scholarly journals Species matter for predicting the functioning of evolving microbial communities

2019 ◽  
Author(s):  
Timothy Giles Barraclough
Keyword(s):  
Microbial Communities ◽  
Resource Use ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Ecological Interactions ◽  
Community Functioning ◽  
Trade Offs ◽  
As Species ◽  
Multiple Species ◽  
Digestive Health

ABSTRACTHumans depend on microbial communities for numerous ecosystem services such as global nutrient cycles, plant growth and their digestive health. Yet predicting dynamics and functioning of these complex systems is hard, making interventions to enhance functioning harder still. One simplifying approach is to assume that functioning can be predicted from the set of enzymes present in a community. Alternatively, ecological and evolutionary dynamics of species, which depend on how enzymes are packaged among species, might be vital for predicting community functioning. I investigate these alternatives by extending classical chemostat models of bacterial growth to multiple species that evolve in their use of chemical resources. Ecological interactions emerge from patterns of resource use, which change as species evolve in their allocation of metabolic enzymes. Measures of community functioning derive in turn from metabolite concentrations and bacterial density. Although the model shows considerable functional redundancy, species packaging does matter by introducing constraints on whether enzyme levels can reach optimum levels for the whole system. Evolution can either promote or reduce functioning compared to purely ecological models, depending on the shape of trade-offs in resource use. The model provides baseline theory for interpreting emerging data on evolution and functioning in real bacterial communities.

scholarly journals Eco-evolutionary feedbacks and the maintenance of metacommunity diversity in a changing environment

2020 ◽  
Author(s):  
Aidan P. Fielding ◽  
Jelena H. Pantel
Keyword(s):  
Environmental Change ◽  
Feedback Loop ◽  
Competitive Ability ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Landscape Scale ◽  
Phenotypic Evolution ◽  
Species Sorting ◽  
As Species ◽  
Multiple Species

AbstractThe presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored for single communities, its implications for eco-evolutionary dynamics at the metacommunity scale are unknown. We developed a simulation model for the evolution of a quantitative trait that influences both an organism’s carrying capacity and its intra- and interspecific competitive ability. In the model, multiple species inhabit a variable three-patch landscape, and we varied the connectivity level of the species among patches, the presence and pace of directional environmental change, and the strength of competition between the species. Our results reflect some patterns previously observed in evolving metacommunity models, such as species sorting and community monopolization. However species sorting was more likely to occur in evolving communities without dispersal, and monopolization was observed only when environmental change was very rapid. We also detected an eco-evolutionary feedback loop between local phenotypic evolution at one site and competition at another site, which maintains species diversity in some conditions. The existence of a feedback loop maintained by dispersal indicates that eco-evolutionary dynamics in communities operate at a landscape scale.

scholarly journals Evolutionary dynamics of microbial communities in bioelectrochemical systems

2019 ◽  
Author(s):  
Lukasz Szydlowski ◽  
Anatoly Sorokin ◽  
Olga Vasieva ◽  
Susan Boerner ◽  
Veyacheslav Fedorovich ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Evolutionary Dynamics ◽  
Nutrient Utilization ◽  
Microbial Consortia ◽  
Bioinformatics Pipeline ◽  
Initial Inoculum ◽  
Selective Enrichment ◽  
Custom Made ◽  
A Minor

SUMMARYBio-electrochemical systems can generate electricity by virtue of mature microbial consortia that gradually and spontaneously optimize performance. To evaluate selective enrichment of these electrogenic microbial communities, five, 3-electrode reactors were inoculated with microbes derived from rice wash wastewater and incubated under a range of applied potentials. Reactors were sampled over a 12-week period and DNA extracted from anodal, cathodal, and planktonic bacterial communities was interrogated using a custom-made bioinformatics pipeline that combined 16S and metagenomic samples to monitor temporal changes in community composition. Some genera that constituted a minor proportion of the initial inoculum dominated within weeks following inoculation and correlated with applied potential. For instance, the abundance of Geobacter increased from 423-fold to 766-fold between −350 mV and −50 mV, respectively. Full metagenomic profiles of bacterial communities were obtained from reactors operating for 12 weeks. Functional analyses of metagenomes revealed metabolic changes between different species of the dominant genus, Geobacter, suggesting that optimal nutrient utilization at the lowest electrode potential is achieved via genome rearrangements and a strong inter-strain selection, as well as adjustment of the characteristic syntrophic relationships. These results reveal a certain degree of metabolic plasticity of electrochemically active bacteria and their communities in adaptation to adverse anodic and cathodic environments.

scholarly journals Interactions between strains govern the eco-evolutionary dynamics of microbial communities

