scholarly journals Nutrient levels and trade-offs control diversity in a serial dilution ecosystem

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Amir Erez ◽  
Jaime G Lopez ◽  
Benjamin G Weiner ◽  
Yigal Meir ◽  
Ned S Wingreen
Keyword(s):  
Resource Competition ◽  
Nutrient Supply ◽  
Serial Dilution ◽  
Community Diversity ◽  
Ecosystem Stability ◽  
Early Bird ◽  
Trade Offs ◽  
Dilution Culture ◽  
Serial Dilution Culture ◽  
High Diversity

Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.

scholarly journals Inter-laboratory validation of the serial dilution culture—most probable number method for enumerating viable phytoplankton

2018 ◽  
Vol 31 (1) ◽  
pp. 491-503
Author(s):  
Hugh L. MacIntyre ◽  
John J. Cullen ◽  
Shannah Rastin ◽  
Magdalena Waclawik ◽  
Kimberly J. Franklin ◽  
...  
Keyword(s):  
Serial Dilution ◽  
Most Probable Number ◽  
Probable Number ◽  
Dilution Culture ◽  
Serial Dilution Culture

scholarly journals Liquid Serial Dilution Is Inferior to Solid Media for Isolation of Cultures Representative of the Phylum-Level Diversity of Soil Bacteria

2004 ◽  
Vol 70 (7) ◽  
pp. 4363-4366 ◽  
Author(s):  
Liesbeth Schoenborn ◽  
Penelope S. Yates ◽  
Bronwyn E. Grinton ◽  
Philip Hugenholtz ◽  
Peter H. Janssen
Keyword(s):  
Soil Bacteria ◽  
Serial Dilution ◽  
Bacterial Phyla ◽  
Pasture Soil ◽  
Solid Media ◽  
Dilution Culture ◽  
Serial Dilution Culture ◽  
Bacterial Lineages

ABSTRACT Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria, Verrucomicrobia, and Gemmatimonadetes and of other poorly represented bacterial lineages were isolated in earlier experiments with solidified versions of the same media. We conclude that, contrary to expectation, liquid serial dilution culture is inferior to culturing on solid media for isolating representatives of many bacterial phyla from soil.

Molecular and structural antioxidant defenses against oxidative stress in animals

2011 ◽  
Vol 301 (4) ◽  
pp. R843-R863 ◽  
Author(s):  
Reinald Pamplona ◽  
David Costantini
Keyword(s):  
Oxidative Stress ◽  
Life History ◽  
Antioxidant Properties ◽  
Epigenetic Inheritance ◽  
Antioxidant Defenses ◽  
Redox Systems ◽  
Traditional Concept ◽  
Trade Offs ◽  
Antioxidant Mechanisms ◽  
High Diversity

In this review, it is our aim 1) to describe the high diversity in molecular and structural antioxidant defenses against oxidative stress in animals, 2) to extend the traditional concept of antioxidant to other structural and functional factors affecting the “whole” organism, 3) to incorporate, when supportable by evidence, mechanisms into models of life-history trade-offs and maternal/epigenetic inheritance, 4) to highlight the importance of studying the biochemical integration of redox systems, and 5) to discuss the link between maximum life span and antioxidant defenses. The traditional concept of antioxidant defenses emphasizes the importance of the chemical nature of molecules with antioxidant properties. Research in the past 20 years shows that animals have also evolved a high diversity in structural defenses that should be incorporated in research on antioxidant responses to reactive species. Although there is a high diversity in antioxidant defenses, many of them are evolutionary conserved across animal taxa. In particular, enzymatic defenses and heat shock response mediated by proteins show a low degree of variation. Importantly, activation of an antioxidant response may be also energetically and nutrient demanding. So knowledge of antioxidant mechanisms could allow us to identify and to quantify any underlying costs, which can help explain life-history trade-offs. Moreover, the study of inheritance mechanisms of antioxidant mechanisms has clear potential to evaluate the contribution of epigenetic mechanisms to stress response phenotype variation.

scholarly journals Biogeochemical versus ecological consequences of modeled ocean physics

2017 ◽  
Vol 14 (11) ◽  
pp. 2877-2889 ◽  
Author(s):  
Sophie Clayton ◽  
Stephanie Dutkiewicz ◽  
Oliver Jahn ◽  
Christopher Hill ◽  
Patrick Heimbach ◽  
...  
Keyword(s):  
Primary Production ◽  
Ocean Circulation ◽  
Mixed Layer ◽  
Phytoplankton Biomass ◽  
Phytoplankton Community ◽  
Resource Competition ◽  
Nutrient Supply ◽  
Zooplankton Biomass ◽  
Global Ocean ◽  
Competition Theory

