Effect of ecotype and Enteromorpha polysaccharide supplementation on the growth performance of indigenous chickens in Northwest Ethiopia.

The study was conducted to compare the growth performance of indigenous chickens and evaluate the effect of Enteromorpha prolifera (EP) supplementation on the growth of chickens. A total of 180 indigenous chicken ecotypes (Sinan, Dembecha, North Achefer, and Jawi) were used in the study. Chicken ecotype and sex had a highly significant (p < 0.001) effect on body weight and average daily gain (ADG). The highest final body weight (1811.5 ± 16.6 g) and ADG at twenty weeks of age (12.76 ± 0.12 g) were recorded for the Jawi ecotype, followed by the North Achefer. A significantly higher body weight and ADG in male chickens than female chickens were observed. The EP supplemented (EP +) chickens showed a significantly (P < 0.05) higher body weight and ADG than the non-supplemented (EP-) chickens. The interaction effect of ecotype and feed type was not statistically significant on body weight in the starter and grower phases, except at week 9. In the first four weeks, the highest (100%) and lowest (91.7%) survivability rates were recorded for the Sinan ecotype and the Jawi ecotype, respectively. In general, the Jawi and North Achefer ecotypes had better growth performance, and the Sinan ecotype relatively showed better survivability. EP supplementation could improve the growth performance of chickens.

Morphological Differentiation, Yield, and Cutting Time of Lolium multiflorum L. under Acid Soil Conditions in Highlands.

Livestock production in the basins of the northern macro-region of Peru has as its primary source pastures of Lolium multiflorum L. 'Cajamarquino ecotype' (ryegrass CE) in monoculture, or in association with white clover Ladino variety, for feeding. The objective of this research work was the morphological characterisation, yield evaluation, and cutting time evaluation of two local genotypes (LM-58 and LM-43) of Lolium multiflorum L. in six locations. An ANOVA was performed to compare fixed effects and interaction. It was determined that the LM-58 genotype is intermediate, growing semi-erect, with a dark green colouring and 0.8 cm broadleaf, and can reach an average stem length of 46 cm, up to 1.6 cm. day-1, achieving fourth-leaf growth at 28 days under appropriate management conditions. Despite the differentiated characteristics, according to BLASTn evaluation, the ITS1 sequences showed a greater than 99.9% similar identification to Lolium multiflorum L., characterising it as such. It was determined that the LM-58 genotype outperforms LM-43, achieving a forage yield of 4.49 Mg. ha-1, a seed production of 259.23 kg. ha-1, and an average of 13.48% crude protein (CP). The best biomass yield (49.10 Mg. ha-1.yr-1) is reached at 60 days; however, at 30 days, there is a high level of CP (14.84%) and there are no differences in the annual protein production at the cutting age of 60 and 45 days. With the results of the present study, LM-58 from a selection and crossbreeding of 680 ryegrass EC accessions emerges as an elite genotype adapted to the conditions of the northern high Andean zone of Peru.

Competition and drought affect cleistogamy in a non-additive way in the annual ruderal Lamium amplexicaule.

Competition affects mixed-mating strategies by limiting available abiotic or biotic resources such as nutrients, water, space, or pollinators. Cleistogamous species produce closed (cleistogamous, CL), obligately selfed, simultaneously with open (chasmogamous, CH), potentially outcrossed flowers. The effects of intraspecific competition on fitness and cleistogamy variation can range from limiting the production of costly CH flowers because of resource limitation, to favouring CH production because of fitness advantages of outcrossed, CH offspring. Moreover, the effects of competition can be altered when it co-occurs with other environmental variations. We grew plants from seven populations of the ruderal Lamium amplexicaule, originating from different climates and habitats, in a common garden experiment combining drought, interspecific competition, and seasonal variation. All these parameters have been shown to influence the degree of cleistogamy in the species on their own. In spring, competition and drought negatively impacted fitness, but the CL proportion only increased when plants were exposed to both treatments combined. We did not observe the same results in autumn, which can be due to non-adaptive phenotypic variation, or to differences in soil compactness between seasons. The observed responses are largely due to phenotypic plasticity, but we also observed phenotypic differentiation between populations for morphological, phenological, and cleistogamy traits, pointing to the existence of different ecotypes. Our data do not support the hypothesis that CL proportion should decrease when resources are scarce, as plants with reduced growth had relatively low CL proportions. We propose that variation in cleistogamy could be an adaptation to pollinator abundance, or to environment-dependent fitness differences between offspring of selfed and outcrossed seeds, two hypotheses worth further investigation. This opens exciting new possibilities for the study of the maintenance of mixed-mating systems using cleistogamous species as models that combine the effects of inbreeding and reproductive costs.

