People are exposed to environments containing various pathogens, which have multiple interactions with human cells or tissues. Pathogens can survive in the host environment by regulating pathogenic conditions such as virulence and invasiveness. At the same time, host cells resist the invasion of pathogens by mobilizing their own immune system. However, researchers mainly focus on the physiological functions of sRNAs in pathogens and have gained limited knowledge about the interactions between pathogens and hosts. How to use highly sensitive and high-resolution methods to study the interactions between pathogens and hosts have become a major challenge in the current research. By reviewing relevant studies, we summarize the commonly used techniques and experimental processes for studying the interactions between pathogens and hosts, aiming to improve the understanding about the mechanisms and principles of these experimental techniques and provide technical references for the research on interactions between pathogen sRNAs and host targets.

In bacterial cells, RNase HI usually degrades RNA in the RNA/DNA hybrids to prevent the accumulation of primers in replication and the formation of R-loops in transcription, thus maintaining genomic stability and normal life activities. The recognition of substrates by RNase HI mainly depends on DNA- and RNA-binding grooves, and the catalysis of substrates by RNase HI mainly depends on the DEDD motif and a histidine located in a flexible loop near the active site. Metal ions represented by Mg²⁺ play an important role in the catalytic process. The mode of action of RNase HI is determined by the type of ssDNA overhangs on RNA/DNA hybrids. In the presence of a 5′ ssDNA overhang or in the absence of any overhang on RNA/DNA hybrids, RNase HI functions as a non-sequence-specific endonuclease to degrade RNA randomly. In the presence of a 3′ ssDNA overhang on RNA/DNA hybrids, RNase HI relies on 5′-exonuclease activity for the successive degradation of RNA. RNase HI, Rep, DinG, and UvrD are recruited near the replication forks by interacting with the six residues of the C-terminal tail of single-stranded DNA-binding protein (SSB), and may resolve replication-transcription conflicts in a cooperative manner. The deletion of RNase HI or the decrease in RNase HI activity will cause a series of harmful events such as DNA structural instability, gene mutation, transcriptional machinery backtracking, and replication incoordination. RNase HI has shown great application prospects in antisense technology, R-loop detection, and targeted therapy combined with antibiotics. The cooperative mechanism of primer degradation by RNase HI and other enzymes is also worth studying in the future.

[Background] Long-term continuous cropping of tobacco (Nicotiana tabacum) leads to the accumulation of autotoxins, which aggravates the incidence of tobacco bacterial wilt (TBW) caused byRalstoniasolanacearum and causing great economic losses of tobacco production. [Objective] To develop a compound bacterial agent capable of controlling TBW in the field with long-term continuous cropping of tobacco. [Methods] We formulated compound bacterial agents with screened strains capable of degrading autotoxins. Orthogonal design and single factor experiments were employed to optimize the strain ratio and the dosages of additives. The inhibition performance of the compound bacterial agent on TBW was evaluated in a greenhouse and in a field with continuous cropping of tobacco for 15 years. [Results] Orthogonal experiments showed that the optimal ratio ofBacillus sp. NO1,Brucella sp. NO8,Bacillus sp. NO9, andBacillus sp. NO10 in the compound bacterial agent was 1:3:4:2. Single factor experiments showed that the best vector was silica. The best wetting agent and dispersant were sodium hexametaphosphate (SHMP) and sodium butylnaphthalene sulfonate (SBNS), respectively, which were optimized to be added at the dosages of 2%. The optimal concentration of the stabilizer glycerin was 1.0%. Pot experiments showed that both the degradation rate of six autotoxins and the inhibition rate of TBW by the compound bacterial agent reached over 78%. The results of the field experiment showed that the compound bacterial agent diluted by 100 folds had significant degradation effects on six autotoxins in the tobacco field with continuous cropping for 15 years. Moreover, the agent significantly increased the height, stem circumference, and waist leaf length and width of tobacco plants, thus promoting the growth and development of tobacco. In addition, the agent regulated the rhizosphere microbiota of tobacco, as manifested by the decreased relative abundance ofClostridium_sensu_stricto_1,Ralstonia, andCellulomonas and the increased relative abundance ofDevosia,Flavobacterium, andSphingomonas. The agent decreased the incidence rate and disease index of TBW from 92.22% and 48.19% to 18.15% and 9.52%, respectively, with a control effect of 80%. [Conclusion] The optimized compound bacterial agent significantly reduces the incidence rate and disease index of TBW in the field with long-term continuous cropping of tobacco, which provides a solution for the prevention and control of TBW.

