Comparative evaluation of Tobit and Free Ion Activity Models for optimizing genotype-specific permissible arsenic limits in rice soil and irrigation water.

Counteracting effects of a pesticide-free cultivation system on soil microorganisms, meso- and macrofauna

Molecular insights into melatonin-mediated stress tolerance in Dendrobium: Integrating antioxidant defense, hormonal networks, and omics approaches.

Quantification of rice root anatomical traits such as cortical aerenchyma lacunae is key to understanding rice adaptation to diverse water regimes and to support climate-smart breeding. Aerenchyma lacunae contributes to rice internal gas transport and influences methane emissions from flooded systems and can also limit rice water conductivity. It could be an interesting anatomical trait for breeding, however, large-scale anatomical phenotyping remains limited because manual analysis of root cross-sections is labor-intensive, subjective, and difficult to scale across heterogeneous imaging conditions. Existing pipelines often require parameter tuning and do not generalize well across environments. We developed a deep learning pipeline based on a vision transformer architecture to automatically segment rice root cross-sections and quantify cortical aerenchyma lacunae. The model was trained on 1,760 annotated images collected across multiple countries, growth stages, cultivation systems, and experimental contexts, using a collaboratively defined annotation protocol. The final model achieved high segmentation accuracy, with mean intersection over union values exceeding 0.92 for cortical tissues and lacunae. Quantification of the lacuna-to-cortex ratio showed strong agreement with manual annotations, with a coefficient of determination of 0.98 on an independent test set. An independent expert review indicated that model predictions were at least as consistent as manual annotations and reduced large annotation inconsistencies. The pipeline is released as open-source software and includes an interactive online demonstrator, and is accompanied by an online test dataset to support testing and reproducibility. Application across six experimental use cases revealed reproducible differences in aerenchyma lacunae across genotypes, water regimes, environments, and developmental stages. This work provides a robust, scalable, and transferable tool for automated root anatomical phenotyping under heterogeneous experimental conditions. Transformer-based segmentation enables consistent and high-throughput quantification of lacunae, facilitating integration of these anatomical traits into breeding, physiological studies, and climate-smart crop improvement programs.

Brucellosis remains one of the most significant zoonotic diseases worldwide, and the absence of licensed human vaccines highlights the need for novel vaccine platforms and reproducible laboratory-scale manufacturing strategies. In the present study, the replication efficiency of a recombinant capripoxvirus expressing a Brucella antigen was evaluated in Vero cells cultured under serum-free conditions using two 3D carrier-based cultivation systems. Vero cells were cultivated in serum-free medium either on Cytodex 1 microcarriers in a 500-mL reusable spinner flask operated in repeated-batch mode or on BioNOC II® macrocarriers in single-use 500-mL BelloCell™ 500AP vessels integrated into the BelloStage™-3000 system and operated according to the Tide Motion principle with medium recirculation. Cells were infected with recombinant SPPV(TKΔ)-OMP16 at a multiplicity of infection of 0.1, and total cell yield, metabolic parameters, and virus production were subsequently monitored throughout cultivation. The microcarrier and macrocarrier systems achieved maximum total cell yields of 7.0 × 10⁸ and 3.1 × 10⁹ cells, respectively. Peak virus titers reached 5.75 log₁₀ TCID₅₀/mL at 120h post-infection in the microcarrier system and 7.25 log₁₀ TCID₅₀/mL at 168h post-infection in the macrocarrier system, corresponding to a 1.5 log₁₀ increase in virus titer (p < 0.01). After normalization to the working culture volume, the macrocarrier system exhibited 4.4-fold higher volumetric cell productivity. In addition, virus productivity normalized to the total number of cells present at the time of infection was approximately sevenfold higher than that observed in the microcarrier system. These findings demonstrate that the macrocarrier-based dynamic cultivation system enables superior total cell yield and enhanced recombinant virus production under serum-free laboratory-scale conditions. KEY POINTS: • BioNOC II® macrocarriers increased volumetric cell productivity by 4.4-fold compared with Cytodex 1. • BioNOC II® macrocarriers increased peak virus titers by 1.5 log₁₀ TCID₅₀/mL. • Cell-specific viral productivity was approximately sevenfold higher in the macrocarrier-based bioreactor system.

