Search Results (2,224)

Multipartite genomes are thought to confer evolutionary advantages to bacteria by providing greater metabolic flexibility in fluctuating environments and enabling rapid adaptation to new ecological niches and stress conditions. This genome architecture is commonly found in plant symbionts, including nitrogen-fixing rhizobia, such as Rhizobium leguminosarum bv. trifolii TA1 (RtTA1), whose genome comprises a chromosome and four extrachromosomal replicons (ECRs). In this study, the transcriptomic responses of RtTA1 to partial nutrient limitation and low acidic pH were analyzed using high-throughput RNA sequencing. RtTA1 growth under these conditions resulted in the differential expression of 1035 to 1700 genes (DEGs), which were assigned to functional categories primarily related to amino acid and carbohydrate metabolism, ribosome and cell envelope biogenesis, signal transduction, and transcription. These results highlight the complexity of the bacterial response to stress. Notably, the distribution of DEGs among the replicons indicated that ECRs played a significant role in the stress response. The transcriptomic data align with the Rhizobium pangenome analysis, which revealed an over-representation of functional categories related to transport, metabolism, and regulatory functions on ECRs. These findings confirm that ECRs contribute substantially to the ability of rhizobia to adapt to challenging environmental conditions. Full article

Davidia involucrata has an ancient origin, representing a remnant from the paleotropical flora that thrived during the Tertiary period. Altitudinal gradient acts as a natural testing ground for studying climate change, and research on the distribution patterns of microorganisms along altitudinal gradients is crucial in understanding the adaptability of D. involucrata to climate change. In our study, we examined sample sites ranging from 1600 to 2200 m in elevation, which are part of the primary habitat zone for Davidia involucrata within the Xuebaoding National Nature Reserve. In 2021, field surveys were conducted across four altitudinal gradients (1600 m, 1800 m, 2000 m and 2200 m) of the D. involucrata distribution in the nature reserve. The sampling plots were set in each altitudinal gradient, and three representative and healthy mature trees were selected as sample trees for each plot. Rhizosphere soils were used to test the soil stoichiometry characteristics and root zone microbial communities. Our findings indicated pronounced differences in soil total carbon (TC) and total phosphorus (TP) content and C:P and N:P ratios between the four altitude sites (p < 0.05). Analysis of the bacterial communities revealed higher richness (PD and Chao1 indexes) at ASL2000 and ASL2200 (high altitude) compared to ASL1600 and ASL2000 (low altitude) (p < 0.05). Non-metric multidimensional scaling analysis demonstrated a distinct clustering of bacterial communities between the high and low altitudes (p < 0.01). At the phylum level, Proteobacteria and Acidobacteria were predominant at high altitudes, while Actinobacteria and Chloroflexi dominated at low altitudes. The core microbiome, shared among all altitudes, comprised 377 genes. The analysis of differential abundance revealed notable disparities in the prevalence of certain bacterial genera with altitude, with Arthrobacter and Acidothermus experiencing the most pronounced shifts (p < 0.05). This confirmed that environmental factors significantly influenced bacterial community structure and abundance. Spearman’s rank correlations revealed that both Chao1 and PD indices were positively correlated with elevation, TC, and TN, with Chao1 showing stronger relationships. Both indices were negatively correlated with MAT, while only Chao1 exhibited a significant negative correlation with pH. Linear regression analysis further confirmed the significant associations between Chao1 index and elevation, TN, MAT, and pH. Furthermore, redundancy analysis demonstrated that altitude (ASL) and TN were the primary factors shaping soil bacterial community composition, explaining 21.32% and 30.70% of the variance, respectively. Altitude significantly influenced microbial community structure (p = 0.003). Distinct microbial taxa showed specific associations with environmental gradients, suggesting niche specialization in response to soil conditions. These findings suggest that altitude influences soil nutrient characteristics and microbial community composition in the D. involucrata habitat, offering insights into the ecological factors affecting this endangered species. Full article

