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1. Developing an Appropriate Evolutionary Baseline Model for the Study of Human Cytomegalovirus

   https://doi.org/10.1093/gbe/evad059  

   Howell, Abigail A; Terbot, John W; Soni, Vivak; Johri, Parul; Jensen, Jeffrey D; Pfeifer, Susanne P (April 2023, Genome Biology and Evolution)

   Qian, Wenfeng (Ed.)

   Abstract Human cytomegalovirus (HCMV) represents a major threat to human health, contributing to both birth defects in neonates as well as organ transplant failure and opportunistic infections in immunocompromised individuals. HCMV exhibits considerable interhost and intrahost diversity, which likely influences the pathogenicity of the virus. Therefore, understanding the relative contributions of various evolutionary forces in shaping patterns of variation is of critical importance both mechanistically and clinically. Herein, we present the individual components of an evolutionary baseline model for HCMV, with a particular focus on congenital infections for the sake of illustration—including mutation and recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization—and describe the current state of knowledge of each. By building this baseline model, researchers will be able to better describe the range of possible evolutionary scenarios contributing to observed variation as well as improve power and reduce false-positive rates when scanning for adaptive mutations in the HCMV genome. 

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2. Dynamics and variability in the pleiotropic effects of adaptation in laboratory budding yeast populations

   https://doi.org/10.7554/eLife.70918  

   Bakerlee, Christopher W; Phillips, Angela M; Nguyen Ba, Alex N; Desai, Michael M (October 2021, eLife)

   Evolutionary adaptation to a constant environment is driven by the accumulation of mutations which can have a range of unrealized pleiotropic effects in other environments. These pleiotropic consequences of adaptation can influence the emergence of specialists or generalists, and are critical for evolution in temporally or spatially fluctuating environments. While many experiments have examined the pleiotropic effects of adaptation at a snapshot in time, very few have observed the dynamics by which these effects emerge and evolve. Here, we propagated hundreds of diploid and haploid laboratory budding yeast populations in each of three environments, and then assayed their fitness in multiple environments over 1000 generations of evolution. We find that replicate populations evolved in the same condition share common patterns of pleiotropic effects across other environments, which emerge within the first several hundred generations of evolution. However, we also find dynamic and environment-specific variability within these trends: variability in pleiotropic effects tends to increase over time, with the extent of variability depending on the evolution environment. These results suggest shifting and overlapping contributions of chance and contingency to the pleiotropic effects of adaptation, which could influence evolutionary trajectories in complex environments that fluctuate across space and time. 

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3. Parallel Evolution towards Increased Motility in Long-Term Cultures of Escherichia coli, Even Though Motility was Not Required for Long-Term Survival

   https://doi.org/10.1128/spectrum.02330-21  

   Henderson, Autumn L.; Moreno, Angie; Kram, Karin E. (June 2022, Microbiology Spectrum)

   Gao, Beile (Ed.)

   ABSTRACT Escherichia coli can survive for long periods in batch culture in the laboratory, where they experience a stressful and heterogeneous environment. During this incubation, E. coli acquires mutations that are selected in response to this environment, ultimately leading to evolved populations that are better adapted to these complex conditions, which can lead to a better understanding of evolutionary mechanisms. Mutations in regulatory genes often play a role in adapting to heterogeneous environments. To identify such mutations, we examined transcriptional differences during log phase growth in unaged cells compared to those that had been aged for 10 days and regrown. We identified expression changes in genes involved in motility and chemotaxis after adaptation to long-term cultures. We hypothesized that aged populations would also have phenotypic changes in motility and that motility may play a role in survival and adaptation to long-term cultures. While aged populations did show an increase in motility, this increase was not essential for survival in long-term cultures. We identified mutations in the regulatory gene sspA and other genes that may contribute to the observed differences in motility. Taken together, these data provide an overall picture of the role of mutations in regulatory genes for adaptation while underscoring that all changes that occur during evolution in stressful environments are not necessarily adaptive. IMPORTANCE Understanding how bacteria adapt in long-term cultures aids in both better treatment options for bacterial infections and gives insight into the mechanisms involved in bacterial evolution. In the past, it has been difficult to study these organisms in their natural environments. By using experimental evolution in heterogeneous and stressful laboratory conditions, we can more closely mimic natural environments and examine evolutionary mechanisms. One way to observe these mechanisms is to look at transcriptomic and genomic data from cells adapted to these complex conditions. Here, we found that although aged cells increase motility, this increase is not essential for survival in these conditions. These data emphasize that not all changes that occur due to evolutionary processes are adaptive, but these observations could still lead to hypotheses about the causative mutations. The information gained here allow us to make inferences about general mechanisms underlying phenotypic changes due to evolution. 

