Search Results (1,786)

Some actinobacterial species have been reported to improve plant growth due to their roles as biostimulants and biological control agents. In this study, the effect of actinobacterial isolate 27, obtained from the rhizospheric soil of melon plants and identified as Streptomyces calvus, was evaluated on the growth of Arabidopsis thaliana and tomato plants. In Arabidopsis, in vitro assays showed that after seven days of interaction, isolate 27 increased fresh weight by 1.4-, 1.5-, and 2.3-fold and lateral root number by 1.7-, 1.3-, and 2.5-fold under physical contact and split-plate systems (MS and ISP2 media), respectively, compared with non-inoculated plants. An increased β-glucuronidase (GUS, encoded by the uidA gene) signal was observed in primary and lateral roots of the Arabidopsis DR5::uidA reporter line during both interaction types, suggesting the activation of auxin-responsive pathways. In addition, isolate 27 rescued the rhd6 (root hair defective 6) mutant phenotype, restoring root hair formation. Gas chromatography-mass spectrometry (GC-MS) analysis revealed that isolate 27 emitted volatile organic compounds (VOCs), including an alcohol and several sesquiterpenes, and that this profile changed during interaction with Arabidopsis plantlets. In soil-based pot assays, inoculation with isolate 27 significantly enhanced the development of Arabidopsis plants after 23 days, both when applied alone and in co-inoculation with Trichoderma atroviride. Furthermore, isolate 27 stimulated tomato plant growth, leading to significant increases in fresh and dry biomass, as well as shoot and root lengths after 28 days. Overall, these results demonstrate that S. calvus isolate 27 promotes plant growth and development through the production of bioactive compounds that modulate plant growth pathways, including hormonal responses, highlighting its potential as a bioinoculant for sustainable and productive agricultural systems. Full article

Root exudates are key drivers of rhizosphere microbial assembly, yet their effects across coexisting plant species with different functional roles remain unclear. We examined the effects of root exudates from five desert steppe species in Inner Mongolia: one constructive species, two dominant species, and two accompanying species. Exudates were collected hydroponically and applied to bulk soil in a three-week incubation experiment. Microbial communities were analyzed using high-throughput sequencing, functional prediction, and co-occurrence network analysis. Exudate addition significantly altered bacterial community composition, reducing bacterial richness, while fungal communities showed weaker responses. Exudates from constructive and dominant species enriched Actinobacteria, including Rubrobacter, Arthrobacter, and Solirubrobacter, and increased functional groups linked to chemoheterotrophy and nitrogen transformation. In contrast, exudates from accompanying species induced distinct microbial assemblages without promoting Actinobacteria dominance. Exudate addition also increased bacterial network complexity, suggesting enhanced microbial interactions. Soil pH decreased and available nitrogen and phosphorus increased, strongly correlating with bacterial community shifts. Overall, root exudates mediate species-specific microbial assembly and functional reorganization in desert steppe soils, driven mainly by plant functional roles rather than taxonomic relatedness. This study provides new insights into how plant-derived substrates regulate microbial communities and nutrient cycling in arid ecosystems. Full article

The human gut microbiota represents a complex and dynamic ecosystem of trillions of microorganisms that play a fundamental role in maintaining physiological homeostasis, regulating metabolism, and modulating the immune system. This narrative review explores the biochemical intricacies of the gut microbiome, focusing on the dominant phyla (Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Verrucomicrobia, Fusobacteria) and their specific contributions to host health. A critical emphasis is placed on the metabolic outputs of these microorganisms, such as short-chain fatty acids (SCFAs) like butyrate, which serve as vital energy sources and anti-inflammatory signaling molecules. Conversely, the review examines how dysbiosis, the disruption of microbial balance, is mechanistically linked to the pathogenesis of diverse conditions, including obesity, diabetes mellitus, inflammatory bowel disease (IBD), and gout. Furthermore, it highlights the profound impact of dietary interventions on microbial architecture, notably, how non-digestible carbohydrates promote beneficial taxa and eubiosis, while high-fat and high-sugar diets drive metabolic endotoxemia and systemic inflammation. By synthesizing current knowledge on microbial biotransformations of proteins and polyphenols, this work underscores the bidirectional relationship between nutrition and the microbiome. Ultimately, understanding these biochemical interactions is essential for developing targeted probiotic, prebiotic, and nutritional strategies to prevent and manage chronic metabolic and inflammatory disorders. Full article