Organic farming encourages soil management practices that can improve soil health and fertility by increasing soil organic matter inputs and system sustainability. This study evaluated the effect of three years of continuous organic farming and intercropping orchard treatments on soil microbial diversity, microbial enumeration, respiration, soil fertility and fruit yields. Organic management resulted in higher soil organic matter content, Olsen P, and water holding capacity, but did not affect soil pH, electrical conductivity (EC), K, or Na levels. Growth parameters measured on all fruit trees were not significantly different among treatments. The enumeration of bacteria was significantly higher in organic plots when compared to conventionally managed plots. Soil respiration and substrate-induced respiration were significantly higher in the organic diverse plots in comparison to both conventional systems. The genomic analysis of prokaryotes (16S rRNA) and eukaryotes/fungi (ITS) revealed a significantly higher number of taxa, Shannon H index, and Equitability index in the organic systems for both prokaryotes and eukaryotes, in comparison to conventional farming, all of which are indicators of system sustainability. The relative abundance of Operational Taxonomic Units (OTUs) previously reported as diazotrophs, denitrifiers, or involved in the sulfur cycle, as well as Arbuscular Mychorrizae Fungi (AMF)/glomeromycotan, were highest in the organically managed soils than in the conventional plots. A multivariate correlation network clustering revealed that the microbial communities within the organic and conventional soils had strong dissimilarities regarding soil microbial niches. Our work provides evidence that organic management can be used for increasing soil microbial diversity and soil health, leading to higher levels of sustainability in fruit orchard systems. Full article

Background: Lactiplantibacillus plantarum is a species found in a wide range of ecological niches, including vegetables and dairy products, and it may occur naturally in the human gastrointestinal tract. The precise mechanisms underlying the beneficial properties of these microbes to their host remain obscure. Although Lactic acid bacteria are generally regarded as safe, there are rare cases of the emergence of infections and antibiotic resistance by certain probiotics. Objective: An in silico whole genome sequence analysis of putative probiotic bacteria was set up to identify strains, predict desirable functional properties, and identify potentially detrimental antibiotic resistance and virulence genes. Methods: We characterized the genomes of three L. plantarum strains (54B, 54C, and 55A) isolated from Ethiopian traditional cottage cheese. Whole-genome sequencing was performed using Illumina MiSeq sequencing. The completeness and quality of the genome of L. plantarum strains were assessed through CheckM. Results: Analyses results showed that L. plantarum 54B and 54C are closely related but different strains. The genomes studied did not harbor resistance and virulence factors. They had five classes of carbohydrate-active enzymes with several important functions. Cyclic lactone autoinducer, terpenes, Type III polyketide synthases, ribosomally synthesized and post-translationally modified peptides-like gene clusters, sactipeptides, and all genes required for riboflavin biosynthesis were identified, evidencing their promising probiotic properties. Six bacteriocin-like structures encoding genes were found in the genome of L. plantarum 55A. Conclusions: The lack of resistome and virulome and their previous functional capabilities suggest the potential applicability of these strains in food industries as bio-preservatives and in the prevention and/or treatment of infectious diseases. The results also provide insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates. Full article

