Search Results (10)

Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article

The soil microbiota is a key component of agroecosystems, and understanding its traits is crucial for effective agronomic management. Among beneficial microorganisms, arbuscular mycorrhizal fungi (AMFs) are mutually associated with grapevine (Vitis vinifera L.), enhancing the ability of this cropping system to adapt to soil conditions and bolstering its resistance and resilience against abiotic stresses, particularly drought, by promoting root growth and enhancing the roots’ absorption surface. The objective of this on-field study was to determine AMF species richness and diversity along with their relation to soil chemical, physical, and biological characteristics in two adjacent organic vineyards in Central Italy. The two tested vineyards of the autochthonous cv. Aleatico differed by the presence of grafted (Vitis berlandieri × V. riparia rootstock; AL-420) or own-rooted (ungrafted V. vinifera L.; AL-ORV) vines. To this aim, soil and root samples were collected and geo-referenced. Analysis of the AMF species colonizing roots of both AL-ORV and AL-420 revealed the presence of four species: Scutellospora alterata, Paraglomus laccatum, Acaulospora laevis, and A. baetica, with S. alterata being the most frequent. Mycorrhization parameters were higher in the roots of grafted plants compared to ungrafted ones. A high beta-glucosidase (BG):N-acetylglusosaminidase (NAG) ratio in two tested vineyards indicated that microbes utilized more cellulose than chitin and peptidoglycan as dominant C resources. A negative correlation between mycorrhization rate (MyCP) and BG was observed, likely because AMFs form mutualistic relationships with plants, depending on the host plant for carbon. Results revealed a positive correlation between the degree of mycorrhizal association and the species involved, with the presence of copper and nickel among metals. Negative correlations were found concerning soil clay content along with beta-glucosidase. In conclusion, the grapevine root system was characterized by a differential symbiotic relationship with AMF species, whose development is influenced by the root genotype, soil texture, and biochemistry. Specifically, the increased frequency of AMFs in relation to copper content strengthens the evidence of their role in maintaining a vine’s production capacity in the event of soil contamination by this element. Full article

Aeschynomene indica rhizobia (AIRs) are special classes of bacteria capable of nodulating without nodulation factors and have photosynthetic capacity. With an aim to characterize the structural variations in Bradyrhizobium genomes during its evolution, the genomes of AIRs and the reference Bradyrhizobium strains were compared utilizing molecular biology, bioinformatics, and biochemistry techniques. The presence of symbiotic nitrogen fixation (nif) genes and photosynthetic genes, as well as components of the T3SS (Type III secretion system) and T3CP (Type III chaperone) in the genome of AIRs, was also assessed. Additionally, the origin, evolutionary history, and genes associated with the NF-independent nodulation pattern in AIRs were explored. The results indicate that horizontal gene transfer events have occurred in AIRs, and three distinct origins of AIRs were estimated: early differentiated AIRs, non-symbiotic Bradyrhizobium, and non-AIRs. In contrast to the significant genetic transformations observed in the second and third groups, the first group of AIRs displays a rich evolutionary history, exhibits high species diversity, and primarily relies on vertical transmission of nitrogen fixation and photosynthetic genes. Overall, the findings provide a fundamental theoretical foundation for gaining a deeper understanding of the phylogeny and genealogy of AIRs. Full article

The arising of the Cyber–Physical Systems’ vision and concepts drives technological evolution toward a new architectural design for the infrastructure of an environment referred to as a Smart Environment. This perspective alters the way systems within Smart City landscapes are conceived, designed, and ultimately realized. Modular architecture, resource-sharing techniques, and precise deployment approaches (such as microservices-oriented or reliant on the FaaS paradigm) serve as the cornerstones of a Smart City cognizant of multiple Cyber–Physical Systems composing it. This paper presents a framework integrating Digital Decisioning, encompassing the automated combination of human-derived knowledge and data-derived knowledge (e.g., business rules and machine learning), to enhance decision-making processes and application definition within the Smart City context. Full article