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4. Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes

   https://doi.org/10.1093/ismejo/wraf081  

   Putnam, Emily E; May, Robert; Freeman, Nina; Arrigan, Dillon; Boylan, Andrew; Childs, Laura H; Wolfe, Benjamin E (May 2025, The ISME Journal)

   Abstract Studies of microbial interactions often emphasize interactions with large, easily measurable growth differences and short-term ecological outcomes spanning just a few generations. However, more subtle interactions, such as those without obvious phenotypes, may play a significant role in shaping both the short-term ecological dynamics and the long-term evolutionary trajectories of microbial species. We used the cheese rind model microbiome to examine how two fungal species, Penicillium camemberti and Geotrichum candidum, impact global gene expression and genome evolution of the bacterium Pseudomonas carnis LP. Even though fungi had limited impacts on the growth of P. carnis LP, approximately 4–40% of its genome was differentially expressed, depending on the specific fungal partner. When we evolved this Pseudomonas strain alone or in co-culture with each of the fungi, we observed frequent mutations in global regulators of nitrogen regulation, secondary metabolite production, and motility, depending on the fungus. Strikingly, many strains with mutations in the nitrogen regulatory gene ntrB emerged when evolved alone or with G. candidum, but not with P. camemberti. Metabolomic and fitness experiments demonstrate that release of free amino acids by P. camemberti removes the fitness advantages conferred by ntrB mutations. Collectively, these results demonstrate that even in the absence of major short-term growth effects, fungi can have substantial impacts on the transcriptome and genomic evolution of bacterial species. 

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5. Viral infection impacts volatile organic compound production in the coccolithophore Gephyrocapsa huxleyi

   https://doi.org/10.1101/2025.02.09.637333  

   Buchholz, Holger H; Mojica, Kristina DA; Comstock, Jacqueline; Collart, Lindsay; Giovannoni, Stephen J; Halsey, Kimberly H (February 2025, bioRxiv)

   Abstract Volatile Organic Compounds (VOCs) are a diverse collection of molecules critical to cell metabolism, food web interactions, and atmospheric chemistry. The eukaryotic coccolithophoreGephyrocapsa huxleyi, an abundant coastal eukaryotic phytoplankter, forms massive blooms in coastal upwelling regions, which are often terminated by viruses (EhVs).G. huxleyiproduces organosulfur VOCs such as dimethyl sulfide (DMS) and halogenated metabolites that play key roles in atmospheric chemistry. Here we resolved the role of lytic viral infection by EhV207 on VOC production of the model strainG. huxleyiCCMP374. Our analysis identified 79 VOCs significantly impacted by viral infection, particularly during cell lysis, with sulfur containing VOCs like DMS dominating the profiles. Viral lysis results in a nearly six-fold increase in VOC production and generated a previously unrecognized range of VOCs, including 15 sulfur, 22 nitrogen, 2 phosphorus, 19 oxygen and 17 halogen-containing compounds. These findings reveal that viral infection ofG. huxleyireleases VOCs which are much more diverse than previously recognized. We further show that EhV207 primarily accelerates existing metabolic processes inG. huxleyiand facilitates the release of pre-existing intracellular VOCs rather than inducing novel biochemical pathways. This wide range of VOCs may be produced on a massive scale during coccolithophore bloom-and-bust cycles, with important impacts on coastal biogeochemistry and surface ocean/atmosphere interactions. 

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