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Objectives To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014–18 and the Danish AMR surveillance programme in 2016–19. Methods WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV , 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype–phenotype concordance was determined for all isolates. Transferability of mef (C)- mph (G)-carrying plasmids was assessed by conjugation experiments. Results mph (A), mph (B), mef (B), erm (B) and mef (C)- mph (G) were detected in E. coli and Salmonella , whereas erm (C), erm (42), ere (A) and mph (E)- msr (E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph (A) operon structures were observed in azithromycin-susceptible (n  = 50) and -resistant (n  = 136) isolates. mef (C)- mph (G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by IS CR2 or Tn As1 and associated with IncIγ and IncFII plasmids. Conclusions Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef (C)- mph (G) and erm (42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph (A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales. [ABSTRACT FROM AUTHOR]

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance. Authors carry out a longitudinal genomic analysis of Salmonella enterica serovar Concord isolates from various geographical locations, to reconstruct population diversity, evolution and antimicrobial resistance distribution. [ABSTRACT FROM AUTHOR]

Aim: Theoretical, experimental and observational studies have shown that biodiversity–ecosystem functioning (BEF) relationships are influenced by functional community structure through two mutually non‐exclusive mechanisms: (1) the dominance effect (which relates to the traits of the dominant species); and (2) the niche partitioning effect [which relates to functional diversity (FD)]. Although both mechanisms have been studied in plant communities and experiments at small spatial extents, it remains unclear whether evidence from small‐extent case studies translates into a generalizable macroecological pattern. Here, we evaluate dominance and niche partitioning effects simultaneously in grassland systems world‐wide. Location: Two thousand nine hundred and forty‐one grassland plots globally. Time period: 2000–2014. Major taxa studied: Vascular plants. Methods: We obtained plot‐based data on functional community structure from the global vegetation plot database "sPlot", which combines species composition with plant trait data from the "TRY" database. We used data on the community‐weighted mean (CWM) and FD for 18 ecologically relevant plant traits. As an indicator of primary productivity, we extracted the satellite‐derived normalized difference vegetation index (NDVI) from MODIS. Using generalized additive models and deviation partitioning, we estimated the contributions of trait CWM and FD to the variation in annual maximum NDVI, while controlling for climatic variables and spatial structure. Results: Grassland communities dominated by relatively tall species with acquisitive traits had higher NDVI values, suggesting the prevalence of dominance effects for BEF relationships. We found no support for niche partitioning for the functional traits analysed, because NDVI remained unaffected by FD. Most of the predictive power of traits was shared by climatic predictors and spatial coordinates. This highlights the importance of community assembly processes for BEF relationships in natural communities. Main conclusions: Our analysis provides empirical evidence that plant functional community structure and global patterns in primary productivity are linked through the resource economics and size traits of the dominant species. This is an important test of the hypotheses underlying BEF relationships at the global scale. [ABSTRACT FROM AUTHOR]

Invasions of alien plants pose a serious threat to native biodiversity and ecosystem processes. Forests are considered more resistant to invasion due to limited light availability in understories. However, disturbance and abiotic stress may open tree canopies and promote invasion. Their combined effects together with the resistance of resident species may determine the numbers and abundances of invasive species. Here we explore how canopy openness, water stress, and taxonomic and functional properties of resident communities affect the invasion by a frequent single invasive species (Aster lanceolatus and Impatiens parviflora) compared to that by multiple invaders in Central European lowland forests. Different abiotic factors and species-specific mechanisms of invasiveness determined the success of single versus multiple invaders. The massive spread of A. lanceolatus was associated with the long-distance seed dispersal and exploitation of available resources by fast growth resulting in formations of compact clonal patches in disturbed, open-canopy floodplain forests. The success of I. parviflora was caused by avoiding competition via tolerating less favorable conditions under the dense tree canopy on drier sandy soils. A. lanceolatus thus suppressed resident species richness, while I. parviflora spread in communities of higher functional and phylogenetic diversity. Multiple invasive species, mostly represented by subordinate species with low cover, colonized forests that were rich in resident species. We conclude that a combination of intense disturbance and stress favor the invasion of single dominant species that act as drivers of changes in native communities. Multiple invasive species colonize forests with less extreme conditions acting more as passengers who increase rather than decrease forest diversity. [ABSTRACT FROM AUTHOR]

