scholarly journals Mapping Gene-Microbe Interactions: Insights from Functional Genomics Co-culture Experiments between Saccharomyces cerevisiae and Pseudomonas spp

2020 ◽  
Author(s):  
Guillaume Quang N’guyen ◽  
Mani Jain ◽  
Christian R Landry ◽  
Marie Filteau
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Functional Genomics ◽  
Gene List ◽  
Biotic Interactions ◽  
Microbial Evolution ◽  
Microbial Interactions ◽  
Variable Degree ◽  
Evolutionary Trajectory ◽  
Microbe Interactions ◽  
The Impact

AbstractMicrobial interactions contribute to shape ecosystems and their functions. The interplay between microorganisms also shapes the evolutionary trajectory of each species, by imposing metabolic and physiological selective pressures. The mechanisms underlying these interactions are thus of interest to improve our understanding of microbial evolution at the genetic level. Here we applied a functional genomics approach in the model yeast Saccharomyces cerevisiae to identify the fitness determinants of naïve biotic interactions. We used a barcoded prototroph yeast deletion collection to perform pooled fitness competitions in co-culture with seven Pseudomonas spp natural isolates. We found that co-culture had a positive impact on fitness profiles, as in general the deleterious effects of loss of function in our nutrient-poor media were mitigated. In total, 643 genes showed a fitness difference in co-culture, most of which can be explained by a media diversification procured by bacterial metabolism. However, a large fraction (36%) of gene-microbe interactions could not be recaptured in cell-free supernatant experiments, showcasing that feedback mechanisms or physical contacts modulate these interactions. Also, the gene list of some co-cultures was enriched with homologs in other eukaryote species, suggesting a variable degree of specificity underlying the mechanisms of biotic interactions and that these interactions could also exist in other organisms. Our results illustrate how microbial interactions can contribute to shape the interplay between genomes and species interactions, and that S. cerevisiae is a powerful model to study the impact of biotic interactions.

scholarly journals Restricted access to beneficial mutations slows adaptation and biases fixed mutations in diploids

2017 ◽  
Author(s):  
Daniel A. Marad ◽  
Gregory I. Lang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Microbial Evolution ◽  
Beneficial Mutations ◽  
Recombination Hotspot ◽  
Restricted Access ◽  
Evolution Experiment ◽  
Homozygous Mutations ◽  
Key Aspects ◽  
The Impact ◽  
Diploid Populations

ABSTRACTPloidy varies considerably in nature. Yet, our understanding of the impact of ploidy on adaptation is incomplete. Many microbial evolution experiments characterize adaptation in haploid organisms, but few focus on diploid organisms. Here, we perform a 4,000-generation evolution experiment using diploid strains of the yeast Saccharomyces cerevisiae. We show that the rate of adaptation and spectrum of beneficial mutations are influenced by ploidy. Haldane’s sieve effectively restricts access to beneficial mutations in diploid populations, leading to a slower rate of adaptation and a spectrum of beneficial mutations shifted towards dominant mutations. Genomic position also plays an important role, as the prevalence of homozygous mutations is largely dependent on their proximity to a recombination hotspot. Our results demonstrate key aspects of diploid adaptation that have previously been understudied and provide support for several proposed theories.

scholarly journals Strain-Specific Responses by Saccharomyces cerevisiae to Competition by Non-Saccharomyces Yeasts

Fermentation ◽  
2021 ◽  
Vol 7 (3) ◽  
pp. 165
Author(s):  
Cristobal A. Onetto ◽  
Anthony R. Borneman ◽  
Simon A. Schmidt
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Yeast Species ◽  
Microbial Interactions ◽  
Fermentation Performance ◽  
Competitive Fitness ◽  
Sequential Fermentation ◽  
Saccharomyces Yeast ◽  
Negative Impacts ◽  
The Impact ◽  
Saccharomyces Yeasts

