The study of bacterial sociality, understanding when and how bacteria interact and the consequences of those interactions, has rapidly grown in popularity over the last 20 years. This has revealed that bacteria engage in a remarkable variety of social interactions, including complex cell-cell communication, the exchange of an arsenal of inhibitory molecules, and the sharing of metabolites. These interactions can have significant consequences for the host or environment they reside in, and numerous mechanisms of interaction have attracted significant interest for their therapeutic potential. The present special issue contains eight review articles addressing three major questions in bacterial sociality (Who is where? How are they interacting? And what are the implications of this?) alongside five methods-focused articles that introduce some particularly valuable approaches for the study of bacterial interactions.
Although the study of microbes started with type strains and reference genomes, advances in sequencing technology and new interest in mixed microbial communities have made us aware that a single genome cannot and does not reflect the diversity of a given bacterial species. Bacteria rarely occupy an environmental or host niche alone and quickly diversify into strains upon colonization of a new niche. The genetic diversity present within a phylogenetically related set of bacterial strains (the 'pangenome') is influenced by the niche that they occupy and how they interact with the other microorganisms that they share that niche with. In this review, I examine how the social lives of bacteria can affect their genetic diversity and the bioinformatic techniques that we use to detect that diversity.
The spatial organization of microbiomes illuminates their structure, function, and relationship to their host. Using fluorescence spectral imaging to discriminate up to 16 fluorophores and using combinations of probes to generate unique spectral signatures, combinatorial labeling and spectral imaging-fluorescence in situ hybridization (CLASI-FISH) has been deployed to analyze spatial organization in oral, gut, and marine microbiomes. In dental plaque, imaging revealed the structural role of Corynebacterium matruchotii in organizing the plaque biofilm and revealed previously unrecognized complexity in dental plaque corncob structures. Tongue dorsum biofilms showed a patchy organization around a core of host epithelial cells projecting from the tongue surface, with anaerobes located near the core and oxygen-tolerant taxa near the surface. Taxa that are prominent in these tongue dorsum communities can reduce nitrate to nitrite and thus may play an important role in human nitrate metabolism. In contrast with the highly structured organization of oral biofilms, analysis of the gut microbiome by CLASI-FISH showed a mixed community, indicating that the rate of mixing in the gut is high enough to overcome the tendency of bacterial replication to generate single-taxon patches. Application of CLASI-FISH to blades of kelp showed a dense biofilm with clusters of cocci near the kelp surface, bacteria invading the kelp tissue, and rod-shaped and filamentous bacteria extending into the water column. Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host-microbiome interaction.
Alzheimer's disease (AD) is a complex neurodegenerative disorder involving amyloid-β deposition, tau aggregation, neuroinflammation, synaptic dysfunction, and microvascular and epigenetic changes. Although recent therapeutic developments have energised the field, effective and widely accessible disease-modifying treatments remain limited. This reflects both the biological complexity of AD and the continuing challenge of validating drug targets in the central nervous system (CNS). Chemical probes are small molecules designed to investigate the function of specific proteins in biological systems. When selected and used carefully, they provide powerful tools for testing how particular targets and pathways contribute to AD biology. High-quality chemical probes for AD targets must have high selectivity, confirmed target engagement, and CNS exposure adequate for the specific biological question, with low efflux, and biomarker evidence that the intended target is engaged in brain-relevant tissue. CNS penetration should be interpreted alongside mechanism-appropriate pharmacodynamic biomarkers, since cerebrospinal fluid measurements and modelled Kp,uu do not always directly reflect brain exposure. Chemical probes have shaped current understanding of major AD-relevant pathways, including amyloid precursor protein processing by BACE1 and γ-secretase, tau phosphorylation and aggregation, epigenetic regulation, and neuroinflammatory signalling. Several compounds initially developed as potential therapies have provided valuable mechanistic insight, even where they did not translate into clinical benefit. New modalities, including targeted protein degradation, molecular glues, and peptides, are expanding the range of AD biology that can be studied. These developments illustrate the value and limitations of chemical probes and underline the need for rigorous probe selection, validation, and experimental design in AD research.