2021 ◽  
Author(s):  
Akshit Goyal ◽  
Leonora S. Bittleston ◽  
Gabriel E. Leventhal ◽  
Lu Lu ◽  
Otto X. Cordero
Keyword(s):  
Microbial Communities ◽  
Evolutionary Dynamics ◽  
Metagenomic Sequencing ◽  
Ecological Interactions ◽  
Base Pairs ◽  
Pitcher Plant ◽  
Naturally Occurring ◽  
Relevant Level ◽  
Over Time

AbstractGenomic data has revealed that genotypic variants of the same species, i.e., strains, coexist and are abundant in natural microbial communities. However, it is not clear if strains are ecologically equivalent, or if they exhibit distinct interactions and dynamics. Here, we address this problem by tracking 10 microbial communities from the pitcher plant Sarracenia purpurea in the laboratory for more than 300 generations. Using metagenomic sequencing, we reconstruct their dynamics over time and across scales, from distant phyla to closely related genotypes. We find that interactions between naturally occurring strains govern eco-evolutionary dynamics. Surprisingly, even fine-scale variants differing only by 100 base pairs can exhibit vastly different dynamics. We show that these differences may stem from ecological interactions in the communities, which are specific to strains, not species. Finally, by analyzing genomic differences between strains, we identify major functional hubs such as transporters, regulators, and carbohydrate-catabolizing enzymes, which might be the basis for strain-specific interactions. Our work shows that strains are the relevant level of diversity at which to study the long-term dynamics of microbiomes.

scholarly journals Eco-Evolutionary Feedbacks and the Maintenance of Metacommunity Diversity in a Changing Environment

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1433
Author(s):  
Aidan P. Fielding ◽  
Jelena H. Pantel
Keyword(s):  
Environmental Change ◽  
Feedback Loop ◽  
Competitive Ability ◽  
Evolutionary Dynamics ◽  
Resource Competition ◽  
Landscape Scale ◽  
Phenotypic Evolution ◽  
Species Sorting ◽  
As Species ◽  
Multiple Species

The presence and strength of resource competition can influence how organisms adaptively respond to environmental change. Selection may thus reflect a balance between two forces, adaptation to an environmental optimum and evolution to avoid strong competition. While this phenomenon has previously been explored in the context of single communities, its implications for eco-evolutionary dynamics at the metacommunity scale are largely unknown. We developed a simulation model for the evolution of a quantitative trait that influences both an organism’s carrying capacity and its intra- and interspecific competitive ability. In the model, multiple species inhabit a three-patch landscape, and we investigated the effect of varying the connectivity level among patches, the presence and pace of directional environmental change, and the strength of competition between the species. Our model produced some patterns previously observed in evolving metacommunity models, such as species sorting and community monopolization. However, we found that species sorting was diminished even at low rates of dispersal and was influenced by competition strength, and that monopolization was observed only when environmental change was very rapid. We also detected an eco-evolutionary feedback loop between local phenotypic evolution at one site and competition at another site, which maintains species diversity in some conditions. The existence of a feedback loop maintained by dispersal indicates that eco-evolutionary dynamics in communities operate at a landscape scale.

scholarly journals Steering ecological-evolutionary dynamics during artificial selection of microbial communities

2018 ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Communities ◽  
Artificial Selection ◽  
Evolutionary Dynamics ◽  
Ecological Interactions ◽  
Evolutionary Trajectory ◽  
Community Function ◽  
Selection Strategies ◽  
Effective Selection ◽  
Orthogonal Components ◽  
Selection Of

AbstractMicrobial communities often perform important functions that arise from interactions among member species. Community functions can be improved via artificial selection: Many communities are repeatedly grown, mutations arise, and communities with the highest desired function are chosen to reproduce where each is partitioned into multiple offspring communities for the next cycle. Since selection efficacy is often unimpressive in published experiments and since multiple experimental parameters need to be tuned, we sought to use computer simulations to learn how to design effective selection strategies. We simulated community selection to improve a community function that requires two species and imposes a fitness cost on one of the species. This simplified case allowed us to distill community function down to two fundamental and orthogonal components: a heritable determinant and a nonheritable determinant. We then visualize a “community function landscape” relating community function to these two determinants, and demonstrate that the evolutionary trajectory on the landscape is restricted along a path designated by ecological interactions. This path can prevent the attainment of maximal community function, and trap communities in landscape locations where community function has low heritability. Exploiting these observations, we devise a species spiking approach to shift the path to improve community function heritability and consequently selection efficacy. We show that our approach is applicable to communities with complex and unknown function landscapes.

