Search Results (1,176)

The lotus–fish co-culture (LFC) system leverages plant–fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal–fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC’s ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation. Full article

Reclaimed land refers to artificially created soil formed by filling in seawater, leading to rapid ecological changes. Undeveloped reclaimed areas offer opportunities to explore previously unknown soil ecological resources. The Shihwa reclaimed land is an undeveloped area where microbiome-based studies of the microbial community have not yet been conducted. The soil from the Sihwa reclaimed land (SR, SL) showed higher pH (8.9), EC (7.5 dS/m), and Na⁺ content (13.4 cmol⁺/kg), but lower levels of organic matter and phosphorus compared to typical agricultural soils (NL, NS). These unfavorable conditions had a negative effect on lettuce growth, as both fresh and dry weights in the SL treatment (32.5 g and 0.39 g, respectively) were significantly lower than those in the NL treatment (40.4 g and 0.45 g). At the phylum level, Actinobacteria (51.6%) dominated the original reclaimed soil (SR), but after lettuce cultivation (SL), there was an increase in Cyanobacteria (25.3%) and Proteobacteria (29.4%). At the order level, Streptomycetales (35.2%) and Bacillales (13.5%) were predominant in SR, whereas in SL, Oscillatoriales (23.5%)—which have photosynthetic ability—as well as organic matter-degrading orders such as Rhodobacterales and Flavobacteriales, became dominant. For the eukaryotic community at the phylum level, Ascomycota was predominant in all samples; however, in NL, the relative proportions of Chlorophyta (22%) and Mucoromycota (8.9%) were higher, indicating increased diversity. At the order level, Eurotiales (28.5%), Hypocreales (20.2%), and Wallemiales (14.4%) were predominant in SR, but after lettuce cultivation, Wallemiales disappeared and Eurotiales increased to 40.0%. Additionally, Glomerellales and Sordariomycetes_o were detected only in SL and NL, suggesting that symbiotic fungal activity in the rhizosphere was promoted. Full article

Plant Growth Promoting Rhizobacteria, PGPR, can protect plants against soil-borne diseases and abiotic stress conditions. The primary objective of this study was to evaluate the effects of different PGPRs (TF1, TF2, TF3, and TF4) on the rhizosphere microbial community of silage maize in a saline–alkaline field via Illumina MiSeq high-throughput sequencing technology. Results demonstrated that different PGPRs significantly increased the harvest density (by 21.31–45.16%), plant height (by 9.12–19.98%), stem diameter (by 30.07–45.78%), and biomass (by 33.20–65.36%) of silage maize, TF3 treatment significantly increased the fresh weight (by 32.50%), while the other treatments could increase the fresh weight but not significantly. Four microbial agents significantly reduced the contents of soil available phosphorus (AP), electrical conductivity (EC), and neutral phosphatase activity (NPA), while significantly increasing the contents of available potassium (AK), ammonium nitrogen (NH₄⁺-N), nitrate nitrogen (NO₃⁻-N), chitinase activity (ChtA), and urease activity (UA). Specifically, TF2 and TF3 treatments significantly decreased the soil pH value, while not for TF1 and TF4. Microbiome analysis showed that four microbial agents significantly increased the relative abundances of beneficial microorganisms, such as Arthrobacter, Blastococcus, MNDI, Chaetomidium, Alternaria, Sarocladium, Acremonium, and Clonostachys, and significantly decreased the relative abundances of Gibberella and Fusarium. Mental analysis showed that the soil bacterial community structure did not significantly correlate with soil biochemical properties, while the soil fungal community structure significantly and positively correlated with pH. Maize yield significantly and positively correlated with NH₄⁺-N, OM, AP, EC, UA, ChtA, and NPA. Full article

