Article
Immunology
Meaghan Castledine, Pawel Sierocinski, Mhairi Inglis, Suzanne Kay, Alex Hayward, Angus Buckling, Daniel Padfield
Summary: Antagonistic coevolution between hosts and parasites has important implications in ecology and evolution. This study found that increasing the genetic diversity of parasites may give them an evolutionary advantage in long-term coevolution.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Amanda Glaser-Schmitt, Meike J. Wittmann, Timothy J. S. Ramnarine, John Parsch
Summary: This study examined the maintenance mechanisms of a regulatory SNP in the X-linked Drosophila melanogaster gene fezzik, revealing that variation at this site may be maintained through both sexually antagonistic and temporally fluctuating selection. The derived variant at this SNP is predicted to be female-beneficial and mostly recessive, with variable dominance estimates. Additionally, gene expression and genotype at this locus are associated with sex-dependent starvation resistance, suggesting a potential phenotypic target of selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Qi Su, Alex McAvoy, Joshua B. Plotkin
Summary: This study explores how social interactions and the identity of opponents impact the emergence and stability of prosocial behavior. The research finds that human beings' sophisticated cognitive abilities allow them to adapt their behavior based on social context and the identity of their opponents. It is revealed that contextualized behavior significantly enhances cooperation, even in populations with a small number of social contexts. Increasing the number of social contexts further greatly promotes cooperation.
Article
Ecology
Kaitlyn E. Kortright, Benjamin K. Chan, Benjamin R. Evans, Paul E. Turner
Summary: This study investigates the coevolutionary dynamics between bacteria and lytic phages. The results show that both arms-race dynamics (ARD) and fluctuating-selection dynamics (FSD) are possible outcomes of coevolution. However, only the ARD bacteria demonstrate the predicted trade-off between phage resistance and antibiotic sensitivity.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2022)
Article
Evolutionary Biology
E. Rodriguez-Exposito, F. Garcia-Gonzalez
Summary: This study used the seed beetle Callosobruchus maculatus to investigate the impact of mating system and population subdivision on sexual conflict evolution. The results revealed that the population spatial structure can modulate resistance of females to male harm, highlighting the significance of ecological context in the evolution of sexual conflict.
Article
Ecology
Jake N. Barber, Aysha L. Sezmis, Laura C. Woods, Trenton D. Anderson, Jasmyn M. Voss, Michael J. McDonald
Summary: Microbial communities are made up of many species that coexist on small spatial scales, and the evolution of coexistence between competing species can occur after long periods of coevolution. Genetic sequencing and mutation analysis have identified genes that can modify interactions between species, allowing for stable coexistence to evolve from intense competition.
Article
Multidisciplinary Sciences
Jean-Sebastien Pierre, Solenn Stoeckel, Eric Wajnberg
Summary: The advantage and fixation of sex in many eukaryote species is considered a evolutionary puzzle. Several hypotheses have been proposed to explain this phenomenon, including negative frequency-dependent selection, competition between siblings, genetic and ecological factors. Recent studies suggest that these different factors can act together to promote the fixation of sexual reproduction in populations.
Review
Ecology
Masato Yamamichi, Andrew D. Letten, Sebastian J. Schreiber
Summary: Growing evidence suggests that temporally fluctuating environments play a crucial role in maintaining variation within and between species. However, studies of genetic variation within populations have been primarily conducted by evolutionary biologists, while population and community ecologists have focused more on species diversity. This article reviews theoretical and empirical studies in population genetics and community ecology, exploring the connection between the "temporal storage effect" and diversity maintenance. By comparing and synthesizing ecological and evolutionary approaches, the authors aim to enhance our understanding of diversity maintenance in nature.
Article
Mathematics, Interdisciplinary Applications
Dong Mu, Xiongping Yue
Summary: This paper investigates the implications of environmental heterogeneity and environmental preference on the evolution of cooperation in supply networks. By using cellular automata and game reward schemes like the Prisoner's Dilemma Game and Snowdrift Game, the study shows that higher levels of cooperation are observed with increasing heterogeneous environment, and that environmental preference significantly impacts the evolution of cooperation.
