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1. Rival phytoplankton contribute to the cross protection of Prochlorococcus from oxidative stress

   https://doi.org/10.1128/aem.01128-24  

   Calfee, Benjamin C; Bowden, Emily C; Zinser, Erik R (May 2025, Applied and Environmental Microbiology)

   Bose, Arpita (Ed.)

   ABSTRACT The marine cyanobacteriumProchlorococcusnumerically dominates the phytoplankton communities in all lower latitude, open ocean environments. Having lost the catalase gene,Prochlorococcusis highly susceptible to exogenous hydrogen peroxide (H₂O₂) produced at the ocean’s surface. Protection by H₂O₂-scavenging heterotrophic “helper” bacteria has been demonstrated in laboratory cultures and implicated as an important mechanism ofProchlorococcussurvival in the ocean. Importantly, some other phytoplankton can also scavenge H₂O₂, suggesting these competing microbes may inadvertently protectProchlorococcus. In this study, we assessed the ability of co-occurring phytoplankton, the cyanobacteriumSynechococcusand picoeukaryotesMicromonasandOstreococcus, to protectProchlorococcusfrom H₂O₂exposure when cocultured at ecologically relevant abundances. All three genera could significantly degrade H₂O₂and diminishProchlorococcusmortality during H₂O₂exposures simulating photochemical production and rainfall events. We suggest that these phytoplankton groups contribute significantly to the H₂O₂microbial sink of the open ocean, thus complicating their relationships with and perhaps contributing to the evolutionary history ofProchlorococcus.IMPORTANCEThe marine cyanobacteriumProchlorococcusis the most abundant photosynthetic organism on the planet and is crucially involved in microbial community dynamics and biogeochemical cycling in most tropical and subtropical ocean waters. This success is due, in part, to the detoxification of the reactive oxygen species hydrogen peroxide (H₂O₂) performed by “helper” organisms. Earlier work identified heterotrophic bacteria as helpers, and here, we demonstrate that rival cyanobacteria and picoeukaryotic phytoplankton can also contribute to the survival ofProchlorococcusduring exposure to H₂O₂. Whereas heterotrophic bacteria helper organisms can benefit directly from promoting the survival of carbon-fixingProchlorococcuscells, phytoplankton helpers may suffer a twofold injury: production of H₂O₂degrading enzymes constrains already limited resources in oligotrophic environments, and the activity of these enzymes bolsters the abundance of their numerically dominant competitor. These findings build toward a better understanding of the intricate dynamics and interactions that shape microbial community structure in the open ocean. 

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2. Tersicoccus phoenicis (Actinobacteria), a spacecraft clean room isolate, exhibits dormancy

   https://doi.org/10.1128/spectrum.01692-25  

   Tirumalai, Madhan; Ali, Sahar; Fox, George E; Widger, William (August 2025, Microbiology Spectrum)

   Tischler, Dirk (Ed.)

   ABSTRACT Space missions or spacecraft equipment destined for sensitive environments, such as Mars, Europa, or Enceladus, are required to be designed to avoid forward contamination. Spacecraft are assembled in clean rooms (SACs) employing treatments to eliminate microbial contamination. However, some organisms can survive the cleaning procedures. Characterization of these populations, through both culture-based and sequencing methods, reveals that the majority consists of spore-forming bacteria. However, a smaller group of non-spore-forming organisms, primarily classified within the orderMicrococcalesof the phylumActinobacteria(Actinomycetota), exists in some SACs. Despite their repeated occurrence and isolation, actinobacterial strains associated with SACs have not been studied for their dormancy potential. Here, we show for the first time that a non-spore-forming SAC isolate,Tersicoccus phoenicis(Micrococcales), enters dormancy under nutrient starvation. Dormancy inMicrococcus luteusinvolves a universal stress protein and a resuscitation-promoting factor (Rpf). Genes for these proteins are widely found in actinobacteria, includingT. phoenicis. We show that dormantT. phoenicis(Micrococcales) can be revived through the addition of the Rpf to the media. Dormancy, as observed in the SAC actinobacterial isolateT. phoenicis, could well be a common trait adopted by other actinobacterial strains under the stressful conditions of spacecraft clean rooms or the ISS (International Space Station). This has implications for the persistence, identification, and recovery of such microbes from cleanroom facilities.IMPORTANCENASA’s long-range goal of a human mission to the Mars surface raises issues relating to planetary protection. The concerns of forward contamination require that spacecraft assembly clean rooms (SACs) be maintained to inhibit microbial survival. However, despite these efforts, distinct microbial communities persist. Here, we show that a SAC isolate,T. phoenicis, exhibits dormancy, a state in which the cells are viable but not cultivable. Dormancy may help non-spore-forming organisms survive in the clean room environments utilized for space missions. This has implications for improving cleaning procedures. 

