Bacterial evolution articles within Nature Communications

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  • Article
    | Open Access

    Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.

    • Erqin Li
    • , Ronnie de Jonge
    •  & Alexandre Jousset

  • Article
    | Open Access

    Dating early bacterial evolution is challenging due to the limited bacterial fossil record. Here Wang and Luo use the close evolutionary relationship between Alphaproteobacteria and mitochondria to leverage the eukaryotic fossil record in dating Alphaproteobacteria origin and diversification.

    • Sishuo Wang
    •  & Haiwei Luo

  • Article
    | Open Access

    Long-term infection of cystic fibrosis patients with Pseudomonas aeruginosa is often accompanied by a reduction in bacterial growth rate. Here, La Rosa et al. use adaptive laboratory evolution to increase the growth rate of clinical isolates, and identify mechanisms and evolutionary trajectories that, in reverse direction, may help the pathogen to adapt to the patients’ airways.

    • Ruggero La Rosa
    • , Elio Rossi
    •  & Søren Molin

  • Article
    | Open Access

    The Candidate Phyla Radiation (CPR) constitutes a large group of bacterial lineages with small cell sizes and limited biosynthetic capabilities. Here, Moreira et al. study the biology and genome of Vampirococcus lugosii, an epibiotic parasite of other bacteria, supporting parasitism as a common lifestyle of CPR bacteria.

    • David Moreira
    • , Yvan Zivanovic
    •  & Purificación López-García

  • Article
    | Open Access

    Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, Ellabaan et al. use a statistical approach to identify putative mobilisation elements and other features associated with ARG transfer among bacterial clades to predict the potential future dissemination of known ARGs.

    • Mostafa M. H. Ellabaan
    • , Christian Munck
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    The photosynthesis performed by trees makes them an important sink for atmospheric carbon dioxide, but trees are also sources of the potent greenhouse gas methane. Here the authors find that tree bark in some common lowland species is colonized by methane oxidizing bacteria that can reduce tree methane emissions by ~ 36%.

    • Luke C. Jeffrey
    • , Damien T. Maher
    •  & Scott G. Johnston

  • Article
    | Open Access

    It is unclear how gut-dwelling E. coli bacteria often emerge to cause systemic infection in chickens. Here, Mageiros et al. use population genomics and pangenome-wide association studies to identify genetic elements associated with pathogenicity in avian E. coli.

    • Leonardos Mageiros
    • , Guillaume Méric
    •  & Samuel K. Sheppard

  • Article
    | Open Access

    Vibrio cholerae uses a type VI secretion system (T6SS) to kill neighbouring competitors. Here, Santoriello et al. show that a T6SS gene cluster (Aux3) exists as a mobile, prophage-like element in some environmental strains, and as a stable truncated form in pandemic isolates. They propose that Aux3 acquisition increased competitive fitness of pre-pandemic V. cholerae.

    • Francis J. Santoriello
    • , Lina Michel
    •  & Stefan Pukatzki

  • Article
    | Open Access

    Game theory has contributed much to the understanding of social evolution. In an elegant combination of experimental tests and modelling, this study suggests that when bacteria face intense competition, repeated retaliation outcompetes a single tit-for-tat response to attack.

    • William P. J. Smith
    • , Maj Brodmann
    •  & Kevin R. Foster

  • Article
    | Open Access

    Gene tandem amplifications can drive bacterial evolution. Here, Belikova et al. identify copy number variations of lipoprotein-encoding genes in Staphylococcus aureus clinical isolates, and show that the loci expand and contract during bacterial growth in vitro and in mice, leading to changes in immunostimulatory capacity.

    • Darya Belikova
    • , Angelika Jochim
    •  & Simon Heilbronner

  • Article
    | Open Access

    Beta-lactam antibiotics and beta-lactamase inhibitors compete for the same binding site on beta-lactamases; thus, mutations that increase beta-lactamase activity likely increase also susceptibility to the inhibitor. Here, Russ et al. identify rare mutations in the ampC beta-lactamase gene that escape this adaptive tradeoff specifically for certain drug combinations.

    • Dor Russ
    • , Fabian Glaser
    •  & Roy Kishony

  • Article
    | Open Access

    The emergence of multidrug resistance (MDR) in bacteria represents a global threat to human health. Here, Cazares et al. identify a family of MDR megaplasmids carrying large arrays of antibiotic resistance genes in Pseudomonas strains from various sources, including P. aeruginosa clinical isolates.

    • Adrian Cazares
    • , Matthew P. Moore
    •  & Craig Winstanley

  • Article
    | Open Access

    The authors study the interactions between chromosomal mutations and horizontally acquired genes in the evolution of antibiotic resistance in experimental evolution assays. They identify constraints that may allow better prediction and control of antibiotic resistance evolution.