Abstract. We present a systematic study of the differences generated by coupling the same ecological–biogeochemical model to a 1°, coarse-resolution, and 1∕6°, eddy-permitting, global ocean circulation model to (a) biogeochemistry (e.g., primary production) and (b) phytoplankton community structure. Surprisingly, we find that the modeled phytoplankton community is largely unchanged, with the same phenotypes dominating in both cases. Conversely, there are large regional and seasonal variations in primary production, phytoplankton and zooplankton biomass. In the subtropics, mixed layer depths (MLDs) are, on average, deeper in the eddy-permitting model, resulting in higher nutrient supply driving increases in primary production and phytoplankton biomass. In the higher latitudes, differences in winter mixed layer depths, the timing of the onset of the spring bloom and vertical nutrient supply result in lower primary production in the eddy-permitting model. Counterintuitively, this does not drive a decrease in phytoplankton biomass but results in lower zooplankton biomass. We explain these similarities and differences in the model using the framework of resource competition theory, and find that they are the consequence of changes in the regional and seasonal nutrient supply and light environment, mediated by differences in the modeled mixed layer depths. Although previous work has suggested that complex models may respond chaotically and unpredictably to changes in forcing, we find that our model responds in a predictable way to different ocean circulation forcing, despite its complexity. The use of frameworks, such as resource competition theory, provides a tractable way to explore the differences and similarities that occur. As this model has many similarities to other widely used biogeochemical models that also resolve multiple phytoplankton phenotypes, this study provides important insights into how the results of running these models under different physical conditions might be more easily understood.

scholarly journals High functional diversity stimulates diversification in experimental microbial communities

2016 ◽  
Vol 2 (6) ◽  
pp. e1600124 ◽  
Author(s):  
Alexandre Jousset ◽  
Nico Eisenhauer ◽  
Monika Merker ◽  
Nicolas Mouquet ◽  
Stefan Scheu
Keyword(s):  
Ecosystem Services ◽  
Functional Diversity ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Bacterial Species ◽  
Focal Species ◽  
Evolutionary Diversification ◽  
The Impact ◽  
High Diversity

There is a growing awareness that biodiversity not only drives ecosystem services but also affects evolutionary dynamics. However, different theories predict contrasting outcomes on when do evolutionary processes occur within a context of competition. We tested whether functional diversity can explain diversification patterns. We tracked the survival and diversification of a focal bacterial species (Pseudomonas fluorescens) growing in bacterial communities of variable diversity and composition. We found that high functional diversity reduced the fitness of the focal species and, at the same time, fostered its diversification. This pattern was linked to resource competition: High diversity increased competition on a portion of the resources while leaving most underexploited. The evolved phenotypes of the focal species showed a better use of underexploited resources, albeit at a cost of lower overall growth rates. As a result, diversification alleviated the impact of competition on the fitness of the focal species. We conclude that biodiversity can stimulate evolutionary diversification, provided that sufficient alternative niches are available.

scholarly journals The evolution of competitive ability for essential resources

2019 ◽  
Author(s):  
Joey R. Bernhardt ◽  
Pavel Kratina ◽  
Aaron Pereira ◽  
Manu Tamminen ◽  
Mridul K. Thomas ◽  
...  
Keyword(s):  
Competitive Ability ◽  
Community Dynamics ◽  
Species Coexistence ◽  
Resource Competition ◽  
Environmental Gradients ◽  
Light Limitation ◽  
Major Question ◽  
Trade Offs ◽  
Resource Requirements ◽  
Competitive Abilities

AbstractCompetition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species’ minimum resource requirements, their R*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered - to what extent are species’ competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposed Chlamydomonas reinhardtii for approximately 285 generations to seven environments in chemostats which differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.

scholarly journals Dynamical persistence in resource-consumer models

2020 ◽  
Author(s):  
Itay Dalmedigos ◽  
Guy Bunin
Keyword(s):  
Fixed Points ◽  
Competitive Exclusion ◽  
Resource Competition ◽  
Exclusion Principle ◽  
Ecological Communities ◽  
Competitive Exclusion Principle ◽  
Stable Equilibria ◽  
Species Being ◽  
Abundance Fluctuations ◽  
High Diversity

We show how highly-diverse ecological communities may display persistent abundance fluctuations, when interacting through resource competition and subjected to migration from a species pool. This turns out to be closely related to the ratio of realized species diversity to the number of resources. This ratio is set by competition, through the balance between species being pushed out and invading. When this ratio is smaller than one, dynamics will reach stable equilibria. When this ratio is larger than one, fixed-points are either unstable or marginally stable, as expected by the competitive exclusion principle. If they are unstable, the system is repelled from fixed points, and abundances forever fluctuate. While marginally-stable fixed points are in principle allowed and predicted by some models, they become structurally unstable at high diversity. This means that even small changes to the model, such as non-linearities in how resources combine to generate species’ growth, will result in persistent abundance fluctuations.

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