Search Results (294)

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article

Background: Developments in biology, genetics, soil science, plant breeding, engineering, and agricultural microbiology are driving advances in soil microbiology and microbial biotechnology. Material and methods: The literature for this review was collected by searching leading scientific databases such as Embase, Medline/PubMed, Scopus, and Web of Science. Results: Recent advances in soil microbiology and biotechnology are discussed, emphasizing the role of microorganisms in sustainable agriculture. It has been shown that soil and plant microbiomes significantly contribute to improving soil fertility and plant and soil health. Microbes promote plant growth through various mechanisms, including potassium, phosphorus, and zinc solubilization, biological nitrogen fixation, production of ammonia, HCN, siderophores, and other secondary metabolites with antagonistic effects. The diversity of microbiomes related to crops, plant protection, and the environment is analyzed, as well as their role in improving food quality, especially under stress conditions. Particular attention was paid to the diversity of microbiomes and their mechanisms supporting plant growth and soil fertility. Conclusions: The key role of soil microorganisms in sustainable agriculture was highlighted. They can support the production of natural substances used as plant protection products, as well as biopesticides, bioregulators, or biofertilizers. Microbial biotechnology also offers potential in the production of sustainable chemicals, such as biofuels or biodegradable plastics (PHA) from plant sugars, and in the production of pharmaceuticals, including antibiotics, hormones, or enzymes. Full article

Nitrogen (N) availability often limits primary productivity in terrestrial ecosystems, and arbuscular mycorrhizal fungi (AMF) can enhance plant N acquisition. This study investigated the interactive effects of N fertilization and AMF inoculation on N uptake, plant performance and phenolic acid content in Hyssopus officinalis L., with the aim of promoting sustainable N management in H. officinalis cultivation. A factorial randomized complete block design was employed to evaluate four AMF inoculation strategies (no inoculation, root inoculation, soil inoculation and combined root–soil inoculation) across three N application rates (0, 0.5 and 1,1 g N pot⁻¹ (7 L)) in a controlled greenhouse environment. Combined root and soil AMF inoculation alongside moderate N fertilization (0.5 mg N pot⁻¹) optimized N use efficiency, maximizing plant biomass and bioactive compound production. Compared to non-inoculated controls, this treatment combination increased N uptake by 30%, phosphorus uptake by 24% and potassium uptake by 22%. AMF colonization increased chlorophyll content and total phenolic compounds under moderate N supply. However, excessive N application (1 g N pot⁻¹) reduced AMF effectiveness and secondary metabolite accumulation. Notably, AMF inoculation without N fertilization yielded the highest levels of anthocyanin and salicylic acid, indicating differential N-dependent regulation of specific biosynthetic pathways. The interaction between AMF and N demonstrated that moderate N fertilization (0.5 g N pot⁻¹) combined with dual inoculation strategies can reduce total N input requirements by 50%, while maintaining optimal plant performance. These findings provide practical insights for developing N-efficient cultivation protocols in medicinal plant production systems, contributing to sustainable agricultural practices that minimize environmental N losses. Full article

Calendula officinalis L. is a widely used medicinal plant whose secondary metabolism and morphology are influenced by light. This study evaluated the effects of 2 and 4 h end-of-day (EOD) red/far-red (R:FR) and green (G) light on the growth, physiology, and phytochemical profile of hydroponically grown C. officinalis under a constant red/blue light background, compared with a red/blue control without EOD treatment. Morphological, physiological (gas exchange, chlorophyll fluorescence), biochemical (chlorophyll, anthocyanin), and chemical composition (attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) and Gas Chromatography-Mass Spectrometry (GC-MS)) were evaluated. EOD G 2 h enhanced photosynthetic pigments, anthocyanins, and biomass, while control plants showed higher phenolic content. EOD R:FR induced stem elongation but reduced pigment and metabolite accumulation. GC-MS revealed organ-specific metabolic specialization, with flowers displaying greater chemical diversity than leaves. EOD G favored sesquiterpene diversity in flowers, while EOD R:FR increased nitrogen-containing compounds and unsaturated fatty acids. Vibrational data supported these shifts, with spectral signatures of esters, phenolics, and lipid-related structures. Bioactive compounds, including α-cadinol and carboxylic acids, were identified across treatments. These findings demonstrate that EOD light modulates physiological and metabolic traits in C. officinalis, highlighting EOD G as an enhancer of biomass and phytochemical richness for pharmaceutical applications under controlled conditions. Full article