Developing high-efficiency mixed forests or converting low-efficiency pure forests into near-natural mixed forests with optimal structure and function is a crucial aspect of forest management. In the initial stages of afforestation or stand improvement, fertilization and planting distance significantly influence the formation and development of mixed forests. This study investigated how nutrients and planting distance affect root competition between five-year-old Chinese pine (Pinus tabuliformis) and one-year-old Chinese white poplar (Populus tomentosa) and identified the factors influencing the competitive ability of these two species. Field planting experiments used three fertilization gradients (63 g·m⁻², 125 g·m⁻², and 250 g·m⁻²) of Stanley compound fertilizer with an N:P:K ratio of 2:1:1 and two planting distances (25 cm and 50 cm). Each experimental group was planted in circular plots with a radius of 0.5 m, yielding a total of nine plots. The effects of different fertilization concentrations and planting distances on root distribution were analyzed both horizontally and vertically. Pearson correlation analysis was used to assess the relationship between roots and soil nutrients, while Levins’ niche overlap formula evaluated the differences in root competition between the species. Furthermore, principal component analysis quantified the relationships between impact factors and the root competitiveness of the two species. Results indicated that both species primarily allocated their fine root biomass to the shallow 0–10 cm layer. Pinus tabuliformis primarily extended to the southwest, while Populus tomentosa predominantly grew to the north. Both species exhibited enhanced root growth at moderate nutrient concentrations of 125 g·m⁻². At a planting distance of 50 cm from Pinus tabuliformis, Populus tomentosa seedlings demonstrated superior root growth compared to those planted 25 cm apart. Pinus tabuliformis demonstrated greater competitive ability in the deeper 10–30 cm soil layers compared to Populus tomentosa, which showed the opposite pattern in the shallow 0–10 cm layers. Furthermore, available phosphorus (contribution rate of one impact factor on the competitiveness indexes, CR: −0.998), organic matter (CR: −0.978), total nitrogen (CR: −0.947), and alkali-hydrolysable nitrogen (CR: −0.937) significantly negatively impacted the competitiveness indexes of Pinus tabuliformis. The fine root surface area, volume, and length of Populus tomentosa also significantly negatively affected its competitiveness indexes, with all contribution rates exceeding an absolute value of 0.847. Results indicated that the root distributions of Pinus tabuliformis and Populus tomentosa overlapped spatially, with each species exhibiting advantages in different regions. Therefore, in future plantation reconstruction and forest management, it is essential to thoroughly evaluate root, soil, and fertilizer factors, adjusting planting distances accordingly, to effectively mitigate competition between the two species and successfully establish a mixed forest. Full article

Understanding how climate change influences the geographical distribution of species within an ecological niche is essential for predicting habitat shifts and informing conservation efforts. This study evaluates the impact of climate change on habitat suitability and ecological connectivity of wych elm (Ulmus glabra Huds.) in Türkiye. The study explores the future distribution of U. glabra and how its connectivity is affected by habitat fragmentation arising from changing climatic conditions. Contextually, this paper aims to achieve two primary objectives: estimating the potential geographical ranges of U. glabra under different climate scenarios and assessing alterations in ecological connections between current and future habitats. The maximum entropy (MaxEnt) model was used along with Morphological Spatial Pattern Analysis (MSPA), and the Probability of Connectivity (PC) index was applied to show possible transformations in distribution patterns of U. glabra over time. The findings suggest that there will be a reduction in the suitability of locations for the species. Moreover, it is expected that under future climate scenarios, ecological connectivity will decline, especially from 2061 to 2100 in the SSP585 scenario. Notably, significant alterations are anticipated during the latter half of the twenty-first century, mainly outside the coastal areas of the Black Sea, where extensive regions would become unsuitable. Additionally, the species is projected to shift its range, decreasing its presence in inland regions while expanding along the coasts. The results show the vulnerability of this species against climate change, thereby demanding adaptive conservation measures to preserve it within the forest ecosystems of Türkiye. Full article

Marine biodiversity is increasingly threatened by overfishing and marine pollution. A comprehensive understanding of the biodiversity in the Yellow and Bohai Seas is essential for resource conservation. This study conducted a large-scale survey of fishery resources in the Yellow and Bohai Seas to investigate fish community structure and diversity using eDNA technology. The results showed that 57 and 65 fish species were recorded in spring and summer, respectively, with 46 species identified in both seasons. A total of nine dominant species were identified in spring, mainly belonging to Perciformes, while seven dominant species were identified in summer, primarily from Clupeiformes. In different regions, no significant differences in fish α diversity were observed between spring and summer. However, significant seasonal differences were found in both α and β diversity. At the spatial level, fish species in the Yellow and Bohai Seas occupied similar ecological niches. However, at the temporal level, there are certain differences in the ecological niches of fish communities between seasons. Phylogenetic diversity showed no significant differences at the spatial scale, yet notable seasonal variations were observed at the temporal scale, with spring (661.46) significantly exceeding summer (540.30). The Mantel test indicated that nitrate and salinity were key environmental factors influencing α diversity. RDA analysis revealed that the dominant species in spring were mainly influenced by chlorophyll-a and water temperature, while those in summer were mainly affected by water depth, nitrite, water temperature, and salinity. Full article

