Probiotic microbiota in roots can enhance nutrient uptake and stress tolerance, thereby improving plant growth. [Objective] To identify elite microbial resources from alfalfa roots. [Methods] We used eight functional bacterial strains isolated from the roots of Medicago sativa var. ‘Caoyuan No. 3’ and eight synthetic microbial communities (synthetic microbial communities, SynComs) composed of different strains for seed soaking treatments under 0, 200, and 250 mmol/L NaCl stress conditions. The germination potential (rate), radicle (embryonic shoot) length, and seed fresh weight were measured, and the effectiveness of the bacterial strains and SynComs in improving stress tolerance and growth was comprehensively evaluated via the membership function method. The effects of strains isolated from roots on alfalfa seed germination were thus evaluated. [Results] Under non-saline conditions, seed soaking had no significant impact on alfalfa seed germination. However, under salt stress, seed soaking significantly enhanced seed germination. Under 200 mmol/L and 250 mmol/L NaCl stress, MS8 was the most effective strain in promoting seed germination. Compared with the control treated with sterile water, MS8 treatment improved the germination potential by 76.67%. Compared with the control, the seeds treated with SynCom 1 exhibited increases of 113.04% to 405.41% in germination rate, significant increases of 47.87% to 56.67% in radicle length, significant increases of 19.13% to 24.01% in embryonic shoot length, and significant rises of 157.64% to 1 300.00% in fresh seed weight. [Conclusion] Under 200 mmol/L and 250 mmol/L NaCl stress, SynCom 1 was the most effective synthetic microbial community in enhancing seed germination, outperforming strain MS8. This study provides a theoretical foundation and technical support for the subsequent development of efficient functional bacterial agents to enhance the salt tolerance of alfalfa.

Hexavalent chromium [Cr(VI)] is a widespread and highly toxic heavy metal contaminant commonly found in industrial effluents from electroplating, metallurgy, and dye manufacturing. Due to its strong oxidizing nature, high solubility, and severe biological toxicity, Cr(VI) is recognized as a priority contaminant to be managed in aquatic and terrestrial environments. Although conventional treatment technologies can rapidly reduce Cr(VI) concentrations, they often entail high costs, pose risks of secondary pollution, and are susceptible to environmental fluctuations. Bioreduction of Cr(VI) has emerged as a promising alternative, offering advantages such as low energy requirements, environmental compatibility, and operational sustainability. This review provides a comprehensive overview of the core mechanisms underlying Cr(VI) bioreduction, which involve key chromate reductases, intracellular and extracellular electron transfer pathways, gene regulatory networks, and adaptive strategies of microbial communities under stress. Furthermore, we discuss the synergistic contributions of metabolic pathways, such as denitrification and sulfur cycling, to elucidate electron competition and pathway modulation in complex multi-contaminant systems. Subsequently, we analyze the effects of environmental parameters including pH, temperature, Cr concentration, and electron donor types on bioreduction efficiency. Representative studies are discussed to illustrate detoxification performance, community succession, and ecological restoration outcomes under field conditions. Finally, this review envisions future advances in microbial remediation through the application of synthetic biology to construct engineered microbial strains, the use of multi-omics technologies to elucidate metabolic pathways, and the integration of artificial intelligence (AI) with in situ sensing technologies for dynamic regulation. It further outlines a developmental framework centered on “intelligent detection-adaptive response-multifunctional coordination”, providing both a theoretical foundation and technological guidance for the in situ remediation of Cr(VI) contamination.

Colorectal cancer (CRC), a common malignant neoplasm of the digestive system globally, demonstrates pathological progression that is intricately linked not only to dysbiosis of the gut microbiota but also to the oral microbial ecosystem. The emerging concept of the “oral-gut axis” offers novel insights into the regulation of microbial interactions across different organs. Recent research indicates that Peptostreptococcus, a predominant genus within the oral microbiome, exhibits spatiotemporal correlations with the initiation and progression of CRC. This genus may influence intestinal microecological changes and CRC pathogenesis through the “oral-gut axis”. We explore the microbial interactions between oral and intestinal ecosystems, examining the multidimensional associations between specific Peptostreptococcus species (such as P. stomatis and P. anaerobius) and CRC development. Key considerations include the population heterogeneity of these species among CRC patients with varying clinical profiles, their dynamic evolution during the adenoma-carcinoma sequence, and their spatial distribution across different pathological stages. We synthesize mechanistic evidence illustrating the role of Peptostreptococcus in promoting tumorigenesis by enhancing cancer cell proliferation, inducing epithelial-mesenchymal transition, and remodeling the tumor microenvironment. Additionally, this article assesses the clinical potential of Peptostreptococcus as predictive biomarkers and therapeutic targets for CRC. Finally, we propose future directions for the development of targeted microbial intervention strategies against oral-derived pathogens, with the aim of stimulating scientific interest and encouraging further investigation in this emerging research area.

