Eco-evolutionary dynamics reshape microbial respiratory responses to warming

Earth System Models project a strong positive carbon–climate feedback from microbial respiration, the largest biotic carbon flux to the atmosphere. Yet experimental studies show that under sustained warming, the thermal sensitivity of microbial respiration often attenuates, through mechanisms that are debated and absent from models. I propose that attenuation is an emergent eco-evolutionary property: evolutionary temperature compensation lowers baseline respiratory rates within lineages; species sorting shifts biomass toward lineages with lower baseline rates; and species interactions reshape the aggregate response, all conditioned by substrate. The pace of these trait and compositional changes relative to warming determines how quickly attenuation develops. Embedding these dynamics in trait-based models could improve carbon–climate projections.

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Microbes and their habitats shape postglacial ecosystems

As glaciers retreat worldwide, microorganisms drive initial proglacial soil development. Ruka et al. reveal that microbial communities are strongly structured by the distinct biological habitats established during primary succession. The trajectories of postglacial ecosystems are thus shaped by reciprocal interactions between biological habitats and their associated microbial communities.

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Trends at 50: a mission that matters

What makes a great review article in your field? As more research is published every day, it has become increasingly difficult to keep up with the latest developments and to ensure that you are hearing from the leading scientists driving these innovations and advances. How do you know what is new and what is valuable?

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Microbiome sharing and the shift to relational privacy

Concerns about big data privacy are growing. While much of the current privacy framework focuses on individuals, protections must also account for relational risks. In this article, we use the microbiome as an example to demonstrate the limitations of applying existing individual-centered privacy frameworks to biological data that can reveal information about interacting individuals.

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Outer membrane lipoprotein sensing for T6SS retaliation

The type VI secretion system (T6SS) is an antimicrobial weapon that Gram-negative bacteria use to outcompete other microbes within polymicrobial communities. Recently, Kolesnikov et al. reported that Pseudomonas aeruginosa can use the T6SS in a precise and responsive manner by sensing T6SS attack via the outer membrane lipoprotein TagQ.

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Cross-kingdom endosymbiosis rewires the rhizobiome for fungal pathogenicity

Soil-borne fungal pathogens undermine crop health by disrupting the protective rhizosphere microbiome. Zhou et al. uncovered a cross-kingdom endosymbiotic mechanism that enables Fusarium oxysporum f. sp. lycopersici to subvert rhizosphere protection: intracellular bacterial endosymbionts drive fungal metabolic reprogramming to produce a selective toxin, thereby suppressing keystone beneficial rhizobacteria.

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Bacteriophages versus priority pathogens: resistance mechanisms, therapeutic challenges, and opportunities for novel combinations

Antimicrobial resistance poses a critical global health threat, and renewed interest in bacteriophage (phage) therapy highlights its potential as a targeted alternative to antibiotic monotherapy. However, phage resistance in bacteria remains a key limiting factor in phage therapy, driven by evolutionary adaptations to phage exposure. Antibacterial modalities (antibiotics, adjuvants, antimicrobial peptides, and RNA-based therapeutics) could help overcome these barriers and represent untapped potential for synergistic, precision antimicrobial interventions when combined with phage therapy. Importantly, bacterial physiology and environmental context could strongly influence treatment outcomes, underscoring the need for clinically relevant models for testing combinations. Integration of multi-omics and artificial intelligence-driven approaches could help predict patterns for the development of precision therapies and support the development of novel antimicrobial interventions.

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Hidden potential for mixotrophy in soil protists

Mixotrophy, the ability of a single protist to combine phototrophy and phagotrophy, is widely recognized as an important functional strategy in aquatic ecosystems, where it shapes food-web structure and carbon cycling. In soil, however, mixotrophy remains largely overlooked despite increasing evidence for trophic flexibility among protists. Here, we argue that this neglect may reflect conceptual and methodological limitations rather than ecological absence. We highlight inconsistencies in trait-based classifications, delineate feeding traits that enable certain forms of mixotrophy, and evaluate soil microhabitats that support mixotrophic activity. Recognizing mixotrophy in soil challenges traditional views of distinct trophic categories and reveals its potential contributions to soil carbon fluxes. Incorporating mixotrophy into soil ecology is therefore essential for developing mechanistic and predictive models of terrestrial ecosystem functioning.

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Hidden carbon: uncovering the diversity and function of polyhydroxyalkanoates

Polyhydroxyalkanoates (PHAs) are a widespread family of microbial carbon-storage polymers. Ecological studies often focus on polyhydroxybutyrate (PHB), obscuring the broader chemical diversity. We argue that PHA monomer composition should be treated as a microbial trait and propose a multiscale framework, from the single cell to the ecosystem level, to reveal hidden carbon dynamics.

