The role of ecological theory in microbial ecology

Prosser, James I.; Bohannan, Brendan J. M.; Curtis, Tom; Ellis, Richard J.; Firestone, Mary K.; Freckleton, Robert P.; Green, Jessica L.; Green, Laura; Killham, Ken; Lennon, Jack J.; Osborn, A. Mark; Solan, Martin; Gast, Christopher J. van der; Young, J. Peter W.

doi:10.1038/nrmicro1643

Cited by 851 publications

(712 citation statements)

References 62 publications

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“…Microbial ecology has shown that many mechanisms controlling metazoans apply similarly to microorganisms [18]. This study contributes to this literature with an example of positive density dependence.…”

Section: Discussionmentioning

confidence: 70%

Experimental demonstration of an Allee effect in microbial populations

et al. 2016

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Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: ‘Everything is everywhere, but the environment selects’. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml −1 under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data.

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Section: Discussionmentioning

confidence: 70%

Experimental demonstration of an Allee effect in microbial populations

et al. 2016

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“…Positive species-energy relationships have been investigated at the field and lab scales (Srivastava and Lawton, 1998;Hurlbert, 2006). However, the species-energy theory has largely been examined from an macroecological framework and remains nascent within microbial ecology as a discipline; but see discussions by Prosser et al, 2007. An exception to this has been presented in a study focused on the energy-diversity relationships in arctic seafloor microbial ecosystems (Bienhold et al, 2012).…”

Section: Diversity-productivity Relationshipsmentioning

confidence: 99%

Trade-offs between microbiome diversity and productivity in a stratified microbial mat

et al. 2016

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Productivity is a major determinant of ecosystem diversity. Microbial ecosystems are the most diverse on the planet yet very few relationships between diversity and productivity have been reported as compared with macro-ecological studies. Here we evaluated the spatial relationships of productivity and microbiome diversity in a laboratory-cultivated photosynthetic mat. The goal was to determine how spatial diversification of microorganisms drives localized carbon and energy acquisition rates. We measured sub-millimeter depth profiles of net primary productivity and gross oxygenic photosynthesis in the context of the localized microenvironment and community structure, and observed negative correlations between species richness and productivity within the energyreplete, photic zone. Variations between localized community structures were associated with distinct taxa as well as environmental profiles describing a continuum of biological niches. Spatial regions in the photic zone corresponding to high primary productivity and photosynthesis rates had relatively low-species richness and high evenness. Hence, this system exhibited negative speciesproductivity and species-energy relationships. These negative relationships may be indicative of stratified, light-driven microbial ecosystems that are able to be the most productive with a relatively smaller, even distributions of species that specialize within photic zones.

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“…Notwithstanding the importance of soil microbial processes at all scales, the observations of these processes in their spatial context is hindered by soil opacity, the complex pore spaces, and variations in properties across scales from pores to aggregates, pedon, and field. Additionally, the lack of quantitative ecological models hinders effective application of experimental methods for systematic hypothesis testing, generalization, and organization of experimental information [Prosser et al, 2007;O'Donnell et al, 2007;Faust and Raes, 2012].…”

Section: Introductionmentioning

confidence: 99%

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

Ebrahimi

2014

Water Resources Research

110

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The dispersal rates of self-propelled microorganisms affect their spatial interactions and the ecological functioning of microbial communities. Microbial dispersal rates affect risk of contamination of water resources by soil-borne pathogens, the inoculation of plant roots, or the rates of spoilage of food products. In contrast with the wealth of information on microbial dispersal in water replete systems, very little is known about their dispersal rates in unsaturated porous media. The fragmented aqueous phase occupying complex soil pore spaces suppress motility and limits dispersal ranges in unsaturated soil. The primary objective of this study was to systematically evaluate key factors that shape microbial dispersal in model unsaturated porous media to quantify effects of saturation, pore space geometry, and chemotaxis on characteristics of principles that govern motile microbial dispersion in unsaturated soil. We constructed a novel 3-D angular pore network model (PNM) to mimic aqueous pathways in soil for different hydration conditions; within the PNM, we employed an individual-based model that considers physiological and biophysical properties of motile and chemotactic bacteria. The effects of hydration conditions on first passage times in different pore networks were studied showing that fragmentation of aquatic habitats under dry conditions sharply suppresses nutrient transport and microbial dispersal rates in good agreement with limited experimental data. Chemotactically biased mean travel speed of microbial cells across 9 mm saturated PNM was $3 mm/h decreasing exponentially to 0.45 mm/h for the PNM at matric potential of 215 kPa (for 235 kPa, dispersal practically ceases and the mean travel time to traverse the 9 mm PNM exceeds 1 year). Results indicate that chemotaxis enhances dispersal rates by orders of magnitude relative to random (diffusive) motions. Model predictions considering microbial cell sizes relative to available liquid pathways sizes were in good agreement with experimental results for unsaturated soils. The new modeling platform enables quantitative consideration of key biophysical factors (e.g., pore space heterogeneities and hydration conditions) governing microbial interactions in 3-D soil pore spaces.

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The role of ecological theory in microbial ecology

Cited by 851 publications

References 62 publications

Experimental demonstration of an Allee effect in microbial populations

Experimental demonstration of an Allee effect in microbial populations

Trade-offs between microbiome diversity and productivity in a stratified microbial mat

Microbial dispersal in unsaturated porous media: Characteristics of motile bacterial cell motions in unsaturated angular pore networks

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