Search Results (476)

Soil contamination in industrial areas often involves complex mixtures of contaminants, making remediation a significant challenge. Microbe-assisted phytoremediation offers a promising solution, yet its success depends on understanding interaction between plants, microorganisms, and contaminants in rhizosphere. This study examined the effects of organic (oil sludge) and inorganic (Zn) contaminants, applied individually and in combination, on the rhizosphere bacterial community of Miscanthus × giganteus Greef et Deu (M×g), with emphasis on strains exhibiting plant growth-promoting, hydrocarbon-degrading, and metal-tolerant traits. A one-season greenhouse experiment included soils spiked with Zn (1650 mg kg⁻¹) and/or oil sludge (15 mL kg⁻¹). Oil sludge exerted a stronger influence on the taxonomic structure of rhizobacterial communities than Zn, largely shaping the patterns observed under co-contamination. Zn exposure increased the relative abundance of Actinobacteriota, whereas oil sludge favoured Proteobacteriota. Both contaminants, individually and together, enhanced the proportion of Sphingomonadaceae. Across all treatments, taxa with potential plant-growth-promoting traits were present, while co-contaminated soil harboured microorganisms capable of hydrocarbon degradation, heavy metal tolerance, and plant growth promotion. These findings highlight the adaptive capacity of the M×g rhizobiome and support its application in phytoremediation. The isolation and characterisation of rhizosphere-associated strains provide basis for developing microbial bioagents to enhance biomass production and remediation efficiency in multi-contaminated environments. Full article

Seed-associated microbiomes represent an underexplored frontier in synthetic community (SynCom) design, particularly in forage legumes such as lucerne (Medicago sativa L.), where early microbial assembly can shape plant development. Crop wild relatives (CWRs) harbour more diverse seed microbiomes and may contain microbes with greater functional potential than domesticated lucerne. To test this, SynComs were constructed from seed-borne bacteria isolated from M. laciniata (drought-resilient) and M. littoralis (salt-tolerant). Two three-strain SynComs were assembled from taxa consistently shared across lucerne and its CWRs, and a third six-strain ‘Mix’ SynCom combined both sets. The aim of this study was to assess whether these SynComs exert phenotypic effects on lucerne growth when used as seed inocula alongside the native microbiome during early development and later vegetative stages under well-watered and drought conditions. Inoculation enhanced germination and early growth, with the Mix SynCom producing the strongest gains. Microbiome profiling at 24 days revealed treatment-specific restructuring, with enrichment of beneficial taxa and microbial coalescence. While early-stage benefits diminished at later stages, and drought ultimately reduced biomass across all treatments, the findings demonstrate that CWR-derived SynComs can enhance lucerne establishment and early growth while restructuring host microbiomes, providing a framework for seed-applied microbial solutions in sustainable agriculture. Full article

Noccaea species (formerly Thlaspi) are Brassicaceae plants renowned for their capacity to hyperaccumulate zinc (Zn), cadmium (Cd), and nickel (Ni), which has made them model systems in studies of metal tolerance, phytoremediation, and plant adaptation to extreme environments. While their physiological and genetic responses to metal stress are relatively well characterised, the extent to which these traits influence microbiome composition and function remains largely unexplored. These species possess compact genomes shaped by ancient whole-genome duplications and rearrangements, and such genomic traits may influence microbial recruitment through changes in secondary metabolism, elemental composition, and tissue architecture. Here, we synthesise the current findings on how genome size, metal hyperaccumulation, structural adaptations, and glucosinolate diversity affect microbial communities in Noccaea roots and leaves. We review evidence from bioimaging, molecular profiling, and physiological studies, highlighting interactions with bacteria and fungi adapted to metalliferous soils. At present, the leaf microbiome of Noccaea species remains underexplored. Analyses of root microbiome, however, reveal a consistent taxonomic core dominated by Actinobacteria and Proteobacteria among bacterial communities and Ascomycetes, predominantly Dothideomycetes and Leotiomycetes among fungi. Collectively, these findings suggest that metal-adapted microbes provide several plant-beneficial functions, including metal detoxification, nutrient cycling, growth promotion, and enhanced metal extraction in association with dark septate endophytes. By contrast, the status of mycorrhizal associations in Noccaea remains debated and unresolved, although evidence points to functional colonisation by selected fungal taxa. These insights indicate that multiple plant traits interact to shape microbiome assembly and activity in Noccaea species. Understanding these dynamics offers new perspectives on plant–microbe co-adaptation, ecological resilience, and the optimisation of microbiome-assisted strategies for sustainable phytoremediation. Full article