    • Andreas Porse
    • , Leonie J. Jahn
    •  & Morten O. A. Sommer

  • Article
    | Open Access

    Newly acquired plasmids are frequently lost due to fitness costs. Here, Zhang et al. show that the evolution of satellite plasmids with gene deletions can reduce fitness costs by driving down the copy number of full plasmids and thus favor maintenance of the full plasmid and its novel accessory genes.

    • Xue Zhang
    • , Daniel E. Deatherage
    •  & Jeffrey E. Barrick

  • Article
    | Open Access

    Phagocytosis is a typically eukaryotic feature that could be behind the origin of eukaryotic cells. Here, the authors describe a bacterium that can engulf other bacteria and small eukaryotic cells through a phagocytosis-like mechanism.

    • Takashi Shiratori
    • , Shigekatsu Suzuki
    •  & Ken-ichiro Ishida

  • Article
    | Open Access

    Listeria monocytogenes isolates are highly heterogeneous and exhibit different levels of virulence. Here, the authors identify hypervirulent isolates that represent a hybrid sub-lineage of the major lineage II harbouring virulence factors from Listeria ivanovii and wall teichoic acids found in major lineage I.

    • Yuelan Yin
    • , Hao Yao
    •  & Xin’an Jiao

  • Article
    | Open Access

    Recent studies have identified a large, phylogenetically distinct clade of bacteria, the candidate phyla radiation (CPR). Here, Méheust and colleagues analyze almost 3600 genomes to characterize the protein family content of CPR versus other bacteria and archaea.

    • Raphaël Méheust
    • , David Burstein
    •  & Jillian F. Banfield

  • Article
    | Open Access

    Chemosynthetic microbial communities in hydrothermal environments receiving meteoric and geothermal fluids are understudied. Here, Colman et al. use metagenomics to study one such community from a hot spring at Yellowstone National Park, revealing exceptional biodiversity and unique functional potential.

    • Daniel R. Colman
    • , Melody R. Lindsay
    •  & Eric S. Boyd

  • Article
    | Open Access

    Development of bacterial resistance to an antibiotic can lead to collateral sensitivity to another drug. Here, the authors study collateral sensitivity conferred by mutations in the horizontally acquired β-lactamase CTX-M-15, and identify antibiotic combinations that constrain the evolution of resistance.

    • Carola E. H. Rosenkilde
    • , Christian Munck
    •  & Morten O. A. Sommer

  • 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

    The evolution of resistance to an antibiotic can render bacteria more susceptible, or more resistant, to a second antibiotic. Here, Nichol et al. provide evidence that the final outcome can be fairly stochastic and depends on the shape of the evolutionary fitness landscape.

    • Daniel Nichol
    • , Joseph Rutter
    •  & Jacob G. Scott

  • Article
    | Open Access

    Staphylococcus epidermidis is carried asymptomatically by virtually all humans but is also a major cause of nosocomial infection. Here, the authors study 141 isolates from healthy carriage and 274 isolates from clinical infections, and identify genes and genetic elements associated with pathogenicity.

    • Guillaume Méric
    • , Leonardos Mageiros
    •  & Samuel K. Sheppard

  • Article
    | Open Access

    Since the 1980s, hypervirulent clonal-group CG23 serotype K1 Klebsiella pneumoniae has been recognised as a prominent cause of community-acquired liver abscess and other severe infections. Here, the authors investigate the genomic evolutionary history of CG23 and suggest a new reference strain for CG23.

    • Margaret M. C. Lam
    • , Kelly L. Wyres
    •  & Kathryn E. Holt

  • Article
    | Open Access

    Mutations in gene pmrB are found in Pseudomonas aeruginosa isolates from cystic fibrosis patients. Here, Bricio-Moreno et al. show in a mouse model of respiratory infection that the mutations enhance bacterial adherence to epithelial cells and resistance to lysozyme, but also increase antibiotic susceptibility.

    • Laura Bricio-Moreno
    • , Victoria H. Sheridan
    •  & Daniel R. Neill

  • Article
    | Open Access

    Sexual recombination and mutation rate may play different roles in adaptive evolution depending on the fitness landscape. Here, Peabody et al. examine how the two factors affect the rate of adaptation of an E. coli strain capable of sexual recombination, under different conditions during experimental evolution.

    • George L. Peabody V
    • , Hao Li
    •  & Katy C. Kao

  • Article
    | Open Access

    The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.