Investigating the microbial community structure and stress-tolerance mechanisms in the rhizospheres of salt-adapted plants along saline lakes is critical for understanding plant–microbe interactions in extreme environments and developing effective strategies for saline–alkaline soil remediation. This study explored the rhizosphere microbiomes of four salt-adapted species (Suaeda glauca, Artemisia carvifolia, Chloris virgata, and Limonium bicolor) from the Yuncheng Salt Lake region in China using high-throughput sequencing. Cultivable salt-tolerant plant growth-promoting rhizobacteria (PGPR) were isolated and characterized to identify functional genes related to stress resistance. Results revealed that plant identity and soil physicochemical properties jointly shaped the microbial community composition, with total organic carbon being a dominant driver explaining 17.6% of the variation. Cyanobacteria dominated low-salinity environments, while Firmicutes thrived in high-salinity niches. Isolated PGPR strains exhibited tolerance up to 15% salinity and harbored genes associated with heat (htpX), osmotic stress (otsA), oxidative stress (katE), and UV radiation (uvrA). Notably, Peribacillus and Isoptericola strains demonstrated broad functional versatility and robust halotolerance. Our findings highlight that TOC (total organic carbon) plays a pivotal role in microbial assembly under extreme salinity, surpassing host genetic influences. The identified PGPR strains, with their stress-resistance traits and functional gene repertoires, hold significant promise for biotechnological applications in saline–alkaline soil remediation and sustainable agriculture. Full article

Climate change causes major agricultural losses, driven both by the rise of plant diseases and by extreme weather events such as droughts and floods. Increased precipitation can lead to waterlogging of important crops. The roots of plants submerged in water have limited access to oxygen, which leads to hypoxia, which, in turn, reduces plant resistance to other factors, e.g., plant pathogens. On the other hand, beneficial microorganisms can help plants oppose abiotic stress, e.g., by producing plant hormones or osmoprotectants such as trehalose, to increase plant tolerance to drought. It turns out that plant-beneficial microorganisms can also increase plant resistance to waterlogging. This can be achieved by various mechanisms that involve the production of 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which reduces the amount of ethylene accumulated in the submerged roots. This can stimulate the production of reactive oxygen species scavengers that protect plants from the oxidative stress caused by less efficient anaerobic metabolism, produce plant hormones that help plants to better adapt to low-oxygen conditions, and shape the plant microbiome, supporting plant growth in waterlogging conditions. This review outlines plant responses to waterlogging and discusses examples of microorganisms that improve plant tolerance, focusing on their underlying mechanisms. Full article

The plant microbiome plays a role in pathogen defense, but its role in different resistant varieties and ecological niches remains unclear. This study used 16S rRNA and ITS sequencing to investigate microbial communities and interactions in disease-resistant (PT) and susceptible (Bourbon) coffee varieties of five ecological niches: leaves, fruits, roots, rhizosphere soil, and non-rhizosphere soil. We found that the microbial communities differed significantly between the two varieties. The resistant variety was enriched in beneficial bacteria from the Actinobacteriota phylum and a stable, modular microbial network dominated by saprotrophic fungi. In contrast, the susceptible variety had a higher abundance of opportunistic pathogens and stress-indicator fungi, including Neurospora spp., which were more prominent in the rhizosphere and non-rhizosphere soils. These networks were fragile and dominated by pathotrophic fungi, reflecting ecological imbalance. Our findings show that plant disease resistance is influenced not only by host genetics but also by co-evolutionary interactions with the microbiome. These insights provide a foundation for developing targeted biocontrol strategies to manage plant-associated microbial communities. Full article

