scholarly journals The effect of dilution on eco‐evolutionary dynamics of experimental microbial communities

2021 ◽  
Author(s):  
Thomas Scheuerl ◽  
Veijo Kaitala
Keyword(s):  
Microbial Communities ◽  
Evolutionary Dynamics

scholarly journals Comprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Chaofang Zhong ◽  
Maozhen Han ◽  
Pengshuo Yang ◽  
Chaoyun Chen ◽  
Hui Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microbial Communities ◽  
Virulence Factors ◽  
Evolutionary Dynamics ◽  
Content Type ◽  
Pan Genome ◽  
Gastrointestinal Pathogen ◽  
High Level ◽  
Core Genes ◽  
Isolated Species

ABSTRACT The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging. Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections. IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.

scholarly journals Rampant prophage movement among transient competitors drives rapid adaptation during infection

2021 ◽  
Author(s):  
Christopher W. Marshall ◽  
Erin S. Gloag ◽  
Christina Lim ◽  
Daniel J. Wozniak ◽  
Vaughn S. Cooper
Keyword(s):  
Microbial Communities ◽  
Chronic Infection ◽  
Evolutionary Dynamics ◽  
Functional Genes ◽  
Rapid Adaptation ◽  
Chronic Infections ◽  
Global Regulators ◽  
New Genes ◽  
Biofilm Production ◽  
Genes Encoding

AbstractInteractions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes. However, integrated prophages can also insert into functional genes and impart a fitness benefit by disrupting their expression, a process called active lysogeny. Here, we show that active lysogeny can fuel rapid, parallel adaptations in establishing a chronic infection. These recombination events repeatedly disrupted genes encoding global regulators, leading to increased cyclic-di-GMP levels and elevated biofilm production. The implications of prophage-mediated adaptation are broad, as even transient members of microbial communities can alter the course of evolution and generate persistent phenotypes associated with poor clinical outcomes.One Sentence SummaryBacteriophage act as genetic regulators that are key to establishing chronic infections and are rapidly shared among co-infecting strains.

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

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Li Xie ◽  
Wenying Shou
Keyword(s):  
Microbial Communities ◽  
Artificial Selection ◽  
Species Interactions ◽  
Evolutionary Dynamics ◽  
Species Coexistence ◽  
Evolutionary Trajectory ◽  
Community Function ◽  
Link Type ◽  
Selection Strategies ◽  
Effective Selection

AbstractMicrobial communities often perform important functions that depend on inter-species interactions. To improve community function via artificial selection, one can repeatedly grow many communities to allow mutations to arise, and “reproduce” the highest-functioning communities by partitioning each into multiple offspring communities for the next cycle. Since improvement is often unimpressive in experiments, we study how to design effective selection strategies in silico. Specifically, we simulate community selection to improve a function that requires two species. With a “community function landscape”, we visualize how community function depends on species and genotype compositions. Due to ecological interactions that promote species coexistence, the evolutionary trajectory of communities is restricted to a path on the landscape. This restriction can generate counter-intuitive evolutionary dynamics, prevent the attainment of maximal function, and importantly, hinder selection by trapping communities in locations of low community function heritability. We devise experimentally-implementable manipulations to shift the path to higher heritability, which speeds up community function improvement even when landscapes are high dimensional or unknown. Video walkthroughs: https://go.nature.com/3GWwS6j; https://online.kitp.ucsb.edu/online/ecoevo21/shou2/.

scholarly journals Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

2021 ◽  
Author(s):  
Vincent Somerville ◽  
Hélène Berthoud ◽  
Remo S. Schmidt ◽  
Hans-Peter Bachmann ◽  
Yi Hélène Meng ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Negative Impact ◽  
Bacterial Species ◽  
Starter Culture ◽  
Streptococcus Thermophilus ◽  
Starter Cultures ◽  
Lactobacillus Delbrueckii ◽  
Shotgun Metagenomics

AbstractUndefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.

scholarly journals The effect of dilution rate and transfer interval on eco-evolutionary dynamics of experimental microbial communities

2020 ◽  
Author(s):  
Thomas Scheuerl ◽  
Veijo Kaitala
Keyword(s):  
Microbial Communities ◽  
Dilution Rate ◽  
Evolutionary Dynamics ◽  
Experimental Studies ◽  
Study Data ◽  
Substantial Impact ◽  
Predator Prey ◽  
Structural Modifications ◽  
Underlying Mechanisms ◽  
Transfer Interval

All organisms are susceptible to the environment and changing environmental conditions can infer structural modifications in predator-prey communities. A change in the environment can influence, for example, the mortality rate of both the prey and the predator, or determine how long the interaction between both partners is. This may have a substantial impact on ecological, but also evolutionary dynamics. Experimental studies, in which microbial populations are maintained by a repeated dilution into fresh conditions after a certain period of time, are able to dissipate underlying mechanisms in a controlled way. By design, dilution rate (modifying mortality) and transfer interval (determining the time of interaction) are crucial factors, but they often receive little attention in experimental design. We study data from a live predator-prey (bacteria and ciliates) system used to gain insight into eco-evolutionary principles and apply a mathematical model to predict how various dilution rates and transfer intervals would affect such an experiment. We find the ecological dynamics to be surprisingly robust for both factors. However, the evolutionary rates are expected to be affected. Our work predicts that the evolution of the anti-predator defence in the bacteria, and the evolution of the predation efficiency in the ciliates, both decrease with higher dilution rate, but increase with longer transfer intervals. Our results provide testable hypotheses for future studies of predator-prey systems and we hope this work will help improving our understanding how ecological and evolutionary processes together shape composition of microbial communities.

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 Toward a dynamical understanding of microbial communities

2020 ◽  
Vol 375 (1798) ◽  
pp. 20190248 ◽  
Author(s):  
Paul B. Rainey ◽  
Steven D. Quistad
Keyword(s):  
Microbial Community ◽  
Horizontal Gene Transfer ◽  
Microbial Communities ◽  
Dynamic Systems ◽  
Evolutionary Dynamics ◽  
Microbial Community Composition ◽  
System Function ◽  
Theme Issue ◽  
Microbial Community Ecology

The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

scholarly journals Trait Evolution in Microbial Communities

2020 ◽  
Author(s):  
Lihong Zhao ◽  
Benjamin J Ridenhour ◽  
Christopher H Remien
Keyword(s):  
Microbial Communities ◽  
Population Dynamic ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Relative Fitness ◽  
Dynamic Parameters ◽  
Population Dynamic Model ◽  
Host Health ◽  
And Shifts ◽  
Over Time

Understanding the evolutionary dynamics of microbial communities is a key step towards the goal of predicting and manipulating microbiomes to promote beneficial states. While interactions within microbiomes and between microbes and their environment collectively determine the community composition and population dynamics, we are often concerned with traits or functions of a microbiome that link more directly to host health. To study how traits of a microbiome are impacted by eco-evolutionary dynamics, we recast a classic resource-mediated population dynamic model into a population genetic framework which incorporates traits. The relative fitness of each group of microbes can be explicitly written in terms of population dynamic parameters, and corresponding evolutionary dynamics emerge. Using several example systems, we demonstrate how natural selection, mutation, and shifts in the environment work together to produce changes in traits over time.

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