Mining microbiomes for microproteins
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Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost
Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.
Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis
Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.
Professional demand analysis for teaching Chinese to speakers of other languages: a text mining approach on internet recruitment platforms
The rapid development of international education in China highlights the growing importance of employment analysis in Teaching Chinese to Speakers of Other Languages (TCSOL). This study explores the enterprise demands for TCSOL professionals using text mining techniques to analyze recruitment data collected from four major platforms: Boss Zhipin, Zhaopin.com, 51job.com, and Liepin.com. Combining descriptive statistics, LDA topic modeling, BERT-BiLSTM-CRF-based named entity recognition, and co-occurrence network analysis were used. Results show that there is a high demand for TCSOL professionals, especially for small-scale enterprises located in first-tier cities such as Beijing, Shanghai, Guangzhou, and Shenzhen. Employers tend to favor candidates with at least a bachelor’s degree and 1–3 years of work experience. The topic model highlighted three central themes in job descriptions, emphasizing a shift toward a more diverse skill set. Named entity recognition identified essential attributes such as “communication ability”, “teaching experience”, “bachelor’s degree or above” and “responsibility” as core recruitment requirements. The co-occurrence network analysis revealed the importance of “teaching” and “priority” as core skill nodes. Time series analysis showed seasonal fluctuations in recruitment demand, peaking during spring recruitment and graduation periods. A hierarchical model of talent demand and development in TCSOL is proposed, integrating the perspectives of employers, job seekers, educators, and policymakers. This study provides valuable insights for aspiring TCSOL professionals, offering guidance to better align talent training with market needs and improve employment prospects.
Protein signatures predict coral resilience and survival to thermal bleaching events
Coral bleaching events from thermal stress are increasing globally in duration, frequency, and intensity. While bleaching can cause mortality, some corals survive, reacquire symbionts, and recover. We experimentally bleached Montipora capitata to examine molecular and physiological differences between corals that recover (resilient) and those that die (susceptible). Corals were collected and monitored for eight months post-bleaching to identify genets with long-term resilience. Using an integrated systems-biology approach that included quantitative proteomics, 16S rRNA sequencing to characterize the coral microbiome, total coral lipids, symbiont community composition and density, we explored molecular-level mechanisms of tolerance in corals pre- and post-bleaching. Prior to thermal stress, resilient corals have a more diverse microbiome and abundant proteins essential for carbon acquisition, symbiont retention, and pathogen resistance. Protein signatures of susceptible corals showed early symbiont rejection and utilized urea for carbon and nitrogen. Our results reveal molecular factors for surviving bleaching events and identify diagnostic protein biomarkers for reef management and restoration.
Brine management with zero and minimal liquid discharge
Zero liquid discharge (ZLD) and minimal liquid discharge (MLD) are brine management approaches that aim to reduce the environmental impacts of brine discharge and recover water for reuse. ZLD maximizes water recovery and avoids the needs for brine disposal, but is expensive and energy-intensive. MLD (which reduces the brine volume and recovers some water) has been proposed as a practical and cost-effective alternative to ZLD, but brine disposal is needed. In this Review, we examine the concepts, technologies and industrial applications of ZLD and MLD. These brine management strategies have current and potential applications in the desalination, energy, mining and semiconductor industries, all of which produce large volumes of brine. Brine concentration and crystallization in ZLD and MLD often rely on mechanical vapour compression and thermal crystallizers, which are effective but energy-intensive. Novel engineered systems for brine volume reduction and crystallization are under active development to achieve MLD and/or ZLD. These emerging systems, such as membrane distillation, electrodialytic crystallization and solvent extraction desalination, still face challenges to outcompete mechanical vapour compression and thermal crystallizers, underscoring the critical need to maximize the full potential of reverse osmosis to attain ultrahigh water recovery. Brine valorization has potential to partially offset the cost of ZLD and MLD, provided that resource recovery can be integrated into treatment trains economically and in accordance with regulations.
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