The bacterial stringent response refers to the adaptive reaction that bacteria exhibit when faced with adverse environmental conditions, altering their metabolism and reducing the growth rate to enhance survival and adaptability. The rapid accumulation of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp in this article, mediates the stringent response, playing a crucial role in microbial adaptation to environmental changes. The levels of (p)ppGpp within bacteria are regulated by RelA/SpoT homologue (RSH) proteins, which include small alarmone synthetases (SASs), small alarmone hydrolases (SAHs), and bifunctional proteins such as Rel. Furthermore, recent studies have identified a new bacterial alarmone, adenosine tetraphosphate (ppApp) and adenosine pentaphosphate (pppApp), collectively referred to as (p)ppApp, which is involved in the regulation of various biological processes in bacteria. The enzymes involved in (p)ppGpp metabolism vary among different bacterial species. This study systematically classifies and reviews the structural and biochemical characteristics of the known RSH proteins and summarizes their biochemical functions, aiming to promote further exploration and development in this field.

Organic contamination of crops poses a threat to the safety of food products and human health, and it is urgently needed to be solved. Endophytic bacteria are indispensable in microecosystems. In recent years, researchers have screened and isolated endophytic bacteria with the function of degrading pollutants from the environment. These bacteria have been used to regulate the metabolic processes of organic pollutants in crops, which achieve the efficient reducing of toxic organic pollutants in crops. This paper reviews the research progress in the reduction of toxic organic pollutant accumulation in crops by functional endophytic bacteria, focusing on the degradation genes, products, and pathways of toxic organic pollutants in crops after the colonization of functional endophytic bacteria. Furthermore, it discusses the factors affecting the degradation efficiency of functional endophytic bacteria and emphasizes the importance of these bacteria in reducing organic pollutants in crops. This review provides ideas and a basis for the further utilization of endophytic bacteria to control the risk of organic contamination in crops.

[Objective] Streptomyces rapamycinicus has large biosynthetic potential with 55 natural product biosynthetic gene clusters (BGCs), most of which have not yet been identified. This study aims to obtain a series of novel compounds by Bacterial Artificial Chromosome (BAC) library-based cloning of novel BGCs from S. rapamycinicus on a large scale and then heterologously expressing them in model Streptomyces strains. [Methods] The bioinformatics analysis of the novelty of BGCs screened out 11 unknown BGCs encoding non-ribosomal peptides, polyketides or terpenoids, from S. rapamycinicus SIPI RP202. Then, we cloned these BGCs by constructing a BAC library and screening via PCR, and then introduced them into three heterologous expression hosts by conjugative transfer. Finally, LC-MS was employed to detect whether these BGCs were successfully expressed after fermentation in three media and fermentation broth extraction with two approaches. Novel compounds were separated, purified, and structurally elucidated. [Results] An unknown terpenoid BGC was successfully expressed in Streptomyces albus Del14. Three novel aromatic meroterpenoids, rapamylic acids A-C, were identified. Then, the potential biosynthetic pathways of rapamylic acids A-C were proposed based on their structural features and BGC. [Conclusion] We successfully unlocked a silent BGC from S. rapamycinicus by large-scale BGC cloning and heterologous expression, providing an alternative strategy for the activation of silent BGCs from other Streptomyces strains. Meanwhile, the discovery of this kind of novel meroterpenoids expands the structural diversity of bacterial terpenoids.