Article
Mathematics, Applied
Anuran Pal, Supratim Sengupta
Summary: We analyze a cooperative decision-making model based on individual aspiration levels in the framework of a public goods game. Sensitivity to payoff differences and dynamic aspiration levels affects individual satisfaction and subsequent behavior. The efficiency of aspiration level updates determines the collective outcome of strategy changes. Our work shows that even a small fraction of nodes restructuring their connections can promote cooperation across a wide range of learning efficiencies.
Article
Physics, Mathematical
Jeremie Unterberger
Summary: We investigate a class of Markovian models that describe the growth of a clonal biological population in a randomly fluctuating environment. The population consists of several phenotypes that are related through stochastic switching. The growth rate of the population, known as Lambda, is self-averaging in the infinite time limit and can be interpreted as the fitness of the population in the context of Darwinian evolution. However, due to the finite observation time T, the growth rate fluctuates. We derive a formula for the variance of the time-averaged growth rate in terms of the stationary probability distribution for the phenotypes. This formula is applicable in general cases and for the specific case of two states, an explicit expression for the stationary probability has been obtained. We briefly present the applications of our main formula in studying survival strategies of biological populations.
JOURNAL OF STATISTICAL PHYSICS
(2022)
Review
Microbiology
Demetris Taliadoros, Eva H. Stukenbrock
Summary: Identifying traits involved in plant-pathogen interactions is a major objective in molecular plant pathology. Evolutionary analyses using genome sequences of fungal plant pathogens have led to important discoveries related to virulence and adaptation. Positive selection leaves specific signatures in genome alignments and can be identified using statistical genetics methods. This review highlights the significant contribution of evolutionary genomics in discovering virulence-related traits and studying plant-pathogen ecology and adaptive evolution.
CURRENT OPINION IN MICROBIOLOGY
(2023)
Article
Ecology
Sam Paplauskas, June Brand, Stuart K. J. R. Auld
Summary: Ecological factors play a significant role in shaping the coevolution of host-parasite interactions. Biotic and abiotic forces influence the evolutionary trajectories of organisms, amplifying or diluting parasitism as a selective force on hosts and parasites. The wider ecology drives variation in host evolution of resistance, leading to coevolutionary divergence in response to changing environmental conditions.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Statistics & Probability
Niloy Biswas, Alison Etheridge, Aleksander Klimek
Summary: The article discusses populations in which the fitness of different genetic types fluctuates in time and space, focusing on two genetic types and the effects of short bursts of selection and genetic drift on genetic variation. Using models and mathematical methods, the article explores the evolutionary processes of populations in fluctuating environments.
ELECTRONIC JOURNAL OF PROBABILITY
(2021)
Article
Physics, Condensed Matter
Peican Zhu, Xin Hou, Yangming Guo, Jiwei Xu, Jinzhuo Liu
Summary: Researchers proposed a co-evolving mechanism to study the effects of applying different updating rules on the level of cooperation in interactive diversity scenarios. Through extensive experiments and simulation results analysis, they found that with an increase in the proportion of Type-T players, individuals tended to adopt the strategy of cooperation even if the temptation to defect was relatively large.
EUROPEAN PHYSICAL JOURNAL B
(2021)
Article
Microbiology
Bryden Fields, Emma K. Moffat, Ellie Harrison, Stig U. Andersen, J. Peter W. Young, Ville-Petri Friman
Summary: Genetic diversity influences facilitative and competitive interactions between different genospecies in the Rhizobium leguminosarum species complex, which can impact bacterial community composition, diversity, and functioning.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Xiaoxuan Zheng, Martin T. Jahn, Mingming Sun, Ville-Petri Friman, Jose Luis Balcazar, Jinfeng Wang, Yu Shi, Xin Gong, Feng Hu, Yong-Guan Zhu
Summary: This study found that in organochlorine pesticide-contaminated soils, the relative abundance of bacteria was lower, but the diversity of viruses was higher, and these viruses contained genes related to pesticide degradation and metabolism. The diversity and abundance of these genes increased with the severity of pesticide contamination. Functional experiments demonstrated that virus-encoded genes were able to degrade pesticide precursors, promoting bacterial growth at sub-inhibitory pesticide concentrations.
