Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: May 7, 2021

In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of new (and often complex) environments can be tackled with a combination experimental evolution next generation sequencing. This allows analyse real-time populations in imposed factors or during interaction host, by screening for genotypic changes over multitude identical cycles. Experimental (EE) coupled comparative genomics has indeed facilitated monitoring bacterial understanding processes. Basically, EE studies had long been done on single strains, allowing reveal dynamics targets selection uncover correlation between changes. However, species are always evolving relation other have not only environment itself but also biotic dynamically shaped species. Nowadays, there is growing interest apply under environments. this paper, we provide non-exhaustive review systems increasing complexity (from species, synthetic communities) particular focus plants plant-associated microorganisms. We highlight some controlling functioning their responses emphasize importance considering complex studies.

Language: Английский

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Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Aug. 13, 2022

Abstract The extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how does so, remains unexplored. Here, we evolve three Klebsiella strains and their mutants parallel. Their comparison reveals different phenotypic genotypic evolutionary changes alter virulence-associated traits. Non-capsulated populations accumulate mutations reduce exopolysaccharide production increase biofilm formation yield, whereas most capsulated become hypermucoviscous, signature of hypervirulence. Hence, environments primarily occurs by fine-tuning expression the capsular locus. same conditions selecting for gene wzc leading hypermucoviscosity also result increased susceptibility antibiotics ramA regulon. This implies general adaptive processes outside host can affect evolution role infection outcomes may be by-product such adaptation.

Language: Английский

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Loss of Heterozygosity and Its Importance in Evolution

Journal of Molecular Evolution, Journal Year: 2023, Volume and Issue: 91(3), P. 369 - 377

Published: Feb. 8, 2023

Abstract Loss of heterozygosity (LOH) is a mitotic recombination event that converts heterozygous loci to homozygous loci. This mutation widespread in organisms have asexual reproduction like budding yeasts, and also an important frequent tumorigenesis. Mutation accumulation studies demonstrated LOH occurs at rate higher than the point rate, can impact large portions genome. Laboratory evolution experiments yeasts revealed often unmasks beneficial recessive alleles confer fitness advantages. Here, I highlight advances understanding dominance, fitness, phenotypes laboratory evolved yeast strains. discuss best practices for detecting intraspecific interspecific clones populations. Utilizing strain backgrounds offers opportunity advance our this type shaping adaptation genome wild, domesticated, clinical

Language: Английский

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Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes

Journal of Molecular Evolution, Journal Year: 2023, Volume and Issue: 91(3), P. 311 - 324

Published: Feb. 8, 2023

Abstract Following the completion of an adaptive evolution experiment, fitness evaluations are routinely conducted to assess magnitude adaptation. In doing so, proper consideration should be given when determining appropriate methods as trade-offs may exist between accuracy and throughput. Here, we present three instances in which small changes framework or execution significantly impacted outcomes. The first case illustrates that discrepancies conclusions can arise depending on approach evaluating fitness, culture vessel used, sampling method. second reveals variations environmental conditions occur associated with material. Specifically, these subtle greatly affect microbial physiology leading pH distorting measurements. Finally, last reports heterogeneity CFU formation time result inaccurate conclusions. Based each case, considerations recommendations presented for future experiments.

Language: Английский

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The use of experimentally evolved coral photosymbionts for reef restoration

Trends in Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

Language: Английский

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On Protein Loops, Prior Molecular States and Common Ancestors of Life

Journal of Molecular Evolution, Journal Year: 2024, Volume and Issue: 92(5), P. 624 - 646

Published: April 23, 2024

The principle of continuity demands the existence prior molecular states and common ancestors responsible for extant macromolecular structure. Here, we focus on emergence evolution loop prototypes - elemental architects protein domain Phylogenomic reconstruction spanning superkingdoms viruses generated an evolutionary chronology with six distinct phases defining a most parsimonious progression cellular life. Each phase was marked by strategic prototype accumulation shaping structures functions ancestors. last universal ancestor (LUCA) cells (LUCellA) defined stem lines that were structurally functionally complex. saga highlighted transformative forces. LUCA lacked biosynthetic ribosomal machinery, while pivotal LUCellA essential DNA biosynthesis modern transcription. Early proteins therefore relied RNA genetic information storage but appeared initially decoupled from it, hinting at shifts processing. Urancestral types suggest advanced folding designs present early stage. An exploration geometric properties revealed gradual replacement α-helix β-strand bracing over time, paving way dominance other types. AlphFold2-generated atomic models accretion described patterns fold emergence. Our findings favor ‛processual' model evolving aligned Woese's vision communal world. This prompts discussing 'problem ancestors' challenges lie ahead research in taxonomy, complexity.