Ammonia-oxidizing bacteria play important roles in nitrogen transformation and agricultural-waste valorization; however, their large-scale application is often limited by high cultivation costs and insufficient functional stability. This study aimed to develop a low-cost and stable microbial consortium for converting cattle manure wastewater into a bioactive fermentation broth and to investigate its underlying mechanisms. The heterotrophic ammonia-oxidizing bacterium Ensifer sp. S2-8-1 was used as the core strain, and Bacillus subtilis was employed as the auxiliary strain. Three cultivation systems were compared: S2-8-1 monoculture, simultaneous co-culture, and a staged consortium (SYC). Among them, SYC exhibited the best overall performance, maintaining the highest viable bacterial density and reaching 3.93 × 10⁷ CFU·mL⁻¹ on day 12. In a soil-maize pot experiment, SYC significantly enhanced rhizosphere nitrification, increased NO₃⁻-N availability, and promoted maize growth, resulting in a 41.4% increase in whole-plant dry matter compared with the water control. The consortium also improved photosynthetic performance and cytokinin accumulation. Comparative metatranscriptomic analysis revealed significant upregulation of heterotrophic ammonia oxidation-related genes (CYP450) and cytokinin-related genes (miaA and LOG) in S2-8-1 under SYC conditions, suggesting coordinated activation of nitrogen transformation and plant growth-promoting signaling pathways. The staged "pre-modification followed by synergy" consortium effectively converts cattle manure wastewater into a stable and bioactive fermentation broth, enhancing both microbial biomass production and plant growth-promoting activity. This strategy provides a scalable approach for livestock wastewater valorization and the development of compound microbial fertilizers.

ABSTRACT Objective Quality of life (QoL) is an individual’s perception of life quality based on cultural values, goals, and standards in physical, psychological, social, and environmental aspects. The objective of this study was to investigate the associations between demographic characteristics, health information factors, and the QoL of durian farmworkers. Additionally, proposed implementation strategies were developed based on factors associated with the QoL. Methods This cross-sectional study was designed to assess the QoL of 160 durian farmworkers in Nakhon Si Thammarat province, Thailand. Participants were selected through purposive sampling, and a face-to-face interview was conducted using a structural questionnaire that collected general demographic characteristics and health information. The validated, Thai-translated World Health Organization Quality-of-Life Scale (WHOQOL-BREF) tool was used to collect data on the QoL. The multiple linear regression analysis was used to examine the factors associated with the QoL. The finding factors were used to propose implementation strategies aligned with the RE-AIM principles (Reach, Effectiveness, Adoption, Implementation, and Maintenance). Results The majority (83.1%) of durian farmworkers reported a good QoL, with an overall mean score of 106.9 (range: 80–130). Domain-specific scores of physical health 27.1 (range: 20–34), mental health 25.3 (range: 16–30), social relationships 12.8 (range: 8–15), and environment 31.8 (range: 16–40) were within the good level. The results showed that stress, age, marital status, and annual income were significantly associated with the QoL (p < .05). Based on four key factors, proposed implementation strategies were developed, including expected outcome, activities, lead person, timelines, resources, and the evaluation method for RE-AIM alignment. Conclusion The study highlights age, marital status, annual income, and stress as key factors influencing the QoL of durian farmworkers. The proposed implementation strategies, may help inform health promotion and community-based initiatives aimed at improving the well-being of durian farmworkers and potentially similar fruit cultivation systems.

