UC Riverside

Vegetation, a key component of terrestrial ecosystems, regulates the mass, momentum, and energy fluxes between the land surface and the atmosphere. The 6th Intergovernmental Panel on Climate Change (IPCC) reports evident climate change will continue to accelerate impacts on the biophysical and structural characteristics of vegetation and water resources into the next century. Given the undeniable role of vegetation in land–atmosphere interactions, its ever-changing composition and functionality can significantly impact the water and energy balance on earth. This underscores the necessity for considering vegetation dynamics in simulating terrestrial water cycles and watershed responses under current and future climates. This paper reviews the physical processes and parameters used within three widely used hydrological models, SWAT (Soil and Water Assessment Tool), WRF-Hydro (Weather Research and Forecasting Model Hydrological Modeling system), and the VIC (Variable Infiltration Capacity), to parameterize vegetation dynamics. We reviewed the relative strengths and limitations of each model's physical processes to represent vegetation as a dynamic component, including recent advancements in modeling vegetation dynamics and their potential to decrease model uncertainty, particularly in the context of climate variability and land use/land cover changes. The paper highlights the shortcomings of LAI for correctly capturing the timing and magnitude of plant physiological activity in evergreen coniferous forests where light and temperature are not the only growth constraints. Recommendations for future model improvements and research directions are discussed, emphasizing the opportunity for incorporating remote sensing data to address some of the current shortcomings. These enhancements are essential for improving water resource management and ensuring sustainable watershed management in the face of ongoing environmental changes.

Abstract: Many past studies have predicted the steady-state production and maintenance of abiotic O2 and O3 in the atmospheres of CO2-rich terrestrial planets orbiting M dwarf stars. However, the time-dependent responses of these planetary atmospheres to flare events—and the possible temporary production or enhancement of false-positive biosignatures therein—has been comparatively less well studied. Most past works that have modeled the photochemical response to flares have assumed abundant free oxygen, like that of the modern or Proterozoic Earth. Here we examine in detail the photochemical impact of the UV emitted by a single flare on abiotic O2/O3 production in prebiotic, CO2-dominated atmospheres of M dwarf planets with CO2 levels ranging from 3% to 80% of 1 bar. We find that a single flare generally destroys O2 and O3 over short timescales while modestly enhancing their column densities over intermediate timescales. We simulate the spectral observables of both the steady-state atmosphere and time-dependent spectral response over the flare window for both emitted and transmitted light spectra. Over the course of the flare, the O3 UV Hartley band is decreased by a maximum of 47 ppm. In both emitted and transmitted light spectra, the 9.65 μm O3 band is hidden by the overlapping 9.4 μm CO2 band for all scenarios considered. Overall, we find that the possible enhancements of abiotic O3 due to a single flare are small compared to O3’s sensitivity to other parameters such as CO2 and H2O abundances or the availability of reducing gases such as H2.

Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.

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The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.

Phyling is a fast, scalable, and user-friendly tool supporting phylogenomic reconstruction of species phylogenies directly from protein-encoded genomic data. It identifies orthologous genes by searching a sample's protein sequences against a Hidden Markov Models marker set, containing single-copy orthologs, retrieved from the BUSCO database. In the final step, users can choose between consensus and concatenation strategies to construct the species tree from the aligned orthologs. Phyling efficiently resolves large phylogenies by optimizing memory usage and data processing. Its checkpoint system enables users to incrementally add or remove samples without repeating the entire search process. For analyses involving closely related taxa, Phyling supports the use of nucleotide coding sequences, which may capture phylogenetic signals missed by protein sequences. The benchmark results show that Phyling substantially runs faster than OrthoFinder, a Reciprocal Best Hit based method, while achieving equal or better accuracy.

The fungus Conoideocrella luteorostrata is a recently discovered pathogen of invasive elongate hemlock scale insects (EHS; Fiorinia externa) in Christmas tree farms in the eastern U.S. Here, we report a scaffold-level genome and assembly along with an initial survey of biosynthetic gene clusters for strain ARSEF 14590 from EHS.

A draft genome sequence was assembled and annotated for an uncultured archaeon reconstructed from shotgun metagenomes obtained from Antarctic endoliths. The assembled genome is 1.99 megabases and encodes 2,405 predicted protein-coding genes. This genome sequence provides insights into the microbial diversity and functional potential of extremophiles inhabiting Antarctic rock environments.