Adenosine diphosphate-ribosylation (ADPr) is a reversible post-translational modification that is catalyzed by adenosine diphosphate-ribosyltransferases (ARTs) and adenosine diphosphate- ribosylhydrolases (ARHs), and it widely occurs in eukaryotes and prokaryotes. ARHs are a class of key enzymes that can reverse ADPr modification of specific amino acid residues or specific sites/sequences of DNA and RNA. They can regulate the physiological metabolism, signal transduction, gene expression, and other key life processes in bacteria or hosts, playing an important role in the inter/intraspecific competition, stress responses, and pathogenicity of bacteria. This article reviews the classification, structural characteristics, and catalytic mechanisms of bacterial ARHs, aiming to enrich our understanding about the catalytic mechanisms and biological functions of ARHs in bacterial life.

Galactose is a ubiquitous monosaccharide in nature, serving not only as a primary carbon source for bioenergy metabolism but also as a precursor for various biological synthesis reactions. In eukaryotic cells, galactose or its derivatives can act as signaling molecules to participate in intercellular communication. Recent studies have revealed that galactose can modulate bacterial virulence by regulating intracellular signal transduction. Accordingly, galactose is considered an underappreciated environmental regulator in bacterial infection. However, the specific regulatory mechanisms remain incompletely elucidated. This review integrates the latest research findings to summarize the bacterial galactose metabolic pathway, the biological implications of galactose metabolism in bacterial virulence and interactions with hosts, and the key proteins (enzymes) in the galactose metabolism pathway as potential targets for developing novel vaccines. It offers new insights and reference for comprehending bacterial infection mechanisms and exploring innovative antibacterial strategies.

[Objective] To screen and identify cadmium (Cd)-tolerant bacteria with plant growth-promoting effect from contaminated soil of a mining area in Guangxi, characterize the strain screened out in terms of the Cd tolerance, Cd²⁺ removal efficiency, plant growth-promoting effect, and influence on rice growth under Cd stress, and demonstrate the potential of the strain in plant growth and soil remediation. [Methods] Cd-tolerant bacteria were isolated by the dilution coating method and Cd²⁺ concentration gradient acclimation and further identified based on the morphological, physiological, biochemical characteristics and the 16S rRNA gene phylogenetic tree. The Cd tolerance, Cd²⁺ removal efficiency, and plant growth-promoting effect of the target strain were measured by microdilution, inductively coupled plasma mass spectrometry, and colorimetry. Finally, the effect of the strain on the growth of rice plants under Cd stress was investigated by a pot experiment. [Results] Twelve strains of bacteria with good tolerance to Cd²⁺ were isolated from heavy metal-contaminated soil, and one strain with the best tolerance to Cd was identified as Achromobacter sp. A81, which could grow in the presence of 800 mg/L Cd²⁺. Strain A81 cultured with 10 mg/L Cd²⁺ for 7 days showed the maximum Cd²⁺ removal rate of 44.66%. Both the supernatant and cells of strain A81 demonstrated the ability to adsorb Cd²⁺. Under Cd stress, the strain secreted a large amount of extracellular polymeric substances (EPS) primarily composed of insoluble and soluble proteins. Furthermore, this strain was capable of fixing nitrogen, solubilizing phosphorus, and secreting siderophores, indole-3-acetic acid (IAA), and 1-aminocyclopropane-l-carboxylate (ACC) deaminase, demonstrating remarkable plant growth-promoting effect. Pot experiment results revealed that compared with the group subjected to Cd stress, the rice plants inoculated with strain A81 showed increases of 9.08%, 39.59%, 41.94%, and 73.58% in plant height, root length, stem diameter, and fresh weight, respectively. [Conclusion] This study investigated the Cd tolerance, Cd removal efficiency, and plant growth-promoting effect of Achromobacter sp. A81 and assessed the application potential of this strain in Cd-contaminated soil remediation, providing a scientific basis and high-quality strain resources for the microbial remediation of heavy metal pollution and green agricultural development.

