The order Lysobacterales consists of three families (Rhodanobacteraceae, Lysobacteraceae and Marinicellaceae), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members within order Lysobacterales have relied heavily on 16S rRNA gene sequences, leading to taxonomic ambiguities at the familial level. With the advancement of sequencing technologies, an increasing number of whole-genome sequences have been available, providing an opportunity to revisit the taxonomy of families in Lysobacterales. In this study, we revisited the taxonomy of Lysobacterales by focusing on family-level reclassification based on phylogenomic frameworks. A total of 218 genome sequences, including 217 strains from Lysobacterales and 1 from Nevskiales (used as an outgroup), were collected for phylogenetic analysis. Phylogenetic relationships were inferred based on UBCG (up-to-date bacterial core gene) approach using 92 core genes and a concatenated protein phylogeney based on 227 single-copy orthologous proteins. Additionally, genomic similarity metrics, including average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI) and core-proteome average amino acid identity (cpAAI), were employed to assess the taxonomy of order Lysobacterales. Our results support the proposal of one novel family and the reassignment of six genera across different families within Lysobacterales, emphasizing the need for a refined family-level taxonomy. In addition, four novel species belonging to the family Lysobacteraceae were also confirmed. This study provides an updated familial framework for Lysobacterales, laying a robust foundation for future detailed taxonomic revisions at the genus and species levels.

Reductive soil disinfestation (RSD) significantly alters soil characteristics, yet its combined effects with bacterial inoculation on subsequent rhizospheric microbial community composition remains poorly understood. To address this knowledge gap, we investigated the effects of RSD and endophytic Brevibacillus laterosporus inoculation on the composition, network, and predicted function of peanut rhizospheric bacteria and fungi. Our results demonstrated that RSD and B. laterosporus inoculation substantially increased rhizospheric bacterial diversity while reducing fungal diversity. Specifically, B. laterosporus-enhanced RSD significantly reshaped the bacterial community, resulting in increased relative abundances of Chloroflexi, Desulfobacterota, and Myxococcota while decreasing those of Firmicutes, Gemmatimonadota, and Acidobacteriota. The fungal community exhibited a more consistent response to RSD and B. laterosporus amendment, with reduced proportions of Ascomycota and Gemmatimonadota but an increase in Chytridiomycota. Network analysis revealed that B. laterosporus inoculation and RSD enhanced the bacterial species complexity and keystone taxa. Furthermore, canonical correspondence analysis indicated strong associations between the soil bacterial community and soil properties, including Eh, EC, NO₃⁻-N, and SOC. Our findings highlight that the shifts in bacterial taxa induced by B. laterosporus inoculation and RSD, particularly the keystone taxa identified in the network, may contribute to the suppression of soil-borne pathogens. Overall, this study provides a novel insight into the shifts in rhizospheric bacterial and fungal communities and their ecological functions after bacteria inoculation and RSD treatment.

The rhizospheric microbial community plays a crucial role in the growth and ecological adaptation of truffles. Although extensive research has been conducted on bacterial communities in truffle habitats, the spatial variation and functional implications across different regions and soil compartments remain poorly understood in the current literature. In this study, soil bacterial communities were analyzed using 16S rRNA high-throughput sequencing across truffle-producing (Tuber sinense) and non-producing sites in Quercus aliena forests in Panzhihua, China. To capture microhabitat-level variation, soils were classified into three compartments: rhizosphere soil tightly adhering to ectomycorrhizal roots (TRS), rhizoplane soil loosely attached to roots (TRE), and bulk soil from truffle zones without visible roots (TBS), with corresponding controls (RS, RE, BS) collected from truffle-free forests. An alpha diversity analysis revealed that truffle-producing soils harbored significantly higher bacterial richness than control soils, while beta diversity indicated more clustered community composition in truffle-associated soils. A taxonomic analysis showed that T. sinense occurrence was associated with enrichment of specific bacterial taxa, including Chloroflexi, Anaeromyxobacteraceae, and Bradyrhizobium, whereas widespread taxa such as Firmicutes and Bacteroidota were more abundant in control soils. To further identify microbial indicators closely associated with truffle presence, we employed random forest modeling, which highlighted Pseudomonas, Streptomyces, and Bradyrhizobium as key genera distinguishing truffle-associated rhizospheres. These findings suggest that T. sinense may influence the composition of rhizospheric microbial communities, thereby constructing a favorable rhizospheric microenvironment. This work provides new insights into the microbial ecology of T. sinense and lays a foundation for future truffle domestication and cultivation efforts.

Optimizing fertilization strategies is key to increasing peanut yields and maintaining soil health, but it is still unclear how the proportion of basal fertilizer (applied before sowing) and topdressing (applied through drip irrigation during growth) systematically affects the “soil microbe plant” system under integrated drip irrigation and water–fertilizer management. This study set up four fertilization strategies—no fertilizer (F1), full basal fertilizer (F2: N–P₂O₅–K₂O = 343.9–123.0–120.0 kg·hm⁻² applied at sowing), drip irrigation with full water-soluble fertilizer (F3: total NPK input same as F2, applied via drip irrigation at flowering–pegging, pod-setting, and pod-filling stages in a 6:2:2 ratio), and 50% basal fertilizer + 50% water-soluble fertilizer (F4: basal applied at sowing, water-soluble applied via drip irrigation at the three growth stages in a 2:4:4 ratio)—to explore their effects on the soil nutrient availability, enzyme activity, bacterial community, and plant nutrient uptake throughout the entire growth stage of peanuts. The results showed that drip irrigation and topdressing strategies significantly improved soil-available nutrients and enzyme activity in the later stages of growth, with the F4 treatment showing the most significant advantage. This treatment not only significantly improved bacterial diversity and community functional redundancy and maintained a stable presence of multifunctional beneficial bacterial genera but also significantly increased nitrogen, phosphorus, and potassium uptake and fertilizer use efficiency. Partial least-squares structural equation modeling (PLS-SEM) reveals that fertilization strategies mainly indirectly drive yield increase by regulating microbial communities and enzyme activity. In summary, under the condition of equal nutrient input, the strategy of evenly matching nutrient supply with peanut demand was achieved, which not only ensured high yield and efficiency but also enhanced soil microecological stability. It is the optimal strategy for integrating water and fertilizer into the drip irrigation of summer peanuts under the conditions of this experiment.

A rhizosphere-derived bacterial isolate, GYB4201^T, was subjected to taxonomic and functional characterization. The strain consisted of Gram-stain-negative, strictly aerobic rods and was positive for both catalase and oxidase activities. Core-genome phylogeny placed GYB4201^T within the Pseudomonas putida group, in which it occupied an independent and well-supported branch. Pairwise ANI and dDDH values relative to the most closely related type strains were below the accepted species boundaries. Its phenotypic and chemotaxonomic profiles provided additional evidence for taxonomic distinction. The cellular fatty acid composition was dominated by C_16:0, Summed Feature 8 and Summed Feature 3. Phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were the principal polar lipids, while ubiquinone-9 was the predominant respiratory quinone. Functional assays demonstrated phosphate and potassium solubilization, indole-3-acetic acid production, CAS-positive siderophore-related activity, and inhibitory activity against Sclerotium rolfsii. Pot experiments further showed that inoculation with GYB4201^T reduced peanut southern blight severity and promoted peanut growth. Positive but non-significant trends were observed in several root architectural traits. These taxonomic and functional data support the recognition of GYB4201^T as a novel species of the genus Pseudomonas, for which the name Pseudomonas gilva sp. nov. is proposed. The type strain is GYB4201^T (=CFCC 17085^T = ICMP 25013^T).