Two phenylacetaldehyde dehydrogenases, originating from Escherichia coli K-12 (FeaB-K-12) and Sphingopyxis fribergensis Kp5.2 (FeaB-Kp5.2), were immobilized on powdery silica carrier with various functionalization. First, the suitability of these carriers for application in combination with phenylacetaldehydes and phenylacetic acids was studied. Out of two carriers functionalized differently, mesoporous cellular foam, whose surface was modified with 3-glycidyloxypropyl groups (MCF-G), showed promising results. Hence, this carrier was further tested at 17 different immobilization conditions. Despite both enzymes showing high immobilization efficiency, the initial activities were relatively low compared to the free enzymes. Interestingly, the immobilized FeaB-Kp5.2 on MCF-G-Kw showed about 80% of retained activity after two months of incubation at 0 °C, indicating that the immobilization enhances the stability of this enzyme. In contrast, no changes in the temperature stability of FeaB-Kp5.2 due to immobilization could be noted. However, relative enzyme activities towards all three substituted phenylacetaldehydes could be increased by the immobilization to approximately 130%. The most active and stable powdery immobilizate was MCF-G-Kw-FeaB-Kp5.2 at pH 8. In addition, FeaB-Kp5.2 was also immobilized and tested on monolith silica carrier for continuous catalysis to produce phenylacetic acids. Full article

Understanding the succession of soil microbial carbon metabolism functions is crucial for elucidating carbon cycling mechanisms during ecosystem restoration in sandy lands. Soils were collected from Caragana korshinskii shrubland sites across a restoration chronosequence (0, 10, 30, 50, and 70 years) in the Mu Us Sandy Land. Biolog carbon source utilization analysis and metagenomic sequencing were employed to characterize the successional patterns of microbial carbon metabolism functions—a shift in carbon metabolism strategies from acquisition to conservation, and a transition in functional diversity from generalism to specialization. The results indicated that microbial communities exhibited two associated successional shifts in functional characteristics: carbon source utilization tended to transition from simple to complex substrates, while functional gene expression showed a progressive shift from broad multi-pathway patterns toward pathway-specific specialization. AWCD values increased continuously with restoration duration, and carbon source utilization patterns diverged significantly around 30 years. Early-stage sites (0–30 years) primarily utilized simple carbon sources, whereas late-stage sites (50–70 years) shifted toward more complex and diverse substrates. Principal component analysis revealed that 27 carbon sources contributed 91.3% of the variance to PC1. Microbial community structure succession revealed that Actinobacteria peaked at 10 years (43.63%), Proteobacteria peaked at 30 years (45.66%), and taxa such as Bacilli and Solirubrobacter dominated at 50–70 years. Carbon metabolism pathways exhibited stage-specific succession: glycolysis and the ED pathway were active in early stages, acetate metabolism dominated with the 3HB cycle peaking in intermediate stages, and the CBB cycle increased in later stages while methane metabolism shifted from high to low contribution. These two associated successional shifts occurred along the same restoration chronosequence, with the progressive transition in substrate utilization accompanying the development of specialist functional characteristics. These findings provide insights into the successional dynamics of microbial carbon metabolism during vegetation restoration, offering a microbiological basis for optimizing ecological restoration practices and enhancing soil carbon sequestration in sandy lands. Full article

This study aims to explore the effects of micro-polluted river water on nitrogen and microbial communities of paddy field soil under different irrigation modes. The experiment was conducted in a water-saving park in Nanjing. By establishing three water quality conditions—clean water, micro-polluted river water, and alternating irrigation—and two moisture conditions—flood irrigation and controlled irrigation—this study investigates the effects of different irrigation patterns on soil nitrogen and microbial communities. The results indicate that, under flood irrigation, the input of micro-polluted river water can effectively alleviate NH₄⁺-N loss during the heading stages of rice growth by 49.3%. Moisture conditions are the primary factor influencing microbial community structure. Although the input of micro-polluted river water reduces community stability, rotation irrigation can increase microbial abundance and enhance network complexity, thereby enhancing the system’s resilience. Redundancy analysis shows that soil moisture, pH, and ion content are the key environmental factors driving microbial distribution. The clean and polluted water rotation irrigation model performs best in maintaining soil nitrogen and microbial health. Rotation irrigation promotes the enrichment of key functional groups, such as Actinobacteria, effectively increasing rice yield. This study provides a theoretical basis for promoting sustainable agricultural production through water resource management. Full article

In the present study, we conducted three treatments with different cadmium concentrations and three different soil types selected for grape cultivation to assess the accumulation and migration characteristics of Cadmium (Cd) in the soil–grape system in different years. The change in Cd fractions in soil and the transfer and accumulation of Cd in different soil–grape systems were analyzed to evaluate the health risks of pulp cadmium accumulation to grape consumers. The results showed that after the planting of the grape, the active Cd fraction increased by 1~3 times and the stable fraction decreased by 1~3 times compared to before planting grapes. It gradually began to stabilize as the cultivation period progressed. The bioaccumulation factor (BCF) of Cd in different parts of grape was ranked as: root (0.094~2.590) > stem (0.117~2.112) > leaf (0.008~0.621) > seed (0.010~0.195) > skin (0.000~0.148) > pulp (0.000~0.156). High Cd concentration inhibited the transfer of Cd from the soil and root to the aboveground part of the grape. The Cd of grape pulp has no health risks. Cd pollution significantly altered the soil microbial community, suppressing Actinobacteria while enriching Acidobacteria. The results of this study will help to clarify migration patterns between different soil–grape systems and providing effective data and theoretical support for the management of Cd pollution in vineyard soils. Full article