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3. The Agrobacterium fabrum efflux pump PecM is produced in response to the plant exudate 4-hydroxybenzaldehyde to avoid disruption of central metabolism

   https://doi.org/10.1128/jb.00150-25  

   Ghosh, Arpita; Grove, Anne (July 2025, Journal of Bacteriology)

   Becker, Anke (Ed.)

   ABSTRACT Agrobacterium fabrum is a phytopathogen that causes crown gall disease. In the rhizosphere, it encounters plant exudates, some of which are toxic, such as 4-hydroxybenzaldehyde (4HBA). Others, including 4-hydroxybenzoate (4HB), participate in the induction of virulence genes.A. fabrum encodes the transcription factor PecS, which has been reported to enhance bacterial fitness in the rhizosphere. The gene encoding PecS is divergent from pecM, which encodes an efflux pump. PecS represses both pecS and pecM, as evidenced by increased expression in the presence of the PecS ligand urate and by elevated pecM expression in a pecS disruption strain. We report here that the expression ofpecM is induced selectively by 4HBA. Expression of genes encoding enzymes involved in the degradation of 4HB is induced by both 4HBA and 4HB, as expected; however, overexpression ofpecM attenuates the induction by 4HBA, suggesting that 4HBA is a substrate for PecM. Consistent with this inference, untargeted metabolomics shows that 4HBA accumulates intracellularly whenpecM is disrupted. Analysis of PecS by thermal stability assay and DNase I footprinting suggests that 4HBA is not a ligand for PecS. Taken together, our data suggest that 4HBA is a substrate for PecM.IMPORTANCEPlant roots secrete a number of compounds that may be toxic to bacteria residing in the surrounding soil. One such bacterium is Agrobacterium fabrum, which infects plants and induces tumor formation. We show here that an A. fabrum strain in which the efflux pump PecM has been disrupted accumulates 4-hydroxybenzaldehyde, and that this plant root exudate induces the expression of pecM. Our data suggest that PecM and PecS, a transcription factor that regulates pecM expression, both function to promote A. fabrum fitness in the rhizosphere. As a competitive advantage in the rhizosphere is a prerequisite for subsequent plant infection, our data contribute to a more complete understanding of the A. fabrum infection process. 

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4. 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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5. Biophysical modeling reveals the transcriptional regulatory mechanism of Spo0A, the master regulator in starving Bacillus subtilis

   https://doi.org/10.1128/msystems.00072-25  

   Zhang, Yujia; Palma, Cristina_S D; Chen, Zhuo; Zarazúa-Osorio, Brenda; Fujita, Masaya; Igoshin, Oleg A; Eichenberger, Patrick (May 2025, mSystems)

   Svensson, Sarah L (Ed.)

   ABSTRACT In starvingBacillus subtilisbacteria,the initiation of two survival programs—biofilm formation and sporulation—is controlled by the same phosphorylated master regulator, Spo0A~P. Its gene,spo0A,is transcribed from two promoters, Pvand Ps,that are, respectively, regulated by RNA polymerase (RNAP) holoenzymes bearing σ^Aand σ^H. Notably, transcription is directly autoregulated by Spo0A~P binding sites known as 0A1, 0A2, and 0A3 box, located in between the two promoters. It remains unclear whether, at the onset of starvation, these boxes activate or repressspo0Aexpression, and whether the Spo0A~P transcriptional feedback plays a role in the increase inspo0Aexpression. Based on the experimental data of the promoter activities under systematic perturbation of the promoter architecture, we developed a biophysical model of transcriptional regulation ofspo0Aby Spo0A~P binding to each of the 0A boxes. The model predicts that Spo0A~P binding to its boxes does not affect the RNAP recruitment to the promoters but instead affects the transcriptional initiation rate. Moreover, the effects of Spo0A~P binding to 0A boxes are mainly repressive and saturated early at the onset of starvation. Therefore, the increase inspo0Aexpression is mainly driven by the increase in RNAP holoenzyme levels. Additionally, we reveal that Spo0A~P affinity to 0A boxes is strongest at 0A3 and weakest at 0A2 and that there are attractive forces between the occupied 0A boxes. Our findings, in addition to clarifying how the sporulation master regulator is controlled, offer a framework to predict regulatory outcomes of complex gene-regulatory mechanisms. IMPORTANCECell differentiation is often critical for survival. In bacteria, differentiation decisions are controlled by transcriptional master regulators under transcriptional feedback control. Therefore, understanding how master regulators are transcriptionally regulated is required to understand differentiation. However, in many cases, the underlying regulation is complex, with multiple transcription factor binding sites and multiple promoters, making it challenging to dissect the exact mechanisms. Here, we address this problem for theBacillus subtilismaster regulator Spo0A. Using a biophysical model, we quantitatively characterize the effect of individual transcription factor binding sites on eachspo0Apromoter. Furthermore, the model allows us to identify the specific transcription step that is affected by transcription factor binding. Such a model is promising for the quantitative study of a wide range of master regulators involved in transcriptional feedback. 

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