Objective Nitrous oxide (N₂O)-reducing microbes are the only known microbial group capable of eliminating N₂O. The abundance, diversity, community structure, and influencing factors of their functional gene (nosZ) are critical for N₂O removal. Cunninghamia lanceolata is a widely planted timber species in southern China, and its rhizosphere represents a hotspot for both N₂O production and reduction. However, the spatial distribution pattern of nosZ Ⅰ genes and their driving factors in the rhizosphere soils of C. lanceolata plantations remain unclear. Methods We investigated the rhizosphere soils of C. lanceolata plantations from five state-owned forest farms—Qiujiashan, Wuyi, Guanzhuang, Xiayang, and Xiapu—in Fujian Province. Quantitative PCR and amplicon sequencing were employed to analyze the abundance, diversity, and community structure of nosZ Ⅰ genes and to identify their key environmental drivers. Results Dissolved organic carbon concentrations in rhizosphere soils ranged from 6.91 mg/kg to 23.52 mg/kg, being significantly lower in Guanzhuang and Xiayang than in Wuyi, Qiujiashan, and Xiapu. The nosZ I gene abundance ranged from 4.76×10⁶ copies/g to 36.50×10⁶ copies/g, reaching 36.50×10⁶ copies/g and 29.08×10⁶ copies/g in Guanzhuang and Xiayang, respectively, which significantly exceeded those in Qiujiashan, Wuyi, and Xiapu. Dissolved organic carbon emerged as the primary driver of nosZ I gene abundance, which implied that low dissolved organic carbon may promote the proliferation of N₂O-reducing bacteria. The Shannon index of nosZ I genes ranged from 4.41 to 5.67, being significantly higher in Xiayang than in Wuyi and Xiapu and the lowest in Xiapu. Total carbon was the key factor affecting the Shannon index. The nosZ I community structures in Qiujiashan, Guanzhuang, and Xiapu were similar, whereas that of Xiayang was significantly different from the others. Soil pH was identified as the main driver of community structure, and Xiayang had a significantly higher pH than the other sites. The dominant bacterial class in the rhizosphere soils of all five forest farms was Gammaproteobacteria. Xiayang had significantly lower relative abundance of Gammaproteobacteria but significantly higher relative abundance of Alphaproteobacteria than other farms. Conclusion Soil carbon content and pH are key environmental factors regulating the abundance, diversity, and community structure of N₂O-reducing bacteria in the rhizosphere soils of C. lanceolata plantations, potentially influencing N₂O removal and mitigation potential. Therefore, the management strategies for C. lanceolata plantations should consider regulating soil carbon content and pH to optimize N₂O mitigation effects and alleviate global climate change.

Nitrification inhibitors can affect the biological transformation process of ammonium nitrogen to nitrate nitrogen in soil by inhibiting the activity of ammonia-oxidizing bacteria (AOB). Objective To investigate the effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) on the community structure and assembly mechanisms of AOB in coastal saline-alkaline paddy soil. Methods To study the effects of the typical nitrification inhibitor DMPP addition on the diversity, community structure, and community assembly process of AOB in soil under two salinity levels. Pot experiments and high-throughput sequencing were employed to determine the diversity, community structure, and community assembly process of AOB. Results The addition of DMPP increased the alpha diversity of AOB in soil, which reached a significant level in the high-salinity soil. The addition of DMPP significantly changed the community composition of AOB, reducing the relative abundance of taxa with high relative abundance and enriching the taxa with low relative abundance. The decrease in relative abundance of taxa with high relative abundance was the main reason for the inhibition of DMPP on nitrification. Principal coordinates analysis revealed that the community structure of AOB changed significantly after the addition of DMPP, which was more obvious in high-salinity soil. The null model analysis results showed that stochastic processes played a dominant role in the community assembly process of AOB, and the contribution of stochastic processes increased after the addition of DMPP. Canonical correspondence analysis and Mantel’s test indicated that soil pH, electrical conductivity, organic matter, total nitrogen, and alkaline-hydrolyzable nitrogen were the main physicochemical factors influencing changes in AOB community structure. Conclusion DMPP exerted significant impacts on AOB communities in coastal saline-alkaline paddy soils across varying salinity levels, with its inhibitory effects varying substantially with soil salinity.