Article
Ecology
Michael J. Bottery, Jessica L. Matthews, A. Jamie Wood, Helle Krogh Johansen, Jon W. Pitchford, Ville-Petri Friman
Summary: The study found that multidrug-resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to Pseudomonas aeruginosa, but is ineffective against another antibiotic. The level of exposure protection against different carbapenems is determined by differences in antibiotic efficacy and inactivation rate.
Article
Biology
Meaghan Castledine, Daniel Padfield, Pawel Sierocinski, Jesica Soria Pascual, Adam Hughes, Lotta Makinen, Ville-Petri Friman, Jean-Paul Pirnay, Maya Merabishvili, Daniel de Vos, Angus Buckling, Gisela Storz
Summary: With rising antibiotic resistance, there is increasing interest in using bacteriophages to treat pathogenic bacteria. However, one limitation is that bacteria can quickly evolve resistance to phage therapy. This study investigates the parallels between in vitro and in vivo evolutionary dynamics and suggests that in vitro experiments can provide useful insights for predicting clinical outcomes.
Article
Microbiology
Chen Zhu, Ville-Petri Friman, Ling Li, Qicheng Xu, Junjie Guo, Shiwei Guo, Qirong Shen, Ning Ling
Summary: The composition, diversity, and distribution of soil diazotrophs vary across different soil ecosystems, with environmental factors playing a significant role in their abundance and distribution. Cyanobacteria are the most abundant taxa in crust ecosystems, while Proteobacteria dominate other terrestrial ecosystems. Azospirillum zeae, Skermanella aerolata, and four Bradyrhizobium species are identified as key indicator species of potential diazotroph activity.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Evolutionary Biology
Carrie Louise Alderley, Samuel Terrence Edwards Greenrod, Ville-Petri Friman
Summary: This study finds that biofumigation can suppress the growth of Ralstonia solanacearum plant bacterial pathogen, but under low transfer frequency exposure, the pathogen evolves tolerance to allyl-ITC plant allelochemical and develops cross-tolerance to ampicillin beta-lactam antibiotic. The tolerance evolution is linked to insertion sequence movement in multiple genes.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Ecology
Jianing Wang, Waseem Raza, Gaofei Jiang, Zhang Yi, Bryden Fields, Samuel Greenrod, Ville-Petri Friman, Alexandre Jousset, Qirong Shen, Zhong Wei
Summary: Volatile organic compounds (VOCs) produced by soil bacteria have been found to influence the biocontrol potential of plant pathogens due to their antimicrobial activity. This study investigated the adaptation of Ralstonia solanacearum bacteria to VOCs produced by a biocontrol bacterium and how these adaptations affect its virulence. The findings showed that VOC selection led to increased VOC-tolerance and cross-tolerance to antibiotics, resulting in a loss of pathogenicity in plants. The genetic analysis revealed mutations in genes associated with antimicrobial permeability and virulence. Overall, microbial VOCs are important drivers of bacterial evolution and can be utilized in biocontrol to select for less virulent pathogens.
Article
Microbiology
Keming Yang, Xiaofang Wang, Rujiao Hou, Chunxia Lu, Zhe Fan, Jingxuan Li, Shuo Wang, Yangchun Xu, Qirong Shen, Ville-Petri Friman, Zhong Wei
Summary: This study investigates the influence of rhizosphere phage communities on soil suppressiveness and bacterial wilt disease. It shows that healthy plants are associated with phage communities that have stronger control over the pathogen R. solanacearum. Additionally, phages that target pathogen-inhibiting bacteria are more abundant in diseased plant microbiomes. These findings suggest that rhizosphere phage communities play a crucial role in determining bacterial wilt disease outcomes and soil suppressiveness.