Knowledge of forest recovery processes after severe disturbances, such as tropical cyclones, is essential for understanding the mechanisms maintaining forest diversity and ecosystem functioning. However, studies examining the impact of tropical cyclones on forest dynamics are still rare, especially in Northeast Asia. Here, we explore the complex responses of vegetation and soil chemistry to severe tropical cyclone disturbances in Hallasan National Park in South Korea. Vegetation and soil were examined five years before and five years after passages of tropical cyclones in 2012 in natural broadleaf and coniferous forests along an elevation gradient from 950 to 1770 m a.s.l., including the largest population of endemic Abies koreana. Tropical cyclones caused abundant tree mortality, resulting in a 46% decrease in stem basal area. Tropical cyclone disturbances triggered the spread of pioneer trees and shrubs and intense clonal propagation of graminoids, including dwarf bamboo, resulting in less diverse understory vegetation, especially in coniferous forests. In contrast, broadleaf forests at lower elevations experienced only minor disturbance. Opening of canopies after tropical cyclone disturbance led to the decrease in soil cations and doubling of available soil phosphorus stock, which likely contributed to the increased coverage of clonal graminoids, especially in coniferous forests (from 36 to 66%). Hence, increased competition of graminoids and reduction in seed fall and seedling recruitment prevented A. koreana regeneration. The subalpine forest dominated by A. koreana is forecasted to gradual loss due to the fact of temperature increases, intensified tropical cyclones and, particularly, due to the altered competition between dwarf bamboo and fir seedlings. [ABSTRACT FROM AUTHOR]

Taraxacum koksaghyz Rodin, a dandelion from the steppes of south-eastern Kazakhstan, has been known for long time as potential rubber producer, as a temperate region alternative to the tropical rubber tree Hevea brasiliensis Müll. Arg.. In this work, we evaluate Taraxacum bicorne Dahlst. (wild populations), a closely related congener of T. koksaghyz. The taxonomy of T. bicorne is reviewed, population genetic characteristics are analysed by Simple Sequence Repeat markers, and rubber biosynthesis genes are identified by Kompetitive Allele Specific PCR. Rubber content of T. bicorne plants collected in wild is measured using a modified extraction method to minimize amount of material. Taraxacum bicorne is shown to be an outcrossing sexual diploid. Its rubber content is about half of that of T. koksaghyz (~ 3.2% vs. ~ 7.2% of root dry weight), but T. bicorne could be used as a potential rubber source or as a source of germplasm for production of hybrids to improve rubber yield in various environments, because T. bicorne has considerable genetic variation, wider geographical range than T. koksaghyz and grows in different environments. [ABSTRACT FROM AUTHOR]

Salmonella enterica subspecies enterica serotype Choleraesuis is a swine adapted serovar. S. Choleraesuis variant Kunzendorf is responsible for the majority of outbreaks among pigs. S. Choleraesuis is rare in Europe, although there have been serious outbreaks in pigs including two outbreaks in Denmark in 1999–2000 and 2012–2013. Here, we elucidate the epidemiology, possible transmission routes and sources, and clonality of European S. Choleraesuis isolates including the Danish outbreak isolates. A total of 102 S. Choleraesuis isolates from different European countries and the United States, covering available isolates from the last two decades were selected for whole genome sequencing. We applied a temporally structured sequence analysis within a Bayesian framework to reconstruct a temporal and spatial phylogenetic tree. MLST type, resistance genes, plasmid replicons, and accessory genes were identified using bioinformatics tools. Fifty-eight isolates including 11 out of 12 strains from wild boars were pan-susceptible. The remaining isolates carried multiple resistance genes. Eleven different plasmid replicons in eight plasmids were determined among the isolates. Accessory genes were associated to the identified resistance genes and plasmids. The European S. Choleraesuis was estimated to have emerged in ∼1837 (95% credible interval, 1733–1983) with the mutation rate of 1.02 SNPs/genome/year. The isolates were clustered according to countries and neighbor countries. There were transmission events between strains from the United States and European countries. Wild boar and pig isolates were genetically linked suggesting cross-border transmission and transmission due to a wildlife reservoir. The phylogenetic tree shows that multiple introductions were responsible for the outbreak of 2012–2013 in Denmark, and suggests that poorly disinfected vehicles crossing the border into Denmark were potentially the source of the outbreak. Low levels of single nucleotide polymorphisms (SNPs) differences (0–4 SNPs) can be observed between clonal strains isolated from different organs of the same animal. Proper disinfection of livestock vehicles and improved quality control of livestock feed could help to prevent future spread of S. Choleraesuis or other more serious infectious diseases such as African swine fever (ASF) in the European pig production system. [ABSTRACT FROM AUTHOR]