Background and Aims: Severe alcohol-associated hepatitis (SAH) can trigger unstable decompensations in cirrhosis patients. They experience high rates of emergency department visits and hospitalization. We evaluated real-world clinical outcomes following palliative-faecal microbiota transplantation (pFMT) compared to best supportive care (BSC) in this critically ill population. Patients and Methods: From July 2021 to April 2024, 28 patients on pFMT were compared with 37 on BSC. Patients on pFMT received nasoduodenal healthy donor stool infusion daily for 5-days. Patients were followed up for portal hypertension-related events, infections, hospitalizations, extrahepatic organ failure and 6- and 12-months survival. 16S rRNA sequencing on stool samples collected at baseline and on follow up were analysed for changes in relative abundance (RA) of bacterial communities. Results: Patients were matched for age, type of decompensation and liver disease severity at enrolment. Twelve-month survival was 64.3% in pFMT versus 51.4% in BSC groups. pFMT dramatically reduced hospital readmissions (mean 0.76 ± 0.76 vs. 2.29 ± 1.27, p < 0.001). Unstable decompensations beyond 3 months occurred in 14.3% of pFMT versus 64.9% of BSC (p < 0.001). Organ failures were lesser with pFMT: acute kidney injury 7.7% versus 93.8% (p < 0.001), hepatic encephalopathy 7.1% versus 68.2% (p < 0.001). Infection burden was significantly lower (53.6% vs. 83.8%, p = 0.008), particularly infections requiring admission (17.4% vs. 66.7%, p < 0.001) with pFMT. Microbiome analysis revealed progressive expansion of Gram-negative genera in BSC, and beneficial Actinobacteria in pFMT-treated patients at 3, 6, and 12 months. Conclusions: Palliative FMT represents a unique disease-modifying intervention in end-stage alcohol-related cirrhosis, preventing organ failure progression, reducing healthcare utilization, and improving survival trajectories. Full article

Acyl-CoA carboxylase (YCC) complexes generate essential starter and extender units for fatty acid and polyketide biosynthesis in Actinobacteria. In Streptomyces coelicolor, two tri-subunit YCC complexes, acetyl-CoA carboxylase (ACC) and propionyl-CoA carboxylase (PCC), have been characterized. However, comparative genomic analyses indicate that β/ε subunits are more diversified than currently appreciated. Here, we identify a previously unrecognized β/ε pair, AccB2 and AccE2, and demonstrate that they assemble with the canonical α subunit to form a functional YCC complex. Both genes are transcribed in vivo, and co-immunoprecipitation (Co-IP) reveals association with AccA1 and AccA2, with AccE2 showing stronger relative association with AccA1-containing pull-downs. In vitro reconstitution confirms carboxylation activity toward acetyl-CoA, propionyl-CoA, and butyryl-CoA, which is strongly dependent on AccE2. These findings expand the YCC repertoire in S. coelicolor and support a modular assembly model in which alternative β/ε combinations contribute to functional diversification of YCC complexes. Full article

Elemental migration and enrichment are important processes influencing tea plant growth and the assembly of rhizosphere bacterial communities within the rock–soil–plant continuum. This study explores how soil parent materials (granite, quartz schist, and sericite schist) are potentially associated with these processes and their observed associations with the elemental composition of tea leaves. Exploratory statistical analyses revealed distinct, lithology-specific biogeochemical patterns that serve as a foundation for hypothesis generation. In granite soils, chlorite correlated with the mobility of Cr, Pb, Cu, Ni, Mg, and Na, coinciding with shifts in the relative abundances of Verrucomicrobia, Armatimonadetes, and Chloroflexi. In quartz schist, kaolinite exhibited notable correlations with the dynamics of Pb, Cr, Ni, Zn, and As, which were statistically linked to Planctomycetes, Proteobacteria, and Acidobacteria. Complex mineral–microbe interactions were observed in sericite schist soils, where clay minerals (e.g., chlorite, illite) were closely associated with the migration of multiple elements (Pb, K, Ca, Cd, As, Al, Fe, Zn), paralleling structural variations in communities of Actinobacteria, Planctomycetes, Chloroflexi, and Proteobacteria. Potassium (K), calcium (Ca), and manganese (Mn) showed bioaccumulation tendencies in tea leaves across all lithologies, with an enrichment capacity order of Ca > K > Mn > Mg > Na > Al. Exploratory Classification and Regression Tree (CART) analysis suggested that the migration of K, Ca, Cu, Zn, and Hg corresponded most closely with their soil concentrations. Manganese (Mn) exhibited a mineral-associated trend, with kaolinite content as a potential correlate, while cadmium (Cd) migration was statistically linked to the relative abundance of Armatimonadetes. These findings highlight potential candidate relationships between mineralogy, microbes, and elemental mobility rather than confirming causal mechanisms, emphasizing the need for further validation in larger or experimental datasets. Full article