Article
Biotechnology & Applied Microbiology
Shujian Yuan, Ville-Petri Friman, Jose Luis Balcazar, Xiaoxuan Zheng, Mao Ye, Mingming Sun, Feng Hu
Summary: This study investigated the assembly processes of bacterial and viral communities in clean and OCP-contaminated soils in China. The results showed that assembly of bacterial taxa and genes was dominated by a deterministic process, while assembly of viral taxa and AMGs was driven by a stochastic process. Additionally, viruses showed promise for the dissemination of functional genes among bacterial communities in OCP-contaminated soil.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Yian Gu, Zhidan Li, Peng Lei, Rui Wang, Hong Xu, Ville-Petri Friman
Summary: Through sampling in Hongze Lake during both Autumn and Spring, it was found that bacterial sediment communities were governed by deterministic community assembly processes due to abiotic environmental drivers, while distance-decay relationships were relatively stable with both sampling time points for both bacterial and microeukaryotic communities. This suggests that abiotic environmental factors play an important role in explaining mainly bacterial community assembly in the sediment, but other potential drivers, such as spatial heterogeneity and biotic species interactions, also need to be considered.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Ecology
Hanpeng Liao, Chen Liu, Chaofan Ai, Tian Gao, Qiu-E Yang, Zhen Yu, Shaoming Gao, Shungui Zhou, Ville-Petri Friman
Summary: By studying mesophilic and thermophilic bacteria and their viruses during industrial-scale hyperthermophilic composting (HTC), it was found that the dynamics and activity of virus-bacteria are closely related and play an important role in nutrient cycling. The viruses specific to mesophilic bacteria encode and express several auxiliary metabolic genes (AMGs) linked to carbon cycling and impact nutrient turnover alongside bacteria. The positive correlation between nutrient turnover and virus-host ratio suggests a positive relationship between ecosystem functioning, viral abundances, and viral activity. DNA viruses were found to be the main drivers of nutrient cycling during HTC. These findings suggest that viruses could be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.
Article
Biochemistry & Molecular Biology
Bryden Fields, Sara Moeskjaer, William J. Deakin, Emma K. Moffat, Niels Roulund, Stig U. Andersen, J. Peter W. Young, Ville-Petri Friman
Summary: This study compared the impact of different clover varieties and genotypes on the structure of Rhizobium populations in root nodules. The results showed that different clover varieties and genotypes selected for different Rhizobium communities, and the strength of host filtering was positively correlated with symbiotic efficiency.
Article
Microbiology
Samuel T. E. Greenrod, Martina Stoycheva, John Elphinstone, Ville-Petri Friman
Summary: Ralstonia solanacearum species complex (RSSC) is a destructive group of plant pathogenic bacteria and the causative agent of bacterial wilt disease. Experimental studies have attributed RSSC virulence to insertion sequences (IS), transposable genetic elements which can both disrupt and activate host genes. Yet, the global diversity and distribution of RSSC IS are unknown.
Article
Biochemistry & Molecular Biology
Karoline Rehm, Vera Vollenweider, Shaohua Gu, Ville-Petri Friman, Rolf Kuemmerli, Zhong Wei, Laurent Bigler
Summary: In this study, a novel citrate-based siderophore called chryseochelin A was identified and found to promote the health and growth of plants. The structure of this siderophore, along with its unstable isomer chryseochelin B and fatty acid derivative chryseochelin C, was elucidated using NMR spectroscopy and mass spectrometry. It was demonstrated that chryseochelin A can reduce the access to iron of the plant pathogenic bacterium Ralstonia solanacearum, indicating its potential in plant protection.
Article
Evolutionary Biology
Jianing Wang, Xiaofang Wang, Keming Yang, Chunxia Lu, Bryden Fields, Yangchun Xu, Qirong Shen, Zhong Wei, Ville-Petri Friman
Summary: This study compared the evolution of phage resistance-virulence trade-offs in Ralstonia solanacearum bacterium at different temperature environments. The results showed that phages reduced the density of R. solanacearum, but did not affect the final level of phage resistance. Instead, small colony variants with increased growth rate and mutations in the quorum-sensing (QS) signaling receptor gene evolved in both temperature treatments. Interestingly, these variants were also phage-resistant and reached higher frequencies in the presence of phages. Evolution of phage resistance resulted in metabolic costs, leading to reduced biofilm formation and virulence in the bacteria.