Yuying Bao

Carminic acid (CA) is a high-value natural anthraquinone pigment used in foods, cosmetics, textiles, and pharmaceuticals, but its current industrial supply depends largely on extraction from the scale insect Dactylopius coccus, creating constraints in yield, cost, sustainability, and allergen control. This review summarizes recent progress from pathway elucidation to microbial production. We first outline the structure, occurrence, applications, and biosynthetic logic of CA, emphasizing the convergence of type III polyketide assembly with insect-associated tailoring reactions, especially C-glycosylation. We then compare heterologous production strategies in Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, and Aspergillus nidulans, focusing on chassis-specific advantages, bottlenecks, precursor supply, malonyl-CoA engineering, dynamic regulation, enzyme compatibility, compartmentalization, and downstream processing. Structurally related anthraquinone pigments are further discussed to extract broader design principles for pathway diversification and synthetic biology. Finally, we highlight key challenges for industrial translation, including low titers, incomplete enzyme characterization, host–pathway incompatibility, and scalable purification, and propose integrated strategies combining precursor-pathway rewiring, AI-assisted enzyme engineering, biosensor-based regulation, and process optimization to develop competitive microbial cell factories.

Open-pit coal mining in grassland ecosystems causes severe soil degradation and disrupts the native soil microbial communities. However, current remediation research predominantly focuses on plant growth or soil physicochemical properties, with a limited systematic analysis of the soil microbial community during remediation in the grassland coal mine dump. To address this gap, this study used high-throughput sequencing integrated with field experiments to systematically evaluate the effects of plant-microbial combined remediation on soil microbial communities in a coal mine dump located in a fragile, severely cold grassland. Our study revealed divergent restoration of soil bacteria and fungi. Bacterial communities demonstrated a strong recovery capacity, with diversity nearly restored to natural levels, while fungal communities remained significantly suppressed. Restoration treatments, especially AMF inoculation, successfully altered overall microbial structure and increased the abundance of key marker taxa. Network analysis further showed that remediation drove bacterial communities toward greater complexity and cooperation, whereas fungal communities responded with increased modularity. Critically, the assembly of the entire soil microbial community was primarily governed by a total phosphorus gradient, which clearly discriminated between bare dump, natural grassland, and restoration plots. Mixed planting fostered the most resilient bacterial community; however, microbial inoculation within this system proved counterproductive. Fungal resilience remained consistently lower than that of bacteria. Crucially, inoculation fundamentally altered ecosystem multifunctionality in monocultures, demonstrating its essential role in functional enhancement. Our results demonstrate that integrating specific plant combinations with microbial inoculation is key to enhancing soil microbial stability and ecosystem multifunctionality during restoration. In summary, our findings reveal the distinct response of soil microbial communities under remediation, and provide critical insights for the ecological restoration of mining areas.

Soil salinization limits the growth of agricultural crops in the world, requiring the use of methods to increase the tolerance of agricultural crops to salinity–alkali stress. Arbuscular mycorrhizal fungi (AMF) enhance plant stress adaptation through symbiosis and offer a promising strategy for remediation. However, in non-model crops such as oat (Avena sativa L.), research has mainly focused on physiological assessments, while the key genes and metabolic pathways involved in AMF-mediated growth and saline–alkali tolerance remain unclear. In this study, we employed integrated multi-omics and physiological analyses to explore the regulatory mechanisms of AMF in oats under normal and saline–alkali stress. The results indicated that AMF symbiosis significantly promoted oat growth and physiological performance under both normal and saline–alkali stress conditions. Compared to the non-inoculated group under normal conditions, AMF increased plant height and biomass by 8.5% and 15.3%, respectively. Under saline–alkali stress, AMF enhanced SPAD value and relative water content by 16.7% and 7.3%, reduced MDA content by 35.8%, increased soluble protein by 21.8%, and decreased proline by 13.3%. In addition, antioxidant enzyme activities (SOD, POD, and CAT) were elevated by 18.4%, 18.2%, and 14.8%, respectively. Transcriptomic analysis revealed that AMF colonization under saline–alkali stress induced about twice as many differentially expressed genes (DEGs) as under non-saline–alkali stressed conditions. These DEGs were primarily associated with Environmental Information Processing, Genetic Information Processing, and Metabolic Processes. According to metabolomic analysis, a total of 573 metabolites were identified across treatments, mainly comprising lipids (29.3%), organic compounds (36.8%), and secondary metabolites (21.5%). Integrated multi-omics analysis indicated that AMF optimized energy utilization and antioxidant defense by enhancing phenylpropanoid biosynthesis and amino acid metabolism pathways. This study provides new insights into how AMF may enhance oat growth and tolerance to saline–alkali stress.

