Bacterial physiology articles within Nature Communications

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  • Article
    | Open Access

    Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.

    • Jen Nguyen
    • , Vicente Fernandez
    •  & Roman Stocker

  • Article
    | Open Access

    Bacterial stress responses are potential targets for new antimicrobials. Here, Avican et al. present global transcriptomes for 32 bacterial pathogens grown under 11 stress conditions, and identify common and unique regulatory responses, as well as processes participating in different stress responses.

    • Kemal Avican
    • , Jehad Aldahdooh
    •  & Maria Fällman

  • Article
    | Open Access

    Bacterial cell division by cell wall synthesis proteins is guided by treadmilling filaments of the cytoskeleton protein FtsZ. Here authors use nanofabrication, advanced microscopy, and microfluidics to resolve the function of FtsZ treadmilling in the Gram-positive model organism Bacillus subtilis.

    • Kevin D. Whitley
    • , Calum Jukes
    •  & Séamus Holden

  • Article
    | Open Access

    Long-distance extracellular electron transfer has been observed in Gram-negative bacteria. Here, Yang et al. show that a filamentous, unicellular Gram-positive bacterium is capable of bidirectional extracellular electron transfer, and forms centimetre-range conductive networks consisting of 1mm-long cells and conductive appendages.

    • Yonggang Yang
    • , Zegao Wang
    •  & Mingdong Dong

  • Article
    | Open Access

    Bacteria can use type VI secretion systems (T6SSs) to inject toxic effector proteins into adjacent cells, in a contact-dependent manner. Here, the authors provide evidence of contact-independent killing by a T6SS effector that is secreted into the extracellular milieu and then taken up by other bacterial cells.

    • Li Song
    • , Junfeng Pan
    •  & Xihui Shen

  • Article
    | Open Access

    A key feature that differentiates prokaryotic cells from eukaryotes is the absence of an intracellular membrane surrounding the chromosomal DNA. Here, the authors isolate a member of the ubiquitous, yet-to-be-cultivated bacterial phylum ‘Candidatus Atribacteria’ that has an intracytoplasmic membrane apparently surrounding the nucleoid.

    • Taiki Katayama
    • , Masaru K. Nobu
    •  & Hideyuki Tamaki

  • Article
    | Open Access

    Nucleotides pppGpp and ppGpp regulate bacterial responses to nutritional and other stresses, while the potential roles of the related pGpp are unclear. Here, Yang et al. systematically identify proteins interacting with these nucleotides in Bacillus, and show that pGpp has roles distinct from those of (p)ppGpp.

    • Jin Yang
    • , Brent W. Anderson
    •  & Jue D. Wang

  • Article
    | Open Access

    There are several pathways for CO2 fixation in photoautotrophic and chemoautotrophic microorganisms. Here, the authors provide experimental demonstration for the operation of the reductive glycine pathway in a natural microorganism, Desulfovibrio desulfuricans.

    • Irene Sánchez-Andrea
    • , Iame Alves Guedes
    •  & Alfons J. M. Stams

  • Article
    | Open Access

    Bacterial transcriptomic data have been used to predict antibiotic susceptibility in a species- or antibiotic-specific manner. Here, the authors show that global transcriptional disorder is a common stress response in bacteria with low fitness, and present a general approach that can predict bacterial fitness independently of species or type of stress.

    • Zeyu Zhu
    • , Defne Surujon
    •  & Tim van Opijnen

  • Article
    | Open Access

    FasR is a TetR-like transcriptional activator that plays a central role in sensing mycobacterial long-chain fatty acids and regulating lipid biosynthesis in Mycobacterium tuberculosis. Here authors present crystal structures of M. tuberculosis FasR in complex with acyl effector ligands and with DNA, uncovering its molecular sensory and switching mechanisms.

    • Julia Lara
    • , Lautaro Diacovich
    •  & Alejandro Buschiazzo

  • Article
    | Open Access

    The gut microbiota can alter the effects of anticancer fluoropyrimidines such as 5-fluorodeoxyuridine (FUdR) in the model organism C. elegans. Here, the authors show that these effects are further affected by diet, and dietary thymidine and serine increase FUdR toxicity in C. elegans via different mechanisms.

