Preprints
Filtering by Subject: Microbiology
Beneath the Pavement: Understanding mycorrhizal fungi in urban ecosystems and the path forward
Published: 2025-11-03
Subjects: Biodiversity, Biology, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Environmental Studies, Human Ecology, Life Sciences, Microbiology, Social and Behavioral Sciences, Urban Studies and Planning
Urban expansion is reshaping ecosystems worldwide, yet the responses of mycorrhizal fungi—key mediators of plant–soil interactions—remain poorly understood. In this review, we synthesize current knowledge on the environmental and ecological factors shaping mycorrhizal fungal diversity, distribution, and function in cities. We highlight how greenspace and landscape features—including plant [...]
Microplastic interference influences Pseudomonas fluorescens in denitrification efficiency of wastewater treatment
Published: 2025-10-28
Subjects: Ecology and Evolutionary Biology, Microbiology, Pharmacology, Toxicology and Environmental Health
Wastewater treatment plants (WWTP) play an essential role in pathogen and contaminant removal in wastewater. While developed countries treat approximately 70% of industrial wastewater prior to discharge, only about 8% is treated in developing countries. WWTP solutions can reduce the solids load, including microplastics, by up to 98.4%. Still, it is estimated that about 65 million microplastics [...]
Bridging the scales: what can microbial ecologists learn from classic ecology?
Published: 2025-06-30
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Microbiology
The fields of ecology and microbiology have historically developed independently of one another, resulting in each having unique methods, terminology, and concepts. Microbial ecology aims to synthesise these perspectives, merging the molecular and reductionist strengths of the microbiologist with the systems-level viewpoint of the ecologist. However, unifying disciplines with independent [...]
Two Metschnikowia nectar yeast species have similar volatile profiles, but elicit differential foraging in bee pollinators
Published: 2025-06-19
Subjects: Ecology and Evolutionary Biology, Entomology, Life Sciences, Microbiology, Organismal Biological Physiology, Other Microbiology
1. Nectar yeasts are a highly specialized group of fungi that may play key roles in pollination ecology. Nectar yeasts lack an independent dispersal mechanism to access new habitats with fresh resources. Yeasts, bumble bee pollinators, and flowering plants likely take part in a series of diffuse mutualisms, wherein yeast attract bees that provide phoretic travel between flowers. This [...]
Elevating the importance of Risk of Bias assessment for ecology and evolution
Published: 2025-06-17
Subjects: Agriculture, Animal Sciences, Biodiversity, Biology, Ecology and Evolutionary Biology, Entomology, Life Sciences, Marine Biology, Microbiology, Plant Sciences, Research Methods in Life Sciences
Systematic reviews and meta-analyses are key evidence synthesis methods informing research and policy. An assessment of the Risk of Bias (RoB) in included studies is normally considered an essential component of these. However, RoB assessment is rare in ecology and evolutionary biology (EEB), and tools from other fields are seldom adopted. To identify reasons for this limited uptake, we surveyed [...]
Applying Evolutionary Theory to Understand Host-Microbiome Evolution: New Tricks for Old Dogs
Published: 2024-11-27
Subjects: Ecology and Evolutionary Biology, Microbiology
All plants and animals are host to a community of microorganisms, their microbiomes, that have crucial influences on the life history and performance of their hosts. Despite the importance of such host-microbiome relationships, relatively little is known about the role microbiomes play in mediating evolution of the host as well as entire host-microbe assemblages. This knowledge gap is partly due [...]
Gut microbiome composition and function – including transposase gene abundance - varies with age, but not senescence, in a wild vertebrate
Published: 2024-11-14
Subjects: Bioinformatics, Ecology and Evolutionary Biology, Life Sciences, Microbiology, Ornithology
Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambigous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used seven years of longitudinal [...]