Microbial electrosynthesis is a metabolic process in which extracellular electrons are utilized as the primary energy source for carbon fixation. While microbial electrosynthesis has been proposed as a novel concept for ecological primary production, our understanding of how such microorganisms are distributed in natural environments remains limited. In this study, we constructed a laboratory-scale electrochemical cultivation system that simulates electric discharge conditions in deep-sea hydrothermal fields. Microscopic counts revealed increased cell numbers in the electrochemical culture, and 16S rRNA gene analysis revealed a significant enrichment of a novel Thiomicrorhabdus species. Quantitative PCR confirmed proliferation and enrichment of a metagenome-assembled genome (MAG), named the SREC-4. Electrochemical cultivation with 13C-labeled CO₂ as a substrate indicated significant 13C incorporation specifically in Thiomicrorhabdus cells including MAG SREC-4. The genome of MAG SREC-4 revealed the possession of the putative extracellular electron uptake pathway in addition to the autotrophic sulfur-oxidizing aerobic respiration pathways typically found in Thiomicrorhabdus members. The putative extracellular electron uptake pathway was found in a phylogenetic clade in Thiomicrorhabdus mainly formed by strains derived from hydrothermal fields. These results provide the direct experimental evidence from enrichment cultures derived from hydrothermal fields that an organism inhabiting deep-sea hydrothermal fields can grow electrosynthetically, and suggest that this ability is shared by other Thiomicrorhabdus species, specifically those found in similar environments. This finding suggests electrosynthetic growth may be widely distributed in Thiomicrorhabdus populations dwelling in deep-sea hydrothermal fields, the largest natural electrogenic environment on Earth.

Foliar application of metal micronutrients is increasingly adopted in intensive cultivation systems, yet its potential ecological risks to rhizosphere functions remain poorly understood. Here, using the medicinal plant Panax notoginseng as a model, we conducted a gradient foliar amendment experiment with iron (Fe), zinc (Zn), and copper (Cu) to evaluate how aboveground metal inputs regulate rhizosphere soil multifunctionality (MF) through microbial life-history strategies. By integrating 16S rRNA amplicon sequencing, metagenomics, root transcriptomics, and a newly developed quantitative Yield-Acquisition-Stress tolerance (qYAS) framework, we disentangled the microbial mechanisms underlying divergent functional responses to metal amendments. Foliar Fe significantly enhanced multifunctionality, including nutrient provision and element cycling, while Cu and Zn reduced nutrient provision and element cycling, but enhanced plant pathogen abundances. These changes were closely associated with shifts in bacterial life-history strategies: Fe promoted Y-strategists characterized by efficient carbon use, streamlined genomes, and high network connectivity, whereas Cu and Zn enriched AS-strategists with larger genomes and negative associations with multifunctionality. Partial least squares path modeling (PLS-PM) further identified microbial strategies as key mediators linking foliar metal inputs, plant performance, soil properties, and multifunctionality. This study provides a trait-based microbial framework for evaluating foliar metal fertilization and guiding safer nutrient management.

Rising global meat demand and nutritional awareness have fuelled interest in sustainable, ethical protein sources. Animal agriculture generates greenhouse gas emissions, land degradation, and water scarcity, creating a need for plant-based meat alternatives. While plant sources face drawbacks such as incomplete amino acid profiles, anti-nutritional factors, and land requirements. Algae emerge as a superior option, delivering exceptionally high protein content (up to 70% dry weight), complete essential amino acids, omega-3 fatty acids, vitamins, polysaccharides, and potent antioxidants, surpassing plant sources in nutrient density, bioavailability, and environmental footprint. This review evaluates the nutritional, environmental, and technological potential of key algal species (microalgae and macroalgae) for meat substitute applications. Algal formulations excel over plant-based counterparts with superior protein quality (PDCAAS >0.9 vs. often <0.8 for plants), rapid biomass growth (10-50× faster than plants), and no arable land requirements, enabling scalable, low-water production. The review addresses challenges such as off-flavors, digestibility, and cost through solutions such as strain selection, biorefinery optimization, and hybrid cultivation systems. An overview of key market players highlights the growing role of algae in alternative meats. By integrating nutritional and industrial perspectives, this work reveals trends positioning algae at the forefront for health-conscious consumers, advocating a "best-of-everything" approach with diverse species to revolutionize sustainable food systems.

