Bacteria have evolved diverse anti-phage defence systems to counter the constant threat of viral infection. Like all immune systems, these defences must accurately detect infection while avoiding inappropriate activation that could harm the uninfected host. Recent years have witnessed a rapid expansion in the discovery of bacterial immune mechanisms, yet fundamental questions remain about how these systems recognize phage invasion. What molecules or events are reliable indicators of infection? How do the sensory mechanisms underlying immunity ensure rapid and robust activation? And what evolutionary trade-offs do phages face when mutating to evade detection? In this Review, we examine the experimental approaches used to identify phage-based triggers and organize known triggers into three classes: phage nucleic acids, phage proteins and perturbations to host processes. For each class, we summarize current evidence and highlight emerging principles that connect diverse defence mechanisms. By focusing on sensing rather than downstream responses, we aim to provide a cohesive framework for understanding how bacteria discriminate self from non-self, a challenge universal to immune systems across all domains of life.

Microorganisms facilitate both the synthesis and breakdown of bio-based biodegradable plastics, which positions them as central players in the development of a future circular plastics economy. However, advances in microbial production and biodegradation of plastics are often considered in isolation, limiting our ability to integrate these processes into viable circular systems. In this Review, we discuss the contributions of microorganisms across the life cycle of key bio-based polymers, focusing on polyhydroxyalkanoates, bacterial nanocellulose, and the monomers of polylactic acid and polyethylene furanoate, and we critically assess the extent to which current microbial capabilities can support polymer synthesis and degradation. Although the genetic capacity for these processes is widespread, this does not necessarily translate into efficient synthesis or biodegradation in industrial or environmental conditions. Microbial synthesis remains constrained by low volumetric productivity, carbon inefficiencies and downstream processing challenges, whereas biodegradation is highly dependent on material properties and environmental conditions, with efficient biodegradation often limited to managed settings. Thus, achieving an effective circular bio-based plastic economy requires the integration of microbial engineering, polymer chemistry, material science and other disciplines to optimize both production and end-of-life management.

Below every step we take there is groundwater. Out-competing rivers, lakes and wetlands in terms of water quantity and quality, shallow aquifers are an essential reservoir of freshwater for the human population. At the same time, they represent the largest freshwater biome on earth, forming a responsive but vulnerable interface between the highly dynamic surface aquatic and terrestrial ecosystems and the environmentally static deeper zones of the subsurface. Shallow aquifers are home to a vast phylogenetic and functional microbial diversity, regularly surpassing those of surface environments. Predominantly colonized by microorganisms, key drivers of community composition and biogeochemical cycles are the hydrogeological settings, availability of energy and prevailing redox conditions, as well as climate and local to regional anthropogenic activities. Although there is steadily growing knowledge on microbial biodiversity and their potential functions, quantitative data on active key processes, such as carbon cycling, are scarce. We do have a very incomplete idea of the abundances and distribution of viruses, protists and fungi and their ecological role in groundwater. In this Review, we discuss current and future pressures to shallow groundwater ecosystems in terms of microbial community dynamics particularly in light of global and climate change, that is, groundwater pollution and warming.

Many important plant diseases are caused by airborne spores. This review explains the aerobiology of plant pathogens, sampling methods for collection of airborne spores, merits of different post-capture diagnostic methods (microscopy, immunology and DNA-based diagnostics) and non-capture (optical or imaging) methods to classify airborne particles. Different sampling, downstream processing and diagnostic methods can affect the efficiency of detection of certain species due to differences in traits such as spore size, adhesive surfaces, electrostatic charge, hydrophobicity, physical toughness and copy number of target DNA sequences. These considerations and an understanding of dispersal must be understood by all engaged in practical or academic measurement of bioaerosols, whether for plant pathology, fungal ecology or to measure biodiversity. In addition to surveillance of changes in pathogen populations, for example, for antimicrobial resistance or pathotype, the review describes how air sampling can provide accurate and cost-effective forecasting of imminent plant disease. The scale of spore dispersal processes and impacts on sampling strategies (e.g. spatial density of spore traps and sampling height above ground) for broad-acre or small-scale but high-value crops is also discussed. The fundamental concept behind these processes is the aerobiology pathway, which describes the production, release, dispersal, deposition and resulting effect, which, for air-dispersed plant pathogens, is plant disease. In addition to the seasonality to spore production for many fungi, each component of the aerobiology pathway is affected by the weather, which causes different types of spores to be released under different meteorological conditions or at different times of day and to disperse in different ways. Dispersal processes of fungal spores in air have been modelled and apply irrespective of pathogens or non-pathogenic fungi, or to spores of individuals that are insensitive to fungicides or not. Often, we do not know the location of spore sources or their relative source strength, which makes sampling strategies difficult to optimize initially, and the best strategy will vary from pathogen to pathogen and according to the rationale for monitoring and consequences of 'missing' a spore event.

