Phlomoides rotata is a traditional Chinese herbal medicine that grows in the Qinghai–Tibet Plateau region at a 3100–5000 m altitude. Iridoid compounds are the main active compounds of the P. rotata used as medical ingredients and display anti-inflammatory, analgesic, and hepatoprotective properties. To better understand the biological mechanisms of iridoid compounds in this species, we performed a comprehensive analysis of the transcriptome and metabolome of P. rotata leaves from four different regions (3540–4270 m). Global metabolome profiling detected 575 metabolites, and 455 differentially accumulated metabolites (DAMs) were detected in P. rotata leaves from the four regions. Eight major DAMs related to iridoid metabolism in P. rotata leaves were investigated: shanzhiside methyl ester, 8-epideoxyloganic acid, barlerin, shanzhiside, geniposide, agnuside, feretoside, and catalpin. In addition, five soil physical and chemical indicators in P. rotata rhizosphere soils were analyzed. Four significant positive correlations were observed between alkaline nitrogen and geniposide, exchangeable calcium and geniposide, available potassium and shanzhiside, and available phosphorus and shanzhiside methyl ester. The transcriptome data showed 12 P. rotata cDNA libraries with 74.46 Gb of clean data, which formed 29,833 unigenes. Moreover, 78.91% of the unigenes were annotated using the eight public databases. Forty-one candidate genes representing 23 enzymes involved in the biosynthesis of iridoid compounds were identified in P. rotata leaves. Moreover, the DXS1, IDI1, 8-HGO1, and G10H2 genes associated with iridoid biosynthesis were specifically expressed in P. rotata. The integration of transcriptome and metabolome analyses highlights the crucial role of soil physical and chemical indicators and major gene expression related to iridoid metabolism pathways in P. rotata from different areas. Our findings provide a theoretical foundation for exploring the molecular mechanisms underlying iridoid compound accumulation in P. rotata.

Selenium (Se) has garnered increasing attention in the field of nutrition, as it is essential for both humans and animals. Certain microorganisms can enrich inorganic selenium and convert it into organic selenium. The growth and metabolomic profiles of six lactobacilli strains exposed to 50 μg/mL of sodium selenite were performed using gas chromatography tandem time-off light mass spectrometry (GC-TOF-MS) analysis. The addition of selenium significantly increased both the population and weight of the Lacticaseibacillus rhamnosus PS5, Lbs. rhamnosus RT-B, Limosilactobacillus reuteri 3630, and Lmb. reuteri 1663 strains, while those of the other two strains decreased. A total of 271 metabolites were determined, with their concentrations ranked from highest to lowest as follows: organic acids and derivatives, oxygen compounds, lipids and lipid-like molecules, and benzenoids. In certain groups, the concentrations of serine, aspartic acid, trehalose, palmitic acid, methylthreonine, and melibiose increased significantly, whereas glucuronic acid, ribose, ornithine, and methionine were downregulated. The metabolic pathways were significantly associated with ABC transporters, glycine, serine, threonine metabolism, and aminobenzoate degradation and other pathways. Based on these findings, we concluded that the transport, absorption, assimilation, and stress response to selenium by lactobacilli in metabolomic changed. Furthermore, the metabolomic alterations among different types of lactobacilli varied primarily due to their distinct properties.

Selenium (Se) is an essential micronutrient with many beneficial effects for humans and other living organisms. Numerous microorganisms in culture systems enrich and convert inorganic selenium to organic selenium. In this study, Epichloë sp. from Festuca sinensis was exposed to increasing Na₂SeO₃ concentrations (0, 0.1, 0.2, 0.3, and 0.4 mmol/L) in Petri dishes with potato dextrose agar (PDA) for 8 weeks. Epichloë sp. mycelia were immediately collected after mycelial diameters were measured at 4, 5, 6, 7, and 8 weeks of cultivation, respectively. Gas chromatography-mass spectrometer (GC-MS) analysis was performed on different groups of Epichloë sp. mycelia. Different changes were observed as Epichloë sp. was exposed to different selenite conditions and cultivation time. The colony diameter of Epichloë sp. decreased in response to increased selenite concentrations, whereas the inhibitory effects diminished over time. Seventy-two of the 203 identified metabolites did not differ significantly across selenite treatments within the same time point, while 82 compounds did not differ significantly between multiple time points of the same Se concentration. However, the relative levels of 122 metabolites increased the most under selenite conditions. Specifically, between the 4th and 8th weeks, there were increases in 2-keto-isovaleric acid, uridine, and maltose in selenite treatments compared to controls. Selenium increased glutathione levels and exhibited antioxidant properties in weeks 4, 5, and 7. Additionally, we observed that different doses of selenite could promote the production of carbohydrates such as isomaltose, cellobiose, and sucrose; fatty acids such as palmitoleic acid, palmitic acid, and stearic acid; and amino acids such as lysine and tyrosine in Epichloë sp. mycelia. Therefore, Epichloë sp. exposed to selenite stress may benefit from increased levels of some metabolite compounds.