Mangrove restoration efforts have increased in order to help combat their decline globally. While restoration efforts often focus on planting seedlings, underlying chronic issues, including disrupted hydrological regimes, can hinder restoration success. While improving hydrology may be more cost-effective and have higher success rates than planting seedlings alone, hydrological restoration success in this form is poorly understood. Restoration assessments can employ a functional equivalency approach, comparing restoration areas over time with natural, reference forests in order to quantify the relative effectiveness of different restoration approaches. Here, we employ the use of baseline community ecology metrics along with stable isotopes to track changes in the community and trophic structure and enable time estimates for establishing mangrove functional equivalency. We examined a mangrove system impacted by road construction and recently targeted for hydrological restoration within the Rookery Bay National Estuarine Research Reserve, Florida, USA. Samples were collected along a gradient of degradation, from a heavily degraded zone, with mostly dead trees, to a transition zone, with a high number of saplings, to a full canopy zone, with mature trees, and into a reference zone with dense, mature mangrove trees. The transition, full canopy, and reference zones were dominated by annelids, gastropods, isopods, and fiddler crabs. Diversity was lower in the dead zone; these taxa were enriched in ¹³C relative to those found in all the other zones, indicating a shift in the dominant carbon source from mangrove detritus (reference zone) to algae (dead zone). Community-wide isotope niche metrics also distinguished zones, likely reflecting dominant primary food resources (baseline organic matter) present. Our results suggest that stable isotope niche metrics provide a useful tool for tracking mangrove degradation gradients. These baseline data provide critical information on the ecosystem functioning in mangrove habitats following hydrological restoration. Full article

There are hereditary mutations that predispose individuals to cancer development, such as pathogenic variants in the germ line of the tumor protein 53 (TP53) suppressor gene. This leads to a rare condition known as Li–Fraumeni syndrome (LFS), characterized by a high risk of developing multiple cancers throughout life by the precancerous niche that promotes the tumor microenvironment. LFS presents a significant challenge due to its limited therapeutic and chemoprophylactic options. Recently, protocols involving metformin as a prophylactic medication have been developed to target precancerous niches. However, this approach is still in the clinical phase, and no established therapeutic regimen is available. Therefore, new alternatives are needed to impact this disease effectively. Novel studies suggest that Sechium extract, rich in polyphenols, exhibits chemoprophylactic, antineoplastic, anti-inflammatory, and antioxidant activities, all involved in the tumor microenvironment of LFS. However, the specific role of Sechium extract in preventing recurrent neoplastic development in LFS remains unclear. We conducted this research through a case report of an LFS-diagnosed patient who has experienced multiple malignancies and cutaneous neoformations. This patient received a chemoprophylactic supplementation based on Sechium H387 07 extract over 11 years without reporting new primary malignancy events or recurrences, as evidenced by laboratory and positron emission tomography/computed tomography (PET/CT) studies. An extensive literature review on the disease, precancerous niche, tumor microenvironment, and potential mechanisms of Sechium H387 07 extract components was conducted to explain cancer absence in LFS. This review promotes the research and use of polyphenols as powerful chemoprophylactic agents to prevent and treat proliferative diseases like LFS. Full article

