Microbial communities carry out important ecological functions. Their activities emerge from interactions between species, often potentiated by metabolic traits. We lack a quantitative understanding of how these traits shape community properties. Here, we present theory for microbial communities, leveraging concepts from quantitative microbial physiology. We focus on how steady-state metabolic exchanges between species determine their fractional abundances, given their biomass and byproduct yields on nutrients. We start by deriving formal conditions for the steady states of communities of microbes that grow, die and cross-feed metabolites. We describe the metabolic stoichiometry of nutrient uptake and the formation of biomass and byproducts for each species in terms of charge- and chemical-element balanced reactions (macrochemical reactions). Byproducts function as nutrients for other species. Next, we express the relative abundances of species (living and dead), the net metabolic conversion of a community, and the biomass carrying capacity in terms of the metabolic stoichiometry, growth rates and death rates of the species. We show how niche creation can emerge from stoichiometric imbalances in cross-feeding communities. Finally, we discuss how relative species abundances depend on the ATP stoichiometries of intracellular metabolism.

Microbial communities in natural environments are consistently challenged by toxic compounds, such as polycyclic aromatic hydrocarbons (PAHs). The capacity for rapid phenotypic diversification is key to survival in these dynamic and often hostile niches. Here, we report a mechanism by which E. coli generates immediate phenotypic heterogeneity in response to a model PAH, perylene. Utilizing single-cell techniques, we revealed unexpected efflux phenotypic switches occurring in a single division event by examining the asymmetric distribution of perylene, a TolC-related efflux system substrate. Contrary to gradual changes in many generations, the phenotypic switch we observed is abrupt, resulting in daughter cells with distinct efflux phenotypes and asymmetric viability. We ruled out uneven efflux pump distribution and suggested the switch is linked to asymmetric proton motive force. Furthermore, we found a correlation between the age of the inherited pole during division and the propensity for phenotypic switching. New pole cells are identified as more prone to this switch. Our findings reveal a rapid division-based strategy for generating phenotypic diversity that could enhance the adaptive potential and resilience of bacterial populations facing fluctuating environmental toxins.

To address emerging climate and resource threats to global agriculture, we require advanced, plant-to-farm monitoring interventions. This perspective proposes Flora-Fi, an expanded Internet of plants framework leveraging innate intra- and interplant communication (IPC) pathways. By integrating biological signals with digital networks, Flora-Fi enables energy-efficient, early stress detection. We outline a blueprint detailing the next-generation sensing, communication, and data processing infrastructures necessary to realize this holistic crop management paradigm.

Lichens are symbiotic associations between a fungal mycobiont and a photosynthetic photobiont. They thrive in nutrient-poor environments; yet the mechanisms underlying their adaptation to iron limitation remained largely unknown. Here, we characterize the iron acquisition system of Xanthoria parietina, a globally distributed lichen-forming fungus associated with the microalgal photobiont Trebouxia decolorans. We demonstrate that the mycobiont produces the siderophore ferrichrome and possesses the full genetic repertoire not only for siderophore biosynthesis, but also reductive iron assimilation, iron detoxification, and regulation. The ferrichrome-synthesizing non-ribosomal peptides synthetase exhibits a lichen-specific compact architecture but retains functionality when heterologously expressed in a non-lichenized ascomycete. Transcriptomic analysis and ferrichrome quantification reveal substrate-dependent regulation of the siderophore system. Importantly, ferrichrome promotes photobiont growth independent of extracellular iron reduction, indicating direct utilization. These findings provide the functional evidence of siderophore-mediated iron acquisition in a lichen symbiosis and highlight ferrichrome as a key mediator of mutualistic nutrient exchange. The mechanisms underlying the adaptation of lichens to nutrient-poor environments are poorly understood. Here, Happacher et al. show that a globally distributed lichen fungus produces an iron-scavenging molecule that promotes growth of its algal partner.