Background: The bacterial wilt of tomatoes, caused by Ralstonia solanacearum, is a soil-borne plant disease that causes substantial agricultural economic losses. Various nanoparticles have been utilized as antibacterial agents to mitigate pathogenic destructiveness and improve crop yields. However, there is a lack of in-depth research on how nanoparticles affect tomato metabolite levels to regulate the bacterial wilt of tomatoes. Methods: In this study, healthy and bacterial wilt-infected tomatoes were treated with Cu-Ag nanoparticles, and a metabolomics analysis was carried out. Results: The results showed that Cu-Ag nanoparticles had a significant prevention and control effect on the bacterial wilt of tomatoes. Metabolomic analysis revealed that the nanoparticles could significantly up-regulate the expression levels of terpenol lipids, organic acids, and organic oxygen compounds in diseased tomatoes, and enhance key metabolic pathways such as amino acid metabolism, carbohydrate metabolism, secondary metabolite metabolism, and lipid metabolism. These identified metabolites and pathways could regulate plant growth and defense against pathogens. Correlation analysis between the tomato microbiome and metabolites showed that most endophytic microorganisms and rhizospheric bacteria were positively correlated with fatty acyls groups and organic oxygen compounds. Conclusions: This study reveals that Cu-Ag nanoparticles can actively regulate the bacterial wilt of tomatoes by up-regulating the levels of lipid metabolism and organic oxygen compounds, providing an important theoretical basis for the application of nanoparticles in agriculture. Full article

Polyculture, or intercropping, is the practice of growing two or more crops simultaneously in time and space. The milpa is a systematic polyculture involving the simultaneous cultivation of maize (Zea mays), beans (Phaseolus spp.), squash (Cucurbita spp.), and other crops. Milpa polyculture initially emerged in the Mesoamerican region (Mexico and Central America) through the concurrent processes of managing, utilizing, and domesticating its constituent crops. It subsequently spread throughout the Americas via the diffusion of maize and the convergence of its domestication with that of its companion crops and other domesticated plants in the continent. Mesoamerican farmers made an outstanding contribution by domesticating and bringing together crops with contrasting morphological and physiological traits that are ecologically, agronomically, and nutritionally complementary. Despite its importance, few quantitative evaluations of this polyculture exist. However, these evaluations indicate that its productivity and land efficiency use (Land equivalent ratio = 1.34) are comparable to those of other intercrops studied on a global scale. We emphasize the importance of transdisciplinary efforts to study this polyculture and highlight its potential applications related to ecological interactions, plant microbiomes and breeding in order to reach sustainable production goals. Full article

Disease caused by Plasmodiophora brassicae severely disrupts cruciferous crops by altering root physiology and rhizosphere ecology. While pathogen-induced shifts in rhizosphere microbiomes are documented, the mechanisms linking root exudate reprogramming to microbial community remodeling remain poorly understood. Here, we integrated untargeted metabolomics and 16S rRNA sequencing to investigate how root exudates reshape the rhizosphere microbiome of tumorous stem mustard (Brassica juncea var. tumida) through P. brassicae infection. Metabolomic profiling identified 1718 root exudate metabolites, with flavones (e.g., apigenin 7-O-β-D-rutinoside, VIP > 1.5) and phenolic derivatives (e.g., gastrodin) being selectively enriched in infected plants. P. brassicae infection significantly increased rhizobacterial richness (ACE index, p < 0.05) and restructured the community composition, marked by enrichment of Paenibacillus (LDA score > 3.0). Procrustes analysis revealed tight coupling between microbial community shifts and metabolic reprogramming (M² = 0.446, p = 0.005), while Spearman correlations implicated pathogen-induced metabolites like geniposidic acid in recruiting beneficial Paenibacillus. Our results reveal that plant hosts dynamically secrete defense-related root metabolites to remodel the rhizosphere microbiome in response to P. brassicae infection. This dual-omics approach elucidates a chemical dialogue mediating plant–microbe–pathogen interactions, offering novel insights for engineering disease-suppressive microbiomes through root exudate manipulation. Full article