    • Wenfan Ke
    • , James A. Saba
    •  & Eyleen J. O’Rourke

  • Article
    | Open Access

    Bacterial persister cells exhibit a transient non-growing state and antibiotic tolerance. Here, Peyrusson et al. provide evidence of metabolically active Staphylococcus aureus persisters within infected host cells exposed to antibiotics and analyse transcriptomic alterations associated with persistence.

    • Frédéric Peyrusson
    • , Hugo Varet
    •  & Françoise Van Bambeke

  • Article
    | Open Access

    The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.

    • Jesús Cámara-Almirón
    • , Yurena Navarro
    •  & Diego Romero

  • Article
    | Open Access

    Chakraborty et al. show that phagocyte NADPH oxidase (NOX2) collapses the ΔpH of intracellular Salmonella Typhimurium, leading to oxidative damage of cell envelope proteins. Salmonella responds by shifting redox balance from respiration to glycolysis and fermentation, thereby facilitating folding of periplasmic functions.

    • Sangeeta Chakraborty
    • , Lin Liu
    •  & Andres Vazquez-Torres

  • Article
    | Open Access

    The cyanobacterium Synechococcus elongatus is a model organism for the study of circadian rhythms, and is naturally competent for transformation. Here, Taton et al. identify genes required for natural transformation in this organism, and show that the coincidence of circadian dusk and darkness regulates the competence state in different day lengths.

    • Arnaud Taton
    • , Christian Erikson
    •  & Susan S. Golden

  • Article
    | Open Access

    The mechanisms of Z-ring assembly and regulation in bacteria are poorly understood, particularly in non-model organisms. Here, Sogues et al. study the interaction between FtsZ and SepF in Corynebacterium glutamicum, showing an essential interdependence of these proteins for formation of a functional Z-ring.

    • Adrià Sogues
    • , Mariano Martinez
    •  & Pedro M. Alzari

  • Article
    | Open Access

    The ability to grow at acidic pH is crucial for E. coli colonization of the host’s intestine. Here, the authors identify an acid-tolerance response system that is important for E. coli exponential growth at pH 4.2, survival in the mouse intestine, and production of 3-hydroxypropionate during fermentation.

    • Ying Xu
    • , Zhe Zhao
    •  & Guang Zhao

  • Article
    | Open Access

    The enzyme SpoT is important for accumulation of the alarmone (p)ppGpp, which triggers the stringent response in E. coli. Here, Germain et al. show that the protein YtfK promotes SpoT-dependent accumulation of (p)ppGpp and is required for activation of the stringent response during phosphate and fatty acid starvation.

    • Elsa Germain
    • , Paul Guiraud
    •  & Etienne Maisonneuve

  • Article
    | Open Access

    In bacteria, the conserved trans-translation system serves as the primary pathway of ribosome rescue, but many species can also use alternative rescue pathways. Here the authors report that in B. subtilis, the rescue factor BrfA binds to non-stop stalled ribosomes, recruits RF2 but not RF1, and induces transition of the ribosome into an open active conformation.

    • Naomi Shimokawa-Chiba
    • , Claudia Müller
    •  & Shinobu Chiba

  • Article
    | Open Access

    Carbon sources can modulate biofilm formation and host colonization in Vibrio cholerae. Here, Heo et al. show that this process is mediated by a component of the PEP:carbohydrate phosphotransferase system (PTS), which regulates c-di-GMP hydrolysis by interacting with a c-di-GMP phosphodiesterase.

    • Kyoo Heo
    • , Young-Ha Park
    •  & Yeong-Jae Seok

  • Article
    | Open Access

    Individual bacteria within isogenic populations can differ in antibiotic tolerance. Here, Libby et al. show that antibiotic tolerance variability can be driven by ‘noisy’ expression of a gene encoding a (p)ppGpp synthetase, which is in turn regulated by multisite phosphorylation of a transcription factor.