The amino acid membrane transporters of grape species take part in metabolic pathways that play crucial roles in nitrogen trafficking and in the synthesis of secondary metabolites. Therefore, identifying these amino acid transporters and defining their functional properties might have further applications in crop improvement and, hence, relevance to human nutrition. The VvCAT2 (Cation Amino acid Transporter) transporter cDNA has been isolated and cloned into a specific plasmid for over-expression in Escherichia coli. The expressed protein, after purification by Ni²⁺-chelating chromatography, has been functionally characterized in an experimental model of proteoliposomes by measuring the uptake of radiolabeled compounds. Arginine was revealed to be the best substrate, confirming the role of CAT2 in nitrogen trafficking in plant cells and within sub-cellular spaces, given its plausible localization in vacuoles. The transporter activity is modulated by pH, osmotic imbalance and ATP. The transport kinetics have been measured. Overall, the obtained data indicate the capacity of VvCAT2 in transporting arginine, making it a possible target for crop improvement with a relevance to human health. Full article

Drought stress significantly hinders the cultivation of medicinal plants such as licorice (Glycyrrhiza uralensis), valued for its bioactive compounds, glycyrrhizin, and liquiritin. This study aims to investigate how co-inoculation with arbuscular mycorrhizal fungus Rhizophagus irregularis and Trichoderma harzianum can enhance licorice drought tolerance and secondary metabolite production, providing insights for sustainable agriculture in arid regions. The results demonstrate that inoculation with R. irregularis significantly improved biomass, drought stress tolerance, and increased glycyrrhizin and liquiritin concentrations by 29.9% and 3.3-fold, respectively, particularly under drought conditions. Co-inoculation with T. harzianum further boosted glycyrrhizin yield by 93.7%, indicating a synergistic relationship between the two microbes. The expression of key biosynthetic genes, including squalene synthase (SQS1) for glycyrrhizin and chalcone synthase (CHS) for liquiritin, was significantly upregulated, enhancing water use efficiency and the biosynthesis of secondary metabolites. Nutrient analysis showed improved phosphorus uptake, alongside reduced root carbon and nitrogen concentrations, leading to greater nutrient utilization efficiency. These findings suggest that co-inoculating R. irregularis and T. harzianum is a promising approach to improving licorice growth and medicinal quality under drought stress, with broad applications for sustainable crop management. Full article

Filamentous fungi hold critical industrial value for their ability to produce enzymes, antibiotics, organic acids, and food fermentation. GATA transcription factors (TFs) serve as central regulators of nitrogen metabolism, synthesis of secondary metabolites, stress adaptation, and directly influence fungal development and pathogenicity in filamentous fungi. In this review, we primarily discuss the structural characterization, different types, and phylogenetic analysis of filamentous fungi GATA TFs in filamentous fungi. Subsequently, we systematically summarize the multifunctions of GATA TFs in the mycelial growth, morphological differentiation, and conidial development of filamentous fungi. In addition, we explore their functions in the synthesis of secondary metabolites such as antibiotics (e.g., cephalosporins, penicillins) and organic acids (e.g., ganoderic acid, fumaric acid) in filamentous fungi. Furthermore, we focus on the key roles of GATA TFs AreA and AreB in nitrogen and carbon metabolism in filamentous fungi and their potential synergistic regulatory relationships. Finally, we review the important roles of GATA TFs in the adaptation of filamentous fungi to environmental changes. This review provides research ideas for the development of genetically engineered strains with optimized growth characteristics, increased target metabolites in the fermentation production process, and enhanced environmental adaptability. Full article

