Preprints
Filtering by Subject: Microbiology
Pine wilt disease as a holobiont disorder: microbiome assembly as a potential management target
Published: 2026-10-07
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Forest Management, Forest Sciences, Life Sciences, Microbiology, Plant Pathology, Plant Sciences, Terrestrial and Aquatic Ecology
Pine wilt disease (PWD), caused by the pinewood nematode (PWN) Bursaphelenchus xylophilus, continues to expand globally despite decades of pathogen-focused management. Here, we propose that disruption of microbiome assembly within the pine holobiont may contribute to disease progression and help explain variation in disease outcomes and responses to microbial interventions. Drawing on recent [...]
Coordinated interannual change in NEON soil bacterial communities across continental North America
Published: 2026-09-23
Subjects: Agriculture, Biodiversity, Microbiology
Soil bacterial communities change from year to year, but whether these changes are coordinated across distant ecosystems has not been well investigated. We leveraged publicly available soil data from the National Ecological Observatory Network (NEON), and applied statistical analyses to evaluate the temporal changes of soil bacterial communities across continental North America. Data were [...]
Hive product metagenomics: a promising window into honey bee genomics and bee-associated ecosystems
Published: 2026-09-06
Subjects: Apiculture, Entomology, Genomics, Microbiology, Other Genetics and Genomics
Through their pollination services, bees are essential components of ecosystem functioning, supporting biodiversity and contributing to global food production. Among them, honey bees are particularly important, both for their ecological role and their widespread contribution to many agricultural systems and beekeeping. Honey, beeswax and propolis, among other beehive products, have played a [...]
What goes up, must come down: air–soil microbiome connectivity and its implications for ecosystem functioning
Published: 2026-08-28
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Life Sciences, Microbiology
Soils harbor Earth's largest reservoir of microbial diversity, yet enormous numbers of microorganisms are continuously aerosolized, transported through the atmosphere, and redeposited across landscapes. Although soil and the atmosphere have largely been studied separately, here, we propose a conceptual framework that views soils and the atmosphere as a coupled microbiome linked by bidirectional [...]
How many ways are there to be a phage?
Published: 2026-08-27
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Virology
The search for predictive rules for how microbiomes assemble and function rarely include their most abundant members: phages. Nearly a century of phage research has yielded few ecological principles for the impacts of phages within microbial communities – sequencing surveys resolve phage presence but not phage activity, while mechanistic studies of relatively few model phages provide insights [...]
Candidozyma auris (Candida auris) as a harbinger of novel fungal pathogens
Published: 2026-08-25
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Medical Microbiology, Medicine and Health Sciences, Microbiology, Pathogenic Microbiology
Mammals are protected from fungal pathogens by two evolutionary pillars: adaptive immunity and elevated body temperature. Anthropogenic climate change is eroding this thermal barrier, while a concurrent decline in human basal body temperature accelerates convergence from both directions. The emergence of Candidozyma auris (Candida auris), a thermotolerant, multidrug-resistant pathogen that arose [...]
Beyond the mammalian nucleolus—a comparative perspective on nucleolar dynamics in stress and through the life cycle
Published: 2026-08-11
Subjects: Cell and Developmental Biology, Cell Biology, Ecology and Evolutionary Biology, Evolution, Microbiology, Organismal Biological Physiology
Classically the site of ribosomal RNA transcription, processing and early ribosome assembly, the nucleolus is increasingly understood as a dynamic multiphase condensate reshaped by cell state. Most reviews of this plasticity are mammal-centred. Here we set mammals alongside fungi, plants and animal germlines, following the nucleolus through the life cycle under environmental change and through [...]
An assessment of biodiversity data shortfalls for ectomycorrhizal fungi in Canada
Published: 2026-07-22
Subjects: Biodiversity, Botany, Ecology and Evolutionary Biology, Microbiology
Ectomycorrhizal (EcM) fungi play critical roles in global carbon and nutrient cycling. In Canada, vast forest ecosystems dominated by EcM trees are experiencing rapid environmental and anthropogenic change that threaten the symbiosis. Here we quantify and discuss seven biodiversity data shortfalls that constrain our knowledge of EcM fungi in Canada, and impede the development of effective [...]