    • Elizabeth A. Libby
    • , Shlomi Reuveni
    •  & Jonathan Dworkin

  • Article
    | Open Access

    The reservoir for recurrent urinary tract infection in humans is unclear. Here, Mickiewicz et al. detect cell-wall deficient (L-form) E. coli in fresh urine from patients, and show that the isolated bacteria readily switch between walled and L-form states.

    • Katarzyna M. Mickiewicz
    • , Yoshikazu Kawai
    •  & Jeff Errington

  • Article
    | Open Access

    The mechanisms behind CO2 dependency in non-autotrophic bacterial isolates are unclear. Here the authors show that the Staphylococcus aureus mpsAB operon is crucial for growth at atmospheric CO2 levels, and provide evidence indicating that MpsAB represents a bicarbonate concentrating system.

    • Sook-Ha Fan
    • , Patrick Ebner
    •  & Friedrich Götz

  • Article
    | Open Access

    Ammonia-oxidizing bacteria and archaea are major producers of the gases nitrous oxide and nitric oxide. Here, Kits et al. show that a complete ammonia-oxidizing (comammox) bacterium emits nitrous oxide at levels that are comparable to those produced by ammonia-oxidizing archaea.

    • K. Dimitri Kits
    • , Man-Young Jung
    •  & Holger Daims

  • Article
    | Open Access

    Cofactor F420 plays crucial roles in bacterial and archaeal metabolism, but its biosynthetic pathway is not fully understood. Here, the authors present the structure of one of the enzymes and provide experimental evidence for a substantial revision of the pathway, including the identification of a new intermediate.

    • Ghader Bashiri
    • , James Antoney
    •  & Colin J. Jackson

  • Article
    | Open Access

    Extracellular electron uptake (EEU) is the ability of microbes to take up electrons from solid-phase conductive substances such as metal oxides. Here, Guzman et al. show that electrons enter the photosynthetic electron transport chain and are used for CO2 fixation during EEU in a phototrophic bacterium.

    • Michael S. Guzman
    • , Karthikeyan Rengasamy
    •  & Arpita Bose

  • Article
    | Open Access

    Anammox bacteria couple nitrite reduction to ammonium oxidation, with nitric oxide (NO) and hydrazine as intermediates, and produce N2 and nitrate. Here, Hu et al. show that an anammox bacterium can grow in the absence of nitrite by coupling ammonium oxidation to NO reduction, producing only N2.

    • Ziye Hu
    • , Hans J. C. T. Wessels
    •  & Boran Kartal

  • Article
    | Open Access

    Bacteria can become dormant or form spores when starved for nutrients. Here, Gray et al. describe an alternative strategy, or ‘oligotrophic growth state’, showing that non-sporulating Bacillus subtilis cells can survive deep starvation conditions by adopting an almost coccoid shape and extremely low growth rates.

    • Declan A. Gray
    • , Gaurav Dugar
    •  & Leendert W. Hamoen

  • Article
    | Open Access

    Most cyanobacteria are oxygenic photoautotrophs, and fermenters under dark anoxic conditions. Here, the authors analyse genomic sequences of related uncultivated bacteria, inferring their metabolic potential, and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.

    • Paula B. Matheus Carnevali
    • , Frederik Schulz
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Natural genetic transformation in bacteria requires DNA binding at the surface of competent cells. Here, Mirouze et al. show that wall teichoic acids are specifically produced or modified during competence in Bacillus subtilis and promote (directly or indirectly) DNA binding at the cell surface.

    • Nicolas Mirouze
    • , Cécile Ferret
    •  & Rut Carballido-López

  • Article
    | Open Access

    Lysine degradation and the role of the metabolites glutarate and L-2-hydroxyglutarate have remained elusive in many organisms including Escherichia coli. Here authors present a pathway for catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates.