    • Danny Ionescu
    • , Mina Bizic-Ionescu
    •  & Hans-Peter Grossart

  • Article
    | Open Access

    Some antibiotic resistance genes found in pathogenic bacteria might derive from antibiotic-producing actinobacteria. Here, Jianget al. provide bioinformatic and experimental evidence supporting this hypothesis, and propose a specific mechanism for the transfer of these genes between bacterial phyla.

    • Xinglin Jiang
    • , Mostafa M. Hashim Ellabaan
    •  & Sang Yup Lee

  • Article
    | Open Access

    The production of secreted polymers in bacterial biofilms is costly, and therefore mechanisms preventing invasion of non-producing mutants are hypothesized. Here, the authors show that non-producers can evolve the ability to better incorporate into biofilms via phage-mediated interference.

    • Marivic Martin
    • , Anna Dragoš
    •  & Ákos T. Kovács

  • Article
    | Open Access

    Both host diet and phylogeny have been argued to shape mammalian microbiome communities. Here, the authors show that diet predicts the presence of ancient bacterial lineages in the microbiome, but that co-speciation between more recent bacterial lineages and their hosts may drive associations between microbiome composition and phylogeny.

    • Mathieu Groussin
    • , Florent Mazel
    •  & Eric J. Alm

  • Article
    | Open Access

    Antibiotic resistance is common in environmental bacteria, including those living in isolated caves. Here, Pawlowskiet al. study one of these bacterial strains, showing that it is resistant to most clinically used antibiotics through a remarkable variety of mechanisms, some of which are new to science.

    • Andrew C. Pawlowski
    • , Wenliang Wang
    •  & Gerard D. Wright

  • Article
    | Open Access

    The genome of some bacteria consists of two or more chromosomes or replicons. Here, diCenzo et al. integrate genome-scale metabolic modelling and growth data from a collection of mutants of the plant symbiont Sinorhizobium melilotito estimate the fitness contribution of each replicon in three environments.

    • George C. diCenzo
    • , Alice Checcucci
    •  & Marco Fondi

  • Article
    | Open Access

    Chlamydia trachomatis isolates causing a blinding disease (trachoma) form a single lineage that is different from the lineages causing urogenital infections. Here, Andersson et al. show however that trachoma isolates from Australia are more closely related to urogenital strains than to other trachoma isolates.

    • Patiyan Andersson
    • , Simon R. Harris
    •  & Philip M. Giffard

  • Article
    | Open Access

    The division of labour—where individuals specialise on different tasks—is fundamental to many sophisticated and ancient biological systems. Here the authors show that bacteria can deploy a robust and functional division of labour in a matter of days via a single mutation.

    • Wook Kim
    • , Stuart B. Levy
    •  & Kevin R. Foster

  • Article
    | Open Access

    The bacterium Bdellovibrio bacteriovorus invades and kills other bacteria, but it is unclear how it avoids degradation of its own cell wall. Here the authors identify the B. bacteriovorusprotein Bd3460 as an endopeptidase inhibitor that prevents hydrolysis of the predator’s peptidoglycan during invasion of prey.

    • Carey Lambert
    • , Ian T. Cadby
    •  & Andrew L. Lovering

  • Article
    | Open Access

    Some species of social bacteria can chemically modify their nutrient environments, which may influence community interactions. Here, McClean et al.show that changes at a single gene locus in a biofilm-forming bacteria can perturb community structure to the same extent as the loss of an apex predator.

    • Deirdre McClean
    • , Luke McNally
    •  & Ian Donohue

  • Article
    | Open Access

    Yersinia pestis, which evolved from a gastrointestinal pathogen, causes pneumonic and bubonic plague. Here Zimbler et al. show that the gain of a single protein enabled Y. pestisto first cause pneumonic plague, and one amino-acid change in the same protein then allowed the bacteria to efficiently cause bubonic plague.

    • Daniel L. Zimbler
    • , Jay A. Schroeder
    •  & Wyndham W. Lathem

  • Article
    | Open Access

    The relationship between mutations and phenotypic changes associated with drug resistance in bacteria remains unclear. Here, the authors use antibiotic-resistant E. colistrains, obtained by laboratory evolution, to show that resistance profiles can be predicted by changes in expression of a few genes.

    • Shingo Suzuki
    • , Takaaki Horinouchi
    •  & Chikara Furusawa

  • Article |

    Genes acquired by horizontal transfer must be incorporated into existing regulatory networks to become functional. Here, Will et al. show that conserved and horizontally acquired PhoP-regulated genes in Salmonellaare regulated by distinct mechanisms, defined by promoter architecture.

    • W. Ryan Will
    • , Denise H. Bale
    •  & Ferric C. Fang

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