Intercropping has emerged as a promising strategy to improve agroecosystem biodiversity and mitigate some adverse effects associated with intensive monoculture systems. This study evaluated weed infestation and biodiversity responses in a Paulownia-buckwheat intercropping system compared with buckwheat monoculture under the environmental conditions of southwestern Poland. Weed species composition, abundance, and biomass were assessed at different growth stages of buckwheat. Selected agroecosystem components, including soil microorganisms, soil mesofauna, and pollinator abundance, were evaluated. The intercropping system increased Collembola diversity and Acari abundance, while higher diversity and richness of segetal plant species were also observed compared with monoculture. Higher bacterial abundance and dehydrogenase activity were recorded under intercropping, whereas fungal community composition remained generally stable between cultivation systems. Several melliferous weed species were identified within the intercropping system, potentially supporting pollinator activity. Although no statistically significant differences were observed in pollinator-related parameters, nectar productivity and sugar availability tended to be higher under intercropping conditions, suggesting that the Paulownia-buckwheat system may contribute to maintaining pollinator activity and supporting agroecosystem biodiversity. No significant differences in buckwheat yield or biometric traits were found between cultivation systems. Overall, the results indicate that Paulownia-buckwheat intercropping may enhance selected components of agroecosystem biodiversity without reducing crop productivity.

Cobalamin (vitamin B₁₂) is synthesized only by certain bacteria and archaea and is rarely found in plant-derived foods because plants neither synthesize nor require this cofactor. The edible duckweed Wolffia globosa Mankai is unusual in containing bioavailable cobalamin, suggesting a microbial origin. However, how cobalamin biosynthetic capacity is organized within angiosperm-associated microbiomes remains largely unresolved. Here, we investigated bacterial community structure and cobamide biosynthetic potential across the cultivation medium, plant surface, and internal tissues of Mankai to determine how cobalamin production is maintained in this aquatic plant microbiome. Bacterial communities differed significantly among compartments, with the endosphere forming a low-diversity, host-filtered microbiome enriched in specialized taxa. Genome-resolved metagenomics showed that only a minority of endophytic bacteria encoded near-complete cobamide biosynthesis pathways consistent with de novo synthesis. In contrast, many co-occurring taxa lacked multiple biosynthetic steps but were enriched in genes associated with cobamide precursor salvage and remodeling. Network analysis identified putative producer taxa as highly connected hubs linked to salvager populations, consistent with metabolite cross-feeding. Comparative genomic analysis demonstrated reduced cobamide biosynthetic gene complements in endophytic genomes relative to closely related free-living strains, supporting adaptive pathway reduction in the host-associated niche. Cobalamin production in the Mankai endosphere appears to arise from a metabolically interdependent bacterial consortium rather than from single autonomous producers. These findings identify cooperative micronutrient biosynthesis as an organizing principle in plant-associated microbiomes and position Mankai as a tractable model for studying cobamide-mediated microbial cooperation in aquatic crops. Understanding these interactions may support microbiome-informed strategies to stabilize micronutrient production and functional resilience in controlled aquatic plant cultivation systems.

Climate change drives rising atmospheric CO2 , impacting vegetable crops in polyhouses. Elevated CO2 enhances photosynthesis, biomass, and yield while altering quality attributes. This review examines its dual effects on high-value horticultural crops under controlled conditions. Positive outcomes include increased fructose (14.2%), glucose (13.2%), total soluble sugars (17.5%), antioxidant capacity (59.0%), phenols (8.9%), flavonoids (45.5%), ascorbic acid (9.5%), and calcium (8.2%). Conversely, it reduces protein (9.5%), nitrate (18.0%), magnesium (9.2%), iron (16.0%), and zinc (9.4%). Specific responses in lettuce, tomato, and potato are highlighted. CO2 enrichment boosts yield but compromises nutritional quality, necessitating targeted management and breeding strategies.