Language: Английский

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Microbial evolution and ecological opportunity in the gut environment

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1915), P. 20191964 - 20191964

Published: Nov. 20, 2019

Recent genomic and metagenomic studies have highlighted the presence of rapidly evolving microbial populations in human gut. However, despite fundamental implications this intuitive finding for both basic applied gut microbiome research, very little is known about mode, tempo potential functional consequences evolution guts individual hosts over a lifetime. Here I assess relevance ecological opportunity to bacterial adaptation, colonization persistence neonate germ-free mammalian environment as well course an lifetime using data emerging from mouse models provide examples where possible. then briefly outline how continued development application experimental approaches coupled analysis essential disentangling drift selection identifying specific drivers within between populations.

Language: Английский

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Diversification of Bacillus subtilis during experimental evolution on Arabidopsis thaliana and the complementarity in root colonization of evolved subpopulations

Environmental Microbiology, Journal Year: 2021, Volume and Issue: 23(10), P. 6122 - 6136

Published: July 23, 2021

The soil bacterium Bacillus subtilis is known to suppress pathogens as well promote plant growth. However, in order fully exploit the potential natural fertilizer, we need a better understanding of interactions between B. and plants. Here, was examined for root colonization through experimental evolution on Arabidopsis thaliana. populations evolved rapidly, improved diversified into three distinct morphotypes. In understand adaptation that had taken place, single isolates from final transfer were randomly selected further characterization, revealing changes growth pellicle formation medium supplemented with polysaccharides. Intriguingly, certain showed only species they on, but not another species, namely tomato, suggesting A. thaliana specific adaption paths. Finally, mix performed than sum its constituents monoculture, which demonstrated be caused by complementarity effects. Our results suggest genetic diversification occurs an ecological relevant setting roots proves stable strategy colonization.

Language: Английский

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Adaptive laboratory evolution of microbial co‐cultures for improved metabolite secretion

Molecular Systems Biology, Journal Year: 2021, Volume and Issue: 17(8)