Arid desert regions are among the harshest ecological environments on Earth. Halophytes, with their unique physiological characteristics and adaptability, have become the dominant vegetation in these areas. Currently, research on halophytes in this region is relatively limited, particularly concerning studies related to their root endophytic fungi, which have been rarely reported on. Therefore, investigating the diversity and composition of endophytic fungi in halophytes is crucial for maintaining ecological balance in such an arid environment. This study focuses on eight representative angiosperm halophytes from the West Ordos Desert in China (including Nitraria tangutorum, Salsola passerina, Suaeda glauca, Reaumuria trigyna, Reaumuria kaschgarica, Limonium aureum, Apocynum venetum, and Tripolium vulgare), utilizing Illumina MiSeq high-throughput sequencing technology combined with soil physicochemical factor data to analyze the diversity, composition, and ecological functions of their root-associated fungal communities. Ascomycota dominated the fungal composition in most halophytes, particularly among the recretohalophytes, where it accounted for an average of 88.45%, while Basidiomycota was predominant in Suaeda glauca. A Circos analysis of the top 10 most abundant genera revealed Fusarium, Dipodascus, Curvularia, Penicillium, and other dominant genera. Co-occurrence network analysis showed significant differences in fungal networks across halophyte types, with the most complex network observed in excreting halophytes, characterized by the highest number of nodes and connections, indicating tighter fungal symbiotic relationships. In contrast, fungal networks in pseudohalophytes were relatively simple, reflecting lower community cohesiveness. Redundancy analysis (RDA) and Mantel tests demonstrated that soil factors such as organic matter, available sulfur, and urease significantly influenced fungal diversity, richness, and evenness, suggesting that soil physicochemical properties play a critical role in regulating fungal–plant symbiosis. Functional predictions indicated that endophytic fungi play important roles in metabolic pathways such as nucleotide biosynthesis, carbohydrate degradation, and lipid metabolism, which may enhance plant survival in saline–alkaline and arid environments. Furthermore, the high abundance of plant pathogens and saprotrophs in some fungal communities suggests their potential roles in plant defense and organic matter decomposition. The results of this study provide a reference for advancing the development and utilization of halophyte endophytic fungal resources, with applications in desert ecosystem restoration and halophyte cultivation.

Soil microbial communities were investigated under the volcanic extreme environment. Soil bacterial networks exhibited higher stability than fungal networks. Holocene granite had a more complex microbial network than basalt. Soil pH and total protein were key drivers of microbial network stability.

Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment.

Arbuscular mycorrhizal fungi (AMF) are considered to be an essential indicator of ecosystem biodiversity and can increase a plant’s ability to withstand arid conditions. Despite the obvious significance of AMF in the root and rhizosphere system, little is known about how the AMF variety varies between the soil and roots of endangered plants and how this varies depending on habitats in dry and semiarid regions. This study aimed to address this research gap by investigating the characteristics and diversity of AMF colonization in Zygophyllaceae. Using Illumina MiSeq high-throughput sequencing, indigenous AMF in the roots and rhizosphere soil of three endangered plants (Tetraena mongolica, Sarcozygium xanthoxylon, and Nitraria tangutorum Bobr) were investigated. The three threatened plants had different AMF populations in their root and rhizosphere soils, according to a hierarchical clustering analysis. AMF communities in rhizosphere soil were more sensitive to LDA than root AMF communities based on linear discriminant analysis effect size (LEfSe). Glomus, Septoglomus, and Rhizophagus were seen to function as dominant fungi as the soil and root AMF populations carried out their various tasks in the soil and roots as a cohesive collective. Distance-based redundancy analysis (db-RDA) showed that pH, total phosphorus, and accessible potassium were closely associated with AMF communities. The pH of the soil appears to be an important factor in determining AMF community stability. These findings can serve as a guide for the use of AM fungus in the rehabilitation of agricultural land in arid regions. In summary, our work contributed new knowledge for the scientific preservation of these endangered plant species and for the further investigation of the symbiotic link between AMF and endangered plant species.