Amino acids serve as indispensable components and nutrients for living organisms, while recent studies have revealed that amino acid metabolism in pathogenic bacteria plays a pivotal role in their pathogenic processes. This review summarizes current research on the roles of different amino acids in facilitating the pathogenicity of pathogenic bacteria. Specifically, we highlight how Salmonella enterica utilizes l-aspartate to achieve colonization and dissemination within the inflamed intestine, and how branched-chain amino acids indirectly regulate the virulence of Staphylococcus aureusvia the global transcriptional regulator CodY. Additionally, we briefly outline the vital roles of amino acid metabolism throughout the infection processes of pathogenic bacteria. In-depth research into how amino acid metabolism promotes pathogenic processes will deepen our understanding of the underlying mechanisms and provide a theoretical basis for developing novel antibacterial strategies.

Objective Developing plant-microbe combined techniques is significant for addressing the problem of declining cropland quality in China and enriching the approaches for biological remediation of degraded soils. Methods The plant growth-promoting traits of Burkholderia sp. YQ9 were determined by assessing its cellulase, protease, and ammonia production. Subsequently, a pot experiment was conducted to evaluate the effects of different dilutions of Burkholderia sp. YQ9 inoculant and culture medium on the growth of white clover (Trifolium repens) and the physicochemical properties of the rhizosphere soil. Furthermore, high-throughput sequencing was employed to analyze the impacts of different treatments on the structure of the rhizosphere microbial community. Results Burkholderia sp. YQ9 exhibited plant growth-promoting traits, being capable of producing cellulase, protease, and ammonia. White clover improved the pH environment of the rhizosphere soil. Application of the original inoculant of Burkholderia sp. YQ9 promoted white clover growth, significantly enhancing the content of soluble protein and soluble sugar in the shoots and leaves, as well as the levels of available phosphorus and available potassium in the rhizosphere soil, thereby facilitating organic matter decomposition. Analysis of microbial alpha diversity in the rhizosphere soil revealed that both the original inoculant of Burkholderia sp. YQ9 and the culture medium significantly reduced the richness, diversity, and evenness of both fungal and bacterial communities in the rhizosphere soil and altered the composition of the soil microbial community. The correlation analysis further indicated that the microbial community in the rhizosphere soil was correlated with white clover growth and soil physicochemical properties. Conclusion Burkholderia sp. YQ9 not only promoted the growth of white clover but also modified the composition of the rhizosphere microbial community and improved the soil fertility. These findings provide microbial augmentation-based technical support for enhancing cropland quality.

Objective To explore the application of hutC sequence analysis in the identification of Burkholderia cepacia complex (Bcc) at the species level. Methods We compared the sequences of hutC and the amino acid sequences of the encoded proteins and conducted phylogenetic analysis to theoretically assess the feasibility of using hutC for species-level identification of Bcc. Primers targeting the hutC of Bcc were designed, and the amplification conditions were optimized. With those of standard strains as templates, the hutC sequences of representative Bcc species were amplified. The sequencing results were compared with NCBI sequences for phylogenetic analysis to validate the theoretical hypothesis. Additionally, single nucleotide polymorphism analysis of hutC sequences was performed to identify species-level characteristic barcodes of Bcc. Results The hutC gene was relatively conserved between Bcc and non-Bcc. With the designed primers and amplification conditions, a 692 bp fragment of hutC was successfully amplified from 12 Bcc standard strains. Except for one strain with taxonomic errors, the remaining 11 strains had the comparison results consistent with those from the culture collection centers. The phylogenetic analysis based on hutC showed that different Bcc species could be clustered with high bootstrap values. A 12 nucleotide characteristic barcode of hutC was identified, which can rapidly distinguish different species of Bcc. Conclusion The gene hutC can serve as a new housekeeping gene target for accurate identification of Bcc at the complex and species levels.

