The excessive application of nitrogen fertilizers in croplands drives nitrification-induced nitrogen losses, accelerating soil degradation and groundwater nitrate pollution. By synthesizing global nitrogen profiles and field studies, we identify a previously overlooked “enhanced nitrification layer (ENL)” at approximately 0.6 m depth (ranging from 0.3 to 0.9 m) across global croplands. The formation of the ENL relies on the interplay of four key processes: root-mediated nitrogen transport (the conveyor belt), an oxygenated microenvironment sustained by soil texture (the reaction chamber), nitrifier communities (the nitrification engine), and favorable hydrological conditions (the activating switch). This ENL acts as a biogeochemical hotspot, driving subsoil pH declines and nitrate leaching to groundwater. Its identification establishes a precise subsurface target, expanding nitrogen management to address the critical depth of peak transformation alongside surface measures, thereby advancing agroecosystem sustainability. Global cropland subsoil hides a “biogeochemical engine” where crop roots, soil texture, nitrifier communities, and hydrological conditions interact to fuel nitrification, silently driving soil acidification and groundwater nitrate pollution.

Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.

Intermicrobial and host–microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome–host interactions in the gut at high resolution (1 µm). This method combines enzymatic in situ polyadenylation of both bacterial and host RNA with spatial RNA sequencing to increase bacterial RNA recovery and enable transcriptomic analysis of low-abundance and spatially restricted microbial taxa. We benchmark the method against existing spatial transcriptomic workflows, demonstrating improved sensitivity and resolution. Application of this method in a mouse model of intestinal neoplasia revealed the biogeography of the mouse gut microbiome as function of location in the intestine, frequent strong intermicrobial interactions at short length scales and tumor-associated changes in the architecture of the host–microbiome interface. This method is compatible with widely available commercial platforms for spatial RNA sequencing and can therefore be readily adopted to study the role of short-range, bidirectional host–microbe interactions in microbiome health and disease. Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with commercially available spatial transcriptomics platforms.

Plastics drive twin crises: persistent pollution and greenhouse gas emissions. Bio-based approaches using enzymes and microorganisms to depolymerise plastics and valorise monomers show promise but raise societal, ethical and regulatory questions central to Responsible Research and Innovation (RRI). In this Perspective, we reflect on RRI implications of bio-based plastic degradation, informed by stakeholder discussions across the plastics value chain and public engagement. We identify broad support alongside concerns about scalability, interaction with existing recycling, governance and containment of genetically modified organisms, management of additives and contaminants, and the roles of regulation and economic incentives in enabling adoption. Bio-based approaches to plastic degradation have been an intense area of research in recent years, and although they show great promise, they also raise societal, ethical and regulatory questions. Here the authors reflect on the Responsible Research and Innovation (RRI) implications of this growing field, sharing insights they have gained through engagement with stakeholders and the broader public.

Plants use light both as a resource for photosynthesis and as a signal about their environment. In response to light cues, plants can move their organs via directional growth driven by cell expansion. In dense vegetation where light is available in spatially heterogeneous patterns, plants need to navigate this space to improve the position of their photosynthetic tissues. In canopies blue light irradiance and red to far-red light ratio decrease due to absorption by chloroplasts, and these changes regulate distinct processes within the plant. Changes in light environment are detected by cryptochrome and phytochrome photoreceptors, both regulating Phytochrome Interacting Factors (PIFs) and thereby enhancing elongation in hypocotyls, stems and leaves, and inducing upward leaf movement (hyponasty). An additional class of photoreceptors, phototropins, decode horizontal light gradients to produce directional growth towards the light source (phototropism). Here we review the current state of knowledge on these differential growth responses to light cues, with specific emphasis on the regulatory pathways that translate light signaling in differential cell expansion. Downstream of the photoreceptors, the phytohormone auxin induces cell growth in shoot tissues, but also other phytohormones contribute to balancing light responses. Cell expansion is regulated primarily at the level of cell walls and a comparison of different transcriptome datasets reveals that only a small group of cell wall modifying genes are tightly regulated by shade cues. It remains poorly understood which cell layers are causal to the initiation of cellular expansion. Here we combine insights from different differential growth behaviors in different species and organs to generate different hypotheses for the cellular underpinnings of light-driven leaf movements.