[Objective] To studyhydroxyl radical the differentially expressed genes (DEGs) in Halomonas campaniensis XH26 after co-culture with Fe₃O₄ nanoparticles (NPs), and clarify the molecular mechanism of Fe₃O₄ NPs in increasing the ectoine accumulation in strain XH26. [Methods] Strain XH26 was co-cultured with low-, medium-, and high-concentration (0.01, 0.10, and 0.50 g/L respectively in L, M, and H groups) Fe₃O₄ NPs, and the strain cultured without Fe₃O₄ NPs (0 g/L) was taken as the control group (C). Transcriptome sequencing was performed by Illumina HiSeq 300PE. The DEGs between different groups were mined, and key genes were screened for RT-qPCR verification. [Results] Compared with group C, group M showed an increase of 55.67% (708.87 mg/L) in ectoine accumulation, and groups M and H showed increased ferrous ions and antioxidant capacity. The hydroxyl radical content in group H was higher than that in group M. The transcriptomics analysis showed that the DEGs between groups M and C were enriched in arginine/proline metabolism (13), nitrogen metabolism (11), and sulfur metabolism (10) pathways. They were mainly related to the ectoine synthesis pathways (11), electron transport pathways (7), and antioxidant enzyme systems (5). RT-qPCR was employed to verify the expression of lysC, asd, and ectABC involved in ectoine synthesis, astA/B/D/E in arginine metabolic pathway, and argE/H in urea cycle, which showed the results consistent with the results of RNA-seq. [Conclusion] Ectoine is an important stable protective agent for bacterial cells and biomacromolecules. Strain XH26 exposed to the stress of Fe₃O₄ NPs showed increased intracellular reactive oxygen species and altered amino acid/nitrogen metabolism processes. Strain XH26 increased the accumulation of ectoine to cope with the stress of Fe₃O₄ NPs by improving the antioxidant capacity.

[Objective] The basic leucine zipper (bZIP) factors are a group of large and conserved transcription factors in eukaryotes, and they are involved in the growth, development, and infection of pathogenic fungi in plants. This study aims to identify the bZIP transcription factors in the whole genome of Setosphaeria turcica and explore their functions during HT-toxin induction. [Methods] The members of the bZIP family were screened and identified from the genome database of Setosphaeria turcica, and their physicochemical properties, conserved domains, subcellular localization, cis-acting elements, phylogenetic relationship, and protein-protein interaction network were analyzed. The RNA-seq database was used to analyze the expression of bZIP family members during pathogen infection and HT-toxin induction. [Results] Fourteen bZIP family members (StbZIP1–14) were screened from the genome of Setosphaeria turcica, with significant differences in physical and chemical properties. These factors had the lengths of 226–613 aa, relative molecular weights of 25.24–66.30 kDa, isoelectric points of 4.66–10.36, and the subcellular localization in the nucleus. These factors carried 660 cis-acting elements involved in abiotic stress, hormone induction, cell cycle regulation, enhancers, and core promoters. The phylogenetic analysis with 11 other major pathogenic fungi in plants indicated that StbZIPs were clustered into 10 groups and had a clear co-linear relationship with AabZIPs of Alternaria alternata. The expression levels of StbZIP1, StbZIP5, StbZIP7, StbZIP10, and StbZIP11 were significantly correlated with HT-toxin induction, among which StbZIP5 had the highest expression level and demonstrated upregulated expression after 21 days and 28 days of HT-toxin induction. The protein-protein interaction network of StbZIPs predicted three StbZIPs interaction pathways centered on StbZIP5. [Conclusion] The members of the bZIP family of Setosphaeria turcica have significant physicochemical and structural differences, extensive genetic diversity, and significant functional differentiation, playing an important role in transcriptional regulation during HT-toxin induction.

[Objective] To explore the effects of strain CDWB36 and its metabolite pyrroloquinoline quinone (PQQ) on the drought resistance and growth of pepper, so as to provide efficient strain resources for the development and utilization of multifunctional microbial agents. [Methods] A strain CDWB36 was identified based on the morphological characteristics and the 16S rRNA gene-based phylogenetic tree. HPLC and spectroscopy were employed to detect PQQ. The fermentation conditions were optimized by single factor tests with PQQ production as the indicator. The effects of the PQQ-containing microbial agent on the growth, physio-biochemical characteristics, soil nutrients, and rhizosphere microbial community structure of pepper under drought stress were determined by pot experiments. [Results] Strain CDWB36 was identified as Acinetobacter calcoaceticus and it had the ability to produce PQQ. The optimum conditions of strain CDWB36 for producing PQQ were 10 g/L yeast powder, 4 g/L mixed nitrogen sources (ammonium sulfate: glutamic acid: tyrosine=2:1:1), 1.0 g/L MgSO₄, 0.40 g/L CaCl₂, 0.5% inoculum amount, 28 ℃, and pH 6.5. The PQQ production of the strain in shake flasks after 7 days of fermentation at the optimized conditions reached 61.48 mg/L, which increased by 3.3 times compared with that before optimization. Compared with CK, the PQQ-containing microbial agent increased the plant height, stem diameter, aboveground fresh weight, and belowground fresh weight of pepper by 35.05%, 8.22%, 14.41%, and 51.70%, respectively, demonstrating better plant growth-promoting effect than the PQQ solution. Moreover, the PQQ-containing microbial agent significantly improved the activities of antioxidant enzymes and the content of osmoregulatory substances (soluble sugar, soluble protein, and proline) in leaves, while increasing the soil nutrient content. The PQQ-containing microbial agent significantly changed the relative abundance of bacteria and fungi in the rhizosphere soil of pepper, increasing the relative abundance of Bacillus, Aspergillus, and Streptococcus by 1.99 times, 1.38 times, and 8.75 times, respectively, compared with CK. [Conclusion] A. calcoaceticus CDWB36 has the ability to produce PQQ. Optimizing the fermentation conditions can effectively enhance the PQQ production. The fermentation broth of CDWB36 significantly promotes pepper growth under drought stress, and PQQ is a key substance in the broth for promoting pepper growth. Therefore, the strain has broad application prospects in enhancing the stress resistance and promoting the growth of plants.