Th e aim of the study was to evaluate the impact of micro-site conditions on natural regeneration prosperity and quality of Scots pine (Pinus sylvestris L.) in shelterwood regeneration system. Data were collected in four localities across the Czech Republic in 26 forest stands. In each forest stand with pine natural regeneration a square 0.25 ha research plot was established. We evaluated pine regeneration density, dendrometric characteristics (height, diameter of root collar, increment in last five years, crown diameter), quality characteristics including angle of branching and silvicultural value of each individual. As independent explanatory variables we measured light conditions based on hemispheric image analysis, ground vegetation characteristics such as composition and coverage, thickness of surface humus horizons and competition expressed as distance to the nearest individuals of natural regeneration and to the nearest mature tree. Results showed high variability in natural regeneration density (for seedlings higher than 25 cm), its mean values amounted to 4,285 (Hradec) - 18,570 (Plasy) pc.ha-1 with 75% quantile of values 5,714 - 30,000 pc.ha-1. Number of regeneration individuals was significantly influenced by light conditions (the openness and diffuse PPFD (photosynthetic photon flux density) and by ground vegetation characteristics, especially the cover of mosses. Th e dendrometric and growth characteristics (height, diameter, increment, and crown diameter) were significantly influenced by intraspecific competition, but relative values of both the increment and crown diameter depended also on the diffuse PPFD. Relative height increment between 10% and 15% was reached at values higher than 2 MJ-m-2.day of diffuse PPFD corresponding to stand basal area below 25 m2.ha-1. Th e best quality individuals (with straight stem and regular crown) occurred mainly in the upper height class of the natural regeneration. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the seasonal behavior and milk yield of dairy cows of Czech Fleckvieh cattle. The subject of the monitoring was one section (housed in one quarter of barn) with 103 free cubicle beds with an average of 95 lactating dairy cows of Czech Fleckvieh cattle. In the seasons (spring, summer, autumn, winter) temperature (°C), relative humidity (%) and temperature-humidity index (THI) were monitored. Furthermore, behavioral signs were also observed (a total of 4,940 observations): dairy cows were either lying down (3,432 observations) or standing up (1,508 observations). In the conditions that dairy cows were standingupin the cubicle, up to 585 observations were proved. If dairy cows were standing up outside of the cubicle (923 observations), they were either lying on the left side (1,924 observations) or right side (1,508). Significant seasonal influence was found out (p < 0.05) on the number of dairy cows standing up (a maximum of 410 observations in the spring, a minimum of 342 observations in the summer) and then the number of cows lying both on the left (a maximum of 519 observations in the autumn and a minimum of 444 observations in the spring) and on the right side (a maximum of 415 observations in the winter, a minimum of 320 observations in the autumn). The seasonal influence was no significant (p > 0.05) in the remaining behavioral signs. With regard to milk yield, a significant seasonal influence was proved. The highest milk yield was reached with dairy cows in spring (29.27 kg of milk) and the lowest in the autumn (24.58 kg of milk). No significant differences of milk yield were detected between behavioral signs (p > 0.05). The maximum difference of milk yield was found out up to 1.39 kg between dairy cows lying down on the left side (28.35 kg) and the dairy cows standing up in a cubicle (26.96 kg) in the winter but even this difference was not statistically significant (p > 0.05). [ABSTRACT FROM AUTHOR]

Aim To describe the main vegetation types of the Korean zonal forests and explore their relationship with the main environmental and geographic gradients. Location Korean Peninsula. Methods A data set of 3847 relevés of zonal (semi)natural forest stands, together with environmental factors recorded in the field or derived from interpolated climatic data was collected. Using the hierarchical ISOPAM method, the relevés were classified into main forest types and their species composition, diversity and distribution were described. Their differentiation along main environmental gradients was analysed with classification and regression trees. Results Eleven vegetation types of forests were distinguished and assigned to five vegetation classes: Quercetea mongolicae (representing the core of the Korean temperate forests), Vaccinio-Piceetea (subalpine coniferous forest), Fagetea crenatae (rare beech-dominated forest included within a sub-montane and sub-oceanic type of oak-dominated forest), Querco mongolicae- Betuletea davuricae (sub-continental drought- and fire-tolerant forest, differentiated along elevational gradient) and Camellietea japonicae (oceanic evergreen forest). At a higher hierarchical level, these 11 vegetation types were grouped into three clusters, which most probably reflect different vegetation development in the Late Pleistocene and Holocene. Within the three major vegetation clusters, each forest type occupies a distinct environment. The forest types are especially well separated along elevational and temperature gradients. The distribution of individual forest types is joinly driven by total amount of incoming energy and thermal extremes, both affecting water supply to plant communities. Conclusions All distinguished vegetation types can be assigned to the recent syntaxonomic classification system. However, three main vegetation clusters do not correspond to traditionally distinguished syntaxonomic units. Nevertheless, the forest types within these clusters share common species with similar ecology and, especially, migration histories during the late glacial and post-glacial periods. Therefore, we interpret these clusters as biogeographic patterns reflecting vegetation history rather than the current environmental conditions. [ABSTRACT FROM AUTHOR]