Intraspecific variation in photosynthetic thermal acclimation in Fagus crenata seedlings from two populations growing at different elevations in northern Japan.

Plants can acclimate their photosynthesis to growth temperature, but the contribution of local adaptation to intraspecific variation in thermal acclimation of photosynthesis is not fully understood. Here, we experimentally investigated the photosynthetic thermal acclimation in Fagus crenata Blume seedlings from two populations growing at different elevations and temperature regimes (low- and high-elevation sites) in northern Japan. We acclimated seedlings for 14 to 23 days at daytime temperatures of either 22 °C (control) or 27 °C (warm treatment) and obtained photosynthetic temperature-response curves in the range of 19 to 32 °C. The optimum temperature of photosynthesis (Topt) was ~0.6 °C higher in seedlings acclimated at 27 °C than in those acclimated at 22 °C, and it was significantly lower in seedlings with higher stomatal sensitivity to leaf-to-air vapor pressure deficit than in those with lower sensitivity. The effects of warm treatment, population and treatment-population interaction on Topt were not significant in the two-way analysis of variance, but the effect of treatment became significant when stomatal sensitivity to leaf-to-air vapor pressure deficit was included as a covariate in the model. Structural equation modeling indicated that seedlings with lower root biomass had lower Topt because of the high stomatal sensitivity to leaf-to-air vapor pressure deficit. Structural equation modelling also indicated that the way of shifting the Topt differed between the two populations: seedlings from a high-elevation site depended on decreasing photosynthetic rates at low temperatures for the increase in Topt but seedlings from a low-elevation site did not. We suggest that the difference in thermal acclimation of photosynthesis between the two populations may reflect adaptation to different climate regimes and that belowground traits should be considered when investigating thermal acclimation capacity, especially in seedlings.

Multicellular immune ecotypes within solid tumors predict real-world therapeutic benefits with immune checkpoint inhibitors.

Background: Cancer initiation, progression, and immune evasion depend on the tumor microenvironment (TME). Thus, understanding the TME immune architecture is essential for understanding tumor metastasis and therapy response. This study aimed to create an immune cell states (CSs) atlas using bulk RNA-seq data enriched by eco-type analyses to resolve the complex immune architectures in the TME. Methods: We employed EcoTyper, a machine-learning (ML) framework, to study the real-world prognostic significance of immune CSs and multicellular ecosystems, utilizing molecular data from 1,610 patients with multiple malignancies who underwent immune checkpoint inhibitor (ICI) therapy within the ORIEN Avatar cohort, a well-annotated real-world dataset. Results: Our analysis revealed consistent ICI-specific prognostic TME carcinoma ecotypes (CEs) (including CE1, CE9, CE10) across our pan-cancer dataset, where CE1 being more lymphocyte-deficient and CE10 being more proinflammatory. Also, the analysis of specific immune CSs across different cancers showed consistent CD8+ and CD4+ T cell CS distribution patterns. Furthermore, survival analysis of the ORIEN ICI cohort demonstrated that ecotype CE9 is associated with the most favorable survival outcomes, while CE2 is linked to the least favorable outcomes. Notably, the melanoma-specific prognostic EcoTyper model confirmed that lower predicted risk scores are associated with improved survival and better response to immunotherapy. Finally, de novo discovery of ecotypes in the ORIEN ICI dataset identified Ecotype E3 as significantly associated with poorer survival outcomes. Conclusion: Our findings offer important insights into refining the patient selection process for immunotherapy in real-world practice and guiding the creation of novel therapeutic strategies to target specific ecotypes within the TME.

Sustainable Agrochemical Exploitation of Ligurian Aromatic Plant Ecotypes.

