ORCID Profile
0000-0003-3603-7270
Current Organisation
University of Toronto Scarborough
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Publisher: Wiley
Date: 07-09-2023
DOI: 10.1111/PCE.14705
Publisher: Springer Science and Business Media LLC
Date: 20-04-2022
DOI: 10.1038/S43705-022-00120-9
Abstract: Microbial movement is important for replenishing lost soil microbial bio ersity and driving plant root colonization, particularly in managed agricultural soils, where microbial ersity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS licon sequencing. Location had a greater impact on fungal colonizers ( R 2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more ( R 2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil ( R 2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.
Publisher: Scientific Societies
Date: 2022
DOI: 10.1094/PBIOMES-06-21-0039-R
Abstract: Bitter rot is a disease of apple caused by fungi in the genus Colletotrichum. Management begins with removal of infected twigs and fruit from tree canopies to reduce overwintering inoculum. Infected apple fruit are usually tossed to the orchard floor, which is generally managed as herbicide-treated weed-free tree rows, separated by grass drive rows. We monitored decay rates and succession of fungi of apple fruit with bitter rot in tree canopies, and on the soil surface in tree rows, grass drive rows, and nearby erse plant communities. We hypothesized that decay would occur most rapidly within erse plant communities, which would provide a more erse array of potential fungal decomposers. Apple fruit in tree canopies became dry and mummified and had more Colletotrichum gene marker copies the following growing season than did fruit on the soil surface. Of the soil-surface s les, those in grass drive rows and erse plant communities had higher moisture, faster decay rates, and sharper decreases in Colletotrichum gene marker copies than apple fruit in tree rows. Fungal composition across all decaying apple fruit was dominated by yeasts, with higher genus-level richness, ersity, and evenness in fruit from tree canopies than those on the soil surface. In soil-surface apple fruit, we observed clear successional waves of Pichia, Kregervanrija, and [Candida] yeasts, with similar but distinctly erging fungal composition. Our results show that orchard floor management can influence fungal succession in apple fruit with bitter rot but suggests that bitter rot management should primarily focus on removing infected apple fruit from tree canopies.
Publisher: Elsevier BV
Date: 2022
DOI: 10.1016/J.TIBTECH.2021.04.008
Abstract: Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.
Publisher: Springer Science and Business Media LLC
Date: 19-04-2021
DOI: 10.1038/S42003-021-01988-4
Abstract: Fine roots vary dramatically in their functions, which range from resource absorption to within-plant resource transport. These differences should alter resource availability to root-associated microorganisms, yet most root microbiome studies involve fine root homogenization. We hypothesized that microbial filtering would be greatest in the most distal roots. To test this, we s led roots of six temperate tree species from a 23-year-old common garden planting, separating by branching order. Rhizoplane bacterial composition was characterized with 16S rRNA gene sequencing, while bacterial abundance was determined on a subset of trees through flow cytometry. Root order strongly impacted composition across tree species, with absorptive lower order roots exerting the greatest selective pressure. Microbial carrying capacity was higher in absorptive roots in two of three tested tree species. This study indicates lower order roots as the main point of microbial interaction with fine roots, suggesting that root homogenization could mask microbial recruitment signatures.
Publisher: Wiley
Date: 20-10-2023
DOI: 10.1002/JEZ.2665
Abstract: The gut microbiome can influence host fitness and, consequently, the ecology and evolution of natural populations. Microbiome composition can be driven by environmental exposure but also by the host's genetic background and phenotype. To contrast environmental and genetic effects on the microbiome we leverage preserved specimens of eastern fence lizards from allopatric lineages east and west of the Mississippi River but reared in standardized conditions. Bacterial composition was indistinguishable between lineages but responded significantly to host age—a proxy for environmental exposure. This was accompanied by a continuous decrease in bacterial ersity in both lineages, partially driven by decreasing evenness seen only in western lizards. These findings indicate that longer exposure to a homogeneous habitat may have a depreciating effect on microbiome ersity in eastern fence lizards, a response shared by both lineages. We highlight the importance of such effects when extrapolating patterns from laboratory experiments to the natural world.
Publisher: Wiley
Date: 21-09-2022
Abstract: Realized niche breadth is generally expected to be smaller than fundamental niche breadth. For soil microorganisms, this is due in part to competition from co‐occurring microbes, so removing competitors should allow for expanded use of resource and habitats (i.e. ecological release). We hypothesized that conditioning bacterial isolates to biotically cleared soils would allow for niche breadth expansion relative to ancestral bacteria, and that this niche expansion would be driven by habitat‐dependent niche shifts between derived populations. We grew two taxonomically ergent bacteria for 3 months in four biotically cleared soils and a biotically cleared ‘home’ soil. We then assessed changes in the niche breadth and fitness (i.e. growth respiration carbon resource use) of conditioned bacteria. Post‐conditioning, Pseudomonas populations showed the potential for increased growth rate in‐culture and in‐soil when conditioned to soils, and constrained resource use relative to the ancestral population, while Paenibacillus showed minimal changes in soil habitat breadth, but expanded resource use in conditioned populations. When introduced into complex novel environments containing reduced biotic pressure, soil bacteria can undergo rapid niche shifts, but this response varies across taxa and habitats. This suggests that species identity and habitat should interact to shape near‐term niche shifts when microbes establish in new soil environments. Read the free Plain Language Summary for this article on the Journal blog.
Publisher: Wiley
Date: 26-10-2022
DOI: 10.1111/NPH.17774
Abstract: Climate change‐related soil salinization increases plant stress and decreases productivity. Soil microorganisms are thought to reduce salt stress through multiple mechanisms, so erse assemblages could improve plant growth under such conditions. Previous studies have shown that microbiome selection can promote desired plant phenotypes, but with high variability. We hypothesized that microbiome selection would be more consistent in saline soils by increasing potential benefits to the plants. In both salt‐amended and untreated soils, we transferred forward Brassica rapa root microbiomes (from high‐biomass or randomly selected pots) across six planting generations while assessing bacterial (16S rRNA) and fungal (ITS) composition in detail. Uniquely, we included an add‐back control (re‐adding initial frozen soil microbiome) as a within‐generation reference for microbiome and plant phenotype selection. We observed inconsistent effects of microbiome selection on plant biomass across generations, but microbial composition consistently erged from the add‐back control. Although salt amendment strongly impacted microbial composition, it did not increase the predictability of microbiome effects on plant phenotype, but it did increase the rate at which microbiome selection plateaued. These data highlight a disconnect in the trajectories of microbiomes and plant phenotypes during microbiome selection, emphasizing the role of standard controls to explain microbiome selection outcomes.
Location: United States of America
No related grants have been discovered for Terrence Bell.