Evolutionarily Optimal Phage Life-History Traits
Published: 2024-11-09
Subjects: Ecology and Evolutionary Biology, Evolution, Life Sciences, Microbiology, Population Biology
Optimal phage life-history traits are computed from data on phenotypic tradeoffs presented in De Paepe and Tadei (2006). A parameter is introduced, l_e, that describes the loss of virions in the environment. Hygienic interventions increase l_e. The optimal burst size decreases with l_e and the optimal capsid thickness increases with l_e. The optimal viral fitness also decreases with l_e. An [...]
Coexistence theory for microbial ecology, and vice versa
Published: 2024-10-22
Subjects: Ecology and Evolutionary Biology, Microbiology
Classical models from theoretical ecology are seeing increasing uptake in microbial ecology, but there remains rich potential for closer cross-pollination. Here we explore opportunities for stronger integration of ecological theory into microbial research (and vice versa) through the lens of so-called "modern" coexistence theory. Coexistence theory encompasses a body of theory for disentangling [...]
Should I stay or should I go: Transmission trade-offs in mobile genetic elements
Published: 2024-10-17
Subjects: Biology, Ecology and Evolutionary Biology, Life Sciences, Microbiology
Mobile genetic elements (MGEs), including temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. To maximize reproductive fitness, MGEs have to optimize horizontal and vertical transmission. Yet, the cost of horizontal transmission (e.g. phage lysis) puts these transmission modes at odds. Using virulence-transmission [...]
Microbial functional diversity and redundancy: moving forward
Published: 2024-07-04
Subjects: Biodiversity, Ecology and Evolutionary Biology, Microbiology
Microbial functional ecology is expanding as we can now measure the traits of wild microbes that affect ecosystem functioning. Here, we review techniques and advances that could be the bedrock for a unified framework to study microbial functions. We then explore the technical, ecological, and evolutionary processes that could explain environmental patterns of microbial functional diversity and [...]
A minimum data standard for wildlife disease research and surveillance
Published: 2024-05-20
Subjects: Animal Diseases, Biodiversity, Bioinformatics, Diseases, Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Parasitic Diseases, Veterinary Infectious Diseases, Veterinary Medicine, Virology, Virus Diseases
Rapid and comprehensive data sharing is vital to the transparency and actionability of wildlife infectious disease research and surveillance. Unfortunately, most best practices for publicly sharing these data are focused on pathogen determination and genetic sequence data. Other facets of wildlife disease data – particularly negative results – are often withheld or, at best, summarized in a [...]
Revisiting Wolbachia detections: old and new issues in Aedes aegypti mosquitoes and other insects
Published: 2024-05-05
Subjects: Ecology and Evolutionary Biology, Entomology, Life Sciences, Microbiology
Wolbachia continue to be reported in species previously thought to lack them, particularly Aedes aegypti mosquitoes. The presence of Wolbachia in this arbovirus vector is considered important because releases of mosquitoes with transinfected Wolbachia are being used around the world to suppress pathogen transmission and these efforts depend on a lack of Wolbachia in natural populations of this [...]
Datathons: fostering equitability in data reuse in ecology
Published: 2024-04-04
Subjects: Biodiversity, Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Genetics, Genetics and Genomics, Genomics, Life Sciences, Microbiology
Approaches to rapidly collect global biodiversity data are increasingly important, but biodiversity blindspots persist. We organized a three-day Datathon event to improve the openness of local biodiversity data, and facilitate data reuse by local researchers. The first Datathon, organized among microbial ecologists in Uruguay and Argentina assembled the largest microbiome dataset in the region to [...]
Not All Mass Mortality Events are Equal
Published: 2024-03-14
Subjects: Ecology and Evolutionary Biology, Entomology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Population Biology
Mass Mortality Events (MMEs) are defined as novel events involving many individuals dying in a relatively short period of time. In recent years, there has been an increased interest in MMEs due to their perceived increase in frequency. Current definitions are subjective and categorize mortalities varying in magnitude and frequency together. Within this manuscript, Multiple Mortality Events is a [...]