Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 36(7), P. 614 - 623

Published: June 11, 2018

Language: Английский

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Marine Actinomycetes, New Sources of Biotechnological Products

Marine Drugs, Journal Year: 2021, Volume and Issue: 19(7), P. 365 - 365

Published: June 25, 2021

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production secondary metabolites which have uses medical, environmental rehabilitation, industrial applications. Secondary produced by actinomycete species are an abundant source antibiotics, antitumor agents, anthelmintics, antifungals. These actinomycete-derived medicines circulation as current treatments, but actinomycetes also being explored potential sources new compounds to combat multidrug resistance pathogenic bacteria. Actinomycetes a solve concerns another area recent investigation, particularly their utility bioremediation pesticides, toxic metals, radioactive wastes, biofouling. Other applications include biofuels, detergents, food preservatives/additives. Exploring other unique properties will allow for deeper understanding this interesting taxonomic group. Combined with engineering, microbial experimental evolution, enhancement techniques, it reasonable assume that use marine continue increase. Novel products begin be developed diverse applied research purposes, zymology enology. This paper outlines knowledge usage research, focusing on isolates providing direction future research.

Language: Английский

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Microbial Experimental Evolution – a proving ground for evolutionary theory and a tool for discovery

EMBO Reports, Journal Year: 2019, Volume and Issue: 20(8)