Coccolithophores are unicellular marine microalgae capable of producing calcium carbonate exoskeletons composed of micrometric scales called coccoliths. Since they require CO₂ for both calcification and biomass production, they are expected to exhibit a potentially higher CO₂ fixation, making them promising candidates for applications in biological carbon capture systems. In addition, coccoliths themselves are considered high-value products due to their potential applications in many fields such as nanobiotechnology. In this study, a high cell density culture of Chrysotila sp. was tested using the CellDEG® technology, with the objective of maximizing both biomass and coccolith production as a function of light intensity, nitrogen and carbon supply, thanks to a design of experiments (DoE) approach. The optimal conditions identified for biomass production were 600mg L⁻1 of nitrogen and a light intensity of 375µmolm⁻2s⁻1, which allowed the system to reach a final biomass productivity of 0.96g L⁻1 d⁻1. However, coccolith production was found to be very limited under these conditions. Additional experiments assessed the effect of calcium addition and light regime, which did not remarkably affect the PIC:POC ratio. On the other hand, when Chrysotila sp. was cultivated in a semicontinuous system with controlled pH (to maintain the carbonate structure of the coccosphere) with a light bubbling as mixing, a remarkable particulate inorganic carbon versus particulate organic carbon ratio (PIC:POC) of 0.3 was obtained. Semicontinuous feeding was selected for its ability to maintain relatively stable concentrations of nutrients and cells over time. Therefore, semicontinuous cultivation under these conditions is recommended for coccolith production, whereas the CellDEG® system is more suitable for biomass generation. This study allowed us to obtain data on the growth of Chrysotila sp. using semicontinuous and high cell density culture systems, which is innovative given the limited information available in literature regarding the cultivation of this species. KEY POINTS: CellDEG® technology allows high biomass production, but low PIC:POCChanges in calcium concentration or photoperiod cannot increase CellDEG®'s PIC:POCSemicontinuous cultivation yields high PIC:POC but reduces biomass levels.

Shade-driven morpho-physiological plasticity buffers light-water co-limitation in Euterpe precatoria under rainfed field conditions.

The identification and development of high-quality humus sources to enhance the productivity and performance of substrate-based vegetable cultivation systems remains a significant challenge in sustainable agriculture. Protaetia brevitarsis larvae (PBL) exhibit exceptional efficiency in decomposing decaying crop straw and produce nutrient-rich frass with high humic acid content and a complex microbial community. However, its impacts on substrate microecological systems and the underlying functional mechanisms remain unclear, limiting its rational application in substrate cultivation. This study aimed to investigate the effects of PBL frass on substrate microecology and elucidate the associated mechanisms using cherry tomato (Lycopersicon esculentum Mill. var. cerasiforme Alef) pot experiments. Incorporation of 2% or 4% (w/w) PBL frass into cherry tomato cultivation substrates significantly promoted plant growth, characterized by reduced plant height (indicating more robust, dwarf-type growth) and increased aboveground (stem) and belowground (root) biomass. Furthermore, PBL frass application enhanced substrate microbial diversity through two distinct, complementary pathways: (ⅰ) Frass-derived microbes, which possess specific colonization capabilities, directly augmented microbial communities in both the rhizoplane and bulk substrate; and (ⅱ) Organic compounds in PBL frass may have activated a broad range of microbes, enriching the rhizosphere microbiome. This enhanced microbial diversity was associated with an increased abundance of plant-beneficial taxa, which likely contributed to growth promotion and substrate health maintenance. This study uncovers the multifaceted contributions of PBL frass to substrate microbial ecology and reveals its two suggestive regulatory pathways. These results provide a theoretical basis for the sustainable utilization of PBL frass and advance the development of eco-friendly amendments for modern vegetable production.

