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1. Quorum sensing mediates morphology and motility transitions in the model archaeon Haloferax volcanii

   https://doi.org/10.1128/mbio.00906-25  

   Chatterjee, Priyanka; Consoli, Caroline E; Schiller, Heather; Winter, Kiersten K; McCallum, Monica E; Schulze, Stefan; Pohlschroder, Mechthild (June 2025, mBio)

   Newman, Dianne K (Ed.)

   ABSTRACT Quorum sensing (QS) is a population density-dependent mechanism of intercellular communication, whereby microbes secrete and detect signals to regulate behaviors such as virulence and biofilm formation. Although QS is well-studied in bacteria, little is known about cell-cell communication in archaea. The model archaeonHaloferax volcaniican transition from motile rod-shaped cells to non-motile disks as population density increases. In this report, we demonstrate that this transition is induced by a secreted small molecule present in cell-free conditioned medium (CM). The CM also elicits a response from a bacterial QS bioreporter, suggesting the potential for inter-domain crosstalk. To investigate theHfx. volcaniiQS response, we performed quantitative proteomics and detected significant differential abundances of 236 proteins in the presence of CM, including proteins involved in cell structure, motility, glycosylation, and two-component systems. We also demonstrate that a mutant lacking the cell shape regulatory factor DdfA does not undergo shape and motility transitions in the presence of CM, allowing us to identify protein abundance changes in the QS response pathway separate from those involved in shape and motility. In the ∆ddfAstrain, only 110 proteins had significant differential abundance, and comparative analysis of these two proteomics experiments enabled us to identify proteins dependent on and independent of DdfA in the QS response pathway. Our study provides the first detailed analysis of QS pathways in any archaeon, strengthening our understanding of archaeal communication as well as providing the framework for studying intra- and interdomain crosstalk. IMPORTANCEUnderstanding the complex signaling networks in microbial communities has led to many invaluable applications in medicine and industry. Yet, while archaea are ubiquitous and play key roles in nutrient cycling, little is known about the roles of archaeal intra- and interspecies cell-cell communication in environments such as the human, soil, and marine microbiomes. In this study, we established the first robust system for studying quorum sensing in archaea by using the model archaeonHaloferax volcanii. We demonstrated that different behaviors, such as cell shape and motility, are mediated by a signal molecule, and we uncovered key regulatory components of the signaling pathway. This work advances our understanding of microbial communication, shedding light on archaeal intra- and interdomain interactions, and contributes to a more complete picture of the interconnected networks of life on Earth. 

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2. Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy

   https://doi.org/10.1128/msphere.00343-25  

   Dallon, Emma; Moran, Haley M; Chidambaran, Sadhana R; Kian, Arman; Huang, Betty_Y H; Fried, Stephen D; DiRuggiero, Jocelyne (September 2025, mSphere)

   Ellermeier, Craig D (Ed.)

   ABSTRACT Oxidative stress induces a wide range of cellular damage, often causing disease and cell death. While many organisms are susceptible to the effects of oxidative stress, haloarchaea have adapted to be highly resistant. Several aspects of the haloarchaeal oxidative stress response have been characterized; however, little is known about the impacts of oxidative stress at the translation level. Using the model archaeonHaloferax volcanii, we performed RNA-seq and ribosome profiling (Ribo-seq) to characterize the global translation landscape during oxidative stress. We identified 281 genes with differential translation efficiency (TE). Downregulated genes were enriched in ribosomal and translation proteins, in addition to peroxidases and genes involved in the TCA cycle. We also identified 42 small noncoding RNAs (sRNAs) with ribosome occupancy. Size distributions of ribosome footprints revealed distinct patterns for coding and noncoding genes, with 12 sRNAs matching the pattern of coding genes, and mass spectrometry confirming the presence of seven small proteins encoded by these sRNAs. However, the majority of sRNAs with ribosome occupancy had no evidence of coding potential. Of these ribosome-associated sRNAs, 12 had differential ribosome occupancy or TE during oxidative stress, suggesting that they may play a regulatory role during the oxidative stress response. Our findings on ribosomal regulation during oxidative stress, coupled with potential roles for ribosome-associated noncoding sRNAs and sRNA-derived small proteins inH. volcanii, revealed additional regulatory layers and underscored the multifaceted architecture of stress-responsive regulatory networks.IMPORTANCEArchaea are found in diverse environments, including as members of the human microbiome, and are known to play essential ecological roles in major geochemical cycles. The study of archaeal biology has expanded our understanding of the evolution of eukaryotes, uncovered novel biological systems, and revealed new opportunities for applications in biotechnology and bioremediation. Many archaeal systems, however, remain poorly characterized. UsingHaloferax volcaniias a model, we investigated the global translation landscape during oxidative stress. Our findings expand current knowledge of translational regulation in archaea and further illustrate the complexity of stress-responsive gene regulation. 

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3. Evolutionary trends in Bombella apis CRISPR-Cas systems

   https://doi.org/10.1128/msystems.00166-25  

   Ganote, Carrie L; Caesar, Lílian; Rice, Danny W; Whitaker, Rachel J; Newton, Irene_L G (July 2025, mSystems)

   Gilbert, Jack A (Ed.)