Bacillus coagulans has attracted widespread attention in the treatment of irritable bowel syndrome due to its multiple probiotic functions, yet its specific molecular mechanisms remain unclear, and the efficacy of probiotics exhibits significant strain specificity, posing a key bottleneck for practical application. To address this, this study obtained a bile salt-tolerant B. coaguans idrc019 through in vitro screening. This strain demonstrated strong survival and germination in simulated gut conditions, supporting effective intestinal colonization. Further evaluation in an IBS animal model revealed that idrc019 alleviated visceral hypersensitivity and colonic inflammation in a dose-dependent manner. Through enhanced intestinal barrier integrity, microbiota modulation (e.g., Actinobacteria restoration), and elevated metabolites (e.g., kynurenine), the strain exerted IBS-alleviating effects via synchronized immune, microbial, and metabolic regulation. Our findings offer a mechanistically grounded probiotic candidate, underscore functional screening as a critical strategy, and pave the way for clinical application. Full article

Hemp (Cannabis sativa L.) is an important crop, yet little is known about how herbivory and soil microbial communities interact to influence plant performance. In this study, two hemp cultivars, BaOx and Cherry Citrus, were grown under identical greenhouse conditions and exposed to naturally occurring background populations of the two-spotted spider mite (Tetranychus urticae). Plant traits were measured, and rhizosphere soil was sampled for 16S rRNA gene sequencing to compare bacterial community composition and diversity between cultivars. Spider mite injury was assessed using a standardized 0–5 visual damage scale commonly applied in integrated pest management studies. Although the cultivars did not differ significantly in growth traits, Cherry Citrus experienced significantly less spider mite damage than BaOx, suggesting greater tolerance or resistance to herbivory under shared conditions. Rhizosphere bacterial communities differed markedly between cultivars despite identical soil and environmental conditions. BaOx rhizospheres were enriched in Actinobacteria, including taxa associated with decomposition and antimicrobial compound production, whereas Cherry Citrus rhizospheres were enriched in Alphaproteobacteria, particularly nitrogen-cycling and root-associated taxa such as Rhizobium and Reyranella. Alpha diversity metrics did not differ between cultivars; however, beta diversity analyses revealed significant cultivar-level separation, particularly in phylogenetic community structure. Because herbivore pressure and microbial communities were not experimentally manipulated, this observational study identifies ecological associations rather than direct causal relationships. Nevertheless, the results demonstrate that hemp cultivar identity is associated with distinct rhizosphere microbiomes and differential susceptibility to spider mite damage. These findings highlight the potential for integrating cultivar selection and microbiome-informed strategies into sustainable pest management programs for hemp. Full article

Soil-borne diseases have become increasingly serious due to continuous planting. Soil fumigation may be inadequate because of the persistence of soil-borne pathogens on ginger seed rhizome. A combined strategy of soil fumigation and seed rhizome disinfection would be necessary to achieve synergistic control. In this study, the approach of soil fumigation with chloropicrin (CP) coupled with seed rhizome disinfection (Copper, Cu) was first adopted to evaluate the synergistic effects on soil physicochemical properties, enzyme activities and microbial communities, and therefore reveal mechanisms for soil microecological health and crop yield promotion. The results showed the comprehensive strategy could reduce NO₃⁻-N content, and the activities of soil enzymes, while increased NH₄⁺-N content, EX-Cu, and OXI-Cu content, which were positively correlated with ginger yield but negatively correlated with soil-borne pathogens and plant mortality. On the other hand, there was a reduction in bacterial diversity and richness, which was positively correlated with the abundance of soil-borne pathogens. Moreover, some beneficial soil microorganisms’ relative abundance (such as Firmicutes, Actinobacteria, Bacillus, and Sphingomonas.) was increased. The strategy decreased the abundance of Fusarium spp. and Phytophthora spp. by 49.41–90.07% and 43.34–89.21%, respectively. Compared with other treatments, the combination decreased the ginger mortality by 5.70–57.02% and increased the growth of ginger plants and yield by 3.58–139.96%, and 13.11–399.74%, respectively. This study highlights a prospect to promote ginger growth and yield by blocking the transmission of primary infection pathogens in ginger cultivation and improving soil ecological environment. Full article

The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1–3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65–1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and bla_TEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies. Full article

Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal. Results: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin. Conclusions: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies. Full article