The distribution of suitable habitats for medicinal plants is affected by climate, soil, land use, and other factors. Arnebiae Radix, an important traditional Chinese medicinal resource in Xinjiang, includes Arnebia euchroma (Royle) I. M. Johnst. and Arnebia guttata Bunge and is at risk of over-exploitation. This study predicted suitable planting areas by integrating habitat and phytochemical suitability using the MaxEnt model and ArcGIS. The AUC values for A. euchroma and A. guttata were 0.977 and 0.952, with TSS values of 0.829 and 0.725, respectively, validating the high accuracy of the prediction model. Under the current scenario, the areas of suitable habitats for A. euchroma and A. guttata were 108,914 and 176,445 km², mainly distributed along the main mountains in Xinjiang. Under future climate scenarios, the suitable habitat area of A. euchroma increased by 11–18%, except in the ssp126-2090s scenario, while the suitable habitat area of A. guttata area decreased by 3–18%. Both species were influenced by land use/land cover and soil available nitrogen content; additionally, A. euchroma was affected by the precipitation in the driest month, and A. guttata by the mean diurnal range. The content of secondary metabolites was positively correlated with habitat suitability, with soil factors contributing 35.25% to the total secondary metabolite content. Their suitable habitats predominantly occur in grasslands (42–82%). As habitat and phytochemical suitability distributions aligned, the eastern and western sides of the northern Kunlun Mountain Pass emerged as key areas for cultivation. This research can provide a scientific foundation for selecting optimal planting regions for the two Arnebia species. Full article

Mineral nutrition is of vital importance in plant growth and secondary metabolites accumulation, and thereby in the nutritional value of plants. In Lonicera japonica, a preference to nitrate (NO₃⁻−N) in comparison to ammonium (NH₄⁺−N) was found in our previous study, which can be revealed from the rapid growth rate of L. japonica under NO₃⁻−N. This study assessed whether a preference for nitrogen sources could invoke metabolic reprogramming and interrelationships between factors. NO₃⁻−fed plants exhibited substantial enhancement of carbon stimulation, which was strongly and positively correlated with mesophyll conductance. As a result, the elevated carbon flux by NO₃⁻ supplement was shuttled to phenolic metabolites synthesis, including flavones and caffeoylquinic acids compounds. Notably, the stimulation was triggered by changes in the NO₃⁻ and C/N ratio and was mediated by the induction of several enzymes in the phenylpropanoid pathway. On the contrary, NH₄⁺ plants showed an increment in the content of nitrogen, carbohydrates, and amino acids (mainly a strong increase in citrulline and theanine). Within secondary metabolism, NH₄⁺ may involve active lignin metabolism, showing a dramatic increment in hydroxy−ferulic acid and lignin content. This work provides significant insights regarding the mechanisms of L. japonica in response to diverse nitrogen regimes and effective strategies of nitrogen fertilizer input for L. japonica. Full article

Soil, rhizosphere, and plant-associated microorganisms can enhance plant growth and health. A genomic analysis of these microbes revealed the key characteristics contributing to their beneficial effects. Following a field survey in Panama, four bacterial isolates with plant growth-promoting traits (PGPT) in rice (Oryza sativa L.) were identified. In this study, we sequenced, assembled, and annotated the genomes of Lysinibacillus fusiformis C6 and 24, and Bacillus cereus D23 and 59. The C6 genome was 4,754,472 bp long with 10 contigs, 37.62% guanine-cytosine (GC) content, and 4657 coding sequences (CDS). The 24 genome was 4,683,219 bp with five contigs, 37.65% GC content, and 4550 CDS. The D23 genome was 6,199,908 bp long with 18 contigs, 34.84% GC content, and 6141 CDS. The 59 genome was 6,194,462 bp with 21 contigs, 34.87% GC content, and 6122 CDS. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) confirmed that C6 and 24 belong to Lysinibacillus fusiformis, whereas D23 and 59 belong to the Bacillus cereus species. Further results revealed that these bacteria contained genes characteristic of plant growth-promoting bacteria, such as siderophore, phytohormone auxin (IAA) production, and nitrogen-fixing abilities that promote plant growth. Moreover, the antiSMASH database identified gene clusters involved in secondary metabolite production (biosynthetic gene clusters), such as betalactone, NRPS-like, NRP-siderophore, terpene, and RiPP-like clusters. Moreover, diverse and novel biosynthetic clusters (BCGs) have included non-ribosomal peptides (NRPs), polyketides (PKs), bacteriocins, and ribosomally synthesized and post-transcriptionally modified peptides (RiPPs). This work offers new insights into the genomic basis of the studied strains’ plant growth-promoting capabilities. Full article

