Microorganisms have survived and evolved in continuously changing and energy-limited environments for billions of years. Compared with those cultured in laboratories with abundant organic substrates, the microorganisms in natural oligotrophic environments exhibit significant differences in physiological states, gene expression, and protein synthesis. Under extreme and low-energy environmental stress, microorganisms utilize a range of substances such as hydrogen, ferrous ions, minerals, and organic remnants as energy or electron sources. They adjust their gene expression, metabolic pathways, and physiological states through various mechanisms to enhance energy utilization efficiency, adapt to nutrient-scarce conditions, sustain metabolic activities and population survival, and drive material transformation and element cycling. Understanding the physiological states of microorganisms in natural environments and their adaptive mechanisms to low-energy supply is crucial for revealing the microbial origins, evolution, growth, metabolism, dormancy, and the minimum energy requirements for life. This review introduces the formation, evolution, and distribution of natural low-energy environments (i.e., environments deficient in electron donors and carbon sources), as well as the physiological states and survival strategies of microorganisms in these variable low-energy environments. The research in this field advances microbial remediation technology development, extreme environment protection, and bio-mining technology development, representing a frontier in geomicrobiology.

Staphylococcus aureus is one of the common pathogens causing infections. It can attach media or implant surfaces to form biofilms, which makes it difficult to be tackled and leads to the generation of drug resistance, posing a great challenge to clinical treatment. Therefore, it is urgent to develop novel antimicrobials. Pillar[5]arenes, a new class of supramolecular macrocyclic hosts, attracting wide attention due to their highly rigid and symmetrical architectures and controllable cavity sizes, which afford the limitless possibility to create antimicrobial agents with various functional groups and biological activities.[Objective] To synthesize triphenylphosphine pillar[5]arene (TPP) and determine its antibacterial activities and drug resistance with Staphylococcus aureus ATCC 6538, Staphylococcus aureus subsp. aureus (S. subsp. aureus) ATCC 29213, and methicillin-resistant S. aureus ATCC 43300. [Methods] The minimal inhibitory concentration (MIC) and minimal bacteriocidal concentration (MBC) were determined to evaluate the antibacterial activity of TPP. The effects of TPP on biofilm formation were quantified by crystal violet staining, and the content of extracellular polysaccharides in the biofilm was determined by the phenol-sulfuric acid assay. The strain resistance to TPP was examined. [Results] TPP exhibited inhibitory effects on the three strains tested, with a MIC of 15.63 μg/mL for the three strains and a MBC of 125.00 μg/mL for both S. aureus and S. subsp. aureus. However, TPP was unable to kill MRSA even at a concentration of 125.00 μg/mL. The biofilm inhibition rates of TPP at MIC were as high as 72.9%, 69.2%, and 71.8% for the three strains, respectively. The content of extracellular polysaccharides decreased with the increase in the concentration of TPP. S. aureus did not develop resistance to TPP after 20 generations. [Conclusion] This study clarified the antibacterial performance of TPP, providing a theoretical basis for the further development and utilization of TPP in the medicine field.

[Objective] To evaluate the biocontrol and growth-promoting effects and reveal the antifungal mechanisms of the pepper endophyte Bacillus velezensis XY40-1, thus providing elite bacterial strains and technical support for the development of biocontrol agents for pepper Phytophthora blight. [Methods] Plate confrontation, in vivo inoculation assay, and microscopic observation were employed to determine the biocontrol and growth-promoting effects of B. velezensis XY40-1 on pepper. Genomics and metabolomics methods were adopted to determine the antifungal metabolites of the strain and the synthesis pathways of substances involved in antifungal effects, on the basis of which the antifungal mechanisms were explored. [Results] Strain XY40-1 exhibited strong inhibitory effects on six pathogenic fungi: Phytophthora capsici, Sclerotium rolfsii, Colletotrichum scovillei, Alternaria alternate, Fusarium oxysporum, and F. solani, that infected pepper, and it demonstrated broad-spectrum resistance. The strain suspension at 10⁷ CFU/mL showcased the control effect of 66.13%. Moreover, it possessed the abilities to solubilize phosphorus and potassium and fix nitrogen, thus promoting the growth of pepper seedlings. XY40-1 carried a large number of genes involved in the synthesis of ketone and terpenoid antibiotics, which enabled it to produce extracellular metabolites such as nogalamycin, megalomicin, rifaximin, avermectin ala, avermectin, and ansamitocin P-3 to inhibit pathogenic fungi. The synthesis and degradation of ketone bodies, as well as the biosynthetic pathways of terpenoid skeletons and antibiotics, contributed to the antagonistic function of XY40-1. The core metabolic pathway was the biosynthesis of secondary metabolites. [Conclusion] B. velezensis XY40-1, an endophyte of pepper, possesses excellent biocontrol and growth-promoting effects on pepper, being a multifunctional and high-quality strain for the biocontrol of pepper diseases.