[Objective] To study the spatial and temporal distribution characteristics, community structure, and diversity of uncultured myxobacteria in the rhizosphere soil ofPhragmitesaustralis in the Ebinur Lake wetland, so as to enrich the knowledge of myxobacteria resources in saline-alkaline wetlands, lay a foundation for exploiting the myxobacteria resources in extreme environments, and provide data support for the restoration of saline desert ecosystems. [Methods] The rhizosphere soil samples ofP.australis were collected from 10 sites in Ebinur Lake wetland in 3 months, and high-throughput sequencing was conducted for the V4–V5 region of the 16S rRNA gene to reveal the diversity and spatial and temporal distribution of myxobacteria. [Results] The abundance of myxobacteria, as indicated by the presence of 16S rRNA gene tags, ranged from 0.22% to 3.54% of the total bacteria in the Ebinur Lake wetland. The highest diversity was observed in July and at the sampling site 4, suggesting the correlations of genus diversity with both seasons and sample sites. A total of 14 genera of myxobacteria belonging to 8 families of 3 suborders were identified. Among them,Haliangium was the dominant genus, with the relative abundance of 10.83%–71.01%. Network co-occurrence diagrams showed that most of the bacteria interacted with myxobacteria. Spearman correlation analyses showed that the Shannon, Chao1, and ACE indices of bacteria influenced the diversity and richness of myxobacteria. The redundancy analysis (RDA) showed that soil inorganic nitrogen (IN), organic matter (OM), and water-soluble magnesium ions (Mg²⁺) were the main abiotic factors influencing the diversity and community structure of myxobacteria. [Conclusion] The Ebinur Lake wetland is rich in myxobacteria, the diversity and community structure of which present spatial and temporal variations. Biotic factors (bacteria) and abiotic factors (soil physico-chemical properties) jointly affect the diversity of myxobacteria.

[Objective] To analyze the influence of pH on sulfate-reducing properties of sulfate-reducing bacteria enriched from marine sediments, identify the bacterial community composition, predict the key genes of sulfate reduction, and explore the mechanism of sulfate reduction. [Methods] The sulfate reduction rates of sulfate-reducing bacteria at different pH conditions were determined. On this basis, high-throughput sequencing and PICRUSt were employed to analyze the dominant sulfate-reducing bacteria and the relative abundance of sulfate-reducing genes. [Results] The biomass (OD₆₀₀) and sulfate reduction rate of sulfate-reducing bacteria varied significantly under different pH conditions (P＜0.01) and reached their peak values (0.34±0.01 and 96.52%±0.44%, respectively) at pH 5.0. According to the high-throughput sequencing data, the abundance and diversity of bacteria were the highest at pH 5.0. The dominant bacteria werePseudomonas andBacillus, and the assimilatory sulfate reduction-related genes had higher abundance. [Conclusion] Sulfate-reducing bacteria are suitable to be enriched and cultured at pH 5.0. Under this condition, the high sulfate reduction rate is attributed to the assimilatory sulfate reduction pathway. The findings provide experimental support for revealing sulfate reduction mechanism and broaden the germplasm resources of sulfate-reducing bacteria for application.

[Objective] To investigate the effects and mechanism ofLactobacillus plantarum postbiotics at different doses on amelioratingSalmonellaenterica Typhimurium (ST) infection in mice. [Methods] Sixty 5-week C57BL/6 mice were randomized into five groups: Control, ST, CFS-L+ST, CFS-M+ST, and CFS-H+ST.Lactobacillus plantarum postbiotics (cell-free supernatant, CFS) was administrated at low (L), medium (M), and high (H) doses (50, 100, and 200 μL, respectively) for 21 days. On day 22, mice were orally challenged with ST at 3×10⁸ CFU, and the samples were collected three days later. [Results] Compared with the control group, CFS-L+ST and CFS-M+ST groups showed no significant changes in body weight gain, while the CFS-H+ST group showed a significant decrease (P<0.05). The CFS-M+ST and CFS-H+ST groups alleviated ST-induced body weight loss (P<0.05). CFS pretreatment reduced ST-induced bacterial translocation in the colon, liver, spleen, and brain (P<0.05) and alleviated the pathological damages in the colon and spleen. ST reduced the levels of acetic acid and butyric acid in the cecum, which, however, increased in the CFS-M+ST group (P>0.05). Compared with the ST group, CFS-M+ST alleviated the inflammatory response by lowering the levels of pro-inflammatory cytokines including interleukin-1beta (IL-1β), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) (P<0.05) and elevating the levels of anti-inflammatory cytokines including interleukin-4 (IL-4) and interleukin-10 (IL-10) (P<0.05). Moreover, CFS-M+ST suppressed ST-induced inflammation by modulating the nucleotide-binding oligomerization domain-like receptor (NLR) family pyrin domain-containing protein 3 (NLRP3) inflammasome, as indicated by the down-regulated mRNA levels ofNLRP3, apoptosis-associated speck-like protein (ASC), cysteine-dependent aspartate-specific protease 1 (caspase-1), and gasdermin D (GSDMD) (P<0.05). Furthermore, CFS inhibited NLRP3 inflammasome by blocking the upstream key nuclear factor kappa beta (NF-κB) pathway, as indicated by the down-regulated expression levels of myeloid differentiation factor 88 (MyD88), tumor necrosis factor receptor-associated factor 6 (TRAF6), transforming growth factor beta-activated kinase 1 (TAK1), and NF-κB (P<0.05). [Conclusion] L.plantarum postbiotics CFS alleviated theS.enterica Typhimurium infection and inflammatory responses in mice by inhibiting the NF-κB-mediated NLRP3 inflammasome, and the pretreatment with medium-dose CFS showed the best effects.