Published: July 24, 2019

Review24 July 2019Open Access Microbial Experimental Evolution – a proving ground for evolutionary theory and tool discovery Michael J McDonald Corresponding Author [email protected] orcid.org/0000-0002-5735-960X School of Biological Sciences, Monash University, Melbourne, Vic., Australia Search more papers by this author Information *,1 1School *Corresponding author. Tel: +61 3 9905 1697; E-mail: EMBO Reports (2019)20:e46992https://doi.org/10.15252/embr.201846992 See the Glossary abbreviations used in article. PDFDownload PDF article text main figures. ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract experimental evolution uses controlled laboratory populations study mechanisms evolution. The molecular analysis evolved enables empirical tests that can confirm predictions theory, but also lead surprising discoveries. As with other fields life sciences, microbial has become tool, deployed as part suite techniques available biologist. Here, I provide review general findings evolution, especially those relevant microbiologists are new field. relate these results design considerations an experiment suggest future directions working at intersection biology. clonal interference slowed rates fixation asexual population due competition between lineages each carry beneficial mutation coverage length concatenated DNA-sequence read data divided genome de novo occurs spontaneously during period fixed state which allele given genetic locus is frequency 1 barcode short DNA sequence identify individual or lineage haplotype set variants physically linked on single chromosome HGT horizontal gene transfer individuals share common ancestor within time LN natural log LTEE long-term N size parallel similar phenotypes genotypes independently evolving selection coefficient(s) quantitative representation relative fitness reproductive success standing variation present before considered observer Introduction studies now constitute one foundations 1. In particular, bring greater power precision studies, providing means out elaborate explore ideas biology 2. A typical starts culture, just like any microbiology laboratory. Cells inoculated into media left grow until culture reaches high density. Instead throwing using all resultant population, evolutionist transfers dilutes allow continued growth division. This cycle be indefinitely, generations accumulate, will drive adapt environment. simple process carried range systems, summarised Fig Figure Mechanisms propagation evolution(A) Batch requires regular dilution fresh media. These experiments relatively easy establish, since vessels commonly batch culture. scaled large number replicates, example when 96-well plates. (B) Chemostat systems include constant supply medium. provides continuous cultures without fluctuations phase. (C) Microfluidics most precise control over supplements cell cultures. may need custom designed, replicates limited. (D) Emulsion take advantage small cell-containing vesicles form mixing oil, surfactant cells. cells vesicle determined ratio cell, oil. mixed back vortexing centrifuging solution. One select yield per-vesicle rather than rapid 144. (E) Mutation accumulation introduces regular, single-cell bottleneck replicate population. achieved streaking petri dish then choosing colony (founded cell) streak next plate. (F) introduced model organism, often plant mouse, propagate it recovered from organism. analysed subjected further mode allows testing unanticipated organism-specific features environment difficult Download figure PowerPoint Long- short-term approaches Perhaps striking microbes access long scales. generation times up tens pass every day. limited only how experimentalist maintain transfers. easily stored freezer, indefinite period, so saved frozen snapshot restart inevitable accidents happen. longest running, probably famous, (LTEE). comprised 12 E. coli, started 1987 still passaged daily 68,000 later (see here recent 4). What learned running long? Twenty years ago, biologist might have predicted coli would reached optimal after few thousand generations. However, we know continues 61,500 5, 6. key been utilisation citrate (cit+ phenotype), carbon source buffer phenotype significant because species-defining characteristic unable utilised under oxidising conditions 7. effect mutations explicitly cause cit+ dependent "potentiating" do not seem directly influence occurred first 20,000 8. words, particular trait unlikely experiment. there quicker routes many An alternative propagating term evolve shorter time. strong, rapidly. Adapting temperatures, Tenaillon et al propagated 115 2,000 9. Increasing another magnitude, Lang 1,000 Saccharomyces cerevisiae 10, 11. massive replication confers statistical detect change, hundreds shows some questions highly replicated cannot address; however, trends emerging consistent across both long- 12, 13, reviewed below. Repeatability, diminishing returns diversification: predictable Parallel same phenotypes, sometimes mutations, 14. Parallelism driven observed short- species 11, 15-19 (Fig 2A). Repeatability interesting suggests phenotypic outcomes could predictable. To anticipate response environmental changes major goal 20, capacity make accurate desirable. unclear whether about ever enough useful, subject ongoing models 21, 22. Three experiments(A) Genetic parallelism. signature repeated genes independent populations. expected multi-hit mutated six hypothetical 1000-generation (grey shaded) (orange line) Diminishing epistasis. negatively correlated background (figure adapted 25). Stable polymorphism evolve, whereby multiple ecotypes, different niche microcosm, coexist 27. possible outcome successive sweeps mutation, occasionally hampered (D). At onset experiment, adaptation tends slows down 23. LTEE, rate increase follows law, no attained 5. explained epistatic interactions effects lower better 24. Experiments show engineered low-fitness larger if they high-fitness 2B). "diminishing returns" epistasis M. extorquens S. 25, well 26. While return