With the increasing emphasis on health, probiotics have garnered increasing attention due to their safe and beneficial features for intestinal health and have become a hot spot in the fields of food and medicine. In terms of oral drug delivery, it is difficult to select a safe, convenient, and stable carrier. Probiotics can be used as carriers to deliver drugs through the complex in vivo environment without damage and have excellent safety and stability. This review describes the structures, advantages, and disadvantages of five common probiotic-based oral drug delivery approaches: display on spore surface, yeast microcapsules, recombinant probiotic expression, bacterium-like particles, and bacterial ghost, aiming to provide options for the application of oral delivery carriers.

[Objective] To investigate the biosynthetic potential of the endophyte Streptomyces sp. SZC001 in Sinomenium acutum and explore the unknown active natural products. [Methods] SZC001 was isolated by surface sterilizing method and its full-length genome sequence was obtained by third-generation and second-generation sequencing. Then, the biosynthetic potential of SZC001 was evaluated by antiSMASH analysis. Fermentation was carried out with four media, and the compounds were separated and identified by silica gel column chromatography, high-performance liquid chromatography, high-resolution mass spectrometry and nuclear magnetic resonance. The CCK-8 assay was employed to examine the cytotoxicity of the target compounds. [Results] The strain was identified as Streptomyces sp. SZC001, with a genome length of 9 109 166 bp and the G+C content of 71.08%. The antiSMASH analysis showed that the genome of the strain contained a total of 31 biosynthetic gene clusters (BGCs), among which 17 BGCs had less than 40% similarity with the known BGCs. The strain produced several anthracyclines in four media, and the two most abundant compounds 1 and 2 were isolated and identified. Compound 1 is the known compound ε-rhodomycinone and compound 2 is a new compound η-rhodomycinoe, which is derived from α₂-rhodomycinone by derivatization of the hydroxyl group at the C-10 position and transfer of the hydroxyl group at the 6-position to the 11-position of the backbone. Both compounds 1 and 2 showed relatively strong inhibitory effects on two tumor cell lines, with IC₅₀ of 1.55–4.59 μmol/L. [Conclusion] SZC001 is a strain that holds the potential for the exploration of active natural products. The anthracyclines produced by the strain exhibit anti-tumor activities and warrant further development and utilization. This study enriches ε-rhodomycinone derivatives, furnishing a foundation for the subsequent exploitation of the endophytic resources of S. acutum.

Higher alcohols, major metabolic byproducts produced by Saccharomyces cerevisiae during winemaking, are intricately regulated by a multilevel system. While the enzymatic machinery and their encoding genes involved in the metabolic pathways of higher alcohols in S. cerevisiae have been largely elucidated, the transcriptional regulation underlying this process remains poorly understood. This paper, building upon a summary of the metabolic pathways and regulatory strategies of higher alcohols metabolism in yeast, focuses on the transcription factors Aro80p, GATA and Leu3p implicated in the regulation of higher alcohols metabolism in yeast and their mechanisms of action. The review aims to give theoretical insights into a comprehensive understanding of the transcriptional regulation of higher alcohols metabolism in yeast and facilitate the breeding of yeast strains with moderate production of higher alcohols.

[Objective] To explore the regulatory role of the metalloregulator ZntR in metal homeostasis and clarify the effects of ZntR on the oxidative stress resistance and virulence of Vibrio parahemolyticus. [Methods] Growth curve analysis and intracellular metal content quantification were performed to investigate the regulatory effect of ZntR on the metal homeostasis in V. parahaemolyticus. The effects of ZntR on the oxidative stress resistance and virulence of V. parahaemolyticus were explored by the growth curve analysis and the competitive infection assay in the zebrafish model, respectively. The genes regulated by ZntR were identified by RNA sequencing. [Results] The zntR-deleted strain (ΔzntR) exhibited growth defects under zinc, nickel excess and iron restriction conditions, and the growth defects were related to zinc homeostasis disturbance. The overexpression of zntA in ΔzntR promoted the growth under zinc, nickel excess and iron restriction conditions. In the case of zinc excess, ΔzntR demonstrated weakened resistance to H₂O₂-induced oxidative stress. The virulence of ΔzntR was attenuated in a competitive infection assay in the zebrafish model. RNA sequencing revealed that ZntR regulated the expression of several virulence genes. [Conclusion] ZntR modulates zinc homeostasis and improves oxidative stress resistance and virulence of V. parahaemolyticus.

