Evolution with a seed bank: The population genetic consequences of microbial dormancy

Recombination-Driven Genome Evolution and Stability of Bacterial Species

(2017) Purushottam D. Dixit et al.   GENETICS

Multi-colony Wright–Fisher with seed-bank

(2017) Frank den Hollander et al.   INDAGATIONES MATHEMATICAE-NEW SERIES

Persistent bacterial infections and persister cells

(2017) Robert A. Fisher et al.   NATURE REVIEWS MICROBIOLOGY

Resuscitation ofPseudomonas aeruginosafrom dormancy requires hibernation promoting factor (PA4463) for ribosome preservation

(2017) Tatsuya Akiyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial community assembly and evolution in subseafloor sediment

(2017) Piotr Starnawski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

Fisher–Wright model with deterministic seed bank and selection

(2017) Bendix Koopmann et al.   THEORETICAL POPULATION BIOLOGY

Speciation trajectories in recombining bacterial species

(2017) Pekka Marttinen et al.   PLoS Computational Biology

Microscale Insight into Microbial Seed Banks

(2017) Kenneth J. Locey et al.   Frontiers in Microbiology

Drivers of Bacterial Maintenance and Minimal Energy Requirements

(2017) Christopher P. Kempes et al.   Frontiers in Microbiology

Recombination-Driven Genome Evolution and Stability of Bacterial Species

(2017) Purushottam D. Dixit et al.   GENETICS

A new coalescent for seed-bank models

(2016) Jochen Blath et al.   ANNALS OF APPLIED PROBABILITY

Slow Microbial Life in the Seabed

(2016) Bo Barker Jørgensen et al.   Annual Review of Marine Science

How clonal are bacteria over time?

(2016) B Jesse Shapiro   CURRENT OPINION IN MICROBIOLOGY

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

The Built Environment Is a Microbial Wasteland

(2016) Sean M. Gibbons   mSystems

A generation-time effect on the rate of molecular evolution in bacteria

(2015) Cory Weller et al.   EVOLUTION

Gene-flow through space and time: dispersal, dormancy and adaptation to changing environments

(2015) Rafael Rubio de Casas et al.   EVOLUTIONARY ECOLOGY

Genetic Variability Under the Seedbank Coalescent

(2015) Jochen Blath et al.   GENETICS

Real-time monitoring of the metabolic activity of periodontopathic bacteria

(2015) Kazuko Ishiguro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Impermanence of bacterial clones

(2015) Louis-Marie Bobay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

(2015) Florent Lassalle et al.   PLoS Genetics

Resuscitation of the rare biosphere contributes to pulses of ecosystem activity

(2015) Zachary T. Aanderud et al.   Frontiers in Microbiology

Genetic Variability Under the Seedbank Coalescent

(2015) Jochen Blath et al.   GENETICS

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

(2014) Sean M. Gibbons et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin

(2014) James R Doroghazi et al.   BMC GENOMICS

Life-history syndromes: Integrating dispersal through space and time

(2014) Mathieu Buoro et al.   ECOLOGY LETTERS

Natural Competence and the Evolution of DNA Uptake Specificity

(2014) J. C. Mell et al.   JOURNAL OF BACTERIOLOGY

Strong seed-bank effects in bacterial evolution

(2014) Adrián González-Casanova et al.   JOURNAL OF THEORETICAL BIOLOGY

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

The evolution of seed dormancy: environmental cues, evolutionary hubs, and diversification of the seed plants

(2014) Charles G. Willis et al.   NEW PHYTOLOGIST

Bacteriophage therapy: a potential solution for the antibiotic resistance crisis

(2014) Zhabiz Golkar et al.   Journal of Infection in Developing Countries

Persisters, persistent infections and the Yin–Yang model

(2014) Ying Zhang   Emerging Microbes & Infections

DNA Double-Strand Break Repair at −15°C

(2013) Markus Dieser et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial Persister Cell Formation and Dormancy

(2013) Thomas K. Wood et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Resistance of Bacillus subtilis Spore DNA to Lethal Ionizing Radiation Damage Relies Primarily on Spore Core Components and DNA Repair, with Minor Effects of Oxygen Radical Detoxification

(2013) Ralf Moeller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Normalcy of Dormancy: Common Themes in Microbial Quiescence