The use of non-Saccharomyces yeast species generally involves sequential or co-inoculation of a Saccharomyces cerevisiae strain to complete fermentation. While most studies have focused on characterising the impact that S. cerevisiae has on the growth and metabolic activity of these non-Saccharomyces species, microbial interactions work reciprocally. Antagonism or competition of non-Saccharomyces species against S. cerevisiae has been shown to impact subsequent fermentation performance. To date, it remains unclear whether these negative interactions are strain specific. Hence, characterisation of strain-specific responses to co-inoculation would enable the identification of specific S. cerevisiae strain/non-Saccharomyces combinations that minimise the negative impacts of sequential fermentation on fermentation performance. The competitive fitness response of 93 S. cerevisiae strains to several non-Saccharomyces species was simultaneously investigated using a barcoded library to address this knowledge gap. Strain-specific fitness differences were observed across non-Saccharomyces treatments. Results obtained from experiments using selected S. cerevisiae strains sequentially inoculated after Metschnikowia pulcherrima and Torulaspora delbrueckii were consistent with the competitive barcoded library observations. The results presented in this study indicate that strain selection will influence fermentation performance when using non-Saccharomyces species, therefore, appropriate strain/yeast combinations are required to optimise fermentation.

scholarly journals Reciprocal hemizygosity analysis reveals that the Saccharomyces cerevisiae CGI121 gene affects lag time duration in synthetic grape must

2021 ◽  
Author(s):  
Runze Li ◽  
Rebecca C Deed
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Low Temperatures ◽  
Lag Time ◽  
Lag Phase ◽  
Phenotypic Traits ◽  
Time Duration ◽  
Phase Duration ◽  
Grape Must ◽  
The Impact ◽  
Reciprocal Hemizygosity Analysis

Abstract It is standard practice to ferment white wines at low temperatures (10-18 °C). However, low temperatures increase fermentation duration and risk of problem ferments, leading to significant costs. The lag duration at fermentation initiation is heavily impacted by temperature; therefore, identification of Saccharomyces cerevisiae genes influencing fermentation kinetics is of interest for winemaking. We selected 28 S. cerevisiae BY4743 single deletants, from a prior list of open reading frames (ORFs) mapped to quantitative trait loci (QTLs) on chromosomes VII and XIII, influencing the duration of fermentative lag time. Five BY4743 deletants, Δapt1, Δcgi121, Δclb6, Δrps17a, and Δvma21, differed significantly in their fermentative lag duration compared to BY4743 in synthetic grape must (SGM) at 15 °C, over 72 h. Fermentation at 12.5 °C for 528 h confirmed the longer lag times of BY4743 Δcgi121, Δrps17a, and Δvma21. These three candidate ORFs were deleted in S. cerevisiae RM11-1a and S288C to perform single reciprocal hemizygosity analysis (RHA). RHA hybrids and single deletants of RM11-1a and S288C were fermented at 12.5 °C in SGM and lag time measurements confirmed that the S288C allele of CGI121 on chromosome XIII, encoding a component of the EKC/KEOPS complex, increased fermentative lag phase duration. Nucleotide sequences of RM11-1a and S288C CGI121 alleles differed by only one synonymous nucleotide, suggesting that intron splicing, codon bias, or positional effects might be responsible for the impact on lag phase duration. This research demonstrates a new role of CGI121 and highlights the applicability of QTL analysis for investigating complex phenotypic traits in yeast.

scholarly journals Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Peter Higgins ◽  
Cooper A Grace ◽  
Soon A Lee ◽  
Matthew R Goddard
Keyword(s):  
Saccharomyces Cerevisiae ◽  
New Zealand ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Range Expansion ◽  
Copy Number ◽  
Small Scale ◽  
Whole Genome ◽  
Copy Number Changes ◽  
The Impact

Abstract Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

scholarly journals A Markov model of urban evolution: Neighbourhood change as a complex process

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245357
Author(s):  
Daniel Silver ◽  
Thiago H. Silva
Keyword(s):  
Markov Model ◽  
Markov Models ◽  
Past Research ◽  
Hierarchical Approach ◽  
Evolutionary Trajectory ◽  
Complex Process ◽  
Trajectories Of Change ◽  
Neighbourhood Change ◽  
The Impact ◽  
Complexity Theories