This article describes our point of view regarding the security capabilities of classical learning algorithms (CLAs) and quantum mechanisms (QM) in the industrial Internet of Things (IIoT) ecosystem. The heterogeneity of the IIoT ecosystem and the inevitability of the security paradigm necessitate a systematic review of the contributions of the research community toward IIoT security (IIoTsec). Thus, we obtained relevant contributions from five digital repositories between the period of 2015 and 2024 inclusively, in line with the established systematic literature review procedure. In the main part, we analyze a variety of security loopholes in the IIoT and categorize them into two categories—architectural design and multifaceted connectivity. Then, we discuss security-deploying technologies, CLAs, blockchain, and QM, owing to their contributions to IIoTsec and the security challenges of the main loopholes. We also describe how quantum-inclined attacks are computationally challenging to CLAs, for which QM is very promising. In addition, we present available IIoT-centric datasets and encourage researchers in the IIoT niche to validate the models using the industrial-featured datasets for better accuracy, prediction, and decision-making. In addition, we show how hybrid quantum-classical learning could leverage optimal IIoTsec when deployed. We conclude with the possible limitations, challenges, and prospects of the deployment. Full article

The gut microbiome emerges as an integral component of precision medicine because of its signature variability among individuals and its plasticity, which enables personalized therapeutic interventions, especially when integrated with other multiomics data. This promise is further fueled by advances in next-generation sequencing and metabolomics, which allow in-depth high-precision profiling of microbiome communities, their genetic contents, and secreted chemistry. This knowledge has advanced our understanding of our microbial partners, their interaction with cellular targets, and their implication in human conditions such as inflammatory bowel disease (IBD). This explosion of microbiome data inspired the development of next-generation therapeutics for treating IBD that depend on manipulating the gut microbiome by diet modulation or using live products as therapeutics. The current landscape of artificial microbiome therapeutics is not limited to probiotics and fecal transplants but has expanded to include community consortia, engineered probiotics, and defined metabolites, bypassing several limitations that hindered rapid progress in this field such as safety and regulatory issues. More integrated research will reveal new therapeutic targets such as enzymes or receptors mediating interactions between microbiota-secreted molecules that drive or modulate diseases. With the shift toward precision medicine and the enhanced integration of host genetics and polymorphism in treatment regimes, the following key questions emerge: How can we effectively implement microbiomics to further personalize the treatment of diseases like IBD, leveraging proven and validated microbiome links? Can we modulate the microbiome to manage IBD by altering the host immune response? In this review, we discuss recent advances in understanding the mechanism underpinning the role of gut microbes in driving or preventing IBD. We highlight developed targeted approaches to reverse dysbiosis through precision editing of the microbiome. We analyze limitations and opportunities while defining the specific clinical niche for this innovative therapeutic modality for the treatment, prevention, and diagnosis of IBD and its potential implication in precision medicine. Full article

In this paper, we present a two-phase multimodal optimization model designed to efficiently and accurately identify multiple optima. The first phase employs a population-based search algorithm to locate potential optima, while the second phase introduces a novel peak identification (PI) procedure to filter out non-optimal solutions, ensuring that each identified solution represents a distinct optimum. This approach not only enhances the effectiveness of multimodal optimization but also addresses the issue of redundant solutions prevalent in existing algorithms. We propose two PI algorithms: HVPI, which uses a hill–valley approach to distinguish between optima, without requiring prior knowledge of niche radii; and HVPIC, which integrates HVPI with bisecting K-means clustering to reduce the number of fitness evaluations (FEs). The performance of these algorithms was evaluated using the F-measure, a comprehensive metric that accounts for both the accuracy and redundancy in the solution set. Extensive experiments on a suite of benchmark functions and engineering problems demonstrated that our proposed algorithms achieved a high precision and recall, significantly outperforming traditional methods. Full article