(2013) Emily S.C. Rittershaus et al.   Cell Host & Microbe

Models of microbial dormancy in biofilms and planktonic cultures

(2013) Bruce P. Ayati et al.   Communications in Mathematical Sciences

Antibiotics in crisis

(2013) Michael Gross   CURRENT BIOLOGY

Endospores of thermophilic bacteria as tracers of microbial dispersal by ocean currents

(2013) Albert Leopold Müller et al.   ISME Journal

Bacterial genome replication at subzero temperatures in permafrost

(2013) Steven J Tuorto et al.   ISME Journal

Genomic mutation rates that neutralize adaptive evolution and natural selection

(2013) P. J. Gerrish et al.   Journal of the Royal Society Interface

Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis

(2013) Christopher B Ford et al.   NATURE GENETICS

Evaluating evolutionary models of stress-induced mutagenesis in bacteria

(2013) R. Craig MacLean et al.   NATURE REVIEWS GENETICS

Microbial life under extreme energy limitation

(2013) Tori M. Hoehler et al.   NATURE REVIEWS MICROBIOLOGY

Active microorganisms in soil: Critical review of estimation criteria and approaches

(2013) Evgenia Blagodatskaya et al.   SOIL BIOLOGY & BIOCHEMISTRY

Spore formation inBacillus subtilis

(2013) Irene S. Tan et al.   Environmental Microbiology Reports

Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision

(2013) Nobuto Takeuchi et al.   G3-Genes Genomes Genetics

Resistance of Bacterial Endospores to Outer Space for Planetary Protection Purposes—Experiment PROTECT of the EXPOSE-E Mission

(2012) Gerda Horneck et al.   ASTROBIOLOGY

Genomic determinants of sporulation inBacilliandClostridia: towards the minimal set of sporulation-specific genes

(2012) Michael Y. Galperin et al.   ENVIRONMENTAL MICROBIOLOGY

The Infinitely Many Genes Model for the Distributed Genome of Bacteria

(2012) Franz Baumdicker et al.   Genome Biology and Evolution

Alternative Excision Repair of Ultraviolet B- and C-Induced DNA Damage in Dormant and Developing Spores of Bacillus subtilis

(2012) F. H. Ramirez-Guadiana et al.   JOURNAL OF BACTERIOLOGY

DNA Repair and Genome Maintenance in Bacillus subtilis

(2012) J. S. Lenhart et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Germ banks affect the inference of past demographic events

(2012) Daniel Živković et al.   MOLECULAR ECOLOGY

Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment

(2012) Bente Aa. Lomstein et al.   NATURE

Global distribution of microbial abundance and biomass in subseafloor sediment

(2012) J. Kallmeyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Shrinking majority of the deep biosphere

(2012) B. B. Jorgensen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breaking the rules: bacteria that use several DNA polymerase IIIs

(2011) Charles S McHenry   EMBO REPORTS

Microbes in thawing permafrost: the unknown variable in the climate change equation

(2011) David E Graham et al.   ISME Journal

An additional step in the transmission of Yersinia pestis?

(2011) W Ryan Easterday et al.   ISME Journal

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection

(2011) Christopher B Ford et al.   NATURE GENETICS

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

Entry of Yersinia pestis into the Viable but Nonculturable State in a Low-Temperature Tap Water Microcosm

(2011) David R. Pawlowski et al.   PLoS One

Inference of seed bank parameters in two wild tomato species using ecological and genetic data

(2011) A. Tellier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persister Cells

(2010) Kim Lewis   Annual Review of Microbiology

The Speed of Evolution in Large Asexual Populations

(2010) Su-Chan Park et al.   JOURNAL OF STATISTICAL PHYSICS

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Exit from dormancy in microbial organisms

(2010) Jonathan Dworkin et al.   NATURE REVIEWS MICROBIOLOGY

Dormancy contributes to the maintenance of microbial diversity

(2010) S. E. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resuscitation-promoting Factors Reveal an Occult Population of Tubercle Bacilli in Sputum

(2009) Galina V. Mukamolova et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Roles of Small, Acid-Soluble Spore Proteins and Core Water Content in Survival of Bacillus subtilis Spores Exposed to Environmental Solar UV Radiation

(2009) R. Moeller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial awakenings

(2009) Slava S. Epstein   NATURE

On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales

(2009) O. Zhaxybayeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluctuating natural selection accounts for the evolution of diversification bet hedging

(2009) A. M. Simons   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Does Dormancy Increase Fitness of Bacterial Populations in Time-Varying Environments?

(2008) Tufail Malik et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

An Accurate Model for Genetic Hitchhiking

(2008) Anders Eriksson et al.   GENETICS