Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.
\nRegulated protein degradation underlies the timely execution of essential gene expression programs in bacteria. Here, we deployed time-resolved chemoproteomics, text mining of the PubMed and EcoCyc knowledge bases, and machine learning classification to identify proteolytic regulation in exponential and stationary phase Escherichia coli cultures. We experimentally validated the instability of diverse homeostatic and stress response regulators, including the principal cyclic-di-GMP phosphodiesterase PdeH, the N-end rule substrate chaperone ClpS, and all four A-type domain iron–sulfur cluster carriers, IscA, ErpA, NfuA, and SufA. Mutagenesis of the PdeH N-terminal extension abolished ClpXP recognition, thereby impairing stationary phase depletion of PdeH and altering macrocolony biofilm surface morphology. Unstable proteins synthesized in stationary phase such as the morphology regulator BolA, RNA polymerase ω subunit, and the biofilm regulator BssR were implicated in quiescence. Finally, machine learning–assisted substrate identification revealed Lon-mediated degradation of two opposing key regulators of surface adhesion, the RpoS antagonist FliZ and the major biofilm regulator CsgD, suggesting proteolysis may hasten transitions between motility and sessility. Together, these results highlight the role of regulated proteolysis in driving physiological adaptation for this model organism.
", "doi": "10.1073/pnas.2515265123", "issn": "0027-8424", "publisher": "National Academy of Sciences", "publication": "Proceedings of the National Academy of Sciences", "publication_date": "2026-03-10", "series_number": "10", "volume": "123", "issue": "10", "pages": "e2515265123" }, { "id": "authors:rzyk3-nkb31", "collection": "authors", "collection_id": "rzyk3-nkb31", "cite_using_url": "https://authors.library.caltech.edu/records/rzyk3-nkb31", "type": "article", "title": "The 2025 motile active matter roadmap", "author": [ { "family_name": "Gompper", "given_name": "Gerhard", "orcid": "0000-0002-8904-0986" }, { "family_name": "Stone", "given_name": "Howard A", "orcid": "0000-0002-9670-0639" }, { "family_name": "Kurzthaler", "given_name": "Christina", "orcid": "0000-0002-5516-1464" }, { "family_name": "Saintillan", "given_name": "David", "orcid": "0000-0001-9948-708X" }, { "family_name": "Peruani", "given_name": "Fernado", "orcid": "0000-0003-2985-8935" }, { "family_name": "Fedosov", "given_name": "Dmitry A", "orcid": "0000-0001-7469-9844" }, { "family_name": "Auth", "given_name": "Thorsten", "orcid": "0000-0002-6618-2316" }, { "family_name": "Cottin-Bizonne", "given_name": "Cecile", "orcid": "0000-0001-5807-9215" }, { "family_name": "Ybert", "given_name": "Christophe", "orcid": "0000-0002-2793-7229" }, { "family_name": "Cl\u00e9ment", "given_name": "Eric", "orcid": "0000-0002-2068-9699" }, { "family_name": "Darnige", "given_name": "Thierry", "orcid": "0000-0002-3973-981X" }, { "family_name": "Lindner", "given_name": "Anke", "orcid": "0000-0002-5007-9568" }, { "family_name": "Goldstein", "given_name": "Raymond E", "orcid": "0000-0003-2645-0598" }, { "family_name": "Liebchen", "given_name": "Benno", "orcid": "0000-0002-7647-6430" }, { "family_name": "Binysh", "given_name": "Jack", "orcid": "0000-0002-4880-0942" }, { "family_name": "Souslov", "given_name": "Anton", "orcid": "0000-0001-7735-100X" }, { "family_name": "Isa", "given_name": "Lucio", "orcid": "0000-0001-6731-9620" }, { "family_name": "di Leonardo", "given_name": "Roberto", "orcid": "0000-0002-5020-0663" }, { "family_name": "Frangipane", "given_name": "Giacomo", "orcid": "0000-0002-1533-4754" }, { "family_name": "Gu", "given_name": "Hongri", "orcid": "0000-0002-6396-3408" }, { "family_name": "Nelson", "given_name": "Bradley J" }, { "family_name": "Brauns", "given_name": "Fridtjof", "orcid": "0000-0002-6108-9278" }, { "family_name": "Marchetti", "given_name": "M Cristina", "orcid": "0000-0003-3583-4999" }, { "family_name": "Cichos", "given_name": "Frank", "orcid": "0000-0002-9803-4975" }, { "family_name": "Heuthe", "given_name": "Veit-Lorenz", "orcid": "0000-0003-1248-4770" }, { "family_name": "Bechinger", "given_name": "Clemens", "orcid": "0000-0002-5496-5268" }, { "family_name": "Korman", "given_name": "Amos", "orcid": "0000-0001-8652-9228" }, { "family_name": "Feinerman", "given_name": "Ofer", "orcid": "0000-0003-4145-0238" }, { "family_name": "Cavagna", "given_name": "Andrea", "orcid": "0000-0003-2057-5971" }, { "family_name": "Giardina", "given_name": "Irene", "orcid": "0000-0001-6900-1739" }, { "family_name": "Jeckel", "given_name": "Hannah", "orcid": "0000-0002-7080-4907", "clpid": "Jeckel-Hannah" }, { "family_name": "Drescher", "given_name": "Knut", "orcid": "0000-0002-7340-2444" } ], "abstract": "Activity and autonomous motion are fundamental aspects of many living and engineering systems. Here, the scale of biological agents covers a wide range, from nanomotors, cytoskeleton, and cells, to insects, fish, birds, and people. Inspired by biological active systems, various types of autonomous synthetic nano- and micromachines have been designed, which provide the basis for multifunctional, highly responsive, intelligent active materials. A major challenge for understanding and designing active matter is their inherent non-equilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Furthermore, interactions in ensembles of active agents are often non-additive and non-reciprocal. An important aspect of biological agents is their ability to sense the environment, process this information, and adjust their motion accordingly. It is an important goal for the engineering of micro-robotic systems to achieve similar functionality. Many fundamental properties of motile active matter are by now reasonably well understood and under control. Thus, the ground is now prepared for the study of physical aspects and mechanisms of motion in complex environments, the behavior of systems with new physical features like chirality, the development of novel micromachines and microbots, the emergent collective behavior and swarming of intelligent self-propelled particles, and particular features of microbial systems. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter poses major challenges, which can only be addressed by a truly interdisciplinary effort involving scientists from biology, chemistry, ecology, engineering, mathematics, and physics. The 2025 motile active matter roadmap of Journal of Physics: Condensed Matter reviews the current state of the art of the field and provides guidance for further progress in this fascinating research area.
", "doi": "10.1088/1361-648x/adac98", "pmcid": "PMC11836640", "issn": "0953-8984", "publisher": "IOP Publishing", "publication": "Journal of Physics: Condensed Matter", "publication_date": "2025-04-07", "series_number": "14", "volume": "37", "issue": "14", "pages": "143501" } ]