The use of cold plasma (CP) seed treatment is an emerging agricultural technology that exhibits the potential to enhance nodulation and symbiotic nitrogen fixation (SNF) in legumes. CP is composed of a diverse mixture of excited atoms, molecules, ions, and radicals that have the potential to affect the physical properties of the seed and influence gene expressions that could have a lasting impact on the nodulation, SNF, growth, and yield of legumes. The direct participation of the CP in the nodulation process and its correlation with the escalation of nodules and SNF is still not fully understood. This review discussed four areas in the nodulation and SNF process that can directly or indirectly affect CP seed treatments: root–rhizobia signal exchange pathways, root/shoot growth and development, phytohormone production, and the nitrogen fixation process. We also discuss the potential challenges and future research requirements associated with plasma technology to enhance SNF in legumes. Full article

The ecological indicators for the growth and restoration of A. mongolicus populations are important for grasping the regulatory mechanisms of the biogeochemistry cycle, and for providing basic data for the prediction and evaluation of the evolution characteristics of natural A. mongolicus populations. We conducted studies on the eco-stoichiometric characteristics of natural A. mongolicus in different shrub ages, in order to understand the nutrient limitations for the growth and development of A. mongolicus and the synergy between the soil, leaves and roots, and to explore the C, N and P stoichiometric characteristics on A. mongolicus. The results showed the following: (1) The response of C, N and P stoichiometric characteristics in the leaves, roots and soil to changes in shrub age was not completely consistent. The leaf C content was young shrub> mature shrub> middle age shrub. The C content in the root system and C and N content in the soil showed an upward trend with increasing shrub age. The N and P contents of the root system and the P content of the soil showed a downward trend with increasing shrub age. The stoichiometric ratios C:N, C:P and N:P in the leaves, roots and soil showed an upward trend, and the N:P ratios in the leaves and roots were similar. (2) Among the stoichiometric characteristics of the leaves, C, N and P, leaves P and C:P are the most sensitive to shrub age changes, and have ecological implications for the growth and population dynamics of A. mongolicus. The average N:P ratios of young A. mongolicus leaves in young, middle-aged and mature shrubs were 15.32, 18.23 and 21.76, respectively. It can be seen that with an increase in shrub age, the growth of A. mongolicus gradually shifted from being jointly restricted by N and P to being more restricted by P. (3) The N content and the C∶N and N∶P ratios of A. mongolicus are classified as “strictly homoeostasis “, which shows strong plant homoeostasis for environmental adaptability. The N supplemented by symbiotic nitrogen fixation makes A. mongolicus have strong N internal homoeostasis. Therefore, in a desert grassland with low N content, the growth process of A. mongolicus may be easily restricted by P due to the additional N absorbed by it. (4) The C, N and P contents of the leaves, roots and soils of the three shrubs were shown as leaf > root > soil, and the difference was significant (p < 0.05). The correlation analysis showed that the C, N and P contents of the soil, roots and leaves and their stoichiometric ratio characteristics of the three shrubs showed a certain correlation. Among them, the P content of the soil was significantly related to the N:P ratio of the leaves and roots. Therefore, P is likely to become a limiting factor in the plant growth and repair process of the plant ecosystem in the A. mongolicus population. In summary, during the growth of A. mongolicus, special attention should be paid to the balance of nutrients. In order to improve its productivity, it is recommended to reasonably apply P fertilizers in the process of tending management to enhance the soil nutrient status and improve plant nutrient utilization efficiency and homoeostasis. Full article

A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO₂ levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO₂ levels in N₂-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH₄⁺. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles’ pH to prevent the escape of NH₃ and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages. Full article

