Biology subjects

Edwards, J. A.

Publications and source records attributed to Edwards, J. A..

5 recordsLinked to original sources

bioRxiv2026

The hidden multiverse of ecological roles in Fungi

Ecological roles are treated as discrete, bounded units of biological organization, even as evidence shows that many taxa are versatile, performing more than one of them. Each record of versatility represents a boundary crossing, yet current categorical paradigms prevent this cumulative evidence from reshaping the roles themselves. We solve this by introducing the ecological multiverse, a self-correcting framework that turns boundary crossings into a network of role connectivity. Applied to Fungi, the multiverse recasts the major form of plant pathogenicity from an isolated disease role into a central hub linking much of fungal functional space, especially benign plant symbioses and decomposition. By exposing this topology, the multiverse transforms categorical views of ecological function into a dynamic map, revealing pathways of role change as organisms and knowledge evolve.

ecology↗

bioRxiv2025

Breeding of microbiomes conferring salt tolerance to plants

Microbiome breeding by host-mediated selection is a technique to artificially select for microbiomes conferring benefits to plants. Here, we describe leaf ionomics, microbial community composition, and network analyses of a microbiome-breeding experiment to generate microbiomes conferring salt tolerance to Brachypodium distachyon, a model for cereal crops. Plants receiving microbiomes selected to confer tolerance to either sodium- or aluminium-stress produced 69-198% higher total seed weight than plants receiving control microbiomes. Sodium-selected microbiomes reduced leaf-sodium concentration by 50%, whereas aluminium-selected microbiomes had no effect on leaf-tissue nutrient concentration, suggesting different mechanisms underlying microbiome-mediated salt tolerance. By testing these selected microbiomes in a cross-fostering experiment, we show that artificially-selected microbiomes attain (a) ecological robustness contributing to transplantability (inheritance) of microbiome-encoded effects between plants; and (b) network features identifying key bacteria promoting stress tolerance. Combined, these findings elucidate critical mechanisms underlying host-mediated selection as a tool to breed beneficial microbiomes in an agricultural context.

evolutionary biology↗

bioRxiv2024

Glyphosate Effects on Growth and Biofilm Formation in Bee Gut Symbionts and Diverse Associated Bacteria

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and to withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate proliferation within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore the independent gut colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can independently colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure has varying effects on bacterial growth and biofilm formation. These findings imply specific impacts of environmental stressors on microbial biofilms with both ecological and host health-related implications. Importance Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms. We then examine the impact of glyphosate, a widely used herbicide that disrupts the bee microbiota, on their growth and biofilm formation. Our findings demonstrate diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

microbiology↗

bioRxiv2022

Patterns and determinants of the global herbivorous mycobiome

In spite of their indispensable role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. To examine global patterns and determinants of AGF diversity, we generated and analyzed an amplicon dataset from 661 fecal samples from 34 animal species, 9 families, and 6 continents. We identified 56 novel genera, greatly expanding AGF diversity beyond current estimates. Both stochastic (homogenizing dispersal and drift) and deterministic (homogenizing selection) processes played an integral role in shaping AGF communities, with a higher level of stochasticity observed in foregut fermenters. Community structure analysis revealed a distinct pattern of phylosymbiosis, where host-associated (animal species, family, and gut type), rather than ecological (domestication status and biogeography) factors predominantly shaped the community. Hindgut fermenters exhibited stronger and more specific fungal-host associations, compared to broader mostly non-host specific associations in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicated that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya), while those with preferences for foregut hosts evolved more recently (22-32 Mya). This pattern is in agreement with the sole dependence of herbivores on hindgut fermentation past the Cretaceous-Paleogene (K-Pg) extinction event through the Paleocene and Eocene, and the later rapid evolution of animals employing foregut fermentation strategy during the early Miocene. Only a few AGF genera deviated from this pattern of co-evolutionary phylosymbiosis, by exhibiting preferences suggestive of post-evolutionary environmental filtering. Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

microbiology↗

bioRxiv2019

fastq-pair: efficient synchronization of paired-end fastq files

Paired end DNA sequencing provides additional information about the sequence data that is used in sequence assembly, mapping, and other downstream bioinformatics analysis. Paired end reads are usually provided as two fastq-format files, with each file representing one end of the read. Many commonly used downstream tools require that the sequence reads appear in each file in the same order, and reads that do not have a pair in the corresponding file are placed in a separate file of singletons. Although most sequencing instruments capable of generating paired end reads produce files where each read has a corresponding mate, many downstream bioinformatics manipulations break the one-to-one correspondence between reads, and paired-end sequence files loose synchronicity, and contain either unordered sequences or sequences in one or other file without a mate. Trivial solutions to this problem require reading one or both of the DNA sequence files into memory but quickly become limited by computational resources for moderate to large sized sequence files that are common nowadays. Here, we introduce a fast and memory efficient solution, written in C for portability, that synchronizes paired-end fastq files for subsequent analysis and places unmatched reads into singleton files. Fastq-pair is freely available from https://github.com/linsalrob/fastq-pair and is released under the MIT license.

bioinformatics↗