Glacier forelands undergo a transition from oligotrophic to eutrophic conditions during primary succession. Reduced sulfur compounds may serve as an energy source for early microbial colonizers, yet the sulfur oxidation potential and key taxa remain largely unknown. Here, we perform a multi‑omics survey across a 130‑year chronosequence on the Tibetan Plateau. Glacial retreat profoundly reshapes both viral communities (61,394 viral operational taxonomic units, vOTUs) and microbial communities (404 metagenome‑assembled genomes, MAGs). Notably, Oxidative Dissimilatory sulfite reductase (Dsr) operon‑encoding Sulfur‑Oxidizing Bacteria (ODSOB) were specifically enriched within the first 1–5 years after retreat. Their associated viruses predominantly follow a “piggyback‑the‑winner” strategy, influencing host cold shock protein evolution and potentially modulating sulfur oxidation via iron‑sulfur (Fe‑S) cluster assembly. Metatranscriptomics reveals elevated expression of the oxidative Dsr operon and Form‑I ribulose‑1,5‑bisphosphate carboxylase/oxygenase (RubisCO) in early stages, coinciding with higher sulfate, sulfite, sulfide, and dissolved inorganic carbon (DIC)‑to‑dissolved carbon ratios compared to later stages. These findings indicate that ODSOB support DIC fixation and sulfide detoxification during early ecosystem development. Collectively, this study uncovers the eco‑evolutionary dynamics between viruses and microbes in developing ecosystems and provides genomic and functional evidence for ODSOB as key drivers of soil formation and primary succession in glacial forelands. This study shows that in glacier forelands sulfur-oxidizing bacteria and associated viruses are enriched within 1–5 years after glacial retreat. These microbes alter carbon fixation and sulfide detoxification, acting as drivers of primary succession.

Global livestock production faces mounting pressures from climate variability, heat stress, emerging diseases, antimicrobial resistance, and sustainability demands, necessitating transformative nutritional strategies. Next-generation approaches highlight postbiotics, functional amino acids, microbial proteins, nanotechnology-enabled delivery, and nutrition-driven epigenetic regulation. Postbiotics, including short-chain fatty acids and peptides, enhance gut integrity, immunity, and feed efficiency while reducing antibiotic reliance. Functional amino acids modulate the NRF2–KEAP1 pathway, facilitating hepatic proteome remodeling and stress resilience. Sustainable alternatives, such as microbial proteins and nanocarriers, improve nutrient bioavailability with lower environmental costs. Nutritional epigenetics offers a paradigm shift, as one-carbon metabolites (methionine, choline, folate, vitamin B12) influence DNA methylation, histone dynamics, and microRNA regulation, shaping growth, reproduction, and thermotolerance. Future innovations include epigenome-guided diets, parental nutritional programming, digital twin models, and synthetic biology-driven bioactives. Collectively, these advances redefine nutrition as a driver of resilience and sustainability, requiring interdisciplinary integration, rigorous validation, and equitable translation into practice.

Polymerase-mediated DNA synthesis is fundamental to numerous biotechnology applications, but existing programmable synthesis methods depend on exchanging DNA building blocks, thereby increasing reagent use and complicating multistep workflows. Here, we introduce the TEmperature Mediated Primer Exchange Reaction (TEMPER), a programmable platform for arbitrary DNA synthesis that operates solely through temperature control without solution exchange. TEMPER uses hairpin DNA as temperature-responsive building blocks that define specific temperature range for DNA synthesis. The temperature range is determined by the length design of the hairpin, which regulates thermodynamic interactions between DNA molecules and allows selective and sequential DNA synthesis in one-pot. We validate its versatility by developing a DNA data storage writer, a colorimetric temperature indicator, and a temperature data logger, highlighting its broad potential in nanotechnology and biotechnology applications. Polymerase-mediated DNA synthesis has numerous potential biotechnological applications. Here the authors develop TEmperature Mediated Primer Exchange Reaction (TEMPER), a programmable one-pot DNA synthesis method that stores data in DNA via temperature cycles and records thermal history.

Biomolecular condensates formed through liquid–liquid phase separation (LLPS) compartmentalize biochemical reactions without enclosing membranes, enabling spatiotemporal control over diverse cellular processes. Engineering genetically encoded proteins that phase separate in response to defined chemical inputs remains a central challenge for synthetic biology. Here, we report a coiled-coil peptide polymer, M1, that undergoes cofactor-dependent condensation both in vitro and in E. coli. M1 is an ABA triblock construct comprising two terminal helical domains connected by a flexible, intrinsically disordered linker. The terminal domains are derived from a heme-responsive coiled-coil motif that is destabilized in the apo state but assembles into a four-helix bundle upon metalloporphyrin coordination. We demonstrate that M1 forms condensates exclusively in its cofactor-bound state, both in vitro and in cells. In E. coli, these intracellular condensates accumulate at the cell poles in a concentration-dependent manner. Depletion of cellular heme biosynthetic capacity suppressed condensate formation, which was rescued by supplementation with the heme precursor δ-aminolevulinic acid (δ-ALA) and iron, consistent with metalloporphyrin coordination triggering assembly. The condensates retain peroxidase activity characteristic of heme-containing proteins and catalyze the oxidation of Amplex Red to resorufin both in vitro and in living cells. These results establish metalloporphyrin binding as a molecular switch for condensate biogenesis in a structured peptide polymer, directly coupling cofactor coordination, mesoscale assembly, and catalytic function within a single designed system.