makes specific does robust made although true experiencing fluctuating complex environments. Most use unicellular organisms adapting defined-nutrient diverse, co-existing subpopulations niches, evident 6, 27, 28 2C). Diverse heterogeneity experimenter, called eco-evolutionary feedback 29. happens populations, altered production waste products consumption modifications change ecology alters selective pressures experienced 30. observation emphasises its importance real communities mechanism experiments. facilitate fundamental parameters evolution: environment, Understanding, manipulating, factors benefit exerted size, founding genotype determines therefore drives while manipulating variable potentially subtle effects. interpreting setting discussed Population (N) strength forces minimum detected selection, expressed coefficient (s), 1/N, where "N" ineffective Ns < 31. likely experience drift, random sampling frequencies chance deleterious loss mutations. consequence expect slower and, extreme cases, extinction 32. Some designed consequences 33-36, deliberately 1–10 1). If avoid 103–104 recommended. Variation experimenter vary much variation, "fuel" supplied 37. proportional amount 38. start amounts 39-41, founded clone 3, 28, 42 adaptive must fuelled 43, 44, elevated artificially induced supplementing mutagen deleting required mismatch repair. antimicrobial resistance antibiotic global health challenge that, sits disciplines biology, microbiology, genomics 20. measure costs underlie 45-49, probability 49. Mutations occur important biological functions reduction viability 50. Fitness assays Box 1: How fitness) shown confer actually 47, 51-53, always come cost. When costly, resistant microbe secondary compensate primary 54. Since processes, strategies amelioration resistance, drugs, should account 55. promising line research characterise susceptibilities multidrug-resistant strains. order attain strains several compensatory It less able additional Knowledge multidrug targeted drug combinations based clinical pathogenic organism contribute offspring generation. determine degree validate experimentally wide assays. Growth 145, total carrying capacity, biomass 105 speed boundary expansion 141 measures gold standard measurement competitive starting point assay obtain construct marked reference strain. typically modified readily distinguished nature marker accuracy For instance, fluorescent differentiate strain, proportions measured flow cytometry 10 10s thousands counted ratios. Alternatively, mixture spread onto agar plates containing distinction 146, counting Initially, strain 1:1 ratio. Even care taken mix competitors ratio, very initial frequency, difference calculations fitness. Once portion aside competing diluted incubated time, allowing two compete. After competition, again. calculated measurements dividing individuals. done final point. (LN) quotient gives performance compared value passed points, yielding per-generation (s). chosen carefully. too long, extinction, thus reducing calculation s. short, changed detection differences genotypes. bacteriophages Bacteriophages therapies 56, bacteriophage provided insights genetics 57. Bacteriophage genomes small, whole-genome sequencing phage was rise next-generation technologies 58. head exploited 19, 59, 60. ease bacteria co-culture led co-evolutionary dynamics. infecting isolation 61, 62. diverse bacteriophage, increases types 63. bind membrane protein gain entry cell. facilitated detailed λ site 64, 65. Conversely, bacterial modifying encodes protein. conferred efflux pumps, hypothesised targets such pump tandem comprise "evolution proof" treatment strategy 56. principle demonstrated drove MEX pump, thereby restoring sensitivity P. aeruginosa 66. trait. applications. introduction useful properties reductions 67. yeast, crossed "wild-type" promote recombinants possess productivity fast-growing 68. Continuous passaging widely restore ethanol xylose 69-71. example, C321 replace UAG codons UAA. ideal biotechnological applications, incorporation non-standard amino acids code. engineering caused slow growth. 1,000-generation resulted restored rates. Moreover, re-sequencing revealed mutational causes reduced founder 72. novel hosts, conditions. Wolbachia quickly among their hosts conferring infected females. addition, induce insect pathogens. devised Dengue virus amongst mosquitos originally discovered D. melanogaster. suited dispersal mosquito A. aegypti mosquito's intracellular 2 years. newly establish stable infection 73 thereafter eventual public dengue 74. Next, introduce describing full historical recommend books 1, reviews 75-77 exhaustive treatments earlier periods non-microbial 78-81 aspects You get what you for: choices Setting beyond normally adaptation. Adaptation described, including temperatures 9, 82, gradients 55 even levels ionising radiation 83. imagination. parameter pressure differential survival relied upon regardless pressure, adaptations predict. Wildenberg 84 fluorescence-activated sorter brightest 24 h. anticipated expression modulate fluorescence. Instead, periodically multicellular clusters increased brightness advantage. unpredicted did diminish elegance serves demonstrate unpredictability thwart outcomes. general, complicated regime, unpredictable noted complicated, well-designed, elicit selection. sought traits selecting against germ progenitor cooperative mats fluorescens. Although were unexpected, successfully applied 85. Simple environments function Natural expose microorganisms nutrients stresses spatial temporal complexity reflected numbers utilise respond stress. Laboratory 86, inactivate superfluous 87. Many contain source, usually glucose. glucose sole concentration limits 3. h "lag time", enter via pykF, became 88. specialisation cost sources. Studies showed rbs operon, proteins ribose 89, disrupted deleted Measurements ~1% 90. then, disruption genes, sources, maltose, minimal Other yeast concentrations glucose, Genes 91. Whole-genome half disrupt encode negative regulators RAS/PKA pathway ac

