Rapid niche shifts in bacteria following conditioning in novel soil environments

Abstract

1. 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).2. 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 divergent 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.3. 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. 4. 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.

Fertilisation of agricultural soils with municipal biosoilds: Part 2- Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application

“…Moreover, that the MBS-associated bacteria were not more successful in colonising the agricultural soils speaks to the resilience of the resident soil bacterial communities (Hong et al ., 2021; Yates et al ., 2022). The bacterial pathogens responsible for most food-borne illnesses, enterohemorrhagic Escherichia coli , Salmonella enterica and Listeria monocytogenes , all have large genomes, are metabolically diverse, and are well-adapted to grow and compete in soil environments (Brennan et al ., 2022).…”

“…However, given that the MBS-treated and non-treated agricultural soils remained indistinct, it is likely that these few potential bacterial pathogens belong to the extant soil reservoir of background, opportunistic pathogens that would be found in any soil (Brennan et al ., 2022; Banerjee & van der Heijden, 2023). This suggests that little of the MBS bacterial community was actually able to find an exploitable niche in the soil communities and establish resident populations (Yates et al ., 2022). Perhaps with long-term usage, the impact would accrue.…”

Defoliation enhances the positive effects of soil microbial diversity on plant productivity

“…The quantitative studies about the effect of soil microbial diversity on plant productivity as mentioned above were mainly in an undisturbed condition, whereas nature is a collection of multiple influencing factors (Chen et al, 2020; Wagg et al, 2014). Soil microorganisms occupy disparate ecological niches with contrasting life strategies, are very sensitive to the microenvironment in which they live and can respond quickly to environmental stress (Yates et al, 2022). The ‘Cry for help’ hypothesis demonstrates that plants can temporally (dynamically shape microbiota only under stresses) and spatially (coordinate above‐ground light stress and below‐ground microbiota changes) control microbiota composition in response to environmental perturbations (Wang & Song, 2022).…”

Temperature adaptation of soil bacterial communities across the Arctic

“…We found no correlation between the response to 10 °C warming of the ASVs and their predicted optimal growth temperature (Figure 4.7; Madin et al, 2020;Sato et al, 2020). In these databases the optimal growth temperatures of bacterial taxa were collected from isolates under lab conditions, which may differ from the in situ soil environment This could lead to a mismatch between the measured thermal niche of a bacteria taxa in the lab and the realized thermal niche under in situ soil conditions (Deines et al, 2020;Yates et al, 2022). Interestingly, there was a significant difference between the average responses of the ASVs that matched to different groups of temperature responders as defined in the dataset.…”