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Microbial resistance from genotype to metabolic phenotype

Antimicrobial resistance (AMR) poses an escalating global threat, yet surveillance and mechanistic understanding remain anchored in individual resistance genes, an approach that is inadequate for capturing the ecological, genomic, and metabolic complexity through which resistance emerges and spreads. In this opinion article, we argue that genome-scale metabolic models (GEMs) offer a principled framework for advancing AMR research beyond this gene-centric paradigm. Strain-resolved GEMs embed resistance determinants within metabolic networks, with the potential to generate quantitative, context-dependent phenotypic predictions, including minimum inhibitory concentrations and environment-conditional resistance, that sequence-based tools do not provide. Expanded GEM frameworks incorporating mobile genetic elements, horizontal gene transfer, and community-level interactions support ecology-aware resistance profiling. At the therapeutic level, whole-network modelling can identify metabolic vulnerabilities, synthetic lethal interactions, and microbiome-targeted strategies. Integrating GEMs with multiomics and data-driven approaches represents a critical step toward a mechanism-aware AMR platform connecting surveillance, diagnosis, and drug discovery.

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Community context redirects evolutionary trajectories under stress

Adaptation to abiotic stress is typically studied in single-species cultures, yet bacteria inhabit and evolve in multispecies communities where neighboring organisms reshape, for example, nutrient availability, redox state, and cellular physiology. We recently demonstrated that interspecies interactions can alter the fitness effects of antibiotic resistance mutations, and we suggest that this reflects a broader principle. Stress-response networks are extensively cross-regulated and draw upon a shared, finite pool of proteomic and energetic resources. Consequently, activation of one pathway constrains others, creating physiological trade-offs. Because microbial interactions routinely perturb the physiological inputs to these networks, they can systematically redirect evolutionary trajectories under abiotic stress. We discuss the evidence, limitations, and implications of this framework for predicting evolution and understanding microbiome stability.

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Quinone-trapping filaments enhance respiratory capacity

Cells expand respiratory capacity by adding internal membranes or forming cristae. A new study by Kropp and colleagues shows that the Gram-positive bacterium Bacillus subtilis instead builds hollow protein filaments that sequester and transport quinones, extending the cell’s respiratory capacity without adding membranes. This strategy, widespread across Bacillota, reveals an alternative route to bioenergetic expansion.

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When does environmental antimicrobial resistance become a health risk?

Environmental antimicrobial resistance (AMR) only constitutes a meaningful risk when resistant bacteria overcome key ecological and transmission barriers to reach, persist in, and colonize susceptible hosts. By linking exposure, evolution, transmission, and ecology, our framework provides a realistic basis for assessing AMR risks across One Health compartments.

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Siderophores: chemical threads of rhizosphere health

Rhizosphere microbiomes are central to plant nutrition, pathogen suppression, and rhizosphere health, yet their functions remain difficult to predict from taxonomic composition alone. We argue that microbial siderophores offer a chemically explicit route from taxonomic associations to trait-based rhizosphere ecology. These structurally diverse iron-chelating metabolites link iron mobilization to ecological interactions across microbial, plant, and soil-fauna interfaces. In microbe–microbe systems, siderophore structure–receptor compatibility provides a well-established mechanism underlying resource sharing, competitive exclusion, and pathogen suppression. At plant and nematode interfaces, siderophore functions are increasingly evident, although recognition mechanisms remain less resolved. A siderophore-centered perspective can help move rhizosphere microbiome research from descriptive associations toward predictive, testable, and context-specific ecological engineering.

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Flavobacterium spp.

Flavobacterium spp. are rod-shaped, yellow- to orange-pigmented, Gram-negative bacteria that are ubiquitous in terrestrial and aquatic environments. Across these habitats, they are increasingly recognized as versatile members of environmental and host-associated microbiomes. This ecological breadth reflects the ability of Flavobacterium spp. to adapt to diverse environmental niches that support both beneficial and pathogenic lifestyles. Members of the genus are particularly widespread in aquatic ecosystems, including freshwater environments, sediments, and cold polar environments, while others occur in soils and marine-associated habitats.