Published: Aug. 1, 2021

Article9 August 2021Open Access Source DataTransparent process Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion Dimitrios Konstantinidis orcid.org/0000-0002-2134-6823 Structural and Computational Biology Unit, European Molecular Laboratory, Heidelberg, Germany Faculty Biosciences, Heidelberg University, Search more papers by this author Filipa Pereira orcid.org/0000-0002-0557-8480 Eva-Maria Geissen orcid.org/0000-0002-0423-7019 Kristina Grkovska orcid.org/0000-0002-3784-494X Eleni Kafkia orcid.org/0000-0001-9550-4487 Medical Research Council Toxicology Cambridge, UK Paula Jouhten orcid.org/0000-0003-1075-7448 VTT Technical Centre Finland Ltd, Espoo, Yongkyu Kim orcid.org/0000-0002-3336-6741 Saravanan Devendran orcid.org/0000-0002-1540-5241 Michael Zimmermann orcid.org/0000-0002-5797-3589 Kiran Raosaheb Patil Corresponding Author [email protected] orcid.org/0000-0002-6166-8640 Information Konstantinidis1,2, Pereira1,†, Geissen1, Grkovska1, Kafkia1,3, Jouhten4, Kim1,†, Devendran1, Zimmermann1 *,1,3 1Structural 2Faculty 3Medical 4VTT †Present address: Life Science Institute, University Michigan, Ann Arbor, USA Brain Korea Institute Technology, Seoul, South *Corresponding author. Tel: +44 1223 3 35640; E-mail: Systems (2021)17:e10189https://doi.org/10.15252/msb.202010189 PDFDownload PDF article text main figures. Peer ReviewDownload a summary the editorial decision including letters, reviewer comments responses to feedback. ToolsAdd favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract has proven highly effective obtaining microorganisms with enhanced capabilities. Yet, method is inherently restricted traits that are positively linked cell fitness, such as nutrient utilization. Here, we introduce coevolution obligatory mutualistic communities improving fitness-costly metabolites through natural selection. In strategy, metabolic cross-feeding connects target metabolite, despite its cost secretor, survival proliferation entire community. We thus co-evolved wild-type lactic acid bacteria engineered auxotrophic Saccharomyces cerevisiae in synthetic growth medium leading bacterial isolates two B-group vitamins, viz., riboflavin folate. The increased production was specific targeted vitamin, evident also milk, complex environment naturally contains vitamins. Genomic, proteomic metabolomic analyses evolved bacteria, combination flux balance analysis, showed altered regulation towards supply vitamin precursors. Together, our findings demonstrate how metabolism adapts lifestyle exchange. SYNOPSIS shows can be used improvement secretion. Mutualistic exerts selection pressure compound. Lactic were yeast secretion; retained monocultures milk. Multi-omics analysis strains uncovered cellular networks adapt lifestyle. Introduction long-term Escherichia coli experiment (Lenski, 2017) highlighted under well-controlled conditions gain fundamental insights into adaptive processes. These experiments have helped, example, gauging predictability evolutionary outcomes (McDonald, 2019) divergence between fitness trajectories mutation rates clonal asexual populations (Maddamsetti et al, 2015). now well-established tool development biotechnological characteristics (Dragosits Mattanovich, 2013). applications include adaptation harsh (Wallace-Salinas Gorwa-Grauslund, 2013; Stella 2019), substrate utilization (Zhou 2012) boosting metabolically (Portnoy 2011; Tenaillon, 2018). Further, enabled studying emergence stability interspecies interactions antagonism (Koskella Brockhurst, 2014) exchange (Mee 2014; Harcombe studies primarily focus on establishing models cross-feeding, less emphasis molecular basis adaptations. while amino common (Machado 2021) been (Wintermute Silver, 2010), involving other nutrients well studied. approach does not require prior knowledge genetic elements underlying trait wish improve. Thus, applied arbitrarily organisms amenable engineering. particularly attractive when use due legislative or consumer preference considerations, example fermented food products (Burgess 2006). requirement applying evolution, whether organisms, interest correlated (Winkler While minimal underlines elegance success it underscores limited applicability impose toll To enable keeping advantages offered here exert This makes producer. Consider community members wherein each partner depends one essential metabolites. Secretion these will directly coupled both members. Any all compounds, their costs secretors, then subjected via selecting overall growth. tested concept consisting (LAB) produce vitamins (riboflavin folate) When grown nitrogen excess, secretes acids which LAB (Ponomarova 2017). yeast-lactic satisfies obligate mutualism. strains, engineered, products, folate, relevant applications. Beyond direct industrial relevance, study establishes proof feasibility using communities. Results Coevolution selects known secretors (Hugenholtz Smid, 2002). started identifying Lactobacillus plantarum strain from isolate collection could secrete riboflavin. As S. prototrophic riboflavin, auxotrophy deleting RIB4 RIB5 genes. double deletion mutant ability support L. chemically defined medium. survive absence (Fig 1A). Figure 1. A an cultured together experiments. Vitamin secreting selected based presence required biosynthetic genes genome. periodically transferred new media, fitness. Performance