The interception was recognized as an important part of the catchment water balance in temperate climate. The mountainous forest ecosystem at experimental headwater catchment Liz has been subject of long-term monitoring. Unique dataset in terms of time resolution serves to determine canopy storage capacity and free throughfall. Spatial variability of throughfall was studied using one weighing and five tipping bucket rain gauges. The basic characteristics of forest affecting interception process were determined for the Norway spruce stand at the experimental area - the leaf area index was 5.66 - 6.00 m2 m-2, the basal area was 55.7 m2 ha-1, and the crown closure above individual rain gauges was between 19 and 95%. The total interception loss in both growing seasons analyzed was 34.5%. The mean value of the interception capacity determined was about 2 mm. Throughfall exhibited high variability from place to place and it was strongly affected by character of rainfall. On the other hand, spatial pattern of throughfall in average showed low variability. [ABSTRACT FROM AUTHOR]

Cultivation of the Russian dandelion ( Taraxacum koksaghyz) as a rubber producing crop was abandoned more than 50 years ago. Recently the interest in the Russian dandelion has renewed, due to the increasing demand for natural rubber, health problems associated with Hevea rubber and the potential vulnerability of the Hevea production system. Morphological examination and genetic analyses demonstrated that all available ex situ germplasm collections of T. koksaghyz belonged to a single triploid apomictic clone that was misidentified as T. koksaghyz. Morphological, taxonomic and AFLP analyses show that this clone belongs to T. brevicorniculatum a species commonly co-occurring with wild populations of T. koksaghyz in the southeastern Kazakhstan. The type specimen of T. brevicorniculatum is no longer extant and we provide a detailed description and typification, and the characteristics that distinguish it from T. koksaghyz. The investigation of literature reports and herbarium collections indicates that T. koksaghyz seed batches in the past were often contaminated with T. brevicorniculatum. We discuss the possible reasons for the worldwide replacement of T. koksaghyz by a single T. brevicorniculatum clone. New introductions in ex situ collections are urgently needed. [ABSTRACT FROM AUTHOR]

The globally observed trend of changing intensity of tropical cyclones over the past few decades emphasizes the need for a better understanding of the effects of such disturbance events in natural and inhabited areas. On the Korean Peninsula, typhoon intensity has increased over the past 100 years as evidenced by instrumental data recorded from 1904 until present. We examined how the increase in three weather characteristics (maximum hourly and daily precipitation, and maximum wind speed) during the typhoon activity affected old-growth oak forests. Quercus mongolica is a dominant species in the Korean mountains and the growth releases from 220 individuals from three sites along a latitudinal gradient (33-38°N) of decreasing typhoon activity were studied. Growth releases indicate tree-stand disturbance and improved light conditions for surviving trees. The trends in release events corresponded to spatiotemporal gradients in maximum wind speed and precipitation. A high positive correlation was found between the maximum values of typhoon characteristics and the proportion of trees showing release. A higher proportion of disturbed trees was found in the middle and southern parts of the Korean peninsula where typhoons are most intense. This shows that the releases are associated with typhoons and also indicates the differential impact of typhoons on the forests. Finally, we present a record of the changing proportion of trees showing release based on tree-rings for the period 1770-1979. The reconstruction revealed no trend during the period 1770-1879, while the rate of forest disturbances increased rapidly from 1880 to 1979. Our results suggest that if typhoon intensity rises, as is projected by some climatic models, the number of forest disturbance events will increase thus altering the disturbance regime and ecosystem processes. [ABSTRACT FROM AUTHOR]