Abstract Alzheimer’s disease (AD) is a complex neurodegenerative disorder involving amyloid-β deposition, tau aggregation, neuroinflammation, synaptic dysfunction, and microvascular and epigenetic changes. Although recent therapeutic developments have energised the field, effective and widely accessible disease-modifying treatments remain limited. This reflects both the biological complexity of AD and the continuing challenge of validating drug targets in the central nervous system (CNS). Chemical probes are small molecules designed to investigate the function of specific proteins in biological systems. When selected and used carefully, they provide powerful tools for testing how particular targets and pathways contribute to AD biology. High-quality chemical probes for AD targets must have high selectivity, confirmed target engagement, and CNS exposure adequate for the specific biological question, with low efflux, and biomarker evidence that the intended target is engaged in brain-relevant tissue. CNS penetration should be interpreted alongside mechanism-appropriate pharmacodynamic biomarkers, since cerebrospinal fluid measurements and modelled Kp,uu do not always directly reflect brain exposure. Chemical probes have shaped current understanding of major AD-relevant pathways, including amyloid precursor protein processing by BACE1 and γ-secretase, tau phosphorylation and aggregation, epigenetic regulation, and neuroinflammatory signalling. Several compounds initially developed as potential therapies have provided valuable mechanistic insight, even where they did not translate into clinical benefit. New modalities, including targeted protein degradation, molecular glues, and peptides, are expanding the range of AD biology that can be studied. These developments illustrate the value and limitations of chemical probes and underline the need for rigorous probe selection, validation, and experimental design in AD research.
Many Streptomyces species have a signaling-molecule/receptor system for induction of secondary metabolite biosynthetic gene clusters (BGCs). Signaling molecules hitherto discovered and studied contain five-membered heterocycles, and are classified into three groups, including γ-butyrolactones, γ-butenolides, and furans. These molecules except for avenolide-type are biosynthesized by enzymes harboring an AfsA tandem repeat domain. These enzymes (AfsA homologs) catalyze a transfer of β-ketoacyl moiety to the hydroxyl group of dihydroxyacetone phosphate. Alignment of 59 afsA homolog genes showed that 86% (51/59) of them located adjacent to their possible signaling-molecule receptor genes, which reminds us to readily predict their signaling-molecule/receptor system for expression of BGCs. Apparent exception is the case of afsA-arpA system in Streptomyces griseus, whose distance was around 3.91 Mb. Understanding of the signaling-molecule/receptor system may lead to a practical genome mining strategy to awaken silent BGCs through derepression of transcription using the cognate ligands, signaling molecules.
Forest trees are ecologically and economically vital, contributing to carbon sequestration, biodiversity conservation, pollution mitigation, and renewable bioenergy. However, forests worldwide are increasingly threatened by interacting biotic and abiotic stressors, including pathogens, insect pests, drought, heat, and extreme weather events driven by climate change. Drought and heat stress trigger complex physiological and metabolic responses in trees that can reshape their resistance to pathogens. While moderate stress may activate protective mechanisms, severe stress can cause cellular damage, dehydration, and reactive oxygen species accumulation, weakening defense capacity. Emerging evidence highlights additional layers of regulation, including epigenetic mechanisms and the role of beneficial microbiomes in enhancing tree resilience under combined environmental and pathogen pressures. Breeding and genetic improvement are also essential for strengthening adaptation and resistance to emerging diseases. Although advances in forest genetics, long-term field studies, and tree genomics are improving our predictive capacity, major knowledge gaps remain. Addressing how forest trees respond to pathogens under climate change will require multidisciplinary approaches integrating molecular biology, multiomics, big data analytics, remote sensing, ecology, and climate modelling.
Abstract Nuclear receptors (NRs) are ligand-regulated transcription factors that control many physiological processes, from metabolism and inflammation to development and circadian rhythms. Beginning in the 1990s, systematic chemical probe development transformed many ‘orphan’ NRs with unknown endogenous ligands into chemically tractable, well-studied molecular targets, uncovering their physiological functions and potential for therapeutic development. The present review examines how small molecule ligands for peroxisome proliferator-activated receptors, liver X receptors, farnesoid X receptor, pregnane X receptor, and constitutive androstane receptor enabled the scientific community to connect orphan NR activation to specific transcriptional programs, metabolic phenotypes, and disease processes—while emerging tools for liver receptor homolog-1/steroidogenic factor-1, Rev-Erbs, nerve growth factor-induced clone Bs, HNF4, and transcription factor tailless hold promise to do likewise. These tools not only had widespread impact on NR biology but also established many design principles for chemical probes that continue to guide the field today. The NR field demonstrates how systematic chemical probe discovery can enable basic research and de-risk therapeutic hypotheses, providing a roadmap for other chemical probe initiatives in the human proteome.
Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.
Winter physiological processes are often overlooked in climate change studies of boreal forests, despite their critical role in determining tree survival and carbon balance. Winter climate change is reshaping the environmental constraints that govern boreal forest regeneration, placing increasing pressure on the resilience of tree seedlings. The present mini-review summarises how changing non-growing season temperatures and snow conditions influence the seasonal survival of boreal tree seedlings and the carbon dynamics of both seedlings and soil, with implications for successful forest regeneration. Snow insulates boreal vegetation from extreme cold, regulates light and UV exposure, and shapes spring hydrology. Alterations in snow depth, structure, duration, and melt timing modify soil temperatures, gas exchange, and the snow-soil-root-microbe system, increasing root stress and mortality through deeper frost and hypoxia, ultimately resulting in impaired spring recovery. Winter remains one of the most uncertain parts of the boreal carbon budget, as soils, microbes, and roots continue emitting CO2 and climate change is altering these fluxes and their carryover effects. Boreal forests rely on tightly regulated annual cycles in which cold acclimation and frost hardiness are essential for winter survival, yet warming can delay acclimation, increase vulnerability to warm spells, and advance spring phenology, thereby raising frost-damage risk for seedlings. The post-planting resilience of seedlings can be strengthened by targeted silvicultural planning, nursery, and planting practices that better prepare seedlings to withstand increasingly variable and challenging winter conditions. More research is needed on how boreal forest tree seedlings physiologically and phenologically adapt to changing winter conditions.
In this essay, we postulate that biosynthetic gene clusters (BGCs) chemical diversity arises in Streptomyces cultures from allelic variation both within a single BGC-intra-BGC, and across homologous BGCs-inter-BGC. These layers of genetic diversification reshape pathway architecture, modulate catalytic efficiency, and redefine substrate channeling, ultimately expanding the repertoire of specialized metabolites produced by Streptomyces. On one hand, previous metabolic analyses enabled by the one strain-many compounds framework have provided a comprehensive view of such chemical diversity, while enzyme promiscuity has emerged as a key mechanistic driver contributing to this chemical diversification generating expanded suites of structural analogs. On the other hand, large comparative genomics datasets and phylogenomics have revealed recurrent patterns of enzyme modular rearrangement, domain-level substitutions, and regulatory rewiring that underpin vertical metabolite divergence. Together, the interplay of BGC allelic heterogeneity, pathway modularity, and catalytic promiscuity forms a multilayered evolutionary strategy that fuels the emergence of novel chemical space-derived from a single BGC-in Streptomyces cultures.
Plants serve as central hubs of complex network connecting above- and below-ground inhabitants. These relationships are further shaped by abiotic factors that impact the performance of all organisms in direct or indirect contact. Plant immunity orchestrates the outcomes of these interactions through multiple layers of perception, signal integration, and chemical responses. Although biotic and abiotic dynamics are highly visible in the phyllosphere, the soil represents a vast interface of constant interaction, including the effects of abiotic stressors. As a core component of plant immunity, contact with soil organisms contributes to the complex architecture of plant defense, leveraging the second functional genome to bolster an extended plant immune response. Consequently, continuous contact with organisms will serve as a priming stimulus, fostering systemic resilience against future challenges, particularly in a landscape where environmental fluctuations directly modulate pathogen virulence and soil health. In light of recent literature, the present review calls for the integration of ecological contexts into molecular studies of plant immunity, bridging the gap between cellular mechanisms and ecological dynamics to address the challenges of climate uncertainty.