The differences in soil fungal communities in four agricultural areas growing wheat (Triticum aestivum), rapeseed (Brassica napus), and barley (Hordeum vulgare) in the Qinghai Province, namely the Dulan (DL), Gonghe (GH), Huzhu (HZ), and Datong (DT) counties, were investigated using high-throughput sequencing. The region showed highly significant effects on soil pH, organic matter, ammonium nitrogen, nitrate nitrogen, total phosphate, effective phosphate, total sulfur, and effective sulfur (p < 0.01). The crop type resulted in highly significant (p < 0.01) variations in total phosphate and effective phosphate. Principal coordinates analysis and nonmetric multidimensional scaling revealed significant differences in soil fungal diversity and fungal community composition in the soils of three crops or four regions (p < 0.05). Although the soils of the four regions or three crops had similar dominant phyla, classes, and genera, these taxa differed in terms of their relative abundance. Four, 12, 15, and 16 biomarkers with significant linear discriminant analysis effect sizes were identified in the HZ, DL, GH, and DT groups, respectively. A total of 36, 12, and eight significant biomarkers were observed in the wheat, rapeseed, and barley soils, respectively. In addition, altitude and soil physicochemical properties had significant relationships with fungal diversity and community composition (p < 0.05, p < 0.01).

The biodiversity of CO ₂ -assimilating bacterial communities is pivotal for carbon sequestration in agricultural systems. Changes in the diversity, structure, and activity of the soil chemolithoautotrophic bacteria were examined in four agricultural areas, Dulan (DL), Gonghe (GH), Huzhu (HZ), and Datong (DT) counties in Qinghai Province, where wheat, oilseed rape, and barley were planted. This process was performed using Illumina amplicon sequencing of the ribulose-1,5-bisphosphatecarboxylase/oxygenase (RubisCO) gene ( cbbL Form I) and activity data. The diversity, community, and activity of soil autotrophic CO ₂ -fixing bacteria differed significantly across soil sites, whereas cbbL -bearing bacterial diversity and activity were similar across different crop types. RubisCO activity in the HZ region was significantly greater than in the other three regions ( P < 0.001). The overall relative abundance trend of the bacterial taxa was similar among the three crop samples. Moreover, 31, 27, 10, and 8 significant linear discriminant analysis effect sizes were identified in the four regions collected from HZ, DL, DT, and GH, respectively. No significant biomarkers were detected in any of the crop groups. Some soil properties had significant relationships with the autotrophic bacterial community composition. IMPORTANCE: Agricultural soil plays important roles in carbon fixation during carbon capture and storage. Autotrophic bacteria that utilize inorganic compounds as electron donors for growth fix CO ₂ photosynthetically or chemo-autotrophically in diverse ecosystems and affect soil organic carbon sequestration. Soil properties, agronomic management measures, and environmental factors can influence the community composition, abundance, and activity of CO ₂ -assimilating bacteria. This study aims at evaluating the effects of different regions and crop types on the abundance, composition, and activity of CO ₂ -fixing bacteria in agricultural soil.

Background: Lycium chinense has been acknowledged for its substantial nutritional benefits. The “Mengqi No.1” variety of L. chinense is known for its high yield and exceptional quality. Methods: We screened twenty dominant endophytic bacterial genera based on OTUs from L. chinense fruits during three developmental stages. Results: Forty-three differential amino acid metabolites were selected from L. chinense fruits. Five endophytic bacteria (Enterococcus, Escherichia-Shigella, Bacteroides, Pseudomonas, and Bacillus) were dominant genera in green fruit (GF, 16–19 days after flowering), color-changing fruit (CCF, 22–25 days after flowering), and red-ripe fruit (RRF, 31–34 days after flowering). Four endophytic bacterial genera (Enterococcus, Bacillus, Pseudomonas, and Rhodanobacter) showed positive correlation with twenty different amino acid metabolites and negative correlation with seven different amino acid metabolites. Conclusions: Five genes (AST1, ltaE1, TAT1, SHMT2, and SHMT3) indicated positive correlation with seventeen different amino acid metabolites and negative correlation with eight different amino acid metabolites. AST1 gene had a major role in regulating arginine biosynthesis (ko00220); ltaE1, SHMT2, and SHMT3 genes were major in regulating glycine, serine, and threonine metabolism (ko00260); and TAT1 gene had a major role in regulating tyrosine metabolism (ko00350). These findings offer insights into the relationship between amino acid synthesis and endophytic bacteria in L. chinense fruits.