The discovery of Asgard archaea about a decade ago has greatly reshaped our understanding of archaeal evolution and the origin of eukaryotes. Asgards are currently thought to be the closest prokaryotic relatives of eukaryotes and to represent the archaeal host lineage that participated in the endosymbiotic event leading to the first eukaryotic cell. The presence of numerous eukaryotic signature proteins in Asgard genomes supports this view and provides important insights into the deep evolutionary roots of eukaryotic cellular complexity. However, the close relationship between archaea and eukaryotes had been observed for decades, based on features that are shared in different molecular processes. This review discusses the discovery of Asgard archaea in the broader context of archaeal molecular and cellular biology and highlights how earlier findings foreshadowed their emergence. Primarily targeted at newcomers to the field, the review provides an overview of evolutionary innovations across the Archaea domain and discusses molecular and cellular features of cultivated Asgard strains in light of previous archaeal research.

Although it is increasingly recognized that anthropogenic chemicals modulate horizontal gene transfer (HGT), the nature of these interactions is often more complex than a simple promotion or inhibition. The potential for a single chemical to exert opposing, concentration-dependent effects represent a critical and less-explored frontier in microbial ecology. Here, we investigate the last-resort antibiotic polymyxin B, a membrane-targeting peptide, and reveal a concentration-dependent, biphasic regulation of plasmid conjugation. Sub-inhibitory concentrations (0.125-0.5 mg/L) consistently inhibited the transfer of antibiotic resistance genes (ARGs) by up to 65.4%, whereas bactericidal concentrations (≥ 1 mg/L) strongly promoted it by up to 15.9-fold. This regulatory switch is driven by distinct physiological states: low-level exposure triggers defensive responses including reduced membrane permeability, whereas high-level exposure causes catastrophic membrane damage, inducing a synergistic stress response involving oxidative damage (>2-fold ROS increase) and a surge in cellular energy (up to 83.0% ATP increase) that facilitates HGT. High-concentration polymyxin B also promotes plasmid transfer in complex microbial communities derived from activated-sludge biofilms. Our findings reveal a new paradigm for the interaction between chemical stressors and microbial evolution, demonstrating that the ecological impact of contaminants on HGT cannot be predicted by monotonic models and highlighting the role of environmental hotspots in shaping the dissemination of antibiotic resistome.

Characterizing CRISPR interference (CRISPRi) phenotypes presents a fundamental temporal challenge: pre–existing overabundance of target proteins can mask early silencing, requiring extended growth for dilution, yet prolonged repression rapidly selects for escaper mutants. To resolve this, we integrated a tightly regulated CRISPRi system in Pseudomonas putida with an automated mini-bioreactor platform operating in turbidostat mode. By maintaining continuous exponential growth, we mapped the exact temporal dynamics of essential gene silencing. We identified a critical observation window between 17 and 27 hours (7–9.5 cell doublings) where repression exerts its maximum physiological impact, directly preceding population takeover by target-site mutated escapers. Applying this workflow to the arginine biosynthesis pathway, multi-omics profiling disentangled transient physiological buffering from long-term mutational events, and revealing that argH and argG knockdowns trigger highly diverse metabolomic perturbations. This scalable framework overcomes batch culture limitations, ensuring precise temporal control for accurate phenotypic characterization and reliable functional genomics.

Wood, once regarded primarily as a structural material, possesses rich physicochemical complexity that has long been underexplored. In the context of industrialization and carbon imbalance, it is now emerging as a renewable and multifunctional platform for green nano-technologies. Recent advances in wood nanotechnology have enabled the transformation of natural wood into programmable substrates with tailored nanoarchitectures, establishing it as a representative class of bio-based nanomaterials. This review systematically categorizes wood-specific nanoengineering strategies—including thermal carbonization, laser-induced graphenization, targeted delignification, nanomaterial integration, and mechanical processing—highlighting their mechanisms and impacts on wood’s multiscale structural and functional properties. Importantly, these functionalization strategies can be flexibly combined in a modular, “Lego-like” manner, enabling wood to be reconfigured and optimized for diverse application scenarios. We summarize recent progress in applying functionalized wood to sustainable technologies such as energy storage (e.g., metal-ion batteries, Zn–air systems, supercapacitors), water treatment (e.g., adsorption, photothermal filtration, catalytic degradation), and energy conversion (e.g., solar evaporation, ionic thermoelectrics, hydrovoltaics, and triboelectric nanogenerators). These studies reveal how nanoengineered wood structures can enable efficient charge transport, selective adsorption, and enhanced light-to-heat conversion. Finally, the review discusses current challenges—such as scalable fabrication, material integration, and long-term environmental stability—and outlines future directions for the development of wood-based platforms in next-generation green energy and environmental systems.