Humic substances and beneficial microorganisms are key biostimulants for sustainable agriculture and global food security in the face of climate change. Marine bacteria are emerging as a promising source of plant-beneficial microbes, tapping into a microbial diversity as immense as the oceans themselves. However, their potential, limitations, and mechanisms of action––especially in combination with other biostimulants––remain largely unexplored. In this study, we isolated the Streptomyces sp. LAP3 strain from the giant limpet Scutellastra mexicana. We evaluated the efficacy of the marine bacterium, applied alone or in combination with the humic product Leonardite hydrolate (L), in enhancing tomato performance under field conditions. Treatments included: (1) marine Streptomyces (MS), (2) Leonardite hydrolate (L), (3) both biostimulants (MS + L), and (4) a control (CTRL). We assessed growth, photosynthetic performance, antioxidant responses, and fruit yield and quality. Both biostimulants individually improved plant performance, but their combination had a significant synergistic effect, markedly boosting tomato productivity, thermotolerance, and resilience during a heatwave. Enhanced photosynthetic efficiency and antioxidant enzyme activity were associated with improved agronomic traits. These results highlight the potential of combining Streptomyces sp. LAP3 and Leonardite hydrolate as an eco-friendly strategy to increase crop productivity, strengthen stress resilience, promote sustainable agriculture, and reduce reliance on agrochemicals. Full article

The application of plasma technology in agriculture has emerged as a promising approach to enhance plant health and manage microbial interactions, offering potential solutions for sustainable crop production and disease control. This study contributes to this field by exploring the effects of plasma treatments on plant physiology and microbial dynamics, with a focus on their potential to improve agricultural outcomes. This investigation aims to systematically determine optimal plasma seed treatment parameters for enhancing plant vigor and promoting beneficial microbial associations while minimizing pathogenic interactions in Arabidopsis thaliana. This study focuses on understanding the effects of various plasma treatments on chlorophyll content, root length, microbial growth, and microbial quantification in plants and microbes. The treatments involve the use of an atmospheric jet plasma handheld device, a globe plasma, and a glow discharge plasma chamber with air and argon. These treatments were applied for varying time durations from 10 s to 5 min. The results demonstrated that the globe plasma treatment for 1 min significantly enhanced chlorophyll a extraction and root length, outperforming the other treatments. Additionally, the study examined the impact of plasma on plant–microbe interactions to assess whether plasma treatments affect beneficial microbes. Plasma treatments showed minimal impact on most beneficial microbe activity, though species-specific sensitivities were observed, with Pseudomonas cedrina showing moderate growth inhibition, revealing no significant disruption to their activity. The microbial quantification assays indicated that the globe plasma treatment effectively reduced microbial counts, while combined treatment with plant and microbe plasma together did not yield significant changes. Additionally, the chlorophyll estimation of plasma-treated samples indicated that the globe plasma and atmospheric jet plasma treatments were effective in enhancing chlorophyll content, whereas the combined treatment with both plant and microbe plasma did not yield significant changes. These findings suggest that plasma treatments, especially the globe plasma, are effective in improving plant health and controlling microbial activity. Future research should focus on optimizing plasma conditions, exploring the influence of plasma parameters and the underlying mechanisms, and expanding the scope to include a wider range of plant species and microbial strains to maximize the benefits of plasma technology in agriculture. Full article