[Objective] The rhizosphere microorganism-plant combined approach has high application potential for the remediation of heavy metal-contaminated soil. This study observed the effects of adding exogenous plant growth-promoting bacteria (PGPB) on the growth and molybdenum (Mo) accumulation of alfalfa (Medicago sativa), aiming to provide theoretical references for plant-microbial remediation of Mo-contaminated soil. [Methods] The endophytic bacteria were isolated from dominant plants of Mo tailing and they were identified based on morphological characteristics and molecular evidence. The plant growth-promoting (PGP) properties of molybdate-reducing strains were determined. By adding exogenous PGPB into the soil, we investigated the effects of adding exogenous PGPB on the biomass, physiological activity, and Mo accumulation of alfalfa. [Results] Two molybdate-reducing strains M9 and M13 were obtained and identified as Serratia plymuthica based on morphological characteristics, 16S rRNA gene sequence, and gyrB sequence. M9 and M13 had the abilities to fix nitrogen, solubilize phosphorus, solubilize potassium, and secrete indole-3-acetic acid (IAA), siderophores, and 1-amino cyclopropane-1-carboxylic acid (ACC) deaminase. Under Mo stress, the inoculation of M9, M13, and M9+M13 significantly promoted the growth of alfalfa, increasing the plant height, root length, and fresh weight of alfalfa compared with the non-inoculation control group. At the same time, the inoculation increased the chlorophyll content and peroxidase (POD) activity while decreasing the malondialdehyde (MDA) content in alfalfa. M9 and M13 significantly affected the Mo accumulation of alfalfa. The Mo content in the above-ground and under-ground parts of alfalfa inoculated with M9, M13, and M9+M13 significantly decreased compared with that in the non-inoculation control group. The decreased enrichment factor of Mo in alfalfa indicated that inoculation with molybdate-reducing strains reduced the uptake and transport of Mo in alfalfa. [Conclusion] The molybdate-reducing strains M9 and M13 can promote the growth and reduce the Mo content of alfalfa in Mo-contaminated soil. This finding can provide theoretical reference for revealing the mechanism of microbial-enhanced Mo remediation by plants as well as the joint remediation of Mo-contaminated soil by plants and microorganisms.

Collagen is the most abundant protein in mammals, accounting for about one-third of human protein. As an important component of the connective tissue and extracellular matrix, collagen is essential for maintaining physiological functions and repairing injuries and has important applications in the fields of medicine, food, and beauty. The main methods for producing collagen are natural extraction, chemical synthesis, and biosynthesis. Natural extraction from animal connective tissue has ethical issues, unstable quality, and infectious disease risks. Chemical synthesis is costly and it is not easy to synthesize complex collagen structures. Biosynthesis enables the production of recombinant collagen for different purposes by genetic engineering in a more controllable, safer, and more precise manner. However, due to the complex structure of collagen, its biosynthesis depends on specific molecular chaperones and modifying enzymes, and thus the production of recombinant collagen is challenging. In addition, different types of collagen need to form particular tissue structures, such as fibril, reticular, or transmembrane structures, which further increases the difficulty of production. This article clarifies the multifunctionality of recombinant human collagen, reviews the latest progress and challenges in its biosynthesis, and looks forward to future development directions. This review aims to help researchers, engineers, and industry practitioners understand the research trends of recombinant collagen and promote its further development and commercialization in different application fields.

As autotoxic substances secreted by plant roots, phenolic acids such as p-hydroxybenzoic acid (PHBA), are the main factors causing continuous cropping obstacles. [Objective] To study the effects of Microbacterium aurantiacum on the growth of tomato plants and the microbial community structure in rhizosphere soil under PHBA stress. [Methods] We irrigated tomato rhizosphere with the suspension of M. aurantiacum GX14001 and then measured the growth traits of tomato plants and the soil microbial community changes in the rhizosphere soil. [Results] Under the PHBA treatment, GX14001 significantly promoted the growth of tomato plants, increasing the leaf area, stem diameter, and plant height by 244.0%, 156.5%, and 128.0%, respectively. GX14001 increased the richness but did not cause changes in the diversity of bacteria in the rhizosphere soil. Meanwhile, it decreased the richness and diversity of fungi in the rhizosphere soil. At the phylum level, compared with the control group, the GX14001 group showed increased relative abundance of Actinobacteriota, Chloroflexi, and Proteobacteria, with Ascomycetes as the dominant fungal phylum. [Conclusion] M. aurantiacum GX14001 promotes the growth of tomato plants by changing the microbial community structure in the rhizosphere soil. It increases the relative abundance of beneficial microorganisms in the soil to create a favorable environment for tomato growth.

