Long-term history dependence of growth rates of E. coli after nutrient shifts

Christodoulou, D.; Mukherjee, A.; Wegmann, R.; Pagano, A.; Sharma, V.; Linker, S. M.; Chang, Y.-F.; Palme, J. S.; Sauer, U.; Basan, M.

doi:10.1101/2023.08.22.554350

bioRxiv · 10.1101/2023.08.22.554350

Long-term history dependence of growth rates of E. coli after nutrient shifts

Christodoulou, D.·Mukherjee, A.·Wegmann, R.·Pagano, A.·Sharma, V.·Linker, S. M.·Chang, Y.-F.·Palme, J. S.·Sauer, U.·Basan, M.

View original source ↗Export metadata ↓

Abstract

According to a widely accepted paradigm of microbiology, steady-state growth rates are determined solely by current growth conditions1-3 and adaptations between growth states are rapid, as recently recapitulated by simple resource allocation models4. However, even in microbes overlapping regulatory networks can yield multi-stability or long-term cellular memory. Species like Listeria monocytogenes5 and Bacillus subtilis "distinguish" distinct histories for the commitment to sporulation6, but it is unclear if these states can persist over many generations. Remarkably, studying carbon co-utilization of Escherichia coli, we found that growth rates on combinations of carbon sources can depend critically on the previous growth condition. Growing in identical conditions, we observed differences in growth rates of up to 25% and we did not observe convergence of growth rates over 15 generations. We observed this phenomenon occurs across combinations of different phosphotransferase (PTS) substrates with various gluconeogenic carbon sources and found it to depend on the transcription factor Mlc.

Explore related subjects

microbiology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Christodoulou, D., Mukherjee, A., Wegmann, R., Pagano, A., Sharma, V., Linker, S. M., Chang, Y.-F., Palme, J. S., Sauer, U., Basan, M.. 2023-08-25. Long-term history dependence of growth rates of E. coli after nutrient shifts. https://doi.org/10.1101/2023.08.22.554350

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Polyphyletic origins and lineage-specific expansion of chemosensory systems in phylum Actinomycetota

Phylum Actinomycetota (syn. Actinobacteriota or Actinobacteria), one of the largest well-studied bacterial phyla, is renowned for complex morphology, non-motility, ecological versatility, and secondary metabolite production. Chemosensory systems (CSS) are among the most sophisticated prokaryotic signal transduction architectures, yet their evolutionary distribution in this phylum remains poorly understood. Here, a comparative genomic analysis of 693 high-quality genomes spanning the phylum resolves the diversity, distribution, and evolutionary trajectories of CSS. Despite extensive genomic complexity and ecological versatility, only 6.9% of genomes encode complete CSS clusters, confined to a subset of lineages within a few classes, indicating lineage-specific retention or loss. In contrast, two-component systems (TCS) are ubiquitously abundant, with hybrid kinases enriched in CSS-deficient classes, suggesting functional compensation for the absence of dedicated chemosensory pathways. Basal lineages retain simplified CSS (F1 or F5), whereas Actinomycetes show lineage-specific expansion into multiple classes (F5, F8, F9, and ACF), often co-occurring, indicative of enhanced sensory complexity. The phylogeny of CheA homologs shows a polyphyletic distribution, supporting a mosaic evolutionary history shaped by multiple independent acquisitions, diversification, and gene loss. Collectively, our findings show that, unlike motile bacteria, members of Actinomycetota rely predominantly on TCS-driven regulatory networks, with CSS retained only in select lineages where ecological demands require enhanced environmental sensing. This work provides a phylum-wide evolutionary framework for the emergence, diversification, and functional specialization of CSS in non-motile bacteria.

microbiology↗

bioRxiv2026

Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

Photobioreactors (PBRs) coupled to animal housing offer potential for mitigating gaseous emissions such as CO2 and NH3 while simultaneously producing biomass. Here, we present a time-resolved characterization of microbial community dynamics, with a focus on the genetic potential for carbon and nitrogen metabolism. Using a cone-shaped, helical PBR cultivating Arthrospira platensis (Spirulina) and supplied with exhaust air from a chicken house, we characterized microbial communities over continuous exhaust-air exposure and periodic biomass harvesting. Microbiome and gene-centric profiling revealed temporal variation in community composition and in the representation of genes associated with carbon and nitrogen metabolism. Cycle-based dissolved inorganic nitrogen balances showed that the decrease in dissolved inorganic nitrogen was only partially recovered in harvested biomass, while ammonia-oxidizing microorganisms were associated with structured, low-light niches. These observations indicate ammonia-oxidizing potential but do not establish a quantitatively relevant nitrification flux. Structured carrier matrices provided attached-growth niches harboring microbial populations underrepresented in the circulating suspension, while pre-colonized carriers facilitated biomass development during re-inoculation. Overall, our results show that coupling PBRs to agricultural exhaust streams can support biomass production while sustaining spatially structured microbial communities with taxonomic and functional potential. These findings may inform their further development for emission mitigation and circular biomass production.

microbiology↗

bioRxiv2026

Engineered DNA materials shape microbial physiology and ecological selection

Extracellular DNA (eDNA) is both a structural component of microbial biofilms and a potential reservoir of genetic information, yet its role as an ecological material remains largely unexplored. Here we establish engineered extracellular materials as determinants of microbial physiology and community assembly across increasing biological complexity. A three-dimensional DNA hydrogel altered bacterial stress-associated responses, elicited species-dependent phenotypes and transcriptional changes in a defined consortium, and shaped community succession in wastewater-derived microbiomes. Distinct responses to surface-bound oligonucleotides reveal that DNA presentation matters beyond its mere presence. Strikingly, metagenomic sequencing identified rare, hydrogel-specific candidate junctions linking material-derived DNA to microbial genomic sequences, suggesting a previously unexplored interface between extracellular DNA materials and microbial genetic information. These findings reveal a dual role for engineered DNA: its material organization shapes microbial physiology and ecological selection, while its encoded sequences may engage with microbial genomic processes.

microbiology↗