The mycoheterotrophic orchid Gastrodia elata relies entirely on symbiosis with Armillaria for nutrient acquisition during tuber development. The signaling mechanisms underlying this interaction have long been a research focus, and several pathways, such as phytohormone-mediated signaling, have been reported. However, the role of plant-derived extracellular vesicles (PDEVs) in G. elata–Armillaria communication remains unexplored. In this study, we conducted a comprehensive lipidomic analysis of G. elata-derived extracellular vesicles (GDEVs) isolated from juvenile, immature (active symbiosis), and mature tubers. By employing high-resolution mass spectrometry and advanced statistical methods, we established a detailed EV lipidome profile for G. elata, identifying 996 lipid species spanning eight major classes. Distinct lipidomic remodeling was observed throughout tuber maturation. Notably, as the immature stage corresponds to the period of peak symbiotic activity, targeted lipidome comparisons enabled the identification of core lipid markers, particularly Glc-sitosterols and the polyketide 7,8-dehydroastaxanthin, which are highly enriched during active symbiosis and potentially associated with inter-kingdom communication. These findings suggest that developmentally regulated lipid transport via EVs plays a critical role in mediating G. elata–Armillaria interaction. Our work not only illuminates the contribution of vesicle lipids to plant–fungal interaction but also provides a methodological foundation for investigating EV-mediated signaling in non-model plant–microbe systems. Full article

Drought stress poses a significant threat to olive cultivation in Mediterranean regions. This study investigated the resilience and functional adaptation of root-associated and rhizosphere soil microorganisms of four olive cultivars under contrasting water regimes (irrigated vs. drought) across seasons. Using a combination of amplicon-targeted metagenomics, phylogenetic analysis, and text mining of the scientific literature, we identified a conserved core microbiome and revealed that drought stress significantly alters the structure of root-associated—but not rhizosphere soil—bacterial communities. Potential functional profiling indicated that drought conditions enriched for genes involved in stress response pathways, including branched-chain amino acid transport, glutathione S-transferase activity, thioredoxin reductase, and chemotaxis. Text mining co-occurrence networks highlighted strong associations between some key bacterial genera and plant growth-promoting functions like phytohormone production and biocontrol. Furthermore, we identified Solirubrobacter, Microvirga, and Pseudonocardia as the primary contributors to these drought-resilience functions. The stability of the soil microbiome suggests functional redundancy, whereas the restructuring of the root endophytic compartment indicates active plant selection for beneficial microbes. Our findings provide a foundation for developing tailored microbial consortia (SynComs) to enhance drought tolerance in olive trees and support sustainable agriculture in water-limited environments. Full article

Early-onset colorectal cancer (EOCRC) is emerging as a significant global health concern, particularly among individuals under the age of 50. This alarming trend has coincided with an increase in the consumption of processed foods that often rely heavily on synthetic preservatives. At the same time, these additives play a critical role in ensuring food safety and shelf life. Growing evidence suggests that they may contribute to adverse gut health outcomes, which is a known risk factor in colorectal cancer development. At the same time, synthetic preservatives serve essential roles such as preventing microbial spoilage, maintaining color, and prolonging shelf life. Natural preservatives, on the other hand, not only provide antimicrobial protection but also exhibit antioxidant and anti-inflammatory properties. These contrasting functions form the basis of current discussions on their safety and health implications. Despite their widespread use, the long-term health implications of synthetic preservatives remain inadequately understood. This review synthesizes recent clinical, epidemiological, mechanistic, and toxicological data to examine the potential link between synthetic food preservatives and EOCRC. Particular focus is placed on compounds that have been associated with DNA damage, gut microbiota disruption, oxidative stress, and chronic inflammation, which are the mechanisms that collectively increase cancer risk. In contrast, natural preservatives derived from plants and microbes are gaining attention for their antioxidant, antimicrobial, and possible anti-inflammatory effects. While these alternatives show promise, scientific validation and regulatory approval remain limited. This review highlights the urgent need for more rigorous, long-term human studies and advocates for enhanced regulatory oversight. It advocates for a multidisciplinary approach to developing safer preservation strategies and highlights the importance of public education in making informed dietary choices. Natural preservatives, though still under investigation, may offer a safer path forward in mitigating EOCRC risk and shaping future food and health policies. Full article

