Type VI protein secretion systems (T6SSs) are specialized transport apparatus which can target both eukaryotic and prokaryotic cells and play key roles in host–pathogen–microbiota interactions. Therefore, T6SSs have attracted much attention as a research topic during the past ten years. In this review, we particularly summarized the T6SS antibacterial function, which involves an interesting offensive and defensive mechanism of the effector–immunity (E–I) pairs. The three main categories of effectors that target the cell wall, membranes, and nucleic acids during bacterial interaction, along with their corresponding immunity proteins are presented. We also discuss structural analyses of several effectors and E–I pairs, which explain the offensive and defensive mechanisms underpinning T6SS function during bacterial competition for niche-space, as well as the bioinformatics, proteomics, and protein–protein interaction (PPI) methods used to identify and characterize T6SS mediated E–I pairs. Additionally, we described PPI methods for verifying E–I pairs.

Switchgrass (Panicum virgatum L.) is a cellulosic biofuel feedstock and their effects on bacterial communities in deep soils remain poorly understood. To reveal the responses of bacterial communities to long-term switchgrass cultivation through the soil profile, we examined the shift of soil microbial communities with depth profiles of 0–60 cm in five-year switchgrass cultivation and fallow plots. The Illumina sequencing of the 16S rRNA gene showed that switchgrass cultivation significantly increased microbial OTU richness, rather than microbial Shannon diversity; however, there was no significant difference in the structure of microbial communities between switchgrass cultivation and fallow soils. Both switchgrass cultivation and fallow soils exhibited significant negative vertical spatial decay of microbial similarity, indicating that more vertical depth distant soils had more dissimilar communities. Specifically, switchgrass cultivation soils showed more beta-diversity variations across soil depth profile. Through network analysis, more connections and closer relationships of microbial taxa were observed in soils under switchgrass cultivation, suggesting that microbial co-occurrence patterns were substantially influenced by switchgrass cultivation. Overall, our study suggested that five-year switchgrass cultivation could generated more beta-diversity variations across soil depth and more complex inter-relationships of microbial taxa, although did not significantly shape the structure of soil microbial community.

Many bacteria secrete siderophores to enhance iron uptake under iron-restricted conditions. In this study, we found Cupriavidus necator JMP134, a well-known aromatic pollutant-degrading bacterium, produces an unknown carboxylate-type siderophore named cupriabactin to overcome iron limitation. Using genome mining, targeted mutagenesis and biochemical analysis, we discovered an operon containing six open reading frames (cubA-F) in the C. necator JMP134 genome that encodes proteins required for the biosynthesis and uptake of cupriabactin. As the dominant siderophore of C. necator JMP134, cupriabactin promotes the growth of C. necator JMP134 under iron-limited conditions via enhanced ferric iron uptake. Furthermore, we demonstrated that the iron concentration-dependent expression of the cub operon is mediated by the ferric uptake regulator (Fur). Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and resistance to oxidative and aromatic compound stress in C. necator JMP134. In conclusion, we identified a carboxylate-type siderophore, named cupriabactin, which plays important roles in iron-scavenging, bacterial motility, biofilm formation and stress resistance. Importance Since siderophores have been widely exploited for agricultural, environmental and medical applications, the identification and characterization of new siderophores from different habitats and organisms will have great beneficial applications. Here, we identified a novel siderophore-producing gene cluster in C. necator JMP134. This gene cluster produces a previously unknown carboxylate-siderophore, cupriabactin. Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and oxidative stress resistance. Most notably, this system also plays important roles in increasing the resistance of C. necator JMP134 to stress caused by aromatic compounds, which provide a promising strategy to engineer more efficient approaches to degrade aromatic pollutants.