twelve during experiment. originated same parental co-culture. Shown optical density measurements before transfer. Individual shown blue-shaded lines; dark blue line average Riboflavin estimates (n = 134) 5, biological replicates). fluorescence intensity values (440-nm excitation /520-nm emission) supernatants collected after 72 h culturing supplemented Extracellular intracellular levels LC-MS Levels extracellular flavins (FMN + FAD), data available online figure. Data 1 [msb202010189-sup-0003-SDataFig1.zip] Download figure PowerPoint next performed serial transfer derived cultures. Non-shaking facilitate microaerobic preferred strain. non-shaking condition expected check and/or dominance cheater cells (i.e. profit goods but do contribute return) facilitating spatial organization, generally favours co-operators over cheaters (Stump experiment, cultures fresh media whenever reached stationary stage Following 25 transfers, maximal had sevenfold 1B). Only collapsed (after approximately 20 passages), indicating partners remain robust. From populations, isolated planatarum (134 isolates) (6 further characterization. phenotype 134 (circa 160 generations) estimated measuring cell-free supernatant. Notably, 60% secretion, up 5.6-fold increase comparison 1C). Four values, non-improved (D5), verified ultra-performance liquid chromatography (UPLC; Appendix Table S1). amount produced strain, medium, quantified chromatography–mass spectrometry (LC-MS) analysis. secreted 42 ± 16.4 ng/ml isolates, B4 (isolate B 4), 61.1 (3.2-fold increase), another one, E6 E 6), circa 426 208.7 (10-fold increase) 1D). addition investigated Flavin coenzymes, i.e. FAD FMN, constitute biologically active forms well. at similar 1E, S1), FMN undetectable samples. obtain comprehensive picture capacity analysed accumulation flavin coenzymes. exhibited considerable (144 55.1 ng/ml; 14.4-fold strain; two-tailed t-test, P < 0.05) Isolate accumulated 27 14.9 (2.7-fold comparable being observed contrast E6, (C2, C 2, G7, G 7) did show (C2: 60.9 20.7 ng/ml, G7: 18.2 3.2 ng/ml). However, higher amounts (1.7 1.9-fold C2 respectively; 11 6.7 15 16.6 Fig 1E). resulted positive biosynthesis. Our setting links desired compound whole community, even if productivity imposes burden individual Indeed, producing phenotype, strong decrease rate (B4: 0.05, E6: 0.05; 2A). mimicked co-culture availability 2017), strain's OD600 value significantly decreased (two-tailed 0.05), 2B). Additionally, grew better than either only "negative control" D5 production; S1, 2C). monitor closer species dynamics occurred flow cytometry containing Δrib4:rib5 constitutively express red protein (RFP), isolates. Sorting B4, supported 1.5- 3.5-fold 2D), still number 2D). Per OD, somewhat increased, albeit variation across replicates EV1A). ratio change > nature relation whereby tightly EV1B). By provided resources partner, which, turn, bacteria. 2. Effect maximum vertical horizontal lines mark respectively supplementation. Growth kinetics four co-cultured replicates; grey bars mean SD). Yeast (RFP-positive events fluorescence-activated sorting, Methods) panel C. Samples 84 conditioned 2 [msb202010189-sup-0004-SDataFig2.zip] Click expand EV1. Evaluation associated structure Bacterial sorting (FACS) co-cultures. 2C inoculation counts normalized sample time. P-values unpaired t-test. numbers RFP-positive (showed FACS A. Representative image fixed 2C) (RFP positive), seen wide-field microscope, different time points kinetics. scale bar bottom left corner microscope equal 6 μm. aqueous suspension (PBS) attach (auto-aggregation—left), they exhibit mixed (co-aggregation—right). n SD. Estimation light absorbance 570 nm dye bound biofilm monoculture (left), (right) Bar heights average; dots points; 4 replicates. Direct contact necessary co-aggregate form biofilms (Kawarai 2007; Arroyo-López 2012). therefore set out investigate dependent cell–cell Microscopic observation formation extended aggregates EV1C D). compared aggregation forming determine surface promote contact. Evolved aggregate monoculture, aggregating less, independently yeast. Nevertheless, differences small statistically significant EV1E). Furthermore, three tendency corresponding EV1F). indicate there no independence sufficiently vice versa. 20% 40% 2E). Similarly, considerably 2F). displayed 16 49% density, EV2A B). (Appendix S1A) S1B), (˜34% average). Both confirm intended lack aggregation. over-secreting emerged population able enhance supplying vitamin. At time, capability assimilate resource resulting net impact compensated for, efficient EV2. (Δrib4:rib5) yeast-L. respectively. B. C–H. Amino (LC-MS analysis) samples areas curve (AUC) peaks. Regulation pathway precursor successful coevolution, identify changes Genome sequencing reveal any mutations along operon, identified single nucleotide polymorphisms (SNPs) various regulate transcription uptake S2). Evolution reported (Turkarslan fine-tuning regulatory optimizing usage partners. Since none link biosynthesis, decided analyse

Language: Английский

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How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses

Current Genetics, Journal Year: 2022, Volume and Issue: 68(3-4), P. 319 - 342

Published: April 1, 2022

Language: Английский

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