The bacterial immune system: identifying evolved defense adaptations
Published: 2026-05-13
Subjects: Ecology and Evolutionary Biology, Evolution, Microbiology
The last few years have witnessed a rapid expansion of reported bacterial defense mechanisms. Alongside established mechanisms of defense against molecular parasites (e.g. CRISPR-Cas, restriction-modification), hundreds of novel defenses are being described each year, contributing to an ever-expanding ‘bacterial immune system’. Terms like ‘defense’ and ‘immune’ are often used as shorthand for an [...]
Representational limits in detecting ecological change
Published: 2026-04-28
Subjects: Agriculture, Animal Sciences, Biochemistry, Biophysics, and Structural Biology, Biodiversity, Bioinformatics, Biology, Biotechnology, Cell and Developmental Biology, Ecology and Evolutionary Biology, Entomology, Food Science, Forest Sciences, Genetics and Genomics, Immunology and Infectious Disease, Laboratory and Basic Science Research Life Sciences, Life Sciences, Marine Biology, Microbiology, Neuroscience and Neurobiology, Other Life Sciences, Pharmacology, Toxicology and Environmental Health, Physiology, Plant Sciences, Research Methods in Life Sciences, Systems Biology
Detecting ecological change remains a persistent challenge, even in systems with extensive monitoring data and increasingly sophisticated analytical tools. Uncertainty is usually attributed to stochasticity, limited observations, or imperfect models. Here, I argue that an additional and largely overlooked constraint arises from representational limits: systematic ways in which graphs, indicators, [...]
How environmental conditions affect the acquisition, establishment, and persistence of microbial endosymbiosis in insects
Published: 2026-03-26
Subjects: Ecology and Evolutionary Biology, Life Sciences, Microbiology, Other Ecology and Evolutionary Biology, Other Microbiology
Long-term interactions between insect hosts and their internal microbial symbionts are ubiquitous. As these interactions support many aspects of the insect host biology, restrictions to their establishment and maintenance could have important consequences to the survival of insects and functioning of ecosystems. The current literature provides extensive evidence that rapidly changing [...]
From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
Published: 2026-03-17
Subjects: Evolution, Genetics, Genomics, Microbiology
Horizontal gene transfer (HGT), the set of processes by which genetic information is transferred between individuals, has shaped life’s evolution. It is particularly frequent in microbial organisms, where it has driven numerous remarkable adaptations to extreme conditions, anti-microbial agents, or biotic interactions. Its role in spreading novel functions is now documented by countless examples [...]
The lens of the Sonic Holobiont. A perspective on acoustic influence on microbial communities and its application as an additional layer to the holobiont concept.
Published: 2026-03-11
Subjects: Arts and Humanities, Biochemistry, Biophysics, and Structural Biology, Biodiversity, Ecology and Evolutionary Biology, Life Sciences, Microbiology, Other Arts and Humanities, Other Physical Sciences and Mathematics, Physical Sciences and Mathematics
When studying micro and macro biomes in the quest for a more general understanding, we can hardly escape from a holistic perspective. At first, symbiosis was demonstrated to be a ubiquitous phenomenon in living cells, shaping evolutionary patterns across species at very different scales. The “holobiont” concept gains a central role in modern biology. The observation of the complex inter- and [...]
Thermal filtering reveals a cryptic reservoir of thermotolerant yeasts in Sub-Antarctic soils
Published: 2026-03-05
Subjects: Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology
Global climate change is accelerating ecological transformation in Sub-Antarctic ecosystems, where resident biota exhibit narrow thermal tolerances. While microbial responses to warming are increasingly documented, the role of soil yeasts, key players in organic matter decomposition, remains poorly understood. Here, we show that warming acts as a deterministic filter, triggering a profound [...]
Composite virulence: useful metric or conceptual trap?
Published: 2026-02-20
Subjects: Animal Diseases, Animal Experimentation and Research, Animal Sciences, Biodiversity, Biology, Ecology and Evolutionary Biology, Evolution, Immunity, Immunology and Infectious Disease, Immunology of Infectious Disease, Immunopathology, Life Sciences, Medical Microbiology, Microbiology, Other Ecology and Evolutionary Biology, Other Immunology and Infectious Disease, Parasitic Diseases, Parasitology, Pathogenic Microbiology, Plant Pathology, Research Methods in Life Sciences, Zoology
Virulence, defined as the harm an infection causes to its host, is central to evolutionary ecology, yet it remains difficult to quantify because infection impact is multidimensional, dynamic, and context-dependent. Composite measures have therefore emerged to summarise multiple traits into a single estimate of infection-induced harm. However, every composite embeds biological assumptions about [...]