Soil disinfestation has been widely used as an effective strategy to improve soil health and crop yield by suppression of soil-borne plant pathogens, but its effect on soil organic carbon (SOC), a crucial factor linked to climate change, remains unknown. A microcosm trial was conducted to evaluate microbial residue carbon (MRC) and its contribution to SOC under chemical soil disinfestation (CSD) with quicklime (QL) and chloropicrin (CP), as well as anaerobic soil disinfestation (ASD) with maize straw (MASD) and soybean straw (SASD). The SOC concentrations were increased by both CSD and ASD. Also, total SOC-normalized MRC concentration was enhanced, with a considerable increase in soil bacterial and fungal MRC, particularly evident under CP and SASD treatment. Due to broad-spectrum biocidal activities, decreased SOC-normalized microbial biomass carbon (MBC) was consistent with the reductions in bacterial and fungal phospholipid fatty acids (PLFAs), consequently increasing MRC accumulation under CSD. Similarly, ASD decreased fungal PLFAs while shifting bacterial PLFAs from aerobic to anaerobic taxa or from gram-negative to -positive taxa, both of which contributed to both MBC and MRC buildup. Collectively, the findings demonstrate that ASD can efficiently increase SOC concentration, with distinct mechanisms underlying MRC generation when compared to traditional CSD.

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.

Both organic matter and iron oxide (FeO) dynamics pose key roles in soil cadmium (Cd) bioavailability. However, the microbially driven transformation of soil organic matter and FeO and their linkages to Cd fractions remain unclear under reductive soil disinfestation (RSD) with different organic sources, which limits our mechanistic understanding of Cd immobilization by RSD. To address this gap, we conducted a 45 day microcosm experiment using a paddy soil contaminated with 22.8 mg/kg Cd. Six treatments were established: untreated control (CK), waterlogged (WF), and RSD-amended soils with 0.7% or 2.1% wheat straw (LWD, HWD) or soybean meal (LSD, HSD). We systematically assessed soil Cd fractionation, organic carbon and FeO concentrations, and bacterial community structure, aiming to clarify differences in Cd immobilization efficiency and the underlying mechanisms between wheat straw and soybean meal. For strongly extractable Cd, wheat straw RSD reduced the soil Cd concentrations from 6.02 mg/kg to 4.32 mg/kg (28.2%), whereas soybean meal RSD achieved a maximum reduction to 2.26 mg/kg (62.5%). Additionally, the soil mobility factor of Cd decreased from 44.6% (CK) to 39.2% (HWD) and 32.5% (HSD), while the distribution index increased from 58.5% (CK) to 62.2% (HWD) and 66.8% (HSD). Notably, the HWD treatment increased soil total organic carbon, humus, and humic acid concentrations by 34.8%, 24.6%, and 28.3%, respectively. Regarding amorphous FeO, their concentrations increased by 19.1% and 33.3% relative to CK. RSD treatments significantly altered soil C/N ratios (5.91–12.5). The higher C/N ratios associated with wheat straw stimulated r-strategist bacteria (e.g., Firmicutes, Bacteroidetes), which promoted carbohydrate degradation and fermentation, thereby enhancing the accumulation of humic substances. In contrast, the lower C/N ratios of soybean meal increased dissolved organic carbon and activated iron-reducing bacteria (FeRB; e.g., Anaeromyxobacter, Clostridium), driving iron reduction and amorphous iron oxide formation. PLS-PM analysis confirmed that wheat straw RSD immobilized Cd primarily through humification, whereas soybean meal RSD relied on FeRB-mediated FeO amorphization. These findings suggest that Cd immobilization in soil under RSD may be regulated by microbially mediated organic matter transformation and iron oxide dynamics, which was affected by organic materials of different C/N ratios.

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.

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).