Metagenomic investigation of gut microbiome is a comprehensive and rapid technique for the analysis and diagnosis of numerous diseases. The gut microbiome is an intricate ecosystem, coordinated by the interaction of various microbes and the metabolites produced by them, which helps in developing and sustaining immunity and homeostasis. A healthy gut microbiome is driven by different factors, such as nutrition, lifestyle, etc. The current study examines the association of diet to gut microbiome dysbiosis and its role in various disease conditions. Gut microbiome data was collected from 73 patients and tested at BioAro Inc. lab, using shotgun metagenomics through next generation sequencing. It was then analyzed and compared with data from 20 healthy subjects from HMP database. An in-house bioinformatics pipeline (PanOmiQ) and Pathogen Fast Identifier were utilized for secondary analysis, while tertiary analysis was accomplished using R software. Results showed a higher number of opportunistic pathogen microorganisms in the gut microbiome of subjects consuming a meat diet, as compared to those consuming a plant diet. These opportunistic pathogens included Ruminococcus torques (>3.34%), Ruminococcus gnavus (>2.22%), and Clostridium symbiosum (>1.87%). The study also found a higher relative abundance of these pathogens in cancer patients, as compared to healthy subjects. We also observed a highly significant (p < 0.0001) correlation of a meat diet with obesity in comparison to the subjects on a plant diet and the healthy subjects. Our findings suggest that patients following a plant diet have a lower relative abundance of pathogens that are associated with cancer and obesity. These findings provide critical insight into how we can use shotgun metagenomics to study the composition and diversity of the gut microbiome and the effects of a diet on the gut microbiome and its role in metabolic diseases. This is the first report investigating gut microbiota using shotgun metagenomics, correlating with different diseases and diet followed, which might impact the presence of opportunistic pathogens or keystones species. Additionally, it can provide valuable insights to physicians and dietetic practitioners for providing personalized treatment or customizing a diet plan. Full article

The prolonged and intensive use of chemical inputs in agriculture, particularly synthetic fertilizers, has generated a variety of environmental and agronomic challenges. This has intensified the need for alternative, viable, and sustainable solutions. Plant-associated microbes have emerged as promising candidates in this regard. While research has largely focused on bacteria and fungi, comparatively less attention has been paid to other microbial groups such as microalgae and cyanobacteria. These photosynthetic microorganisms offer multiple agronomic benefits, including the ability to capture CO₂, assimilate essential micro- and macroelements, and synthesize a wide range of high-value metabolites. Their metabolic versatility enables the production of bioactive molecules with biostimulant and biocontrol properties, as well as biofertilizer potential through their intrinsic nutrient content. Additionally, several cyanobacterial species can fix atmospheric nitrogen, further enhancing their agricultural relevance. This review aims to summarize the potential of these microorganisms and their application in the agriculture sector, focusing primarily on their biofertilization, biostimulation, and biocontrol capabilities and presents a compilation of the products currently available on the market that are derived from these microorganisms. The present work also identifies the gaps in the use of these microorganisms and provides prospects for developing a suitable solution for today′s agriculture. Full article

Tree plantations can help reverse the negative impacts of deforestation and land degradation worldwide, and soil microbial communities play key roles in tree growth and productivity. We studied microbial communities in the bulk soil of five native species monoculture plantations in the Republic of Panamá to assess how bacteria and fungi were affected by soil chemistry and plant identity after seven years of tree growth. Relative to the other species, Terminalia amazonia accumulated over three times the aboveground biomass and had lower mortality. Soil nutrients, especially phosphorus, were low, and we found no differences in soil chemistry across the five plantation types. Similarly, there was no difference in alpha diversity of the soil microbial communities across plantation types, and the bacterial communities showed no compositional variation or enrichment of any individual taxa. However, soil fungal communities differed in T. amazonia plantations as compared to the others, exhibiting enrichment or absence of specific taxa of arbuscular mycorrhizal fungi and putative phytopathogens. Our results suggest that T. amazonia may associate with certain microbial taxa that help it overcome low nutrient availability in these habitats. Consideration of plant–soil–microbe interactions in restoration efforts may facilitate tree growth and help to promote climate resilient forested areas. Full article