    • Sebastian Knorr
    • , Malte Sinn
    •  & Jörg S. Hartig

  • Article
    | Open Access

    A Paleoproterozoic carbon isotope anomaly is likely linked to burial of oceanic cyanobacteria, but it is not clear how burial occurred. Here, the authors find that, under Paleoproterozoic pCO2 conditions, planktonic cyanobacteria increase exopolysaccharide production and mineralization, leading to aggregation and faster sinking.

    • Nina A. Kamennaya
    • , Marcin Zemla
    •  & Christer Jansson

  • Article
    | Open Access

    Whether electrochemically active bacteria (EAB) can gain energy according to electrode potentials is still unclear. Here, the authors show through transcriptome and deletion mutant analyses that EAB can sense electrode potentials by the Arc system and activate NADH-dependent catabolic pathway to generate ATP.

    • Atsumi Hirose
    • , Takuya Kasai
    •  & Atsushi Kouzuma

  • Article
    | Open Access

    It is unclear whether the transfer of plasmids carrying antibiotic resistance genes can explain their persistence when antibiotics are not present. Here, Lopatkin et al. show that conjugal plasmids, even when costly, are indeed transferred at sufficiently high rates to be maintained in the absence of antibiotics.

    • Allison J. Lopatkin
    • , Hannah R. Meredith
    •  & Lingchong You

  • Article
    | Open Access

    The RNA-binding protein CsrA regulates the expression of hundreds of bacterial genes. Here, Potts et al. use several approaches to assess the contribution of CsrA to global gene expression in E. coli, revealing new binding targets and physiological roles such as in envelope function and iron homeostasis.

    • Anastasia H. Potts
    • , Christopher A. Vakulskas
    •  & Tony Romeo

  • Article
    | Open Access

    Transcription factors MarR and MarA confer multidrug resistance in enteric bacteria by modulating efflux pump and porin expression. Here, Sharma et al. show that MarA also upregulates genes required for lipid trafficking and DNA repair, thus reducing antibiotic entry and quinolone-induced DNA damage.

    • Prateek Sharma
    • , James R. J. Haycocks
    •  & David C. Grainger

  • Article
    | Open Access

    Fast-growing bacteria produce many proteins in excess of what seems optimal for exponential growth. Here, the authors present a mathematical model and experimental evidence supporting that this overexpression serves as a strategic reserve to quickly meet demand upon sudden improvement in growth conditions.

    • Matteo Mori
    • , Severin Schink
    •  & Terence Hwa

  • Article
    | Open Access

    Cooperative behaviour among individuals provides a collective benefit, but is considered costly. Using Pseudomonas aeruginosa as a model system, the authors show that secretion of the siderophore pyoverdine only incurs a fitness cost and favours cheating when its building blocks carbon or nitrogen are growth-limiting.

    • D. Joseph Sexton
    •  & Martin Schuster

  • Article
    | Open Access

    The mechanisms of action of the antibacterial metalloid tellurite are unclear. Here, the authors show that tellurite induces an accumulation of hydroxyl radical and intermediates of heme biosynthesis inE. coli, and that the heme precursor 5-aminolevulinic acid potentiates tellurite toxicity.

    • Eduardo H. Morales
    • , Camilo A. Pinto
    •  & Claudio C. Vásquez

  • Article
    | Open Access

    Enzyme I, a component of the phosphoenolpyruvate-carbohydrate phosphotransferase system (PTS), converts phosphoenolpyruvate to pyruvate. Here, the authors show that Enzyme I facilitates also the reverse reaction during both gluconeogenic and glycolytic growth inE. coli.

    • Christopher P. Long
    • , Jennifer Au
    •  & Maciek R. Antoniewicz

  • Article
    | Open Access

    Direct interspecies electron transfer has been shown in methane-producing communities, but it is unknown how widespread this mechanism is. Here, Haet al. show that anoxygenic photosynthesis can be driven by direct electron transfer from a heterotrophic partner bacterium.

    • Phuc T. Ha
    • , Stephen R. Lindemann
    •  & Haluk Beyenal

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