Algae and bacteria are both the oldest forms of life on our planet, and billions of years of natural evolution have driven the algae and their microbiomes to evolve into interactive phycobionts. Through complex, flexible, intelligent, and multi-interface interactions between algae and bacteria, the functions of both sides of the phycobionts are exquisitely regulated. The creation, innovation, and development of the phycobiont theory shows vital scientific value for revealing the mystery of the origin and evolution of the life on Earth, and this theory is also being transformed into diverse practical applications in significant fields for sustainable development. After centuries of incubation, knowledge accumulation and development, currently, it is the right time to promote Phycosphere Microbiology to develop into an emerging interdiscipline. In this review, we comprehensively discussed the core concepts of Phycosphere Microbiology, sorted out its vital relationships with environment protection, human health maintenance, resource utilization, and green-oriented transition of energy, then reviewed its development history, and summarized the main research achievements during three development periods. Finally, we also proposed and discussed the future development trends and potential research directions for this emerging interdiscipline.

[Objective] Vibrio parahaemolyticus is a major foodborne pathogen that causes acute gastroenteritis in humans. Here, we aim to decipher the mechanisms by which the histidine kinase EnvZ regulates the swarming motility and biofilm formation of V. parahaemolyticus. [Methods] The plasmids pBAD24 and pMal carrying inducible promoters were used to construct the plasmids carrying target genes for overexpression. The recombinant plasmids were introduced into the wild-type strain (WT) and envZ-deleted strain (ΔenvZ) of V. parahaemolyticus. Swarming plates were prepared to measure swarming motility, while biofilm formation was detected by crystal violet staining. The RT-qPCR and bioluminescence reporter assays were employed to explore the mechanisms by which EnvZ regulated the expression of downstream genes. [Results] The swarming motility of ΔenvZ was significantly lower than that of WT, while the introduction of the pBAD24-envZ plasmid into ΔenvZ restored its swarming ability. The transcription levels of the lateral flagellar genes were positively correlated with the swarming motility. The promoter activities of P _scrABC -lux in ΔenvZ and ΔenvZΔompR were lower than those in WT and ΔompR. The swarming ability of ΔenvZ was significantly increased when the Scr system was overexpressed via the pMal-scrABC plasmid, while the overexpression of EnvZ in the strain without scrABC did not change the swarming motility. In addition, ΔenvZ exhibited a significant decrease in biofilm formation compared with WT. The pMal-envZ plasmid restored the biofilm formation of ΔenvZ to the level of WT, whereas the pMal-scrABC plasmid did not have this effect. The promoter activity of the extracellular polysaccharide operon (epsA-J) and the transcription levels of the extracellular polysaccharide genes in ΔenvZ were both significantly lower than those in WT. [Conclusion] The histidine kinase EnvZ enhances the swarming motility of V. parahaemolyticus by regulating the expression of the Scr system and promotes the biofilm formation by regulating the expression of extracellular polysaccharides.