Language: Английский

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Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation

Proceedings of the National Academy of Sciences, Journal Year: 2020, Volume and Issue: 117(43), P. 26868 - 26875

Published: Oct. 14, 2020

Significance Bacteria can obtain genes from other bacteria, or the surrounding environment, by horizontal gene transfer (HGT). While it is clear that HGT very important for microbial populations, not understood how changes rate mechanisms of adaptation. In this study, we evolve populations bacteria Helicobacter pylori and use DNA sequencing to track movement as they spread through population. We show help antibiotic resistance establish at a low frequency in population, even absence antibiotic. find these treatment flourish when treated with antibiotics, showing potentiate adaptation future environmental change.

Language: Английский

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Host diversity slows bacteriophage adaptation by selecting generalists over specialists

Nature Ecology & Evolution, Journal Year: 2021, Volume and Issue: 5(3), P. 350 - 359

Published: Jan. 11, 2021

Language: Английский

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Why do microbes make minerals?

Comptes Rendus Géoscience, Journal Year: 2022, Volume and Issue: 354(G1), P. 1 - 39

Published: Jan. 11, 2022

Prokaryotes have been shaping the surface of Earth and impacting geochemical cycles for past four billion years. Biomineralization, capacity to form minerals, is a key process by which microbes interact with their environment. While we keep improving our understanding mechanisms this (“how?”), questions around its functions adaptive roles (“why?”) less intensively investigated. Here, discuss biomineral several examples prokaryotic biomineralization systems, propose roadmap study microbial through lens adaptation. We also emerging potential in cooperation as important components biofilm architectures. call shift focus from mechanistic aspects biomineralization, order gain deeper comprehension how communities function nature, improve life co-evolution mineral

Language: Английский

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Substrate availability and not thermal acclimation controls microbial temperature sensitivity response to long‐term warming

Global Change Biology, Journal Year: 2022, Volume and Issue: 29(6), P. 1574 - 1590

Published: Nov. 30, 2022

Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change highly sensitive to shifts the mechanisms assumed control microbial physiological response warming. Two have been suggested explain long-term warming impact on physiology: thermal acclimation quantity quality of substrates available metabolism. Yet studies disentangling these two lacking. To resolve drivers physiology warming, we sampled soils from 13- 28-year-old experiments different seasons. We performed short-term laboratory incubations across a range temperatures measure relationships between temperature sensitivity (growth, respiration, use efficiency, extracellular enzyme activity) chemical composition organic matter. observed apparent but only summer, when had exacerbated seasonally-induced, already small dissolved matter pools. Irrespective greater increased enzymatic pool its sensitivity. propose that fresh litter input into system seasonally cancels C-cycling processes decadal Our findings reveal has indirectly affected via reduced availability this system, implying earth models including negative feedbacks may be best suited describe effects soils.

Language: Английский

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Adaptive Laboratory Evolution for algal strain improvement: methodologies and applications

Algal Research, Journal Year: 2020, Volume and Issue: 53, P. 102122 - 102122

Published: Nov. 21, 2020

Language: Английский

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Bacterial evolution during human infection: Adapt and live or adapt and die

PLoS Pathogens, Journal Year: 2021, Volume and Issue: 17(9), P. e1009872 - e1009872

Published: Sept. 9, 2021

Microbes are constantly evolving. Laboratory studies of bacterial evolution increase our understanding evolutionary dynamics, identify adaptive changes, and answer important questions that impact human health. During infections in humans, however, the parameters acting on infecting populations likely to be much more complex than those can tested laboratory. Nonetheless, thought as naturally occurring vivo experiments, which teach us about antibiotic resistance, pathogenesis, transmission. Here, we review recent advances study within-host during infection discuss practical considerations for conducting such studies. We focus 2 possible outcomes de novo mutations, have termed “adapt-and-live” “adapt-and-die.” In adapt-and-live scenario, a mutation is long lived, enabling its transmission other individuals, or establishment chronic infection. adapt-and-die rapidly extinguished, either because it carries substantial fitness cost, arises within tissues block new hosts, outcompeted by fit clones, resolves. Adapt-and-die mutations provide rich information selection pressures vivo, yet they easily elude detection short may difficult sample, could maladaptive term. Understanding how bacteria adapt under each these scenarios reveal insights basic biology pathogenic microbes aid design translational approaches combat infections.

Language: Английский

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A role for bacterial experimental evolution in coral bleaching mitigation?

Trends in Microbiology, Journal Year: 2021, Volume and Issue: 30(3), P. 217 - 228

Published: Aug. 21, 2021

Language: Английский

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