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An approach for broad molecular imaging of the root-soil interface via indirect matrix-assisted laser desorption/ionization mass spectrometry
摘要： Understanding rhizospheric processes is limited by the need for imaging complex molecular transformations at relevant spatial scales within the root soil continuum. Here, we demonstrate a method to enable this analysis by first extracting organic compounds from the rhizosphere onto a PVDF membrane while maintaining their 2D distribution and then imaging the distribution of chemical compounds using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This approach permitted us to visualize and identify compounds on the root surface and presumed root exudates in the rhizosphere. Within a 1.8 cm x 0.6 cm sampling area of a switchgrass rhizosphere, we could observe at least four chemically distinct zones. Using high performance Fourier transform ion cyclotron MS, we were able to accurately annotate numerous molecules co-localized to each of these zones.
关键词： chemical imaging,PVDF membrane,spatial metabolomics,MALDI,rhizosphere,liquid chromatography
更新于2025-09-23 15:21:01
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Microbial Ecology on Solar Panels in Berkeley, CA, United States
摘要： Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.
关键词： microbiome,stress-resistant bacteria,solar panels,metabolomics,metagenomics
更新于2025-09-19 17:15:36
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Validated Ultra-High-Performance Liquid-Chromatography Hybrid High-Resolution Mass Spectrometry and Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry for Salivary Metabolomics
摘要： Whereas urine and blood are typically targeted in clinical research, saliva represents an interesting alternative as its intrinsic metabolome is chemically diverse and reflective for various biological processes. Moreover, saliva collection is easy and non-invasive, which is especially valuable for cohorts in which sample collection is challenging, e.g. infants and children. With this rationale, we established a validated UHPLC-HRMS method for salivary metabolic profiling and fingerprinting. Hereby, 450 μL of saliva was centrifuged and passed over a 0.45-μm polyamide membrane filter, after which the extract was subjected to chromatographic analysis (HSS T3 column) and Q-ExactiveTM Orbitrap-MS. For the majority of the profiled metabolites, good linearity (R2 ≥ 0.99) and precision (coefficient of variance ≤ 15%) was achieved. The fingerprinting performance was evaluated based on the complete metabolome (11,385 components), whereby 76.8% was found compliant with the criteria for precision (coefficient of variance ≤ 30%) and 82.7% with linearity (R2 ≥ 0.99). In addition, the method was proven fit-for-purpose for a cohort of 140 adolescents (6-16 years, stratified according to weight), yielding relevant profiles (45 obesity-related metabolites) and discriminative fingerprints (Q2 of 0.784 for supervised discriminant analysis). Alternatively, LA-REIMS was established for rapid fingerprinting of saliva, thereby using a Nd:YAG laser and Xevo G2-XS QToF-MS. With an acquisition time of 0.5 min per sample, LA-REIMS offers unique opportunities for point-of-care applications. In conclusion, this work presents a platform of UHPLC-HRMS and LA-REIMS, complementing each other to perform salivary metabolomics.
关键词： obesity,fingerprinting,UHPLC-HRMS,salivary metabolomics,LA-REIMS,metabolic profiling
更新于2025-09-19 17:13:59
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Integrated Analysis of Transcriptomic and Metabolomic Data Reveals the Mechanism by Which LED Light Irradiation Extends the Postharvest Quality of Pak-choi (Brassica campestris L. ssp. chinensis (L.) Makino var. communis Tsen et Lee)
摘要： Low-intensity (10 μmol m?2 s?1) white LED (light-emitting diode) light effectively delayed senescence and maintained the quality of postharvest pakchoi during storage at 20 °C. To investigate the mechanism of LED treatment in maintaining the quality of pakchoi, metabolite profiles reported previously were complemented by transcriptomic profiling to provide greater information. A total of 7761 differentially expressed genes (DEGs) were identified in response to the LED irradiation of pak-choi during postharvest storage. Several pathways were markedly induced by LED irradiation, with photosynthesis being the most notable. More specifically, porphyrin and chlorophyll metabolism and glucosinolate biosynthesis were significantly induced by LED irradiation, which is consistent with metabolomics reported previously. Additionally, chlorophyllide a, chlorophyll, as well as total glucosinolate content was positively induced by LED irradiation. Overall, LED irradiation delayed the senescence of postharvest pak-choi mainly by activating photosynthesis, inducting glucosinolate biosynthesis, and inhibiting the down-regulation of porphyrin and chlorophyll metabolism pathways. The present study provides new insights into the effect and the underlying mechanism of LED irradiation on delaying the senescence of pak-choi. LED irradiation represents a useful approach for extending the shelf life of pak-choi.
关键词： postharvest quality,Pak-choi,LED irradiation,RNA-seq,metabolomics
更新于2025-09-19 17:13:59