This paper seeks to advance neighbourhood change research and complexity theories of cities by developing and exploring a Markov model of socio-spatial neighbourhood evolution in Toronto, Canada. First, we classify Toronto neighbourhoods into distinct groups using established geodemographic segmentation techniques, a relatively novel application in this geographic setting. Extending previous studies, we pursue a hierarchical approach to classifying neighbourhoods that situates many neighbourhood types within the city’s broader structure. Our hierarchical approach is able to incorporate a richer set of types than most past research and allows us to study how neighbourhoods’ positions within this hierarchy shape their trajectories of change. Second, we use Markov models to identify generative processes that produce patterns of change in the city’s distribution of neighbourhood types. Moreover, we add a spatial component to the Markov process to uncover the extent to which change in one type of neighbourhood depends on the character of nearby neighbourhoods. In contrast to the few studies that have explored Markov models in this research tradition, we validate the model’s predictive power. Third, we demonstrate how to use such models in theoretical scenarios considering the impact on the city’s predicted evolutionary trajectory when existing probabilities of neighbourhood transitions or distributions of neighbourhood types would hypothetically change. Markov models of transition patterns prove to be highly accurate in predicting the final distribution of neighbourhood types. Counterfactual scenarios empirically demonstrate urban complexity: small initial changes reverberate throughout the system, and unfold differently depending on their initial geographic distribution. These scenarios show the value of complexity as a framework for interpreting data and guiding scenario-based planning exercises.

scholarly journals Potential for transmission of Elizabethkingia anophelis by Aedes albopictus and the role of microbial interactions in Zika virus competence

2019 ◽  
Author(s):  
MG Onyango ◽  
AF Payne ◽  
J Stout ◽  
C Dieme ◽  
L Kuo ◽  
...  
Keyword(s):  
Zika Virus ◽  
Inhibitory Effect ◽  
Microbial Interactions ◽  
Morbidity And Mortality ◽  
Source Of Infection ◽  
Vector Borne ◽  
Complex Relationships ◽  
The Impact ◽  
First Time ◽  
Transmission Barrier

AbstractElizabethkingia anophelis has been the cause of four outbreaks with significant morbidity and mortality. Its transmission routes remain unknown and no point source of infection has been identified. Here we show that E. anophelis can be found in the saliva of Aedes mosquitoes, suggesting the novel possibility of vector-borne transmission of this bacterium. We additionally characterized diverse microbial communities in Aedes midguts, salivary glands and saliva. To the best of our knowledge, this represents the first description of the microbiome of Aedes saliva. Further, we demonstrate that increased abundance of E. anophelis is associated with decreased susceptibility and replication of Zika virus (ZIKV) in the midgut of Aedes mosquitoes, suggesting a novel transmission barrier for arboviruses transmitted by Aedes mosquitoes. Together, these results demonstrate the complex relationships between the mosquito, the midgut microbial community and arboviruses and offer insights into the epidemiology and control of emerging bacterial and viral pathogens.Author SummaryElizabethkingia anophelis has in the recent past caused outbreaks different parts of the world resulting both in morbidity and mortality. Until now, to the best of our knowledge, no study has been able to demonstrate that this bacterium can be transmitted by mosquitoes. We have demonstrated for the first time that Elizabethkingia anophelis is present in the saliva of both infected and non-infected Aedes mosquitoes. Further, we have shown that it confers an inhibitory effect on Zika virus establishment in the midguts of Aedes mosquitoes. Together, these results potentially display the potential for vector borne transmission of E. anophelis as well as a novel transmission barrier of ZIKV. Lastly, we have for the first time characterized salivary microbes of Aedes mosquitoes necessitating the investigation of the impact of salivary microbes in severity of disease in vertebrate hosts.

scholarly journals Evolutionary adaptation after crippling cell polarization follows reproducible trajectories

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Liedewij Laan ◽  
John H Koschwanez ◽  
Andrew W Murray
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Polarization ◽  
Functional Modules ◽  
Evolutionary Adaptation ◽  
Biological Functions ◽  
Fixed Sequence ◽  
Evolutionary Trajectory ◽  
Adaptive Mutations ◽  
Rapid Divergence ◽  
Polarity Gene

Cells are organized by functional modules, which typically contain components whose removal severely compromises the module's function. Despite their importance, these components are not absolutely conserved between parts of the tree of life, suggesting that cells can evolve to perform the same biological functions with different proteins. We evolved Saccharomyces cerevisiae for 1000 generations without the important polarity gene BEM1. Initially the bem1∆ lineages rapidly increase in fitness and then slowly reach >90% of the fitness of their BEM1 ancestors at the end of the evolution. Sequencing their genomes and monitoring polarization reveals a common evolutionary trajectory, with a fixed sequence of adaptive mutations, each improving cell polarization by inactivating proteins. Our results show that organisms can be evolutionarily robust to physiologically destructive perturbations and suggest that recovery by gene inactivation can lead to rapid divergence in the parts list for cell biologically important functions.

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

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