Perturbation of the gut microbiota has been implicated in neurological diseases via communication across the microbiome-gut-brain axis. As a result, the discovery of mechanisms underlying interaction across this axis is becoming increasingly important. The germ-free (GF) mouse model has enabled an improved understanding of the influence of the gut microbiota on brain development and function. By utilizing an advanced spatial profiling approach, we determined transcriptional changes in the brain, improving our understanding of how brain cells function and interact within their microenvironment in the absence of microbiome influence. Targeted regions of interest were selected based on brain regions implicated in neurological disease or reported structural differences between GF mouse brains and those of colonized mice. In the hippocampus, 276 differentially expressed genes (DEGs) were identified, 345 DEGs in the thalamus and 21 DEGs in the pons. Contrastingly, we identified only 2 DEGs in the midbrain and 4 in the medulla oblongata, with no DEGs in the cerebellum or corpus callosum. These data provide an overview of gut microbiota influence on gene expression in the brain, highlighting multiple genes of interest for further investigation in the context of microbiome influence on brain function and their potential relevance to neurological disease.

Bifidobacteria are widely recognized important symbionts of the human gut microbiome, shaping host physiology from birth to adulthood to old age. Their evolutionary success is derived from metabolic versatility, ecological adaptation and intimate host interactions. Equipped with an expansive glycan-degrading repertoire, stress-response systems and specialized cell surface structures, bifidobacteria establish stable gut colonization and influence host immune, metabolic and neuroendocrine functions. Genomics and functional studies have revealed how human-associated members of this genus shape trophic networks, tolerance and resilience within the gut ecosystem. Integration of ecological, metabolic and immunological perspectives now positions the genus Bifidobacterium as an excellent model to support human gut health and its potential use as gut microbiota-based therapeutics.

Carrot production regions worldwide incur enormous annual economic losses due to postharvest white mold caused by Sclerotinia sclerotiorum. Biological control is a promising approach for controlling postharvest pathogens. This study investigated the biocontrol efficacy of using Bacillus velezensis JR4 against Sclerotinia rot and its potential mechanisms of action. The results showed that the JR4 strain achieved 91.1% inhibition of S. sclerotiorum in a dual-culture assay. B. velezensis JR4 was able to produce extracellular enzymes such as protease, cellulase, and chitinase. Applying JR4 bacterial suspension at 1 × 10[8] CFU mL[- 1] on postharvest carrots infected with the pathogen reduced rot incidence by 65.4% and lesion length by 80.6% on day 5. The same concentration increased the levels of total phenolics and total flavonoids, as well as the activity of defense-related enzymes, including peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). It also increased the expression of three defense-related genes in postharvest carrots over four days. Compared to untreated carrots, it exhibited lower levels of cell membrane permeability, malondialdehyde (MDA), superoxide anion (O2[-]), and hydrogen peroxide (H2O2). Furthermore, the cell-free culture filtrate of JR4 showed minimal to no toxicity on WI-38 and Vero cells across all concentrations. The results suggest that B. velezensis JR4 could be an effective and sustainable biocontrol agent for controlling white mold in postharvest carrots. However, further safety assessments are needed for its successful application.

Microsporidia are obligate intracellular eukaryotic parasites. These pathogens belong to an understudied lineage of fungi and can infect most types of animal. Although microsporidia were first discovered over 150 years ago, their impact on humans and agriculturally important animals has become clear only within the last several decades. Microsporidia have the smallest known eukaryotic genomes, and technological advances have been used to highlight the consequences of genomic reduction. Microsporidia have a unique structure known as the polar tube and the mechanisms of how this infectious apparatus is used for invasion of host cells are beginning to be understood. Microsporidia infection has wide-ranging consequences on hosts, and in turn, hosts have evolved immunity against these parasites. Progress has been made in both detecting and treating these infections. This Review provides an overview of the evolution, infection mechanisms and impact of these parasites on their hosts.