Analyzing the nutritional and defensive chemistry of Quercus rugosa provides insight into gall wasp interactions. Quercus rugosa is the most widely distributed white oak species in Mexico. It is the dominant canopy species in its geographic distribution range and has the largest number of associated gall wasp species (Cynipidae: Cynipini). Our main aims were to characterize the nutritional and defensive chemistry of Q. rugosa leaves and determine whether this chemistry differed between leaves with and without galls. We evaluated 60 trees from six populations of Q. rugosa in central Mexico. For each tree, we analyzed the nutritional chemistry (nitrogen, phosphorus, carbon, and carbon/nitrogen ratio) and defensive chemistry (secondary metabolites). Also, we characterized the community of cynipids in the leaf tissue of each tree. We documented 18 cynipid species, and the cynipid communities differed in composition among localities. We recorded the presence of a total of ten phenolics. The composition of nutritional and defensive chemicals differed significantly between leaves with and without galls in each locality. The nutritional and defensive chemical compounds of Q. rugosa were influenced by their associated cynipids. Our results suggest that gall-inducing cynipids influence the production of secondary metabolites in leaves with galls through the reassignment of nutritional compounds by the hosts. Full article

Microbial protein represents a sustainable alternative to conventional animal protein, yet optimizing substrates for fungal cultivation remains critical. This study demonstrates the successful upcycling of chitin waste and aged rice into fungal protein through fermentation with Cordyceps militaris. Substrate formulations (0–20% chitin waste mixed with aged rice) were evaluated for their effects on fungal growth, yield, and metabolite profiles. Results revealed that aged rice alone supported fruiting body yields comparable to fresh rice (9.8 g vs. 9.8 g), with no significant differences in the morphology or growth rate. The addition of 5% chitin waste led to a 17% improvement in yield compared to the control, increasing the average fresh weight of fruiting bodies from 9.8 g to 11.5 g per bottle, while higher chitin levels (20%, T4) suppressed mycelial growth entirely. Fourier-transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) confirmed chitin’s structural complexity and nitrogen-rich composition, which slowed the substrate utilization but enriched secondary metabolites. Liquid chromatography–mass spectrometry (LC-MS) identified 1025 metabolites, including up-regulated bioactive compounds (e.g., cordycepin and piplartine) in chitin-amended substrates, linked to amino acid and lipid metabolism pathways. Safety assessments confirmed the absence of toxins, validating the substrates’ suitability for food applications. These findings highlight chitin waste (≤5%) as a viable nitrogen supplement to aged rice, improving the fungal protein yield and bioactive compound synthesis. This approach advances sustainable biomass valorization, offering a scalable strategy to reduce agricultural waste while producing nutrient-dense fungal protein. Full article

