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1. An adaptive biomolecular condensation response is conserved across environmentally divergent species

   https://doi.org/10.1038/s41467-024-47355-9  

   Keyport_Kik, Samantha; Christopher, Dana; Glauninger, Hendrik; Hickernell, Caitlin_Wong; Bard, Jared_A_M; Lin, Kyle_M; Squires, Allison_H; Ford, Michael; Sosnick, Tobin_R; Drummond, D_Allan (April 2024, Nature Communications)

   Abstract Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry. 

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2. Noisy metabolism can promote microbial cross-feeding

   https://doi.org/10.7554/eLife.70694  

   Lopez, Jaime G; Wingreen, Ned S (April 2022, eLife)

   Cross-feeding, the exchange of nutrients between organisms, is ubiquitous in microbial communities. Despite its importance in natural and engineered microbial systems, our understanding of how inter-species cross-feeding arises is incomplete, with existing theories limited to specific scenarios. Here, we introduce a novel theory for the emergence of such cross-feeding, which we term noise-averaging cooperation (NAC). NAC is based on the idea that, due to their small size, bacteria are prone to noisy regulation of metabolism which limits their growth rate. To compensate, related bacteria can share metabolites with each other to ‘average out’ noise and improve their collective growth. According to the Black Queen Hypothesis, this metabolite sharing among kin, a form of ‘leakage’, then allows for the evolution of metabolic interdependencies among species including de novo speciation via gene deletions. We first characterize NAC in a simple ecological model of cell metabolism, showing that metabolite leakage can in principle substantially increase growth rate in a community context. Next, we develop a generalized framework for estimating the potential benefits of NAC among real bacteria. Using single-cell protein abundance data, we predict that bacteria suffer from substantial noise-driven growth inefficiencies, and may therefore benefit from NAC. We then discuss potential evolutionary pathways for the emergence of NAC. Finally, we review existing evidence for NAC and outline potential experimental approaches to detect NAC in microbial communities. 

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3. Dynamic coexistence driven by physiological transitions in microbial communities

   https://doi.org/10.1073/pnas.2405527122  

   Narla, Avaneesh V; Hwa, Terence; Murugan, Arvind (April 2025, Proceedings of the National Academy of Sciences)

   Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes in exponential growth often modify their environments so strongly that they are forced out of the growth state into stressed, nongrowing states. Such dynamics are typical of ecological succession in nature and serial-dilution cycles in the laboratory. Here, we introduce a phenomenological model, the Community State Model, to gain insight into the dynamic coexistence of microbes due to changes in their physiological states during cyclic succession. Our model specifies the growth preference of each species along a global ecological coordinate, taken to be the biomass density of the community, but is otherwise agnostic to specific interactions (e.g., nutrient starvation, stress, aggregation), in order to focus on self-consistency conditions on combinations of physiological states, “community states,” in a stable ecosystem. We identify three key features of such dynamical communities that contrast starkly with steady-state communities: enhanced community stability through staggered dominance of different species in different community states, increased tolerance of community diversity to fast growing species dominating distinct community states, and increased requirement of growth dominance by late-growing species. These features, derived explicitly for simplified models, are proposed here as principles aiding the understanding of complex dynamical communities. Our model shifts the focus of ecosystem dynamics from bottom–up studies based on fixed, idealized interspecies interaction to top–down studies based on accessible macroscopic observables such as growth rates and total biomass density, enabling quantitative examination of community-wide characteristics. 

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4. Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria in a synthetic community

   https://doi.org/10.1038/s41396-020-00737-5  

   Fritts, Ryan K.; Bird, Jordan T.; Behringer, Megan G.; Lipzen, Anna; Martin, Joel; Lynch, Michael; McKinlay, James B. (August 2020, The ISME Journal)

   Abstract Interactive microbial communities are ubiquitous, influencing biogeochemical cycles and host health. One widespread interaction is nutrient exchange, or cross-feeding, wherein metabolites are transferred between microbes. Some cross-fed metabolites, such as vitamins, amino acids, and ammonium (NH4+), are communally valuable and impose a cost on the producer. The mechanisms that enforce cross-feeding of communally valuable metabolites are not fully understood. Previously we engineered a cross-feeding coculture between N2-fixing Rhodopseudomonas palustris and fermentative Escherichia coli. Engineered R. palustris excretes essential nitrogen as NH4+ to E. coli, while E. coli excretes essential carbon as fermentation products to R. palustris. Here, we sought to determine whether a reciprocal cross-feeding relationship would evolve spontaneously in cocultures with wild-type R. palustris, which is not known to excrete NH4+. Indeed, we observed the emergence of NH4+ cross-feeding, but driven by adaptation of E. coli alone. A missense mutation in E. coli NtrC, a regulator of nitrogen scavenging, resulted in constitutive activation of an NH4+ transporter. This activity likely allowed E. coli to subsist on the small amount of leaked NH4+ and better reciprocate through elevated excretion of fermentation products from a larger E. coli population. Our results indicate that enhanced nutrient uptake by recipients, rather than increased excretion by producers, is an underappreciated yet possibly prevalent mechanism by which cross-feeding can emerge. 

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5. Impacts of ocean acidification on the palatability of two Antarctic macroalgae and the consumption of a grazer

   https://doi.org/10.1017/S095410202400052X  

   Oswalt, Hannah E; Amsler, Margaret O; Amsler, Charles D; McClintock, James B; Schram, Julie B (June 2025, Antarctic Science)

   Abstract Increases in atmospheric CO₂have led to more CO₂entering the world’s oceans, decreasing the pH in a process called ’ocean acidification’. Low pH has been linked to impacts on macroalgal growth and stress, which can alter palatability to herbivores. Two common and ecologically important macroalgal species from the western Antarctic Peninsula, the unpalatableDesmarestia menziesiiand the palatablePalmaria decipiens, were maintained under three pH treatments: ambient (pH 8.1), near future (7.7) and distant future (7.3) for 52 days and 18 days, respectively. Discs ofP. decipiensor artificial foods containing extracts ofD. menziesiifrom each treatment were presented to the amphipodGondogeneia antarcticain feeding choice experiments. Additionally,G. antarcticaexposed to the different treatments for 55 days were used in a feeding assay with untreatedP. decipiens. ForD. menziesii, extracts from the ambient treatment were eaten significantly more by weight than the other treatments. Similarly,P. decipiensdiscs from the ambient and pH 7.7 treatments were eaten more than those from the pH 7.3 treatment. There was no significant difference in the consumption by treatedG. antarctica. These results suggest that ocean acidification may decrease the palatability of these macroalgae to consumers but not alter consumption byG. antarctica. 

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