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Dysbiotic microbiomes and the collapse of plant health

Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut microbiome, where imbalances similarly contribute to host dysfunction and disease. Here, we discuss the current understanding of plant dysbiosis by integrating host–microbiome interactions and emerging analytical methods. Dysbiosis can extend beyond local compartments, affecting systemic processes such as immunity and nutrient acquisition. Advances in sequencing and quantitative metrics now enable its measurement at the population level, while experimental evidence shows that restoring microbial balance can recover plant function. We highlight translational strategies, including microbiome-informed breeding (Microbiome genes or M genes), synthetic microbial communities (SynComs), and soil microbial priming, to enhance plant resilience. We propose a three-tiered framework for studying and interpreting plant microbiome dysbiosis that integrates compositional profiling, functional omics, and host-performance assessment, and we introduce the concept of functional dysbiosis. We also outline how host-genome-informed M-gene selection, metabolite monitoring, and rationally defined microbial community (SynCom) design can translate this framework into practical crop management strategies.

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Dysbiotic microbiomes and the collapse of plant health

Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut mi...

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Plasmid typing challenges in the era of genomic antimicrobial resistance surveillance

Plasmids are central drivers of antimicrobial resistance (AMR) dissemination, yet their modular, recombinogenic genomes defy concepts of relatedness derived from bacterial chromosomes. Long-read sequencing now routinely yields complete plasmid sequences, exposing a key gap: we can reconstruct plasmids but lack agreed principles for comparing them. In response, diverse clustering tools have emerged that emphasise different signals, such as marker genes, whole-sequence similarity, gene content, backbone structure, or explicit rearrangement events. Each encodes a distinct notion of plasmid distance. This review organises these tools into conceptual families, highlights how their assumptions shape surveillance outputs, and proposes hierarchical, multitool strategies and clearer models of plasmid evolution as the basis for scalable and interpretable plasmid-based AMR surveillance.

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From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance

Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better vie...

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The who, how, and when of mother–infant microbial sharing

The establishment of the infant gut microbiome is strongly linked to health outcomes throughout life. Recently, Mueller et al. reported that the majority of strains shared between a mother and an infant are gut-derived, as opposed to vaginally derived, and strain sharing could be observed into the second year of life.

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Wetland virus exposes blind spots in orthonairovirus pathogenesis

Newly recognized human-associated orthonairoviruses are emerging across East Asia, yet their pathogenic mechanisms remain poorly defined. Wang et al. reveal how Wetland virus converges on caspase-3–gasdermin E pyroptosis and fatty acid synthase-dependent hepatic lipid accumulation Wang and colleagues, linking cell death to metabolic injury and exposing major gaps in pathogenesis and host-directed therapy.

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Micronutrients, the gut microbiota, and infection susceptibility in infants

Micronutrient deficiencies are common during infancy, particularly in settings with a high burden of infectious diseases. At the same time, the developing infant gut microbiota is a key determinant of susceptibility to infection from both resident pathobionts and incoming enteric pathogens. Recent human and experimental studies suggest that micronutrients regulate this developing microbial ecosystem in a highly context-dependent manner, with effects varying according to developmental stage, nutritional status, intestinal location, and environmental exposure. In this review, we synthesise current evidence linking micronutrient-microbiota interactions to microbial competition and metabolism, epithelial barrier integrity, and mucosal immunity, and discuss how these interactions may shape susceptibility to enteric and invasive bacterial infections during infancy.

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The textile web as a probiotic interface

Microbiome of the Built Environment research exhibits a marked ‘hard-surface bias’, overlooking the dynamic soft materials that dominate human-microbial exchange. We propose a theoretical reorientation: the home as a textile web of dynamic, porous microbial reactors. Grounded in immunology’s Danger Theory and the principle of ‘tissue-based class control’, these soft interfaces function as an external tissue analog. By treating textiles as designable interfaces (ranging from airway exchange nodes to laundry bioreactors), architecture becomes a site for proactive probiotic rituals. This framework leverages competitive exclusion to support externalized mucosal ‘guard duty’, transitioning from prophylactic sterility to a choreography of domestic care. Notably, this reframing recognizes that hygiene encompasses more than infection prevention: domestic cleaning rituals also shape the microbial ecology that educates the immune system. Ultimately, we frame the living home as a tolerogenic exoskeleton, biologically calibrated to protect and prime the human holobiont.

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From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance

Antimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better viewed as a context-dependent functional state; the same gene can produce different phenotypes depending on the local microenvironment, enzyme kinetics, antibiotic exposure, and bacterial physiology.

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Serratia plymuthica

Serratia plymuthica is a ubiquitous bacterium with broad ecological relevance that can be isolated from soil, water, insects, plants, and fruits. Although widely distributed, it is most frequently isolated from the plant rhizosphere, where it occurs both as a free-living rhizobacterium and as a non-rhizobial endophyte. While several Serratia species are recognized as opportunistic pathogens (e.g., Serratia marcescens), S. plymuthica is primarily recognized for its beneficial interactions with plants and is widely regarded as a plant growth-promoting and biocontrol bacterium.

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