The present essay attempts to stimulate interest and provide insight into the dynamics of internal conflicts, kin selection, and ecological interactions in multicellular, metabolically gifted microorganisms and how these processes may affect biosynthetic gene cluster (BGC) diversity. The multicellular antibiotic-producing soil bacterium Streptomyces provides a useful model for exploring how internal conflicts emerge and are resolved in biology. These organisms must balance two resource-intensive processes that can create internal conflicts-natural product biosynthesis and sporulation. In Streptomyces, there is potential to mitigate these internal conflicts through division of labour, phenotypic specialisation, and extensive gene duplication and diversification, enabling colonies to optimise both natural product production and reproductive success. Horizontal gene transfer further expands gene families and BGCs, introducing new metabolic capabilities while generating opportunities for functional divergence to reduce internal conflict and potentially promote kin selection. Natural product BGCs also possess features that could identify them as 'greenbeards' (kin selection by trait), promoting cooperation among producers and harming non-producers. The coexistence of multiple natural product BGCs and resistance mechanisms in Streptomyces is discussed in the context of the diverse eco-evolutionary processes occurring in structured natural environments, competition among close relatives, recurrent BGC acquisition, and regulatory compatibility encountered by Streptomyces.
In nature, microorganisms exist in multispecies microbial communities containing bacteria, fungi, archaea, and viruses. The organisation, behaviour, and ecological impact of these communities are very much defined by the various interactions between bacteria and fungi within the community, with physical associations, chemical communication, metabolic exchange, and genetic regulation collectively shaping how these interkingdom communities assemble, adapt, and influence their hosts and habitats. Methods of interaction are widely shared across the microbiota of plants, animals, and the built environment; however, interkingdom microbial communities have environmentally specific outcomes, meaning it is critically important to understand bacterial-fungal interactions (BFIs) within the host or environmental context. With recent advances in BFI analysis now providing increasingly detailed resolution of BFIs and their function in the dialogue between interkingdom microbial communities and their growth environment, we can now gain better insight into these fundamental processes. In the present mini-review, we detail the main BFIs observed in these interkingdom microbial communities, and their implications in the context of plant, human, and the health of the built environment. We also discuss tools and methodologies for their analysis and potential use in the development of microbially derived technologies to improve health and well-being. Finally, we endorse the perspective that interkingdom microbial communities should be considered as structured, interdependent networks with analogy to multicellular organisation.
Horizontal gene transfer, mediated by mobile genetic elements such as conjugative plasmids, is recognised as a major driver of bacterial innovation. While predominantly explored in the context of change within individual strains and species, the broad host ranges of many plasmids mean that they can invade not just lineages but communities. This has far-reaching implications for both the fate of the plasmid and our understanding of bacterial adaptation, as well as applications for the functional engineering of microbial communities. In comparison to single-strain systems, in which plasmid invasion is largely determined by a now well-defined set of parameters-conjugation rate, fitness cost of carriage, and segregation loss-the spread of plasmids into communities is vastly more complex: governed by the wide range of dynamics within strains, but also by community dynamics, spatial heterogeneity, and the interactions between strain- and community-level selection. Here, we review the processes by which plasmids can invade communities and discuss how community complexity both constrains and facilitates plasmid spread. We further explore how this mechanistic understanding can be harnessed to enhance microbial community function.
Natural products (NPs) comprise a wide range of bioactive compounds, including therapeutics and antibiotics. Despite several efforts, the discovery of novel NPs has been hindered by frequent rediscoveries of previously known NPs. Computational tools, such as those in genome mining, have helped identify the biosynthetic gene clusters (BGCs) responsible for the biosynthesis of NPs. However, there is a disconnect between the number of uncharacterized BGCs and the number of observed NPs in laboratory conditions. Considering the community and environmental context (C&EC) of NP-producing organisms can inform elicitation strategies to produce novel, uncharacterized NPs. Approaches inspired by nature, such as mimicking environmental conditions, introducing NPs as elicitors, and using multispecies co-cultures, have been proven successful in eliciting different responses in NP biosynthesis in the laboratory. However, the principles that drive how environmental conditions regulate NPs remain poorly understood. Integrating C&EC with genomic and metabolomic data enables the development of more rational, ecology-informed strategies for eliciting silent BGCs and discovering novel NPs.
