Preprints
Filtering by Subject: Environmental Microbiology and Microbial Ecology Life Sciences
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 [...]
Social interactions shape anaerobic, but not aerotolerant, gut microbiome composition in a cooperative breeding species
Published: 2025-06-20
Subjects: Environmental Microbiology and Microbial Ecology Life Sciences, Ornithology
Background Social transmission of microbes has profound impacts on disease epidemiology and host health. However, how social factors influence gut microbiome (GM) transmission in wild populations is not well understood. Here, we use a wild population of the Seychelles warbler, a facultative cooperatively breeding passerine, to determine whether cooperative breeding behaviour influences the GM. [...]
Ground-nesting ants as architects of microbial landscapes
Published: 2025-06-20
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences
As soil ecosystem engineers, ground-nesting ants alter various physicochemical properties of soils globally. However, less is known about how ant behaviors including bioturbation and hygiene affect microbial communities, such as by altering habitat complexity, resource availability, and competitive dynamics. Interactions such as this are increasingly recognized as important components in shaping [...]
Spatial and environmental influences on the assembly of silk microbiomes in a social spider
Published: 2025-06-03
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences
In nesting animals, the built environment can play an important role in host-associated microbiome assembly. However, the sources and processes structuring the resulting microbiome remain underexplored. In the social spider Stegodyphus dumicola, philopatric sisters collectively build and maintain a silken nest, capture prey, and exhibit alloparental care. We used S. dumicola as a test system to [...]
Grazer-induced bioluminescence and toxicity in marine dinoflagellates
Published: 2025-03-10
Subjects: Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Marine Biology, Plant Biology
Marine copepods are the most abundant type of multicellular zooplankton in the global oceans. They imprint their surrounding waters with a unique bouquet of polar lipids; copepodamides. Copepodamides are recognized by prey organisms, who respond by inducing defensive traits including bioluminescence, toxin production, colony size plasticity and structural modifications. Copepodamides are [...]
The BeeBiome Data Portal provides easy access to bee microbiome information
Published: 2025-01-20
Subjects: Apiculture, Bioinformatics, Environmental Microbiology and Microbial Ecology Life Sciences
Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets [...]
Spatial microbial flows: hidden fluxes of detritus, diversity, and function in meta-ecosystems
Published: 2024-09-30
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences
Ecosystems are linked by spatial flows of energy, nutrients, and organisms across ecosystem boundaries, forming a meta-ecosystem. The study of spatial flows has typically focused on fluxes of materials (e.g., nutrients or organic matter) and conspicuous organisms (e.g., fish or insects). However, recent evidence from field studies has suggested that numerically significant spatial flows of [...]
PPSDB : A Linked Open Data knowledge base for protist-prokaryote symbiotic interactions
Published: 2024-08-26
Subjects: Biodiversity, Environmental Microbiology and Microbial Ecology Life Sciences
As the ecological and evolutionary importance of symbiotic interactions between protists (microbial eukaryotes) and prokaryotes (bacteria and archaea) is better appreciated, keeping an overview of their diversity and the literature becomes a growing and ongoing challenge. Here we present the Protist-Prokaryote Symbiosis Database (PPSDB), comprising 789 manually curated interaction statements [...]
Microbial growth in soil
Published: 2024-06-20
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences
The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their growth rate. At the population level, per capita growth rate is a sensitive metric of [...]
A minimum data standard for wildlife disease research and surveillance
Published: 2024-05-19
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 [...]
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: 2024-03-13
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 [...]
Are microbes colimited by multiple resources?
Published: 2024-03-02
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Microbiology, Systems Biology
Resource colimitation --- the dependence of growth on multiple resources simultaneously --- has become an important topic in microbiology due both to the development of systems approaches to cell physiology and ecology, and to the relevance of colimitation to environmental science, biotechnology, and human health. Empirical tests of colimitation in microbes suggest that it may be common in [...]
Divergent responses between lineages of arbuscular mycorrhizal fungi to soil phosphorus and nitrogen availability
Published: 2023-12-12
Subjects: Ecology and Evolutionary Biology, Environmental Microbiology and Microbial Ecology Life Sciences, Life Sciences, Soil Science
Arbuscular mycorrhizal (AM) associations are multifunctional. Two important functions they perform are facilitating nutrient uptake in host plants and protecting plants from biotic stress, among other functions. AM fungal taxa vary in how capably they perform these functions and can also respond differently to environmental selection. Therefore, there is a need to better understand how particular [...]
Elevated CO2 enhances decomposition and modifies litter-associated fungal assemblages in a natural Eucalyptus woodland
Published: 2023-12-12
Subjects: Environmental Microbiology and Microbial Ecology Life Sciences, Terrestrial and Aquatic Ecology
Litter decomposition is a key process governing carbon and nutrient cycles in forest ecosystems that is expected to be impacted by increasing atmospheric carbon dioxide (CO2) concentrations. We conducted two complementary field studies to assess the effects of elevated CO2 on Eucalyptus tereticornis litter decomposition processes. First, we used bags of two different mesh sizes to assess the [...]