[Objective] To construct a recombinant vaccinia virus strain WR that expresses dual reporters (luciferase Fluc and red fluorescent protein mCherry). [Methods] Firstly, the gRNA CRISPR/Cas9 plasmid targeting the J2R region of WR and the plasmid pJSE-Fluc/mCherry carrying the dual reporter genes were constructed. Then, the CRISPR/Cas9 gene editing tool was used to insert the dual reporter genes into the TK region, and thus the recombinant vaccinia virus strain rWR-Fluc/mCherry (rWR) was constructed. The location and sequence of insertion in rWR were analyzed by PCR and sequencing. The recombinant strain rWR was characterized by mCherry/Fluc activity and plaque assays. The recombinant strain rWR was subcultured for 12 passages, and the expression levels of the dual reporter genes and E3L were determined to reveal the genetic stability of the strain. To analyze the replication dynamics of the virus in Vero and HeLa cells, we determined the cytopathic effect (CPE), TCID₅₀, and dual reporter expression of rWR and the wild type (WR) in the infected cells. Furthermore, we evaluated the inhibitory effects of ST-246 as a positive drug on both rWR and WR in vitro by the plaque assay, qPCR, and dual reporter activity measurement. [Results] Fluc and mCherry were accurately inserted into the TK region of WR. The Vero cells infected with rWR showed the activities of dual reporters and the plaque morphology consistent with that of WR. After 12 passages, the dual reporter activities and E3L expression were stably detected in rWR, which indicated that rWR was successfully constructed and genetically stable. The CPE, TCID₅₀, and dual reporter activity in Vero and HeLa cells indicated that replication peaked 48–72 h post-infection with rWR, which was consistent with the replication dynamics of WR. The median effective concentration (EC₅₀) of ST-246 against rWR was in agreement with that against WR, and the EC₅₀ (2–7 nmol/L) obtained by the plaque assay, qPCR, and dual reporter activity measurement showed good consistency (r > 0.500 0 and P < 0.05). [Conclusion] A recombinant vaccinia virus strain rWR simultaneously expressing Fluc and mCherry was successfully constructed, and it was genetically stable. This strain might be used as an in vitro system for rapid screening and characterization of anti-orthopoxvirus drugs with simple operation.

[Objective] Rivers and lakes are important and closely linked aquatic ecosystems, in which microorganisms are important organic components and participate in the transformation of various substances and energy flow. Comparing the bacterial and fungal communities and their co-occurrence networks between rivers and lakes is the key to a deeper understanding of the biogeochemical cycling in aquatic ecosystems of the Qaidam Basin. [Methods] We analyzed the diversity, structures, driving factors, and co-occurrence networks of bacterial and fungal communities in six rivers and four lakes of the Qaidam Basin by next-generation sequencing and statistical analysis methods. [Results] The abundance and diversity of bacteria and fungi in rivers were higher than those in lakes (Wilcoxon, P < 0.01). The most dominant bacterial phylum was Proteobacteria in both rivers and lakes (rivers: 6.0%–63.0%; lakes: 8.0%–61.0%), while the most dominant fungal phylum varied between rivers and lakes, being Ascomycota (0.5%–75.0%) in rivers and unclassified_k_Fungi (3.0%–87.0%) in lakes. The structures of bacterial and fungal communities differed between rivers and lakes (bacteria: R=0.599, P=0.001; fungi: R=0.435, P=0.001). Altitude (Alt), chlorophyll a (Chl-a), and total nitrogen (TN) were significant factors shaping bacterial community structures, while dissolved oxygen (DO), pH, and temperature (Temp) were significant drivers shaping fungal community structures in different aquatic ecosystems. The stability of bacterial and fungal communities varied significantly between habitats. Specifically, bacterial communities were more stable in rivers than in lakes, while fungal communities were more stable in lakes than in rivers. [Conclusion] The bacterial and fungal communities varied between rivers and lakes in the Qaidam Basin, demonstrating spatial heterogeneity. This study can provide data support for the in-depth study of the differences and connections of the microbial community characteristics between rivers and lakes in the Qaidam Basin. Moreover, it lays a theoretical foundation for the protection and management of water resources in this region.

Acarbose, an α-glucosidase inhibitor, regulates the postprandial blood glucose level by competitively inhibiting the activities of sucrase, maltase, and glucamylase in the intestine, serving as an ideal drug ingredient with blood glucose-lowering activity. Acarbose is mainly produced by the fermentation of Actinoplanes sp., and its biosynthetic pathway is mainly divided into four modules: C₇-cyclitol synthesis, deoxyglucosamine synthesis, maltose integration, and extracellular transport of acarbose and its homologues (carbophore cycle). This paper reviewed the advances in the research fields mentioned above, aiming to provide ideas for further exploring the biosynthetic pathways of acarbose, catalytic mechanisms of related enzymes, and molecular modification of fermentation strains.