Antimicrobial resistance (AMR) is a growing global health crisis, with mortality already in the millions and projections of up to 10 million deaths annually by 2050. Traditional discovery strategies, such as one strain many compounds-based screening of large strain collections, have yielded most of our current antibiotics but are slow, resource-intensive, and highly prone to rediscovery. In parallel, high-throughput sequencing has uncovered an enormous reservoir of biosynthetic gene clusters (BGCs), of which only a small fraction has been experimentally characterized, and many show extensive overlap in gene content. This combination of hidden diversity and functional redundancy demands new tools to prioritize, monitor, and rationally activate BGCs. In this review, we discuss how biosensors can be integrated with genome mining to accelerate antimicrobial discovery and BGC dereplication. We summarize the chemical scaffolds, biosynthetic logic and diagnostic enzymatic signatures of major antimicrobial classes, including β-lactams, tetracyclines, macrolides, aminoglycosides, glycopeptides, lincosamides, polyenes, and azoles, and highlighting representative biosensors that target each scaffold. The biosensors discussed use transcription factors, enzymes, aptamers, CRISPR systems and stress-response modules to generate specific and sensitive signals in complex matrices. We argue that translating BGC architecture into biosensor design creates a practical framework to rapidly discriminate from novel activities, but most importantly, to guide the exploration of chemical space around clinically important scaffolds in the era of escalating AMR.
Streptomycetes are known for their production of diverse secondary metabolites, many of which have medicinal applications. The enzymes facilitating the production of these metabolites are encoded in biosynthetic gene clusters (BGCs) with regulatory and transport proteins. Regulation of secondary metabolite biosynthesis is tightly controlled in laboratory conditions, and many natural products have low yields or are not expressed in laboratory cultures. Although transcriptional regulation has been a major focus in the past, translational control has recently emerged as a critical determinant of BGC activity. Due to the energy requirement for translation, evidence suggests a greater degree of translational regulation than transcriptional regulation. Many translation factors impact protein synthesis rates, such as regulatory RNAs, ribonucleases, transcript quality control, ribosome rescue systems, tRNA pools, and antibiotic-induced ribosome mutations. These convergent components respond to environmental cues and metabolic states to coordinate secondary metabolism with demands for growth and development of streptomycetes. A deeper understanding of translational control will not only reveal key functions that control and coordinate specialized metabolism but will also highlight new strategies for activating silent gene clusters and enhancing natural product yields. The present review explores how translation serves as a central regulatory hub for BGC activity and discusses emerging tools to manipulate protein synthesis for natural product discovery and biotechnological advancement.
Defence priming enhances plant responsiveness to future stress following prior exposure, and has been extensively characterised in annual model species as a reversible state associated with faster or stronger defence activation. However, studies in long-lived plants indicate that priming responses can be elicitor-specific, developmentally variable and closely linked to environmental history. In trees, priming is often strongest in early life stages, while in mature individuals defence responses are more frequently associated with direct activation and stabilised regulatory states. Evidence across systems shows that priming can operate over multiple timescales, from short-term reversible responses to longer-lasting effects that influence response thresholds and activation kinetics. Epigenetic mechanisms, including DNA methylation and chromatin modification, contribute to these processes and may persist across cell divisions or developmental transitions. Together, these findings highlight the importance of developmental stage and temporal context in shaping plant defence responses.
Biofilms are challenging samples for microscopy, because they are usually large samples with small features of interest, a fragile nature due to their high water content, and they may be grown on a variety of substrates. Cryo-scanning electron microscopy (cryo-SEM) has long been used to image microbiological components in plant-pathogen interactions, food products, and soil. The main advantage, compared with the more widely available room temperature SEM, is that the rapid sample preparation results in a native-like structure. It has been used to study environmental biofilms, but rarely for medically relevant biofilms. The cryo-SEM workflow starts with freezing the sample, either by high-pressure freezing, plunge-freezing, or slush nitrogen freezing. This is followed by fracture, sublimation, and coating, before the cryo-SEM imaging takes place. The present review aims to give new potential users an overview of the workflow and give examples of the equipment available, while discussing advantages and limitations of specific steps and their suitability for the research of various biofilms.