The orchard inter-planting pattern is being widely used in many countries of the world, but it is relatively new in China. This study evaluated the interrow mono- and mixed-planting of Lolium perenne (Lp) and Medicago sativa (Ms) in orchards on soil nutrient, enzyme activity, and bacterial community diversity in 0–10, 10–20, and 20–40 cm soil layers. The clean tillage orchard was used as control (CK) treatment. Compared with CK, Lp and Lp + Ms. significantly increased the contents of soil organic matter (OM), total nitrogen (TN), and alkali-hydrolyzable nitrogen (AN) in 0–20-cm soil layer, and up-regulated the activities of urease (URE) and alkaline phosphatase (ALP). The Lp treatment significantly increased the relative abundance of Gemmatimonadetes and Planctomycetes in the 0-10-cm soil layer. Besides, cover crops significantly increased the abundance of Actinobacteria, Gemmatimonadetes, and Chloroflexi in the 10–20-cm soil layer and that of Gemmatimonadetes and Chloroflexi in the 20–40 cm soil layer. The redundancy analysis (RDA) showed significant positive correlations of Actinobacteria with ALP, OM and TN and that of Bacteroidetes with available potassium (AK), and Proteobacteria with available phosphorus (AP). Overall, the grass inter-planting improved the soil nutrients, enzymes activities, and bacterial community composition of the soil. Based on these results, inter-planting perennial ryegrass in the apple orchards is a suitable grass-orchard inter-planting strategy in Weibei, Shaanxi Province of China.

Grass residue decomposition is crucial for nutrient cycling in agro-ecosystems, enhancing nutrient utilization efficiency and supporting sustainable crop management. While grass mulching has been widely studied for improving orchard soil fertility, the role of soil microbial communities in decomposing different plant organs remains unclear. Before decomposition, the aboveground and belowground plant parts were harvested and placed in separate litterbags, which were later used for evaluating the decomposition rate and chemical characteristics of the shoots and roots for 40 days (at 10 days intervals). The changes in soil fertility, soil microenvironment, soil microbial community were measured after 0, 1 and 3 months, alongside analysis of key microbial taxa under different residues treatments. The remaining mass of root litter treatment was significantly higher than that of other treatments by 72.97%, 17.53% during 1–10 days and 30–40 days, respectively. During the 40-days period, the release of potassium (K) from root litter reached 58.61%, and the decomposition of lignin was recorded at 56.94%, whereas the release of carbon (C), nitrogen (N), and phosphorus (P) remained relatively stable. Despite no significant changes in nodes, edges, and links at 30 and 90 days, the co-occurrence network of root litter exhibited modularity values of 0.774 and 0.773, respectively. The values were higher than those observed in random networks, indicating the presence of functional modules and enhanced stability within the root microbial community. Litter organs enhanced decomposition rates by positively influencing soil fertility and keystone microbial decomposers, while its soil microenvironment affects decomposition rates. Despite its recalcitrance, the chemical composition of root litter plays a key role in regulating soil microbial community structure and improving soil fertility, thereby maintaining orchard ecosystem functionality.

This preliminary investigation was designed to study the effects of different mixed orchard hays on meat quality, fatty acids, amino acids, rumen intestinal microflora, and the relationship between rumen bacteria and fatty acids in the longissimus dorsi muscle of Saanen dairy goats. In this preliminary investigation, goats were separately fed crop straws (corn and wheat straws) and alfalfa (Medicago sativa L.) (CK group), alfalfa + oats (Avena sativa L.) (group I), alfalfa + perennial ryegrass (Lolium perenne L.) (group II), and hairy vetch (Vicia villosa Roth.) + perennial ryegrass (group III). There were differences in shear force and cooking loss between treatments. The contents of saturated fatty acids (SFAs) C14:0, C16:0, and C18:0 in the CK group were significantly higher than those in other three groups (p < 0.001). The 16S rDNA sequencing results showed that the relative abundance of Proteobacteria in group II were higher than those in other three groups (p < 0.05). Association analysis showed that Prevotella_1 was negatively correlated with C18:0 and significantly positively correlated with C16:1, while Clostridium and Romboutsia showed a positive correlation with monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs). Therefore, feeding mixed hays can increase beneficial fatty acids and the percentages of associated bacteria in rumen and intestines.