Agrobacteriumtumefaciens, a classic model organism for plant-microbe interaction research, is a valuable transgenic tool for plants. Phenolic acids secreted by plants after injury can affect the infection of the host by A. tumefaciens. Objective This study investigated the transcription factor PcaR of A. tumefaciens regarding its effects on the metabolism of simple phenolic acids, regulation of the target gene, and effect on the bacterial tumorigenicity in host plants. Methods The A. tumefaciens strain with atu4546 knockout (Δatu4546) and the complement strain C-Δatu4546 were constructed via the suicide plasmid pEX18Km and the plasmid pUCA19 with a strong promoter, respectively. Both Δatu4546 and C-Δatu4546 were tested for growth with p-hydroxybenzoic acid or protocatechuic acid as the sole carbon source and tumorigenicity on carrot stems and Kalanchoe pinnata leaves. In the wild-type strain C58 and Δatu4546, the reporter gene was in situ inserted into the downstream region of the metabolic target gene atu4549. The regulatory link between atu4546 and the target gene was examined based on the β-galactosidase activity. To investigate the self-regulation of PcaR, we constructed the atu4546 self-promoter reporter plasmid. To identify the binding sites of PcaR, we constructed the upstream promoter region reporter plasmid of the target gene to remove or replace the predicted binding sites and then determined the β-galactosidase activity. Results The knockout of atu4546 did not affect the growth of A. tumefaciens on sucrose, but led to the inability to use p-hydroxybenzoic acid or protocatechuic acid as the sole carbon source. The growth was restored after atu4546 was complemented. The tumor weights of carrot stems and K. pinnata leaves infected by Δatu4546 decreased by 34.90% and 52.58%, respectively, and the number of colonies per 0.1 g tumor decreased by 72.19% and 80.54%, respectively. The knockout of atu4546 led to a 102.04% increase in its own promoter activity, which suggested that atu4546 negatively regulated its own expression. Atu4546 boosted the expression of the atu4547-atu4549 gene cluster, as evidenced by a 74.86% decrease in β-galactosidase activity downstream of the target gene in Δatu4546 compared with that in the wild type. The promoter region sequence alteration experiment identified GTGCGATATATACGAAC as the binding site of PcaR. Conclusion This study shows that the transcription factor PcaR is involved in phenolic acid catabolism, negatively regulates itself and stimulates the transcription of the downstream gene pcaIJF. The binding site of PcaR to the target gene is GTGCGATATACGAAC. The knockout of PcaR attenuates the pathogenicity of A. tumefaciens. This study reveals the dual regulation mechanism in the phenolic acid metabolism-pathogenic signaling pathway and expands the theoretical cognition of plant-microbe interactions.

Objective To investigate the community structure, network complexity, and stability of soil bacteria harboring the alkaline phosphatase gene (phoD) under the application of organic amendments, elucidating their regulatory mechanisms in microbially mediated soil phosphorus (P) transformation and availability. Methods We conducted the experiment within a 13-year long-term maize field trial located in Ya’an, Sichuan. The experiment comprised three mineral P fertilizer treatments: 0, 75, and 150 kg/hm² (designated as P0, P1, and P2, respectively). In 2018, a split-plot design was implemented with organic amendment treatments, where mineral P application was reduced by 30% and supplemented with pig manure (P0+M, 70% P1+M, and 70% P2+M treatments). The phoD-harboring bacterial community structure was characterized by high-throughput sequencing and bioinformatic analyses, which revealed the effects of organic amendments with varying P supply levels on phoD-harboring bacterial communities and their regulation of soil available P. Results As the P supply level increased, both mineral and organic amendments significantly increased the content of soil organic matter (SOM), Olsen-P, and organic P (Po), while significantly decreasing soil pH. P levels and organic amendments markedly altered the community composition and network characteristics of phoD-harboring bacteria. Under low-P conditions (P0, P0+M), Bradyrhizobium icense emerged as both the dominant and indicator species, with its relative abundance decreasing significantly as P application increased. Under P-amended treatments (P1, P2, 70% P1+M, and 70% P2+M), Bradyrhizobium diazoefficiens and Roseateles depolymerans became the predominant species, exhibiting significant increases in relative abundance with higher P inputs. Notably, the relative abundance of all the three dominant species under the application of organic amendments was higher than that in corresponding inorganic P treatments. Furthermore, organic amendments increased the network nodes and connectivity links compared with corresponding mineral P treatments. Random forest analysis further identified B. icense as the strongest predictor of soil available P. The stability of phoD-harboring bacterial networks showed no significant difference across treatments. However, after the removal of dominant species, the network stability declined significantly in all treatments. Conclusion Organic amendments increase the relative abundance of dominant species within the phoD-harboring bacterial community across different P supply levels. They enhance the network complexity of phoD-harboring bacteria, thereby improving the network stability of these bacterial communities and ultimately influencing the availability of soil P.