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1. Microbial diversification is maintained in an experimentally evolved synthetic community

   https://doi.org/10.1128/msystems.01053-24  

   Al-Tameemi, Zahraa; Rodríguez-Verdugo, Alejandra (November 2024, mSystems)

   Harcombe, William R (Ed.)

   ABSTRACT Microbial communities are incredibly diverse. Yet, the eco-evolutionary processes originating and maintaining this diversity remain understudied. Here, we investigate the patterns of diversification forPseudomonas putidaevolving in isolation and withAcinetobacter johnsoniileaking resources used byP. putida. We experimentally evolved four experimental replicates in monoculture and co-culture for 200 generations. We observed thatP. putidadiversified into two distinct morphotypes that differed from their ancestor by single-point mutations. One of the most prominent mutations hit thefleQgene encoding the master regulator of flagella and biofilm formation. We experimentally confirmed thatfleQmutants were unable to swim and formed less biofilm than their ancestor, but they also produced higher yields. Interestingly, thefleQgenotype and other mutations swept to fixation in monocultures but not in co-cultures. In co-cultures, the two lineages stably coexisted for approximately 150 generations. We hypothesized thatA. johnsoniimodulates the coexistence of the two lineages through frequency-dependent selection. However, invasion experiments with two genotypes in monoculture and co-culture did not support this hypothesis. Finally, we conducted an evolutionary “replay” experiment to assess whether the presence or absence ofA. johnsoniiinfluenced the coexistence of morphotypes at the population level. Interestingly,A. johnsoniihad a stabilizing effect on the co-culture. Overall, our study suggests that interspecies interactions play an important role in shaping patterns of diversification in microbial communities. IMPORTANCEIn nature, bacteria live in microbial communities and interact with other species, for example, through the exchange of resources leaked into the external environment (i.e., cross-feeding interactions). The role that these cross-feeding interactions play in shaping patterns of diversification remains understudied. Using a simple bacterial system in which one species cross-feeds resources to a second species (commensal species), we showed that the commensal species diversified into two subpopulations that persisted only when the cross-feeder partner was present. We further observed loss-of-function mutations in flagellar genes that were fixed in monocultures but not in co-cultures. Our findings suggest that cross-feeding species influence patterns of diversification of other species. Given that nutrient leakage is pervasive in microbial communities, the findings from this study have the potential to extend beyond our specific bacterial system. Importantly, our study has contributed to answering the larger question of whether species evolved differently in isolation versus when interacting with other species. 

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2. Community living causes changes in metabolic behavior and is permitted by specific growth conditions in two bacterial co-culture systems

   https://doi.org/10.1128/jb.00075-25  

   Ellis, Elizabeth; Fulte, Sam; Boylan, Skyler; Flory, Alaina; Paine, Katherine; Lopez, Sophia; Allen, Grace; Warya, Kanwar; Ortiz-Merino, Javier; Blacketer, Sadie; et al (June 2025, Journal of Bacteriology)

   Shank, Elizabeth Anne (Ed.)

   ABSTRACT Although bacteria exist in complex microbial communities in the environment, their features and behavior are most often studied in monoculture. While environmental enrichments or complex co-cultures with tens or hundreds of members might more accurately represent the natural communities of bacteria, we sought to create simple pairs of organisms to learn what conditions create successful co-culture and how bacteria change transcriptionally when a partner species is present. We grew two pairs of organisms in co-culture,Pseudomonas aeruginosaandEscherichia coliandLacticaseibacillus rhamnosusandBacteroides thetaiotaomicron. At first, both co-cultures failed, with one organism outcompeting the other. However, through manipulating media and environmental conditions, we created co-cultures with stable member ratios over many generations for each community. We then show that changes in the expression of metabolic genes are present in all studied species, with key catabolic and anabolic pathways often upregulated in the presence of another organism. These changes in gene expression fail to occur in conditions that will not lead to successful co-culture, suggesting they are essential for adapting to and surviving in the presence of others. IMPORTANCEIn 1882, Robert Koch and Fanny Hesse developed the agar plate, which enabled microbiologists to separate individual microbial cells from each other and create monocultures of a single strain of bacteria. This powerful tool has been used in the almost 150 years since to develop a robust understanding of how bacterial cells are structured, how they manage and process their information, and how they respond to the environment to produce behaviors that match their circumstances. We were curious about how the behavior of bacteria, as measured by their gene expression, changes between well-studied monoculture conditions and co-culture. We found that only specific growth conditions permit co-culture and that bacteria change their metabolic strategies in the presence of a partner. 