Plant-to-plant interactions are essential for structuring plant communities and supporting adaptation in nutrient-poor, seasonally dry environments. This study examined the interactions between moss Leucobryum aduncum Dozy & Molk and Oreocharis hainanensis by analyzing microbial communities and physicochemical parameters across various sample types. These included soil [bare (B), O. hainanensis (O), moss (M), and moss + O. hainanensis (MO)], rhizosphere soil [O. hainanensis (ORS), moss (MRS), and moss + O. hainanensis (MORS)], and root [O. hainanensis (OHR), moss (MR), and moss + O. hainanensis (MOR)] using metagenomics sequencing across dry and wet seasons in limestone habitats on Hainan Island. During the dry season, combined plant samples MOR, MO, and MORS showed higher nutrients, supported by microbes that enhance nutrient turnover, which may indicate facilitation. Conversely, during the wet season, increased moisture leads to decreased nutrient levels and microbial communities shift, associated with slower nutrient turnover in combined plant samples, which may reflect competition. According to KEGG analysis, an increase in oxidative phosphorylation and ABC transporters in the dry season supported the facilitative interaction, while quorum sensing and two-component systems supported the competitive interaction in the wet season. These findings show how shifts between facilitation and competition arise from seasonal conditions and microbes in the limestone ecosystem. 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

Natural dyes and pigments are gaining importance as a sustainable alternative to synthetic dyes. Sourced from renewable materials, they are known for their biodegradable and non-toxic properties, offering a diverse range of color profiles and applications across industries such as textiles, cosmetics, food, and pharmaceuticals. This manuscript discusses various aspects of natural dyes and pigments (derived from plants and microbes), including anthocyanins, flavonoids, carotenoids, lactones, and chlorophyll. Furthermore, it highlights the polyphenolic nature of these compounds, which is responsible for their antioxidant activity and contributes to their anticancer, antibacterial, antifungal, antiprotozoal, and immunomodulatory effects. However, natural dyes are often categorized as pigments rather than dyes due to their limited solubility, a consequence of their molecular characteristics. Consequently, this manuscript provides a detailed discussion of key structural challenges associated with natural dyes and pigments, including thermal decomposition, photodegradation, photoisomerization, cross-reactivity, and pH sensitivity. Due to these limitations, natural dyes are currently used in relatively limited applications, primarily in the food industry, and, to lesser extent, in textiles and coatings. Nevertheless, with ongoing research and technological innovations, natural dyes present a viable alternative to synthetic dyes, promoting a more sustainable and environmentally conscious future. Full article

One of the important traits of many plant growth-promoting rhizobacteria (PGPR) is the biocontrol of phytopathogens. Some PGPR metabolize phytohormone abscisic acid (ABA); however, the role of this trait in plant–microbe interactions is scarcely understood. Phytopathogenic fungi produce ABA and use this property as a negative regulator of plant resistance. Therefore, interactions between ABA-producing necrotrophic phytopathogen Botrytis sp. BA3 with ABA-metabolizing rhizobacterium Rhodococcus sp. P1Y were studied in a batch culture and in gnotobiotic hydroponics with sunflower seedlings. Rhizobacterium P1Y possessed no antifungal activity against BA3 and metabolized ABA, which was synthesized by BA3 in vitro and in associations with sunflower plants infected with this fungus. Inoculation with BA3 and the application of exogenous ABA increased the root ABA concentration and inhibited root and shoot growth, suggesting the involvement of this phytohormone in the pathogenesis process. Strain P1Y eliminated negative effects of BA3 and exogenous ABA on root ABA concentration and plant growth. Both microorganisms significantly modulated the hormonal status of plants, affecting indole-3-acetic, salicylic, jasmonic and gibberellic acids, as well as cytokinins concentrations in sunflower roots and/or shoots. The hormonal effects were complex and could be due to the production of phytohormones by microorganisms, changes in ABA concentrations and multiple levels of crosstalk in hormone networks regulating plant defense. The results suggest the counteraction of rhizobacteria to ABA-producing phytopathogenic fungi through the metabolism of fungal ABA. This expands our understanding of the mechanisms related to the biocontrol of phytopathogens by PGPR. Full article