[Objective] Over a prolonged period of growth, the old tea plant ecosystem ofCamellia sinensis 'Fujian Shuixian' in Gujing has acquired a distinctive fir flavor, with the mountainous environment playing a key role in shaping the tea quality. Microbial communities play a vital role in biogeochemical cycling within mountainous ecosystems. Nevertheless, the characteristics of the microbial community within the distinct old tea plant ecosystem remain incompletely understood. [Methods] Samples were collected from both the aboveground and belowground parts of the oldC.sinensis 'Fujian Shuixian' tea garden in Gujing, situated in the central region of the Wuyishan National Park. The samples encompassed the phyllosphere and leaf endosphere, along with soils from the rhizosphere, non-rhizosphere, and surrounding regions. High-throughput sequencing of the 16S rRNA gene and internal transcribed spacer (ITS) region were carried out to assess the bacterial and fungal diversity, respectively. [Results] The richness and diversity of bacterial and fungal communities in the aboveground part were markedly lower than those in the belowground part. Within co-occurrence networks, the modularity index for taxa networks in each niche exceeded 0.4, and the positive correlations in interactions among microbial taxa are greater than the competition. The prevailing phyla, with the relative abundance greater than 1%, wereProteobacteria,Acidobacteriota,Actinobacteriota,Ascomycota, andBasidiomycota, which were present in both above and belowground habitats. Notably, the relative abundance ofProteobacteria,Actinobacteria, andAscomycetes aboveground surpassed that belowground, whereas that ofAcidobacteria andBasidiomycetes displayed an opposite pattern (P＜0.05). The prominent genera (with the abundance exceeding 1%) identified wereMethylobacterium-Methylorubrum,Sphingomonas,Pseudomonas,Amnibacterium,Bacillus,Cladosporium, andFusarium. These genera potentially served as crucial biomarkers in the ecological niches ofC.sinensis 'Fujian Shuixian' within the old tea plant ecosystem in Gujing. [Conclusion] The present study unveiled the unique attributes of bacterial and fungal communities within the old tea plant ecosystem ofC.sinensis 'Fujian Shuixian' in Gujing, delivering valuable scientific insights for disease prevention and biocontrol in tea plant cultivation, tea quality improvement, and the exploration of functional microbial resources.

[Objective] To compare the biotite weathering activities and mechanisms betweenPseudomonas azotoformans F77 andPseudomonas paracarnis P1. [Methods] During the mineral weathering process, the dissolved Fe and Al concentrations, cell number, pH, gluconic acid concentration, and residual glucose concentration in the culture medium were determined to reveal the biotite weathering effects and mechanisms of strains F77 and P1. Furthermore, RNA-seq was employed to explore the molecular mechanism for the difference in the biotite weathering effect between the two strains. [Results] During the 5 days of mineral weathering, strain F77 increased Fe and Al concentrations by 3.3−23.3 folds and gluconic acid concentration by 27.3−53.9 folds the compared with strain P1. Meanwhile, strain F77 showed decreased cell number and medium pH compared with strain P1. The data of comparative transcriptomics showed that strain F77 had more specific genes (2 872) and differentially expressed genes (1 832) than strain P1 (1 903 and 1 258 genes, respectively). Additionally, strain F77 carried more genes involved in the membrane transport, carbohydrate metabolism, cell motility, chemotaxis, and signal transduction than strain P1. Furthermore, strain F77 had higher fold changes in the expression levels of superoxide dismutase and catalase genes as well as higher number and fold changes of the genes involved in gluconic acid synthesis than strain P1. [Conclusion] Strain F77 surpassed strain P1 in weathering the biotite and producing gluconic acid. Strain F77 promoted the biotite weathering by producing gluconic acid. The addition of biotite significantly up-regulated the expression of genes involved in the transmembrane transport, cell movement and chemotaxis, signal induction, and carbon and energy metabolisms in mineral weathering. Furthermore, the genes involved in gluconic acid synthesis and encoding superoxide dismutase and catalase may play a role in the mineral weathering by strain F77.