The fermentation of leaf vegetable waste to produce animal feed reduces the environmental impact of vegetable production and transforms leaf vegetable waste into a commodity. We investigated the effect of exogenous probiotics and lignocellulose enzymes on the quality and microbial community of fermented feed (FF) produced from cabbage waste. The addition of exogenous probiotics resulted in increased crude protein (CP) content (p < 0.05), better odor (moderate organic acid and ethanol, with low ammonia-N, p < 0.05), and a lower relative abundance (RA) of pathogens (below 0.4%, p < 0.05) in FF, compared to without. With the addition of exogenous probiotics, only Pediococcus and Saccharomyces were enriched and symbiotic in FF; these were the keystone taxa to reduce the abundance of aerobic, form-biofilms, and pathogenic microorganisms, resulting in an efficient anaerobic fermentation system characterized by facultative anaerobic and Gram-positive bacterial communities, and undefined saprotroph fungal communities. Thus, inoculation of vegetable waste fermentation with exogenous probiotics is a promising strategy to enhance the biotransformation of vegetable waste into animal feed. Full article

Foodborne pathogens are a major concern for public health. We demonstrate for the first time a partially automated sensing system for rapid (~17 min), label-free impedimetric detection of Escherichia coli spp. in food samples (vegetable broth) and hydroponic media (aeroponic lettuce system) based on temperature-responsive poly(N-isopropylacrylamide) (PNIPAAm) nanobrushes. This proof of concept (PoC) for the Sense-Analyze-Respond-Actuate (SARA) paradigm uses a biomimetic nanostructure that is analyzed and actuated with a smartphone. The bio-inspired soft material and sensing mechanism is inspired by binary symbiotic systems found in nature, where low concentrations of bacteria are captured from complex matrices by brush actuation driven by concentration gradients at the tissue surface. To mimic this natural actuation system, carbon-metal nanohybrid sensors were fabricated as the transducer layer, and coated with PNIPAAm nanobrushes. The most effective coating and actuation protocol for E. coli detection at various temperatures above/below the critical solution temperature of PNIPAAm was determined using a series of electrochemical experiments. After analyzing nanobrush actuation in stagnant media, we developed a flow through system using a series of pumps that are triggered by electrochemical events at the surface of the biosensor. SARA PoC may be viewed as a cyber-physical system that actuates nanomaterials using smartphone-based electroanalytical testing of samples. This study demonstrates thermal actuation of polymer nanobrushes to detect (sense) bacteria using a cyber-physical systems (CPS) approach. This PoC may catalyze the development of smart sensors capable of actuation at the nanoscale (stimulus-response polymer) and macroscale (non-microfluidic pumping). Full article

Microorganisms in terrestrial and marine ecosystems are essential to environmental sustainability. In the marine environment, invertebrates often depend on metabolic cooperation with their endosymbionts. Coral reefs, one of the most important marine ecosystems, are based on the symbiosis between a broad diversity of dinoflagellates of the genus Symbiodinium and a wide phyletic diversity of hosts (i.e., cnidarian, molluscan, poriferan). This diversity is reflected in the ecology and physiology of the symbionts, yet the underlying biochemical mechanisms are still poorly understood. We examined metabolite profiles of four cultured species of Symbiodinium known to form viable symbioses with reef-building corals, S. microadriaticum (cp-type A194), S. minutum (cp-type B184), S. psygmophilum (cp-type B224) and S. trenchii (cp-type D206). Metabolite profiles were shown to differ among Symbiodinium species and were found to be affected by their physiological response to growth in different temperatures and light regimes. A combined Random Forests and Bayesian analysis revealed that the four Symbiodinium species examined primarily differed in their production of sterols and sugars, including a C₂₉ stanol and the two sterols C₂₈Δ⁵ and C₂₈Δ^5,22, as well as differences in metabolite abundances of a hexose and inositol. Inositol levels were also strongly affected by changes in temperature across all Symbiodinium species. Our results offer a detailed view of the metabolite profile characteristic of marine symbiotic dinoflagellates of the genus Symbiodinium, and identify patterns of metabolites related to several growth conditions. Full article