Throughout history, humans have relied on plants as a source of medication, flavoring, and food. Plants synthesize large chemical libraries and release many of these compounds into the rhizosphere and atmosphere where they affect animal and microbe behavior. To survive, nematodes must have evolved the sensory capacity to distinguish plant-made small molecules (SMs) that are harmful and must be avoided from those that are beneficial and should be sought. This ability to classify chemical cues as a function of their value is fundamental to olfaction and represents a capacity shared by many animals, including humans. Here, we present an efficient platform based on multiwell plates, liquid handling instrumentation, inexpensive optical scanners, and bespoke software that can efficiently determine the valence (attraction or repulsion) of single SMs in the model nematode, Caenorhabditis elegans. Using this integrated hardware-wetware-software platform, we screened 90 plant SMs and identified 37 that attracted or repelled wild-type animals but had no effect on mutants defective in chemosensory transduction. Genetic dissection indicates that for at least 10 of these SMs, response valence emerges from the integration of opposing signals, arguing that olfactory valence is often determined by integrating chemosensory signals over multiple lines of information. This study establishes that C. elegans is an effective discovery engine for determining chemotaxis valence and for identifying natural products detected by the chemosensory nervous system.

Dinoflagellates are ecologically important and essential to corals and other cnidarians as phytosymbionts, but their photosystems had been underexplored. Recently, photosystem I (PSI) of dinoflagellate Symbiodinium sp. was structurally characterized using cryo-Electron Microscopy (cryo-EM). These analyses revealed a distinct organization of the PSI supercomplex, including two previously unidentified subunits, PsaT and PsaU, and shed light on interactions between light harvesting antenna proteins and the PSI core. These results have implications with respect to the evolution of dinoflagellates and their association with cnidarians.

The photosynthetic amoeba, Paulinella provides a recent (ca. 120Mya) example of primary plastid endosymbiosis. Given the extensive data demonstrating host lineage-driven endosymbiont integration, we analysed nuclear genome and transcriptome data to investigate mechanisms that may have evolved in Paulinella micropora KR01 (hereinafter, KR01) to maintain photosynthetic function in the novel organelle, the chromatophore. The chromatophore is of alpha-cyanobacterial provenance and has undergone massive gene loss due to Muller's ratchet, but still retains genes that encode the ancestral alpha-carboxysome and the shell carbonic anhydrase, two critical components of the biophysical CO2 concentrating mechanism (CCM) in cyanobacteria. We identified KR01 nuclear genes potentially involved in the CCM that arose via duplication and divergence and are upregulated in response to high light and downregulated under elevated CO2. We speculate that these genes may comprise a novel CO2 delivery system (i.e., a biochemical CCM) to promote the turnover of the RuBisCO carboxylation reaction and counteract photorespiration. We posit that KR01 has an inefficient photorespiratory system that cannot fully recycle the C2 product of RuBisCO oxygenation back to the Calvin-Benson cycle. Nonetheless, both these systems appear to be sufficient to allow Paulinella to persist in environments dominated by faster-growing phototrophs.

MOTIVATION: The study of bacterial genome dynamics is vital for understanding the mechanisms underlying microbial adaptation, growth, and their impact on host phenotype. Structural variants (SVs), genomic alterations of 50 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to the absence of clear reference genomes and the presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing all metagenomic samples in a series (time or other metric) into a single co-assembly graph. The log fold change in graph coverage between successive samples is then calculated to call SVs that are thriving or declining.

Macroecological scaling patterns, such as between prey and predator biomass, are fundamental to our understanding of the rules of biological organization and ecosystem functioning. Although these scaling patterns are ubiquitous, how they arise is poorly understood. To explain these patterns, we used an eco-evolutionary predator-prey model parameterized using data for phytoplankton and zooplankton. We show that allometric scaling relationships at lower levels of biological organization, such as body-size scaling of nutrient uptake and predation, give rise to scaling relationships at the food web and ecosystem levels. Our predicted macroecological scaling exponents agree well with observed values across ecosystems. Our findings explicitly connect scaling relationships at different levels of biological organization to ecological and evolutionary mechanisms, yielding testable hypotheses for how observed macroecological patterns emerge.

The pyrolite model, which can reproduce the upper-mantle seismic velocity and density profiles, was suggested to have significantly lower velocities and density than seismic models in the lower mantle transition zone (MTZ). This argument has been taken as mineral-physics evidence for a compositionally distinct lower MTZ. However, previous studies only estimated the pyrolite velocities and density along a one-dimension (1D) geotherm and never considered the effect of lateral temperature heterogeneity. Because the majorite-perovskite-akimotoite triple point is close to the normal mantle geotherm in the lower MTZ, the lateral low-temperature anomaly can result in the presence of a significant fraction of akimotoite in pyrolitic lower MTZ. In this study, we reported the elastic properties of Fe-bearing akimotoite based on first-principles calculations. Combining with literature data, we found that the seismic velocities and density of the pyrolite model can match well those in the lower MTZ when the lateral temperature heterogeneity is modeled by a Gaussian distribution with a standard deviation of 100 K and an average temperature of dozens of K higher than the triple point of MgSiO3. We suggest that a harzburgite-rich lower MTZ is not required and the whole mantle convection is expected to be more favorable globally.

In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of exponential growth we show power-law relationships that relate variability in the time required to reach a threshold population size to growth rate and inoculum size. Population-growth experiments in E. coli and S. aureus with inoculum sizes ranging between 1 and 100 are consistent with these relationships. We quantify how noise accumulates over time, finding that it encodes-and can be used to deduce-information about the early growth rate of a population.