[Objective] Preliminary studies have identified four protein elicitors from the whole genome of Saccharothrix yanglingensis Hhs.015 that can induce a hypersensitive response (HR) in Nicotiana benthamiana. This study investigated the two elicitors capable of triggering a strong HR and their associated immune mechanisms, aiming to provide a basis for probing into the molecular mechanisms by which Hhs.015 enhances the disease resistance of plants. [Methods] The protein elicitors capable of inducing the immune responses of plants were screened based on the HR and reactive oxygen species (ROS) levels. A prokaryotic expression system was used to purify the proteins. Furthermore, we verified the roles of the protein elicitors in inducing plant disease resistance by observing the disease spots, measuring the activities of defense-related enzymes, and analyzing the expression of defense genes. Additionally, we treated Arabidopsis thaliana seedlings with the protein elicitors to evaluate the plant growth-promoting effects of the elicitors. [Results] The protein elicitors HSyp1 and HSyp2 from Hhs.015 that could induce a HR, callose and ROS deposition, and upregulation of defense genes in N. benthamiana, were screened and found to be soluble. HSyp1 and HSyp2 enhanced the resistance of different plants to Sclerotinia sclerotiorum, Phytophthora capsica, and Valsa mali. Furthermore, HSyp1 and HSyp2 promoted the cotyledon and root development of A. thaliana seedlings, and HSyp2 exhibited stronger plant growth-promoting effect than HSyp1. [Conclusion] This study identified two protein elicitors HSyp1 and HSyp2 capable of triggering immune responses, enhance disease resistance, and promoting growth of plants. The findings provide a theoretical basis for the development of new biocontrol agents and offer experimental evidence for their future field application.

[Objective] To explore the differences and potential associations of endophytic microbial communities in different niches of chili pepper and provide a theoretical basis for the exploration and application of endophytic microbial resources in chili pepper. [Methods] The 16S rRNA and internal transcribed spacer (ITS) genes sequencing were employed to study the community structure characteristics of endophytic bacteria and fungi in different ecological niches (roots, stems, leaves, and fruits) of 91 pepper germplasm accessions, along with functional annotations. Additionally, co-occurrence network analysis and traceability analysis were performed on the endophytic bacterial communities. [Results] The operational taxonomic unit (OTU) of endophytic microbial communities were highly common among the four ecological niches, including 46.36% common bacterial OTUs and 29.66% common fungal OTUs. The diversity of endophytic bacterial and fungal communities in chili pepper exhibited variations across different ecological niches, with the endophytic communities in roots being distinctly separated from those in the other three niches (P<0.05). The Shannon index of endophytic bacteria varied significantly among niches, whereas that of endophytic fungi remained relatively stable. The dominant endophytic bacteria in chili pepper were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being enriched in the roots and Firmicutes and Bacteroidetes being predominant in the fruits. Ascomycota and Basidiomycota, the dominant endophytic fungal phyla, exhibited minimal differences in relative abundance across the four ecological niches. Functional annotation results indicated that chili pepper harbored various endophytic bacteria capable of synthesizing secondary metabolites and antibiotics. Within the fungal community, pathogenic fungi were found to have the highest relative abundance. Additionally, more than 80.0% of the endophytic bacteria in chili pepper originated from their directly associated morphologically lower niches, exhibiting complex interaction networks, strong community stability, and a modular structure. [Conclusion] Compared with the endophytic fungal community, the endophytic bacterial community in chili pepper is sensitive to changes in ecological niches, while the niche specificity of the fungi is comparatively weak. The endophytic bacteria associated with each niche of chili pepper primarily originate from the niche located beneath, exhibiting significant niche enrichment, where the roots serving as a crucial source in shaping the endophytic bacterial community.