The characterization of local improved varieties as well as the reduction of synthetic chemical fertilizers are sustainable approaches in the vision of a new precision Farming. Aim of our study was to improve the geographical characterization of local ecotypes and to identify peculiar features of new crops in terms of bioactive compounds. NMR and LC-MS metabolite profiling approaches followed by multivariate data analysis were applied to characterize local rosemary and garlic ecotypes. With the aim of applying for a protected designation of origin, orthogonal partial least squares discriminant analysis (OPLS-DA) was used to identify representative sensory quality indicators for Vessalico garlic and rosemary "Eretto Liguria" local ecotypes, Variable Influence on Projections (VIP) values of OPLS-DA indicated six metabolites as quality indicators for Vessalico garlic and sixteen metabolites as quality indicators for rosemary "Eretto Liguria". Finally, to discover and utilize new ecotypes in a sustainable way, Vessalico garlic extracts antiviral activity, previously evaluated against Tomato brown rugose fruit virus (ToBRFV), a Tobamovirus affecting tomato crops, was extended to Pepino mosaic virus (PepMV) with positive results.

Identifying potential provenances for climate-change adaptation using spatially variable coefficient models.

BACKGROUND: Selection of climate-change adapted ecotypes of commercially valuable species to date relies on DNA-assisted screening followed by growth trials. For trees, such trials can take decades, hence any approach that supports focussing on a likely set of candidates may save time and money. We use a non-stationary statistical analysis with spatially varying coefficients to identify ecotypes that indicate first regions of similarly adapted varieties of Douglas-fir (Pseudotsuga menziesii (Mirbel) Franco) in North America. For over 70,000 plot-level presence-absences, spatial differences in the survival response to climatic conditions are identified. RESULTS: The spatially-variable coefficient model fits the data substantially better than a stationary, i.e. constant-effect analysis (as measured by AIC to account for differences in model complexity). Also, clustering the model terms identifies several potential ecotypes that could not be derived from clustering climatic conditions itself. Comparing these six identified ecotypes to known genetically diverging regions shows some congruence, as well as some mismatches. However, comparing ecotypes among each other, we find clear differences in their climate niches. CONCLUSION: While our approach is data-demanding and computationally expensive, with the increasing availability of data on species distributions this may be a useful first screening step during the search for climate-change adapted varieties. With our unsupervised learning approach being explorative, finely resolved genotypic data would be helpful to improve its quantitative validation.

Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene.

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Chromosome-scale Genome Assembly of the Rough Periwinkle Littorina saxatilis.

The intertidal gastropod Littorina saxatilis is a model system to study speciation and local adaptation. The repeated occurrence of distinct ecotypes showing different levels of genetic divergence makes L. saxatilis particularly suited to study different stages of the speciation continuum in the same lineage. A major finding is the presence of several large chromosomal inversions associated with the divergence of ecotypes and, specifically, the species offers a system to study the role of inversions in this divergence. The genome of L. saxatilis is 1.35 Gb and composed of 17 chromosomes. The first reference genome of the species was assembled using Illumina data, was highly fragmented (N50 of 44 kb), and was quite incomplete, with a BUSCO completeness of 80.1% on the Metazoan dataset. A linkage map of one full-sibling family enabled the placement of 587 Mbp of the genome into 17 linkage groups corresponding to the haploid number of chromosomes, but the fragmented nature of this reference genome limited the understanding of the interplay between divergent selection and gene flow during ecotype formation. Here, we present a newly generated reference genome that is highly contiguous, with a N50 of 67 Mb and 90.4% of the total assembly length placed in 17 super-scaffolds. It is also highly complete with a BUSCO completeness of 94.1% of the Metazoa dataset. This new reference will allow for investigations into the genomic regions implicated in ecotype formation as well as better characterization of the inversions and their role in speciation.

Flavonoid diversity in bitter and debittered seeds of Andean lupin (Lupinus mutabilis Sweet).

Seeds of ten Andean lupin (Lupinus mutabilis Sweet) ecotypes were collected from different regions of Peru and treated with an aqueous debittering method. Both untreated and treated seeds were analyzed by using LC-MS to investigate flavonoid profiles of different ecotypes and impact of debittering process on these compounds. Thirteen isoflavones (mainly as glycosides of genistein and methoxy-genistein) and eight flavones (glycosylated apigenins and methyl-luteolins) were characterized as the main flavonoids in the seed samples. The untreated lupin seeds contained 187-252 mg/100 g (dry weight) of flavonoids. The main difference among lupin ecotypes was observed in the levels of genistein-malonylhexoside, methoxy-genistein-malonylhexoside, and methyl-luteolin-malonylhexoside. After the debittering treatment, the total flavonoid content in the seeds was decreased to 125-203 mg/100 g dry weight, the aglycones of genistein, methoxy-genistein, and methyl-luteolin being the key distinguishing compounds of ecotypes. The aqueous treatment was effective in degrading flavonoid glycosides and releasing the corresponding aglycones.