Bacterial endophytes have emerged as critical components of plant microbiomes, offering multifaceted benefits ranging from growth promotion to stress resilience. This review synthesizes two decades of research, from 2004 to 2024, on bacterial endophyte identification and applications, highlighting advances in both traditional culture-based techniques and modern omics approaches. The review also focuses on interactions between these microorganisms and their host plants, emphasizing their roles in biocontrol, phytoremediation, and nanoparticle biosynthesis. While significant progress has been made in characterizing cultivable bacterial endophytes, challenges persist in accessing unculturable species and understanding strain-specific functional mechanisms. The integration of metagenomics, metatranscriptomics, and metabolomics has begun unraveling this hidden diversity, revealing novel metabolic pathways and plant–microbe communication systems. There have been limitations in endophyte isolation protocols and field applications, and therefore a need exists for standardized frameworks to bridge lab-based discoveries with agricultural practices. Cutting-edge multi-omics techniques, such as genomics, transcriptomics, metabolomics, proteomics, and phenomics, should be used more in future research to clarify the mechanistic underpinnings of plant–endophyte interactions to thoroughly profile the microbial communities and unlock their functional potential under diverse environmental conditions. Overall, bacterial endophytes present viable paths toward sustainable farming methods, supporting food security and crop resilience in the face of environmental difficulties by providing a transformative opportunity for next-generation agriculture, mitigating climate-related agricultural stressors, reducing dependence on synthetic agrochemicals, and enhancing crop productivity. Full article

Rice (Oryza sativa L.) is a staple crop for over half of the global population; however, pathogenic infections pose significant threats to its sustainable production. Although chemical pesticides are commonly employed for disease control, their prolonged usage has led to pathogen resistance, reduced effectiveness, and non-target toxicity, rendering them unsustainable for agricultural practices. Nanomaterials (NMs) present a promising alternative due to their small size, tunable release properties, and diverse mechanisms for disease resistance. This review examines how NMs can enhance rice disease management through (1) direct pathogen suppression; (2) the activation of plant defense pathways; (3) the formation of nanoscale barriers on leaves to obstruct pathogens; (4) targeted delivery and controlled release of fungicides; and (5) modulation of the microbiome to bolster resilience. Moreover, we critically analyze the agricultural potential and environmental implications of NMs, develop optimized application strategies, and, for the first time, propose the innovative ‘NMs-Rice-Soil’ Ternary System framework. This groundbreaking approach integrates nanotechnology, plant physiology, and soil ecology. The pioneering framework offers transformative solutions for sustainable crop protection, illustrating how strategically engineered NMs can synergistically enhance rice productivity, grain quality, and global food security through science-based risk management and interdisciplinary innovation. Full article

The Asian citrus psyllid (Diaphorina citri) is an economically important pest of citrus as it is a vector of the bacterium (Candidatus Liberibacter asiaticus, CLas) that causes huanglongbing disease (HLB). Understanding the virome of D. citri is important for uncovering factors that influence vector competence, to support biosecurity surveillance, and to identify candidate agents for biological control. Previous studies have identified several D. citri-associated viruses from various geographical populations of this pest. To further investigate virus diversity in this pest, high-throughput sequencing was used to analyse D. citri populations from the Samoan islands of Upolu and Savai’i. Eleven novel viruses from the Yadokariviridae, Botourmiaviridae, Nodaviridae, Mymonaviridae, Partitiviridae, Totiviridae, and Polymycoviridae were identified as well as some that corresponded to unclassified groups. In addition, microbiome analysis revealed the presence of several endosymbiotic microorganisms, including Wolbachia, as well as some plant pathogenic fungi, including Botrytis cinerea. However, the causative agent of HLB disease (CLas) was not detected in the RNA-Seq data. These findings highlight the complex and diverse microbiota associated with D. citri and suggest potential interactions and dynamics between microorganisms and psyllid-associated viruses. Further research is needed to understand the ecological significance of these discoveries, and whether the novel viruses play a role in regulating field populations of the psyllid. Full article