[Objective] To investigate the diversity and community structure of soil bacteria in the farmlands in Qinghai Province. [Methods] High-throughput sequencing was employed to analyze the bacterial community structure and diversity in the soil samples of farmlands growing wheat, oilseed rape, and highland barley in Dulan, Huzhu, Gonghe, and Datong counties. Furthermore, the relationship between bacterial community structure and soil physicochemical properties was analyzed. [Results] The pH, moisture, and organic matter of soil, as well as the Chao1 and Shannon indexes and linear discriminant analysis effect size (LEfSe) of soil bacteria, showed significant differences in some of these indexes (P＜0.01) but no significant differences among the three crops (P > 0.05). The results of principal component analysis (PCA) showed that the bacterial community structure was different among different regions but highly similar in the farmlands of the three crops. A total of 3 127 operational taxonomic units (OTUs) and 3 694 OTUs were common in the four regions and in the farmlands of the three crops, respectively. The OTUs of soil bacteria were identified as 423 species, 450 genera, 276 families, 192 orders, 93 classes of 36 phyla. The four regions or three crops had similar dominant phyla, genera, and species, while these taxa differed in relative abundance. Soil moisture, pH, and organic matter were significantly correlated with Chao1 and Shannon indexes. Soil pH and organic matter had significantly positive or negative correlations with unclassified species, unclassified RB41, and unclassifiedSphingomonas. Chao1 and Shannon indexes had significantly negative correlations with unclassifiedSphingomonas but positive correlations with unclassified RB41 and unclassifiedVicinamibacteraceae. [Conclusion] Regional differences had significant effects on soil physicochemical properties, bacterial community structure and diversity, which were more obvious than those of crop differences.

[Objective] To obtain the proteins of acetyl-CoA synthase (ACS_MU) and PHA synthase (PhaC_MU) fromMassilia sp. UMI-21 by structuring anin vitro recombinant expression system, and to elucidate their roles in the biosynthesis of polyhydroxybutyrate (PHB) using the one-phase reaction system (OPRS). [Methods] Seamless cloning was employed to ligate the acetyl-CoA synthase geneacs_MU and the PHA synthase genephaC_MU amplified fromMassilia sp. UMI-21 to the pQE-80L plasmid to construct the recombinant plasmids. The recombinant plasmids were transformed intoEscherichia coli BL21(DE3), and the recombinant strains were obtained. ACS_MU and PhaC_MU were purified using a 6×His tag, and their activities were determined by the 5, 5′-dithiobis-(2-nitrobenzoic acid) (DTNB) method. With 3HB as a substrate, the one-phase reaction system (OPRS) was employed to validate the functions of ACS_MU and PhaC_MU in the biosynthesis of PHB. [Results] The recombinant strains BL21-pQE-80L-acs_MU and BL21-pQE-80L-phaC_MU were successfully engineered, with the ACS_MU and PhaC_MU yields of 24.8 mg/L and 25.6 mg/L, respectively. The specific activity of ACS_MU was (0.148±0.011) U/mg, and that of PhaC_MU for (R)-3HBCoA was (0.102±0.011) U/mg. Nuclear magnetic resonance hydrogen spectroscopy (¹H-NMR) results showed that products from the all three PHB synthesis pathways, ACS_Pt-PCT_CP-PhaC_Re, ACS_MU-PCT_CP-PhaC_Re, and ACS_MU-PCT_CP-PhaC_MU, in OPRS were PHB. The yields of PHBvia the three pathways were 0.62, 0.76, and 0.64 g/L, respectively. [Conclusion] The genesacs_MU andphaC_MU can be overexpressed in theE.coli expression system to yield active soluble proteins. Compared with the ACS_Pt-PCT_CP-PhaC_Re pathway, substitution of ACS_Pt with ACS_MU increased the PHB yield by 22.58%. The yield of PHB was contingent upon the stability of acetyl-CoA synthase (ACS), which provided acetyl-CoA for reaction under identical PhaC. Replacing PhaC_Re with PhaC_MU decreased the PHB yield by 15.79% compared with ACS_MU-PCT_CP-PhaC_Re. The polymerase PhaC plays a crucial role in PHB synthesis under identical precursor concentrations.