Soil nutrients variability plays a crucial role in paddy growth and yield. Insufficient information on soil nutrient content can lead to inefficient fertilizers application, resulting in either nutrient deficiency or excess in the soil. This study investigates the potential of laser-induced breakdown spectroscopy (LIBS) combined with machine learning for rapid classification of paddy soils from non-granary cultivation systems in Sarawak, Malaysia. Soil samples from irrigated lowland, rainfed lowland, and upland areas were analysed using conventional physicochemical methods and LIBS to evaluate variability in soil properties and spectral characteristics. The LIBS spectra revealed distinct multi-elemental signatures dominated by Ca, Fe, K, and N, while P exhibited weak emission intensity due to both low concentration and intrinsic plasma emission limitations. Principal Component Analysis (PCA) reduced spectral dimensionality, with the first four components explaining 74.38% of the total variance. However, PCA score plots showed substantial overlap among soil groups, indicating limited separability using unsupervised analysis. To address this, a supervised classification approach using Support Vector Machine (SVM) was implemented. The PCA-SVM model achieved an average classification accuracy of 76.42 ± 15.17% under repeated sample-level hold-out validation, which improved to 87.33 ± 12.80% using Leave-One-Sample-Out Cross-Validation (LOSOCV). These results demonstrate that, although intrinsic spectral differences among paddy cultivation categories are subtle, the integration of LIBS with machine learning facilitates effective extraction of discriminative spectral patterns. This study highlights the potential applicability of LIBS as a rapid, multi-element analytical approach for preliminary classification of non-granary paddy cultivation systems, particularly in heterogeneous and resource-limited agricultural environments.

Background/Objectives: The high temperatures associated with climate change represent an important constraint for tomato production in tropical regions, affecting plant growth, reproductive development, and fruit metabolic composition. In this context, protected cultivation systems capable of modifying greenhouse microclimates may help reduce thermal stress and maintain crop productivity. Methods: This study evaluated the effects of two protective environments, diffuse agricultural film (AF) and twin-walled polycarbonate panels with laminar water flow (P), on the agronomic performance and fruit metabolic traits of five grape-tomato hybrids grown under tropical conditions. Microclimatic variables, vegetative growth, yield components, postharvest behavior, and fruit quality attributes were evaluated, with emphasis on carotenoid accumulation. Results: Compared with the agricultural film environment, the polycarbonate system reduced global radiation and photosynthetically active radiation (PAR) and was associated with an increase in yield of approximately 25%, an increase in fruit number of approximately 13%, and an 8% increase in fruit diameter. In addition, some hybrids cultivated under the polycarbonate system showed greater lycopene and β-carotene accumulation, indicating that microclimate moderation may favor carotenoid-related fruit quality depending on genotype. Principal component analysis revealed a clear separation between cultivation environments, with the polycarbonate system more closely associated with yield-related and canopy development traits, whereas the agricultural film environment was linked to biomass accumulation and selected physicochemical attributes. Among the evaluated hybrids, BS IGR0104, Jacy, and GI7545 showed the most favorable combination of agronomic performance and fruit quality traits. Conclusions: These results demonstrate the importance of climate-adaptive protected cultivation systems and hybrid selection for improving tomato productivity under tropical heat conditions.

Cadmium (Cd) contamination in acidified paddy soils poses a major threat to rice safety and necessitates practical remediation strategies compatible with flooded rice cultivation systems. In this study, a Cd-tolerant microalgal strain, Chlorella sorokiniana T003, was isolated and evaluated for its potential to reduce Cd accumulation in rice through a microalgae-based remediation strategy integrated with swine wastewater utilization. Strain T003 maintained growth at Cd concentrations up to 25mg L⁻¹ and removed over 90% of dissolved Cd at 5-25mg L⁻¹, with a removal efficiency of 62% at 50mg L⁻¹. T003 also showed robust growth in untreated swine wastewater, reaching 1.5 × 10¹¹ cells L⁻¹ after 9 d, supporting its suitability for wastewater-based biomass production. In pot experiments, application of T003 cultivated in swine wastewater increased soil pH from 5.61 to 6.60 and reduced rice shoot Cd concentration by up to 75.9% compared with the alkalized control. Field application similarly increased soil pH from 5.60 to 6.11, reduced exchangeable Cd by 49.7%, and decreased grain Cd concentrations by 72.7% and 98.7% in two rice cultivars, respectively. These findings indicate that C. sorokiniana T003 cultivated in swine wastewater can reduce Cd accumulation in rice under field conditions and may provide a biologically based strategy for Cd mitigation in acidified paddy soils while supporting nutrient recycling in crop-livestock systems.

Comparative transcriptomic and metabolomic profiling of forest tea and terrace tea in Sandu, Guizhou, China