Amelanchier alnifolia is a plant known for its nutritional and bioactive properties. Its leaves contain a high concentration of active compounds with significant antioxidant and antidiabetic effects, including strong α-glucosidase inhibitory potential. The combination of these bioactive leaf extracts with prebiotic substances, such as fructooligosaccharides (FOS), galactooligosaccharides (GOS), and chitooligosaccharides (COS), enables the development of functional systems with enhanced beneficial properties. In this study, process optimization for leaves extraction was performed using a Plackett–Burman screening design, which identified key parameters for further optimization using the Box–Behnken design. The optimal extraction conditions were determined as follows: methanol content 58.06%, solid-to-solvent ratio 26.03 m/v, and extraction time 73.56 min. These conditions yielded the highest the total phenolic content (TPC). A comparative analysis of different cultivars revealed significant variations in polyphenol content among them. The formulated lyophilized systems with GOS, FOS and COS positively influenced the chlorogenic acid release profile, while maintaining the extract’s antidiabetic and antioxidant properties. FT-IR analysis confirmed the molecular interactions responsible for these effects. The prebiotic effectiveness of the systems was quantitatively evaluated using two key parameters: the prebiotic index (PI), and the prebiotic activity score (PAS). Microbiological analyses demonstrated the beneficial effects of prebiotic-enriched systems characterized by better prebiotic action on Bifidobacterium strains than the pure extract. These findings suggest that A. alnifolia leaf extracts, in combination with prebiotics, could serve as promising functional ingredients with potential applications in health-promoting and antidiabetic formulations. Full article

The modern livestock industry incorporates widely used antibiotic growth promoters into animal feed at sub-therapeutic levels to enhance growth performance and feed efficiency. However, this practice contributes to the emergence of antibiotic-resistant pathogens in livestock, which may be transmitted to humans through the food chain, thereby diminishing the efficacy of antibiotics in treating bacterial infections. Current research explores the potential of essential oils from derived medicinal plants as alternative phytobiotics. This review examines modern encapsulation strategies that incorporate essential oils into natural-origin matrices to improve their stability and control their release both in vitro and in vivo. We discuss a range of encapsulation approaches utilizing polysaccharides, gums, proteins, and lipid-based carriers. This review highlights the increasing demand for antibiotic alternatives in animal nutrition driven by regulatory restrictions, and the potential benefits of essential oils in enhancing feed palatability and stabilizing the intestinal microbiome in monogastric animals and ruminants. Additionally, we address the economic viability and encapsulation efficiency of different matrix formulations. Full article

The rhizosphere microbiome plays an important role in carbon- and nitrogen-cycling in soil and in the stress response of plants. It also affects the function of the ammonium transporter (AmtB) that senses nitrogen levels inside and outside the cells of the associative nitrogen-fixing bacterium GXGL-4A. However, the potential mechanism of the interaction between the AmtB deletion mutant of GXGL-4A (∆amtB) and microorganisms in the rhizosphere of plants under low-nitrogen stress is still unclear. As revealed by transcriptome analyses, mutation of the amtB gene in GXGL-4A resulted in a significant up-regulation of many functional genes associated with nitrogen fixation and transportation at transcription level. The application of ∆amtB changed the nitrogen level in the rhizosphere of cucumber seedlings and reshaped the microbial community structure in the rhizosphere, enriching the relative abundance of Actinobacteriota and Gemmatimonadota. Based on bacterial functional prediction analyses, the metabolic capacities of rhizobacteria were improved after inoculation of cucumber seedlings with the original strain GXGL-4A or the ∆amtB mutant, resulting in the enhancement of amino acids, lipids, and carbohydrates in the cucumber rhizosphere, which promoted the growth of cucumber plants under a low-nitrogen stress condition. The results contribute to understanding the biological function of gene amtB, revealing the regulatory role of the strain GXGL-4A on cucumber rhizosphere nitrogen metabolism and laying a theoretical foundation for the development of efficient nitrogen-fixing bacterial agents for sustainable agricultural production. Full article