   ABSTRACT Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found inBombella apis.B. apisis an important honey bee symbiont, found primarily in larvae, queens, and hive compartments.B. apisis found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However,B. apisappears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired byB. apisin its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types acrossB. apisstrains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the sameB. apisgenomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for eachB. apisstrain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that theB. apisCRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe. IMPORTANCEHoney bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacteriumBombella apis.B. apisis found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen’s digestive tract. The roles thatB. apismay serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity inB. apismay be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay betweenB. apisand its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host. 

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4. Euprymna berryi as a comparative model host for Vibrio fischeri light organ symbiosis

   https://doi.org/10.1128/aem.00001-25  

   Imes, Avery M; Pavelsky, Morgan N; Badal, Klodia; Kamp, Derrick L; Briseño, John L; Sakmar, Taylor; Vogt, Miranda A; Nyholm, Spencer V; Heath-Heckman, Elizabeth_A C; Grasse, Bret; et al (July 2025, Applied and Environmental Microbiology)

   Rudi, Knut (Ed.)

   ABSTRACT Functional studies of host-microbe interactions benefit from natural model systems that enable the exploration of molecular mechanisms at the host-microbe interface. BioluminescentVibrio fischericolonize the light organ of the Hawaiian bobtail squid,Euprymna scolopes, and this binary model has enabled advances in understanding host-microbe communication, colonization specificity,in vivobiofilms, intraspecific competition, and quorum sensing. The hummingbird bobtail squid,Euprymna berryi,can be generationally bred and maintained in lab settings and has had multiple genes deleted by CRISPR approaches. The prospect of expanding the utility of the light organ model system by producing multigenerational host lines led us to determine the extent to which theE. berryilight organ symbiosis parallels known processes inE. scolopes. However, the nature of theE. berryilight organ, including its microbial constituency and specificity for microbial partners, has not been examined. In this report, we isolated bacteria fromE. berryianimals and tank water. Assays of bacterial behaviors required in the host, as well as host responses to bacterial colonization, illustrate largely parallel phenotypes inE. berryiandE. scolopeshatchlings. This study revealsE. berryito be a valuable comparative model to complement studies inE. scolopes.IMPORTANCEMicrobiome studies have been substantially advanced by model systems that enable functional interrogation of the roles of the partners and the molecular communication between those partners. TheEuprymna scolopes-Vibrio fischerisystem has contributed foundational knowledge, revealing key roles for bacterial quorum sensing broadly and in animal hosts, for bacteria in stimulating animal development, for bacterial motility in accessing host sites, and forin vivobiofilm formation in development and specificity of an animal’s microbiome.Euprymna berryiis a second bobtail squid host, and one that has recently been shown to be robust to laboratory husbandry and amenable to gene knockout. This study identifiesE. berryias a strong symbiosis model host due to features that are conserved with those ofE. scolopes, which will enable the extension of functional studies in bobtail squid symbioses. 

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5. Global phylogeography and microdiversity of the marine diazotrophic photoautotrophs Trichodesmium and UCYN-A

   https://doi.org/10.1128/msphere.00245-25  

   Nguyen, Angie; Ustick, Lucas J; Larkin, Alyse A; Martiny, Adam C (July 2025, mSphere)

   Campbell, Barbara J (Ed.)

   ABSTRACT Photoautotrophic diazotrophs, specifically the generaTrichodesmiumand UCYN-A, play a pivotal role in marine nitrogen cycling through their capacity for nitrogen fixation. Despite their global distribution, the microdiversity and environmental drivers of these diazotrophs remain underexplored. This study provides a comprehensive analysis of the global diversity and distribution ofTrichodesmiumand UCYN-A using the nitrogenase gene (nifH) as a genetic marker. We sequenced 954 samples from the Pacific, Atlantic, and Indian Oceans as part of the Bio-GO-SHIP project. Our results reveal significant phylogenetic and biogeographic differences between and within the two genera.Trichodesmiumexhibited greater microdiversity compared to UCYN-A, with clades showing region-specific distribution.Trichodesmiumclades were primarily influenced by temperature and nutrient availability. They were particularly frequent in regions of phosphorus stress. In contrast, UCYN-A was most frequently observed in regions experiencing iron stress. UCYN-A clades demonstrated more homogeneous distributions, with a single sequence variant within the UCYN-A1 clade dominating across varied environments. The biogeographic patterns and environmental correlations ofTrichodesmiumand UCYN-A highlight the role of microdiversity in their ecological adaptation and reflect their different ecological strategies. These findings underscore the importance of characterizing the global patterns of fine-scale genetic diversity to better understand the functional roles and distribution of marine nitrogen-fixing photoautotrophs.IMPORTANCEThis study provides insights into the global diversity and distribution of nitrogen-fixing photoautotrophs, specificallyTrichodesmiumand UCYN-A. We sequenced 954 oceanic samples of thenifHnitrogenase gene and uncovered significant differences in microdiversity and environmental associations between these genera.Trichodesmiumshowed high levels of sequence diversity and region-specific clades influenced by temperature and nutrient availability. In contrast, UCYN-A exhibited a more uniform distribution, thriving in iron-stressed regions. Quantifying these fine-scale genetic variations enhances our knowledge of their ecological roles and adaptations, emphasizing the need to characterize the genetic diversity of marine nitrogen-fixing prokaryotes. 

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