Metagenomics has enriched our understanding about the composition and functions of digestive tract microbiota in animals. Currently, metagenomic sequencing can generally achieve the classification rate of species between 15% and 45% at the read level. Therefore, improving the alignment rate of microbial reads in metagenomics can help to further mine microbial information from metagenome data. [Objective] To enhance the classification ability for digestive tract microbiota in ruminants by extending the Kraken2 standard database, thereby deeply mining the microbial information from metagenome data. [Methods] A total of 14 827 metagenome-assembled genomes (MAGs) of the rumen fluid, feces, and digestive tracts of cattle, sheep, and goats were collected. After quality control and filtering, 3 095 species-level genome bins (SGBs) were retained. These SGBs were integrated into the Kraken2 standard database following taxonomic classification and functional prediction, and the classification effect was evaluated. [Results] In the genome taxonomy database (GTDB), the 3 095 SGBs were identified as bacteria belonging to 782 genera of 28 phyla (3 053 SGBs) and archaea belonging to 8 genera of 2 phyla (42 SGBs). The functional prediction based on eggNOG annotated the SGBs into 26 clusters of orthologous groups of proteins (COGs). The Kyoto encyclopedia of genes and genomes (KEGG) enrichment categorized the top 25 ortholog groups (KO entries) into 14 pathways. The prediction of carbohydrate-active enzymes (CAZy) showed that 593 SGBs were annotated into six classes of CAZymes: auxiliary activities (AA), carbohydrate esterases (CE), glycosyltransferases (GT), carbohydrate-binding modules (CBM), glycoside hydrolases (GH), and polysaccharide lyases (PL). Among them, GH was the most common class. The addition of 3 095 SGBs to the Kraken2 standard database (May 2024) increased the number of species in the database by 5.00%, extending the size from 87.2 Gb to 98.2 Gb. Furthermore, a study about the effect of diet fiber-to-concentrate ratio on the rumen microbiota of Holstein cows by metagenomics was reassessed, which showed that the integration of SGBs into the database raised the species alignment rate of rumen metagenome reads from (19.35±1.81)% to (51.04±2.05)%. The principal component analysis results at the species level indicated that the extended database enhanced the ability to distinguish rumen microbiota structures under two different diet fiber-to-concentrate ratios. The linear discriminant analysis effect size results indicated that the microbial markers for low-fiber and high-fiber diets were Xylanibacter ruminicola and Aristaeella hokkaidonensis, respectively, in the standard database, whereas they were Prevotella sp. 902800365 and Prevotella sp. 900316445, respectively, in the extended database. [Conclusion] In summary, introducing SGBs to extend the Kraken2 standard database can increase species coverage and improve the alignment rate of species at the metagenome read level, thereby enhancing the understanding of microbial information in metagenome data.

[Objective] Carbon and nitrogen sources play an important role in providing the energy required for fungal growth and increasing secondary metabolite production. This study aims to investigate the effects of carbon and nitrogen restriction on the growth of Inonotus obliquus and the production of triterpenoid secondary metabolites. [Methods] l-glutamine and d-anhydrous glucose were used as the nitrogen and carbon sources, respectively. A nutrient-sufficient medium (0.877 g/L l-glutamine and 20.000 g/L of d-anhydrous glucose) served as the control group (CK). The experimental groups included a nitrogen-limited medium (N-L) with 0.044 g/L l-glutamine and a carbon-limited medium (C-L) with 2.000 g/L d-anhydrous glucose. In the plate experiment, inoculated plates were incubated at 28 ℃ in a constant temperature incubator, and colony diameters were measured and recorded daily. In the shake flask fermentation experiment, samples were collected on the 5th and 10th days to measure biomass, triterpene content, and the expression levels of triterpene synthesis-related genes. [Results] The plate experiment showed that the C-L group had the fastest mycelium extension, but the mycelium was sparse, and the aging was greatly delayed. The N-L group exhibited faster mycelium extension than the CK group but slower than the C-L group, with the fastest mycelium aging. The shake flask fermentation results showed that the N-L group had the highest biomass. qPCR results demonstrated an upregulation trend in most triterpenoid synthase genes under C-L and N-L conditions. GC-MS analysis revealed that both lanosterol and inotodiol content increased in the C-L and N-L groups compared to the CK group. [Conclusion] Nutritional restriction conditions stimulate the accumulation of triterpenes in I. obliquus.