As global climates shift, plants are increasingly exposed to biotic and abiotic stresses that adversely affect their growth and development, ultimately reducing agricultural productivity. To counter these stresses, plants produce secondary metabolites (SMs), which are critical biochemical and essential compounds that serve as primary defense mechanisms. These diverse compounds, such as alkaloids, flavonoids, phenolic compounds, and nitrogen/sulfur-containing compounds, act as natural protectants against herbivores, pathogens, and oxidative stress. Despite the well-documented protective roles of SMs, the precise mechanisms by which environmental factors modulate their accumulation under different stress conditions are not fully understood. This review provides comprehensive insights into the recent advances in understanding the functions of SMs in plant defense against abiotic and biotic stresses, emphasizing their regulatory networks and biosynthetic pathways. Furthermore, we explored the unique contributions of individual SM classes to stress responses while integrating the findings across the entire spectrum of SM diversity, providing a comprehensive understanding of their roles in plant resilience under multiple stress conditions. Finally, we highlight the emerging strategies for harnessing SMs to improve crop resilience through genetic engineering and present novel solutions to enhance agricultural sustainability in a changing climate. Full article

Poa alpigena Lindm is a dominant forage grass in the temperate grasslands of the Qinghai Lake Basin, commonly used for grassland restoration. Soil microorganisms are crucial in material cycling within terrestrial ecosystems. This study aimed to investigate the effects of P. alpigena on the microbial community composition and structure in rhizosphere and non-rhizosphere soils in the Qingbaya grassland area. Using high-throughput sequencing, we identified microbial gene pools and compared microbial diversity. Metagenomic analysis showed that non-rhizosphere soil contained 35.42–36.64% known microbial sequences, with bacteria making up 79.25% of the microbiota. Alpha diversity analysis indicated significantly higher microbial richness and diversity in non-rhizosphere soil, influenced by electrical conductivity, total carbon, and total nitrogen content. LEfSe analysis revealed that Alphaproteobacteria and Betaproteobacteria were major differential taxa in rhizosphere and non-rhizosphere soils, respectively. Key metabolic pathways in rhizosphere microorganisms were related to AMPK signaling, secondary metabolite biosynthesis, and starch metabolism, while non-rhizosphere microorganisms were involved in aromatic compound degradation, purine metabolism, and microbial metabolism in diverse environments. The enrichment of microbial taxa and functional pathways related to methane oxidation in rhizosphere soil suggests a potential role of P. alpigena in shaping microbial processes linked to greenhouse gas regulation, although direct evidence of methane flux changes was not assessed. Similarly, the presence of aromatic compound degradation pathways in non-rhizosphere soil indicates microbial potential for processing such compounds, but no direct measurements of specific contaminants were performed. Full article

The production of microbial metabolites such as (exo)polysaccharides, lipids, or mannitol through the cultivation of microorganisms on sustainable, low-cost carbon sources is of high interest within the framework of a circular economy. In the current study, two non-extensively studied, non-conventional yeast strains, namely, Cutaneotrichosporon curvatus NRRL YB-775 and Papiliotrema laurentii NRRL Y-3594, were evaluated for their capability to grow on semi-defined lactose-, glycerol-, or glucose-based substrates and produce value-added metabolites. Three different nitrogen-to-carbon ratios (i.e., 20, 80, 160 mol/mol) were tested in shake-flask batch experiments. Pretreated secondary cheese whey (SCW) was used for fed-batch bioreactor cultivation of P. laurentii NRRL Y-3594, under nitrogen limitation. Based on the screening results, both strains can grow on low-cost substrates, yielding high concentrations of microbial biomass (>20 g/L) under nitrogen-excess conditions, with polysaccharides comprising the predominant component (>40%, w/w, of dry biomass). Glucose- and glycerol-based cultures of C. curvatus promote the secretion of mannitol (13.0 g/L in the case of glucose, under nitrogen-limited conditions). The lipids (maximum 2.2 g/L) produced by both strains were rich in oleic acid (≥40%, w/w) and could potentially be utilized to produce second-generation biodiesel. SCW was nutritionally sufficient to grow P. laurentii strain, resulting in exopolysaccharides secretion (25.6 g/L), along with dry biomass (37.9 g/L) and lipid (4.6 g/L) production. Full article