Division time (td) for in situ growth measurements demonstrates thermal ecotypes of Karlodinium veneficum.

The toxic dinoflagellate Karlodinium veneficum forms fish killing blooms in temperate estuaries worldwide. These blooms have variable toxicity which may be related to bloom stage and in situ growth rates of the constituent K. veneficum cells. Measurement of in situ growth rates is challenging and methods such as the mitotic index technique require knowledge of the dynamics of cell division. In order to better understand these dynamics, we determined the duration of cell division (td) in four geographically distinct laboratory strains of K. veneficum at three different environmentally relevant temperatures. The results demonstrated that the td value for each strain, growing at strain-specific optimal temperatures, was 1.6 ± 0.1 h. This value corresponded to a range of growth rates from 0.17 ± 0.08 d-1 to 0.62 ± 0.07 d-1. Equivalent values of td spread across four geographically distinct laboratory strains and a nearly fourfold range of growth rates implies that 1.6 h represents the td value of K. veneficum. Additionally, temperature conditions yielding this value for td and the highest growth rates varied among strains, indicating cold-adapted (Norway), warm-adapted (Florida, USA), and eurythermally-adapted (Maryland, USA) strains. These differences have been apparently retained in culture over many years, indicating a conserved genetic basis that suggests distinct thermal ecotypes of the morphospecies K. veneficum. This knowledge together with the first estimate of td for K. veneficum will be useful in future field studies aimed at correlating bloom toxicity with in situ growth rate using the mitotic index technique.

Environmental correlates of adaptive diversification in postglacial freshwater fishes.

Determining how environmental conditions contribute to divergence among populations and drive speciation is fundamental to resolving mechanisms and understanding outcomes in evolutionary biology. Postglacial freshwater fish species in the Northern Hemisphere are ideal biological systems to explore the effects of environment on diversification in morphology, ecology, and genetics (ecomorph divergences) within lakes. To date, various environmental factors have been implicated in the presence of multiple ecomorphs within particular lakes or regions. However, concerted evidence for generalizable patterns in environmental variables associated with speciation across geographical regions and across species and genera has been lacking. Here, we aimed to identify key biotic and abiotic factors associated with ecological divergence of postglacial freshwater fish species into multiple sympatric ecomorphs, focusing on species in the well-studied, widespread, and co-distributed genera Gasterosteus, Salvelinus, and Coregonus (stickleback, charr, and whitefish, respectively). We found that the presence of multiple sympatric ecomorphs tended to be associated with increasing lake surface area, maximum depth, and nutrient availability. In addition, predation, competition, and prey availability were suggested to play a role in divergence into multiple ecomorphs, but the effects of biotic factors require further study. Although we identified several environmental factors correlated with the presence of multiple ecomorphs, there were substantial data gaps across species and regions. An improved understanding of these systems may provide insight into both generalizable environmental factors involved in speciation in other systems, and potential ecological and evolutionary responses of species complexes when these variables are altered by environmental change.

Exploring the influence of host community composition on the outbreak potential of Anaplasma phagocytophilum and Borrelia burgdorferi s.l.

In large parts of the northern hemisphere, multiple deer species coexist, and management actions can strongly influence wild deer communities. Such changes may also indirectly influence other species in the community, such as small mammals and birds, because deer can have strong effects on their habitats and resources. Deer, small mammals and birds play an important role in the dynamics of tick-borne zoonotic diseases. It is, however, relatively underexplored how the abundance and composition of vertebrate communities may affect the outbreak potential, maintenance and circulation of tick-borne pathogens. In this study we focus on the outbreak potential by exploring how the basic reproduction number R0 for different tick-borne pathogens depends on host community composition. We used published data on co-varying roe deer (Capreolus capreolus) and fallow deer (Dama dama) densities following a hunting ban, and different small mammal and bird densities, to investigate how the change in host community influences the R0 of four tick-borne pathogens: one non-zoonotic, namely Anaplasma phagocytophilum ecotype 2, and three zoonotic, namely A. phagocytophilum ecotype 1, Borrelia afzelii and Borrelia garinii. We calculated R0 using a next generation matrix approach, and used elasticities to quantify the contributions to R0 of the different groups of host species. The value of R0 for A. phagocytophilum ecotype 1 was higher with high fallow deer density and low roe deer density, while it was the other way round for A. phagocytophilum ecotype 2. For B. afzelii, R0 was mostly related to the density of small mammals and for B. garinii it was mostly determined by bird density. Our results show that the effect of species composition is substantial in the outbreak potential of tick-borne pathogens. This implies that also management actions that change this composition, can (indirectly and unintentionally) affect the outbreak potential of tick-borne diseases.