Doñana (southern Spain), a region of notable biodiversity richness, is highly threatened by ongoing landscape transformation and climate change. We investigated the local effect of these anthropogenic factors on the temporal range dynamics of Lataste’s viper (Vipera latastei), an Iberian endemic Mediterranean reptile that has apparently become rare over the years in Doñana. Using ecological niche-based models, based on climatic and remote sensing variables, we analyzed historical (1959–1999) and contemporary (2000–2022) records of the species to assess range shifts and identify environmental factors that may influence them. Our results show that V. latastei is mostly restricted to the coastal region of Doñana and that one temperature variable is the most important factor explaining this distribution pattern in both periods. Additional climatic and vegetation variables play a role in its historical distribution, but they become less important in contemporary times, suggesting a niche simplification over time. We found 30.5% of reduction in the species suitable area from historical to contemporary conditions, a reduction that would be even greater (83.37%) in the absence of niche shift. These findings underscore the species’ heightened vulnerability to ongoing environmental changes and highlight the urgent need for targeted conservation strategies. Full article

Rainbow trout, or mykiss (Oncorhynchus mykiss), is one of the most popular species used in aquaculture and has been naturalized worldwide, including in the Central Asian Balkhash basin, which has unique aboriginal fish fauna. Both rainbow trout from European farms and wild mykiss from Kamchatka were introduced to some mountain lakes and rivers of the Balkhash basin about 50 years ago. This study investigates the current distribution and life history traits of the alien species and its possible impact on the local fish fauna. This study showed that the rainbow trout occupies various habitats in the Ili River basin: mountain lakes, fast-flowing mountain rivers, and lowland rivers with slow currents and warm water (up to +27 °C). Rainbow trout from European fish farms dominate the mountain Middle Kolsay Lake, while the wild trout from Kamchatka occupies the small Ulken Kokpak River. Both co-occur in the Chilik River. Contrary to that in other regions, the distribution of rainbow trout in the Balkhash basin remained almost the same after their introduction. Broad intrapopulation variability in terms of size, growth rate, and maturation age was revealed, apparently as a result of adaptation to the new environment and intrapopulation competition. In particular, the growth rate has decreased, but life span, surprisingly, has increased as compared to the originally introduced fish. Intrapopulation variation in growth and maturity patterns was also noted. Differences in skin coloration between highland (cold-water) and lowland (warm-water) populations were discovered. The feeding mode of naturalized trout is insectivorous (insect imago), indicating that it occupies its own niche in the local fish communities. The largest population of rainbow trout was recorded in the Lower Kolsay Lake, lowering the population of native fish species, while in other localities, no negative impact on local fish communities was recorded. Full article

Recently, there has been significant consumer demand for traditional tomato varieties due to their favourable organoleptic qualities; however, the cultivation of these ancient varieties is becoming more restricted due to inadequate shelf life and low productivity. The “Pisanello” is a Tuscany tomato variety mainly cultivated in the provinces of Pisa, Lucca, and Livorno, and the main producers of this ancient tomato are small local farmers. The purpose of this work was, firstly, to study the range of quality parameters of this landrace tomato grown using different cultivation techniques, both in soil and soilless systems. For this purpose, the physicochemical parameters of Pisanello tomatoes grown in six different farms in Tuscany using both soilless and soil methods were investigated. Secondly, Pisanello tomatoes grown using different soilless techniques (rockwool and aeroponics) and soil-grown tomatoes (Pisanello and Goldmar F1) were evaluated from organoleptic and nutraceutical points of view. The sensory profile evaluation of all types of tomatoes under investigation was carried out. The aeroponic cultivation of Pisanello induced higher organoleptic qualities than those of tomatoes cultivated in rockwool (+34% for titratable acidity and +18% for total soluble solids). On the other hand, soilless rockwool-grown tomatoes showed a better sensory profile with respect to aeroponic cultivation. Nevertheless, the Goldmar F1 tomato, morphologically similar to ‘Pisanello’, received lower scores from the sensory panel compared to the Tuscany landrace tomato. This indicates that ancient tomato varieties selected over decades remain the preferred choice for consumers. Therefore, from a long-term viewpoint, the valorisation of local tomato varieties such as Pisanello can promote the regional commercialization of novel niche products originating from ancient fruit thanks to their acceptability by consumers. Full article