Search for: All records

Abstract Streptomycesare key contributors to soil microbiome function, known for their biosynthetic diversity. While advances in -omics technologies have improved our understanding of microbiome composition and metabolic potential, the mechanisms underpinning interspecies interactions remain poorly resolved. Here, we investigate the molecular basis of interactions among four sympatricStreptomycessoil microbiome isolates, focusing on phenotypic, metabolomic and transcriptomic responses. Co-culture experiments revealed that one isolate, strain A, exhibited pronounced phenotypic changes when grown alongside each of the other three strains. Untargeted metabolomics and RNA-seq analyses showed that strain A undergoes distinct metabolic and transcriptional shifts depending on its partner, with the strongest response elicited by strain C. Despite all four strains possessing a conserved desferrioxamine biosynthetic gene cluster, only strain C constitutively produced desferrioxamine B (DFO-B), a hydroxamate siderophore, indicating a role for iron bioavailability in the interaction. Supplementation with DFO-B or iron mimicked the growth stimulation of strain A observed in co-culture with strain C, and CRISPR base editing ofdesDin strain C abolished both DFO production and the phenotypic induction of strain A. However, transcriptomic profiles of strain A varied significantly depending on the partner strain, with distinct sets of biosynthetic gene clusters and metabolic pathways activated in response to strains B and C, suggesting additional cues beyond DFO-B. In contrast, strain D did not elicit growth stimulation in its partners, and itself showed downregulation of amino acid and carbon metabolism when co-cultured with strain C. These findings indicate thatStreptomycesinteractions are not only mediated by siderophore piracy but also involve complex, strain-specific molecular responses. Our findings demonstrate thatStreptomycesinteractions are highly strain-specific and only partly mediated by siderophore piracy, with DFO-B acting as a potent interspecies cue. The divergent molecular responses to different partners suggest nuanced mechanisms of microbial sensing and competition. These insights advance our understanding of microbial crosstalk and highlight the ecological and evolutionary complexity of siderophore-mediated interactions. By integrating transcriptomics, metabolomics, and biochemical assays, we present a robust framework for dissecting microbial interactions, with implications for microbiome engineering and synthetic community design. 

Abstract Key messageThe 2024 ENSO event advanced the timing of spring phenological phases of native shrubs significantly more than non-native shrubs and native trees in a temperate deciduous woodland fragment in Wisconsin, USA. This suggests that, as spring temperatures warm, shrubs will likely play a pivotal role in forest dynamics including contributing to an earlier onset to the growing period and an early start to CO₂assimilation. ContextThe 2023/2024 El Niño Southern Oscillation (ENSO) event brought warmer than average temperatures to the Midwest USA. This presented a unique opportunity to examine how short-term warming might impact the phenology of temperate deciduous forest vegetation. AimTo quantify the impact of an ENSO-driven warm spring on the phenology of temperate deciduous forest vegetation in order to assess how trees and shrubs respond to short-term temperature anomalies. MethodsSpring phenology was recorded twice weekly (2018–2024) on 5 dominant tree species and 5 native and 4 non-native shrub species, in a woodland fragment on the University of Wisconsin Milwaukee campus. In addition, phenological transition dates were extracted from daily Green Chromatic Coordinate (GCC) data from a PhenoCam installed at the site. ResultsIn 2024, the average spring (March–May) temperature (8.7 ± 0.57 °C) was significantly warmer than the 2018–2023 average (6.7 ± 0.28 °C). Compared to the average of the previous 6 years, the timing of budburst in 2024 occurred significantly (p < 0.001) earlier on DOY 76, 82, and 98 for native shrubs, non-native shrubs, and trees, representing advances of 20, 17, and 18 days, respectively. The advance was greater in shrubs than trees suggesting that any future advance to the start of the growing-season in temperate deciduous forests resulting from warmer spring temperatures will likely be driven by early leafing species like shrubs. Notably, the rise in GCC in 2024 (DOY 116) occurred following budburst, indicating that PhenoCam imagery may not fully capture early vegetation phenology. ConclusionEarly leafing shrubs, and in particular native species, were more sensitive to warmer temperatures early in the season than non-native shrubs and native trees. Therefore, as temperatures warm in the future, the onset of growth in temperate deciduous forests is likely to be driven by the early spring phenophases of early leafing species. 

Band-selective excitation short-transient (BEST) sequences are widely used for protein NMR experiments that start with amide proton magnetization, such as 1H-15N HSQC, 1H-15N TROSY, and multidimensional backbone assignment experi- ments, because the optimization of amide proton longitudinal relaxation afforded by the BEST methodology allows for much greater sensitivity when using short scan times. Here we show that the BEST methodology can be easily incorpo- rated in sequences for measuring proton transverse relaxation rates (1H R2), which are typically used to determine para- magnetic relaxation enhancements (PREs). The resulting BEST-HSQC-PRE and BEST-TROSY-PRE experiments afford similar or better sensitivity for measuring PREs compared to previous methods, provide equally accurate measurements of transverse relaxation rates (and therefore PREs), and allow shorter scan times to be used. 

Abstract Distributed Acoustic Sensing (DAS) can enhance earthquake early warning (EEW) by transforming existing fiber-optic cables into dense seismic arrays, including in offshore areas with sparse instrumentation. We present dEPIC (DAS–Earthquake Point-source Integrated Code), the first operational DAS-integrated EEW framework, deployed on a submarine cable in Monterey Bay, California, and designed to operate independently or jointly with ShakeAlert’s EPIC algorithm. dEPIC combines GPU-accelerated machine-learning phase picking, grid-search location, and empirical magnitude estimation, with real-time quality metrics to suppress unstable solutions. In event replays and continuous data tests, dEPIC detected both onshore and offshore earthquakes accurately with sub-second processing time. The modular, edge-computing design enables adaptation to future DAS deployments to improve existing EEW systems like ShakeAlert. 

Abstract BackgroundClimate change is expected to alter fire return intervals in cold and wet forests in the northwestern United States. This coupled with an expected rise in prescribed fires to restore healthy forests, disproportionately increases risk to saplings of tree species adapted to colder and wetter environments that have low fire resistance. To assess this potential impact, we evaluated the impacts of increasing fire intensity onPicea engelmanniiandThuja plicatasapling physiology, morphology, and mortality. This was achieved using established pyro-ecophysiology experiments where saplings were subjected to controlled surface fires across a range of fire intensities and post-fire growth, physiology and mortality were assessed up to 7 months post-fire. ResultsIn this study we demonstrate that the probability of mortality in the saplings of these two conifer species displays a sigmoidal increase with increasing fire intensity. At fire radiative energy dosage levels < 0.6 MJ m⁻², the observed mortality in both species was lower than predicted by existing crown scorch-based models due to their limited sensitivity at small diameters. Prior to sapling death, chlorophyll fluorescence transiently recovers before a rapid decline, though the timing varies by species and fire intensity dosage. A new general sapling mortality model derived from 7 conifer species is presented. ConclusionsOur results provide predictive tools that managers could use to make informed decisions on the potential impacts of fires on conifer saplings growing in cold and wet environments. Results from both species suggest that chlorophyll fluorescence temporal trends could serve as a potential early warning indicator of fire-induced tree mortality, however, future work should explore whether similar responses are observable using remote sensing data from solar-induced chlorophyll fluorescence and assess potential mechanisms underlying this signal. The general sapling mortality model presented in this paper appears to provide an improved method of predicting conifer sapling mortality over existing approaches, however, research is needed to develop coefficients to adjust the model with tree age and environmental factors. Further studies could also explore whether phenotypic plasticity is driving observed tree responses to fire from plants grown from similar environments.