Growth–defense trade-offs shape population genetic composition in an iconic forest tree species

2021 ◽  
Vol 118 (37) ◽  
pp. e2103162118 ◽  
Author(s):  
Olivia L. Cope ◽  
Ken Keefover-Ring ◽  
Eric L. Kruger ◽  
Richard L. Lindroth
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Functional Trait ◽  
Forest Tree ◽  
Ecological Interactions ◽  
Trait Variation ◽  
Trade Offs ◽  
Spatiotemporal Scales ◽  
Evolutionary Consequences ◽  
Selection Of

All organisms experience fundamental conflicts between divergent metabolic processes. In plants, a pivotal conflict occurs between allocation to growth, which accelerates resource acquisition, and to defense, which protects existing tissue against herbivory. Trade-offs between growth and defense traits are not universally observed, and a central prediction of plant evolutionary ecology is that context-dependence of these trade-offs contributes to the maintenance of intraspecific variation in defense [Züst and Agrawal, Annu. Rev. Plant Biol., 68, 513–534 (2017)]. This prediction has rarely been tested, however, and the evolutionary consequences of growth–defense trade-offs in different environments are poorly understood, especially in long-lived species [Cipollini et al., Annual Plant Reviews (Wiley, 2014), pp. 263–307]. Here we show that intraspecific trait trade-offs, even when fixed across divergent environments, interact with competition to drive natural selection of tree genotypes corresponding to their growth–defense phenotypes. Our results show that a functional trait trade-off, when coupled with environmental variation, causes real-time divergence in the genetic architecture of tree populations in an experimental setting. Specifically, competitive selection for faster growth resulted in dominance by fast-growing tree genotypes that were poorly defended against natural enemies. This outcome is a signature example of eco-evolutionary dynamics: Competitive interactions affected microevolutionary trajectories on a timescale relevant to subsequent ecological interactions [Brunner et al., Funct. Ecol. 33, 7–12 (2019)]. Eco-evolutionary drivers of tree growth and defense are thus critical to stand-level trait variation, which structures communities and ecosystems over expansive spatiotemporal scales.

scholarly journals Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

2021 ◽  
Vol 97 (3) ◽  
Author(s):  
Constantinos Xenophontos ◽  
Martin Taubert ◽  
W Stanley Harpole ◽  
Kirsten Küsel
Keyword(s):  
Bacterial Communities ◽  
Species Interactions ◽  
Phylogenetic Diversity ◽  
Molecular Mechanisms ◽  
Linear Models ◽  
Theory Development ◽  
Metabolic Diversity ◽  
Community Functioning ◽  
Metabolic Functions ◽  
Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Yield, resource use efficiency or flavour: Trade-offs of varying blue-to-red lighting ratio in urban plant factories

2022 ◽  
Vol 295 ◽  
pp. 110802
Author(s):  
Hao Zhou ◽  
Rhydian Beynon-Davies ◽  
Nicola Carslaw ◽  
Ian C. Dodd ◽  
Kirsti Ashworth
Keyword(s):  
Resource Use ◽  
Resource Use Efficiency ◽  
Trade Offs ◽  
Use Efficiency

scholarly journals Do soil bacterial communities respond differently to abrupt or gradual additions of copper?

2018 ◽  
Vol 95 (1) ◽  
Author(s):  
Michael McTee ◽  
Lorinda Bullington ◽  
Matthias C Rillig ◽  
Philip W Ramsey
Keyword(s):  
Heavy Metals ◽  
Soil Respiration ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Diversity Indices ◽  
Microbial Populations ◽  
Metal Concentrations ◽  
Soil Bacterial Communities ◽  
Bacterial Richness

ABSTRACTMany experiments that measure the response of microbial communities to heavy metals increase metal concentrations abruptly in the soil. However, it is unclear whether abrupt additions mimic the gradual and often long-term accumulation of these metals in the environment where microbial populations may adapt. In a greenhouse experiment that lasted 26 months, we tested whether bacterial communities and soil respiration differed between soils that received an abrupt or a gradual addition of copper or no copper at all. Bacterial richness and other diversity indices were consistently lower in the abrupt treatment compared to the ambient treatment that received no copper. The abrupt addition of copper yielded different initial bacterial communities than the gradual addition; however, these communities appeared to converge once copper concentrations were approximately equal. Soil respiration in the abrupt treatment was initially suppressed but recovered after four months. Afterwards, respiration in both the gradual and abrupt treatments wavered between being below or equal to the ambient treatment. Overall, our study indicates that gradual and abrupt additions of copper can yield similar bacterial communities and respiration, but these responses may drastically vary until copper concentrations are equal.

Sign in / Sign up

Export Citation Format

Share Document