems using a stratified sampling approach. Dendrometric parameters and indicators of anthropogenic disturbance were analyzed. Land use affected the height of C. micranthum (P=0.002). Although the densities of C. micranthum and E. africana didn’t vary across land use types, the highest densities were recorded in the classified forest. E. africana showed stable population structure under protection in the classified forest. However, C. micranthum and C. edulis presented disturbed demographic structures under anthropogenic pressure. C. edulis had the lowest density (29.86 individuals/ha) and was absent in forests which are refuge areas for threatened and rare plant species, suggesting its vulnerability. Despite signs of regenerative potential in all three species, sustainable use and conservation practices are needed to prevent further degradation.