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3. Spatially organized cellular communities form the developing human heart

   https://doi.org/10.1038/s41586-024-07171-z  

   Farah, Elie N; Hu, Robert K; Kern, Colin; Zhang, Qingquan; Lu, Ting-Yu; Ma, Qixuan; Tran, Shaina; Zhang, Bo; Carlin, Daniel; Monell, Alexander; et al (March 2024, Nature)

   Abstract The heart, which is the first organ to develop, is highly dependent on its form to function^1,2. However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart function remains unclear. Here we integrated single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization to resolve the identity of the cardiac cell types that develop the human heart. This approach also provided a spatial mapping of individual cells that enables illumination of their organization into cellular communities that form distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, which support their specialization according to the cellular ecosystem and anatomical region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell–cell interactions within these communities using in vivo conditional genetic mouse models and in vitro human pluripotent stem cell systems revealed multicellular signalling pathways that orchestrate the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. These detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodelling the human heart offer new insights into structural heart diseases and the engineering of complex multicellular tissues for human heart repair. 

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4. Epigenetic potential affects immune gene expression in house sparrows

   https://doi.org/10.1242/jeb.238451  

   Hanson, Haley E.; Zimmer, Cedric; Koussayer, Bilal; Schrey, Aaron W.; Maddox, J. Dylan; Martin, Lynn B. (March 2021, Journal of Experimental Biology)

   ABSTRACT Epigenetic mechanisms may play a central role in mediating phenotypic plasticity, especially during range expansions, when populations face a suite of novel environmental conditions. Individuals may differ in their epigenetic potential (EP; their capacity for epigenetic modifications of gene expression), which may affect their ability to colonize new areas. One form of EP, the number of CpG sites, is higher in introduced house sparrows (Passer domesticus) than in native birds in the promoter region of a microbial surveillance gene, Toll-like Receptor 4 (TLR4), which may allow invading birds to fine-tune their immune responses to unfamiliar parasites. Here, we compared TLR4 gene expression from whole blood, liver and spleen in house sparrows with different EP, first challenging some birds with lipopolysaccharide (LPS), to increase gene expression by simulating a natural infection. We expected that high EP would predict high inducibility and reversibility of TLR4 expression in the blood of birds treated with LPS, but we did not make directional predictions regarding organs, as we could not repeatedly sample these tissues. We found that EP was predictive of TLR4 expression in all tissues. Birds with high EP expressed more TLR4 in the blood than individuals with low EP, regardless of treatment with LPS. Only females with high EP exhibited reversibility in gene expression. Further, the effect of EP varied between sexes and among tissues. Together, these data support EP as one regulator of TLR4 expression. 

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5. Long-duration environmental biosensing by recording analyte detection in DNA using recombinase memory

   https://doi.org/10.1128/aem.02363-23  

   Kalvapalle, Prashant Bharadwaj; Sridhar, Swetha; Silberg, Jonathan J; Stadler, Lauren B (April 2024, Applied and Environmental Microbiology)

   Rudi, Knut (Ed.)

   ABSTRACT Microbial biosensors that convert environmental information into real-time visual outputs are limited in their sensing abilities in complex environments, such as soil and wastewater, due to optical inaccessibility. Biosensors that could record transient exposure to analytes within a large time window for later retrieval represent a promising approach to solve the accessibility problem. Here, we test the performance of recombinase-memory biosensors that sense a sugar (arabinose) and a microbial communication molecule (3-oxo-C12-L-homoserine lactone) over 8 days (~70 generations) following analyte exposure. These biosensors sense the analyte and trigger the expression of a recombinase enzyme which flips a segment of DNA, creating a genetic memory, and initiates fluorescent protein expression. The initial designs failed over time due to unintended DNA flipping in the absence of the analyte and loss of the flipped state after exposure to the analyte. Biosensor performance was improved by decreasing recombinase expression, removing the fluorescent protein output, and using quantitative PCR to read out stored information. Application of memory biosensors in wastewater isolates achieved memory of analyte exposure in an uncharacterizedPseudomonasisolate. By returning these engineered isolates to their native environments, recombinase-memory systems are expected to enable longer duration andin situinvestigation of microbial signaling, cross-feeding, community shifts, and gene transfer beyond the reach of traditional environmental biosensors.IMPORTANCEMicrobes mediate ecological processes over timescales that can far exceed the half-lives of transient metabolites and signals that drive their collective behaviors. We investigated strategies for engineering microbes to stably record their transient exposure to a chemical over many generations through DNA rearrangements. We identify genetic architectures that improve memory biosensor performance and characterize these in wastewater isolates. Memory biosensors are expected to be useful for monitoring cell-cell signals in biofilms, detecting transient exposure to chemical pollutants, and observing microbial cross-feeding through short-lived metabolites within cryptic methane, nitrogen, and sulfur cycling processes. They will also enablein situstudies of microbial responses to ephemeral environmental changes, or other ecological processes that are currently challenging to monitor non-destructively using real-time biosensors and analytical instruments. 

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