Genetic variation and response to selection of photosynthetic and forage characteristics in Kentucky bluegrass (Poa pratensis L.) ecotypes under drought conditions.

Introduction: Evaluation of the effects of water-limited conditions on the photosynthetic characteristics and forage yield is important for enhancing the forage productivity and drought tolerance in Kentucky bluegrass (Poa pratensis L.). Methods: In the present study, 100 P. pratensis ecotypes collected from different geographical areas in Iran were assessed under well-watered and drought stress conditions. Genetic variation and response to selection for the photosynthetic characteristics [i.e., net photosynthesis rate (A), stomatal conductance (gs), transpiration rate (Tr), chlorophyll content (Chl), and photochemical efficiency (Fv/Fm)] and forage yield [fresh forage yield (FY) and dry forage yield (Dy)] traits were analyzed during the 2018 and 2019 growing seasons. Results and discussion: Drought stress had negative effects on evaluated photosynthesis parameters and significantly reduced dry and fresh forage yields. On average, FY with a 45% decrease and gs with a 326% decrease under drought stress conditions showed the highest reduction rate among forage yield and photosynthesis traits, respectively. Genotypic coefficients of variation (GCV) for FY were lower under drought stress. The estimates of heritability, genetic advance, and genetic advance as percentage of mean showed the predominance of additive gene action for the traits. Overall, the results showed that "Ciakhor", "Damavand", "Karvandan", "Basmenj", "Abr2", "Abrumand", "Borhan", "Hezarkanian", "LasemCheshmeh", "Torshab", and "DoSar" have higher forage yield production with little change between two irrigation regimes, which makes them promising candidates for developing high-yielding drought-tolerant varieties through breeding programs.

Tidal gradients, fine-scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha).

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.

Effects of cadmium and pyrene on earthworm-associated bacterial communities: Unveiling new perspectives for soil pollution management.

Earthworms are considered to be excellent bioindicators of soil pollution. In recent years, there has been increasing interest in examining the effects of soil pollution on earthworm-associated microbiomes, with a particular focus on the gut microbiomes. However, relatively little effort has been invested in comprehensively investigating other microbiomes associated with earthworms and their responses to soil pollution. To fill this gap, we systematically studied the effects of Cd, pyrene, and combined pollution on the bacterial community in different vermicompartments, i.e., burrow wall, gut, and cast, in both epigeic Eisenia fetida and anecic Metaphire guillelmi, using a 2D-terraria incubator and high-throughput sequencing techniques. The results showed that bacterial alpha diversity followed the order of burrow wall > cast > gut, and this did not vary with soil pollution or earthworm ecotypes. Moreover, the dominant phyla in the vermicompartments were similar across different pollution treatments. Principal coordinate analysis (PCoA) revealed that the bacterial communities in different vermicompartments and ecotypes of earthworm were separated from each other, whereas they were grouped together in polluted treatments and unpolluted conditions. These results imply that even in polluted soil, vermicompartment and earthworm ecotypes remain the most significant factors affecting earthworm-associated microbiomes. However, the impacts of soil pollution on the bacterial composition in each vermicompartment were still evident. A comprehensive analysis revealed that the gut bacterial communities are more sensitive to soil contamination than casts and burrow wall in different ecotypes. Additionally, linear discriminant analysis of effect size (LefSe) identified several bacteria in Gemmatimonadota, the Firmicutes phylum in the burrow walls, and Patescibacteria (phyla) in the gut as potential biomarkers for pyrene contamination in soil. This research provides a comprehensive understanding of the effects of soil pollution on earthworm-associated microbiomes, thereby enhancing our understanding of earthworm ecotoxicology and soil pollution management.