[Objective] To provide environmental sustainable, safe, and efficacious management approaches for root rot impacting a range of crops in the unique agro-ecosystems of Gansu and Qinghai Provinces. [Methods] The plate confrontation method and the organophosphorus agar plate were used for preliminary screening of 305 strains of tested bacteria, and the strains obtained from preliminary screening were re-screened with the fermentation broth method. Subsequently, the nitrogen-fixing, phosphate-solubilizing, and potassium-solubilizing abilities of the strains were determined by the Kjeldahl method, ultraviolet spectrophotometry, and flame photometry, respectively. The siderophore-producing activity, the IAA content in the fermentation broth, as well as the acid, alkali, and salt tolerance of the strains, were determined by spectrophotometric methods. Finally, targeting the pathogens causing root rot in various crops in Gansu and Qinghai Provinces, bacterial consortia were constructed with different functional strains for disease prevention and plant growth promotion. The plant growth-promoting and antifungal effects of different consortia were evaluated, and the best consortium was selected. Furthermore, the 16S rRNA gene and gyrB of the strains in the best consortia were sequenced for identification. The root rot-preventing and plant growth-promoting effects of the best consortium were evaluated by the pot culture method. [Results] A total of 86 antagonistic strains and 134 phosphate-solubilizing strains were preliminarily screened out, and 20 antagonistic strains were selected after re-screening, among which strains K87 and LB17 demonstrated excellent broad-spectrum antifungal effects. Specifically, K87 showed inhibition rates of 87.53%, 74.90%, 75.15%, 79.69%, and 88.43% against Fusarium avenaceum, F. equiseti, F. oxysporum, F. solani, and Microdochium bolleyi, respectively. LB17 exhibited inhibition rates of 61.89%, 87.52%, and 87.23% against F. oxysporum, F. solani, and Bipolaris sorokiniana, respectively. Among the 8 strains with superior plant growth-promoting abilities, LB17 had the strongest siderophore-producing activity, with an iron carrier activity unit (su) value of 0.32, and K113 exhibited a good nitrogen-fixing capability, fixing nitrogen at a rate of 0.08 g/L. K87 secreted the highest amount of IAA, which reached 9.87 mg/L. MP6 had the greatest ability to solubilize inorganic phosphorus, with a solubilization rate of 1 470.69 μg/mL, while K85 showed the best performance in solubilizing organic phosphorus, with a solubilization rate of 1 321.23 μg/mL. MP41 excelled in potassium solubilization, with a solubilization rate of 140.33 mg/L. Ultimately, 14 bacterial consortia were constructed, in which T2 exhibited the best synthetic performance, with a nitrogen-fixing rate of 0.212 g/L, a potassium solubilization rate of 86.28 mg/L, and an IAA secretion rate of 16.91 mg/L. Moreover, its inhibition rates against the 6 pathogenic fungi all reached over 60.00%, and even 87.69% against F. equiseti. Strains LB17, K87, and MP6 in this consortium were all identified as Bacillus velezensis. T2 demonstrated significant biocontrol efficacy against root rot in naked barley, with the control effects exceeding 70.00%, and exhibited remarkable plant growth-promoting properties. [Conclusion] This study developed an efficient bacterial consortium for the management of crop root rot and the promotion of crop growth in the unique agro-ecosystems in Gansu and Qinghai Provinces.

Salmonella Enteritidis is a major foodborne pathogen that can cause gastrointestinal infections in both humans and animals. As one of the key genes encoding the iron-sulfur cluster assembly, iscA plays a role in the transport of iron ions and energy metabolism. IscA is a conserved A-type iron-binding protein. [Objective] To study the role of iscA in the infection process of Salmonella by constructing an iscA-deleted mutant (ΔiscA) of Salmonella Enteritidis Z11. [Methods] The unmarked in-frame gene deletion method was employed to construct ΔiscA from the laboratory-preserved Salmonella Enteritidis Z11 strain. The wild type (WT) and ΔiscA were compared in terms of motility and biofilm formation. Additionally, the impact of IscA on the virulence of Salmonella Enteritidis was explored in both RAW264.7 cells and a mouse model. [Results] The deletion mutant ΔiscA was successfully constructed. No significant difference in the growth or biofilm formation was observed between ΔiscA and WT, indicating that the deletion of iscA did not affect the normal growth or biofilm formation of Salmonella Enteritidis. However, ΔiscA exhibited a significantly smaller zone of motility than WT at the time point of 6 h, suggesting that the loss of iscA reduced the motility of Salmonella Enteritidis Z11. In RAW264.7 cells, the adhesion and invasion of ΔiscA significantly decreased to 37% and 20%, respectively, of those of WT. Furthermore, the proliferation rate of ΔiscA in the cells was significantly lower than that of WT. Mouse infection experiments revealed that ΔiscA demonstrated reduced colonization in the jejunum and cecum compared with WT. [Conclusion] iscA is closely associated with the virulence of Salmonella Enteritidis. Its deletion affects the motility, adhesion, invasion, and proliferation, ultimately reducing the colonization in the host intestine and influencing the infection process of Salmonella Enteritidis.