Environmental Adaptation of Psychrophilic Bacteria Subtercola spp. Isolated from Various Cryospheric Habitats.

Subtercola boreus K300T is a novel psychrophilic strain that was isolated from permanently cold groundwater in Finland and has also been found in several places in Antarctica including lake, soil, and rocks. We performed genomic and transcriptomic analyses of 5 strains from Antarctica and a type strain to understand their adaptation to different environments. Interestingly, the isolates from rocks showed a low growth rate and smaller genome size than strains from the other isolation sources (lake, soil, and groundwater). Based on these habitat-dependent characteristics, the strains could be classified into two ecotypes, which showed differences in energy production, signal transduction, and transcription in the clusters of orthologous groups of proteins (COGs) functional category. In addition, expression pattern changes revealed differences in metabolic processes, including uric acid metabolism, DNA repair, major facilitator superfamily (MFS) transporters, and xylose degradation, depending on the nutritional status of their habitats. These findings provide crucial insights into the environmental adaptation of bacteria, highlighting genetic diversity and regulatory mechanisms that enable them to thrive in the cryosphere.

Evolution of immune and stromal cell states and ecotypes during gastric adenocarcinoma progression.

Understanding tumor microenvironment (TME) reprogramming in gastric adenocarcinoma (GAC) progression may uncover novel therapeutic targets. Here, we performed single-cell profiling of precancerous lesions, localized and metastatic GACs, identifying alterations in TME cell states and compositions as GAC progresses. Abundant IgA+ plasma cells exist in the premalignant microenvironment, whereas immunosuppressive myeloid and stromal subsets dominate late-stage GACs. We identified six TME ecotypes (EC1-6). EC1 is exclusive to blood, while EC4, EC5, and EC2 are highly enriched in uninvolved tissues, premalignant lesions, and metastases, respectively. EC3 and EC6, two distinct ecotypes in primary GACs, associate with histopathological and genomic characteristics, and survival outcomes. Extensive stromal remodeling occurs in GAC progression. High SDC2 expression in cancer-associated fibroblasts (CAFs) is linked to aggressive phenotypes and poor survival, and SDC2 overexpression in CAFs contributes to tumor growth. Our study provides a high-resolution GAC TME atlas and underscores potential targets for further investigation.

Soil water stress alters differentially relative metabolic pathways affecting growth performance and metal uptake efficiency in a cadmium hyperaccumulator ecotype of Sedum alfredii.

Modeling plants for biomass production and metal uptake from surrounding environment is strongly dependent on the moisture content of soil. Therefore, experiments were conducted to find out how soil moisture affects the phenotypic traits, photosynthetic efficiency, metabolic profile, and metal accumulation in the hyperaccumulating ecotype of Sedum alfredii (S. alfredii). A total of six water potential gradients were set: 0 ~ -15 kPa (T1), -15 ~ -30 kPa (T2), -30 ~ -45 kPa (T3), -45 ~ -60 kPa (T4), -60 ~ -75 kPa (T5), and -75 ~ -90 kPa (T6). Different water potential treatments had a significant effect on plant growth and metal uptake efficiency. Compared to T3, T2 was more effective in promoting plant growth and development, with an increase in biomass of 23% and 17% in both fresh weight (FW) and dry weight (DW), respectively. T2 and T3 had the highest cadmium (Cd) content in the shoot (280.2 mg/kg) and (283.3 mg/kg), respectively, whereas T1 had the lowest values (204.7 mg/kg). Cd availability for plants in the soil was affected by moving soil moisture cycles. Changes in soil moisture that were either too high or too low compared to the ideal soil water content for S. alfredii growth resulted in a significant reduction in Cd accumulation in shoots. Tryptophan, phenylalanine, and other amino acids were accumulated in T5, whereas only tryptophan and phenylalanine slightly increased in T1. Sugars and alcohols such as sucrose, trehalose, mannitol, galactinol, and mannobiose increased in T5, while they decreased significantly in T1. Interestingly, in contrast to T1, the two impaired metabolic pathways in T5 (galactose and starch metabolism) were identified to be glucose metabolic pathways. These findings provide scientific information (based on experiments) to improve biomass production and metal uptake efficiency in hyperaccumulating ecotype of S. alfredii for phytoremediation-contaminated agricultural fields.

Integrating Pool-seq uncertainties into demographic inference.

Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.