Species dynamics in natural bacterial communities over multiple rounds of propagation

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(11), P. 1766 - 1775

Published: Aug. 22, 2022

Our experimental work illustrates how microbial ecosystems can be shaped by selective pressures over long-term ecological time scales. Natural generally consist of various co-existing species, where community composition describes the frequency at which species or types are present. Overall functionality system is achieved interacting species. Upon short-term selection, for instance transfer to a novel environment, and may change in process referred as sorting. Various factors, such initial from influence this change. Mabisi traditional fermented food Zambia that naturally contains bacterial around twenty unique types. We used six comparable but different natural communities, each split into five identical replicates, 16 propagation cycles novel, common laboratory environment. Composition communities changed upon propagation. The four main factors on composition, i.e. (history), impact environment (adaptation), changes due interaction between random processes (chance) dynamics, was tested using maximum likelihood ratios. Initial seemed determine followed processes. Interestingly, we observed convergence level ecosystem functionality, measured profiles metabolic output. This suggests combinations achieve similar eco-system functionality.

Language: Английский

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Experimental Evolution and the Nature of Biodiversity

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: May 7, 2024

Abstract Why and how did life become so diverse? This has been the central question—or more accurately, obsession—in biology. book attempts to provide an answer by providing account of biodiversity evolves in some simplest biological systems, microbial populations evolving laboratory. approach, experimental evolution, allows us watch evolutionary process unfold real time track adaptation diversification both phenotype genotype along way, making it possible observe processes that have remained stubbornly inaccessible research larger, longer-lived organisms. The provides insight into ecology genetics adaptive diversification, repeated origins novelty innovation, coevolutionary patterns diversity through ends with a sketch general theory diversification.

Language: Английский

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Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

FEMS Microbiology Ecology, Journal Year: 2023, Volume and Issue: 99(10)

Published: Sept. 19, 2023

The influence of community diversity, which can be measured at the level metabolic guilds, on function is a central question in ecology. Particularly, long-term temporal dynamic between community's and its diversity remains unclear. We investigated guild associated by propagating natural microbial communities from traditionally fermented milk beverage diluted to various levels. Specifically, we assessed less abundant types, such as yeast, functionality bacterial compositions over repeated propagation cycles amounting ∼100 generations. starting richness guilds had repeatable effect compositions, profiles, acidity. single guild, yeast our study, played dramatic role function, but interestingly not species sorting trajectories remaining community. Our results together suggest an unexpected niche division evidence ecological selection system.

Language: Английский

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Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 2, 2024

Abstract Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain desired function. However, ecological factors control balance between shaping and propagation are not well understood. Dairy backslopping can as model approach investigate dynamics during serial propagations. In this study, 26 raw milk samples were generate lineages 6 obtained propagation. Bacterial structures analyzed metabarcoding acidification was recorded pH monitoring. The results revealed different types in terms taxonomic composition dynamics. Five reached repeatable structure few steps, with little variation final generations, giving rise stable kinetics. Moreover, these stabilized presented high inter-lineage variability diverse properties. Besides, other characterized levels leading parallel or divergent trajectories. functional properties mainly related relative abundance lactic acid bacteria within communities. These findings highlight short-term schemes fermentation produce wide range intimately linked structure. Importance Microbiome applications require approaches propagating microbial Shaping allows selection properties, while production biomass required inoculate engineered target ecosystem. top-down engineering, where from pool mixed microorganisms acting on variables, major challenge master favor and, conversely, those stability work, dairy blacksloping key role bacterial their open up interesting prospects biotechnological use microbiomes, particularly field fermentation, diversify injecting biodiversity into cheesemaking processes.

Language: Английский

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Phenotypic Disparity

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 143 - 157

Published: May 7, 2024

Abstract This chapter explores how phenotypic disparity, or trait divergence, evolves. Four mechanisms contribute to divergence: drift, epistasis, divergent selection, and ecological interactions like competition. Data from the literature reveals that, as expected, disparity increases through time decreases with population size, at least for bacterial experiments. Epistasis can generate but especially in concert disruptive selection generated by against intermediate phenotypes caused competition predation, are more potent drivers of disparity. Sexual also although it has received rather little focused attention microbial literature.

Language: Английский

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Preface to the second edition

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown, P. vii - viii

Published: May 7, 2024

Extract When I set out to write the first edition of this book over a decade ago, think it would be fair say that experimental evolution was on margins mainstream evolutionary research. am sure not only one have received reviewer comments effect there nothing interesting gained by studying microbes evolving in laboratory as they were just convenient way avoid coding computer simulation. It hard feeling if results one's experiments too clear and clean, wasn't doing real biology. Things are changing. For one, many more researchers making use tool, either for processes directly—the subject book—or means generating phenotypes genotypes further study microbiology, environmental remediation, or industrial processes. another, is an increasing sense within broader field biology can should part portfolio approaches most fundamental problems. If we can't understand simplest systems, what hope do explaining complicated ones? Experimental helps us through plausibility our theories how works.

Language: Английский

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Endorsement

Published: May 7, 2024

Extract Kassen's book lets us see evolution, not as a dusty subject of the past, but vibrant, experimental science that shapes how we understand everything from diseases to biodiversity. Sarah Otto, Professor Zoology & University Killam Professor, The British Colombia, Canada I didn't think it was possible, this massively updated examination evolution is even better than first edition. Rees Kassen has written spectacular synthesis one most exciting areas in today. A must read for any evolutionary biologist. Jonathan Losos, Biology and Director Living Earth Collaborative, Washington St Louis, USA In 2nd edition Experimental Evolution Nature Biodiversity, successfully improves on classic, by offering text emphasizes technical approaches connecting central canon theory. doing so, opened door only teaching can improve our understanding also why an essential tool observing evolution-in-action, identifying mechanistic underpinnings underlie adaptations. This rich scholarly work, reading anyone who seeks grasp powerful revealing happens natural world.

Language: Английский

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An Introduction to Microbial Experimental Evolution

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 14

Published: May 7, 2024

Abstract This chapter provides a brief history of the use microbes to study adaptation and diversification in laboratory foundational principles theory on which subject is based. I review methods used propagate as well those measure key properties interest such fitness. As it now standard practice supplement results selection experiments with genomic data, what often referred evolve-and-resequence experiments, discussion these techniques kinds information obtained included. The closes by briefly introducing examples microbial evolution chosen because they have become emblematic approaches field.

Language: Английский

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The Nature of Biodiversity

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 196 - 202

Published: May 7, 2024

Abstract This final chapter serves three purposes. The first is to summarize the key results in form of a sketch for general theory evolution biodiversity. second place these into broader context evolutionary biology by discussing explicitly limitations experimental approach. third offer some directions forward guide future work on biodiversity, both particular and more generally. These also strike close heart this book, title chapter—the nature

Language: Английский

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Divergent Selection

Oxford University Press eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 41 - 62

Published: May 7, 2024

Abstract This chapter examines the consequences of selection in contrasting environments, with a view to understanding evolution trade-offs underpinning niche specialization and differentiation. I introduce theory pleiotropy that extends Fisher’s geometric model multiple dimensions provides framework for fitness trade-offs, so ecological specialization, across environments. A review experimental literature shows due divergent evolve readily laboratory costs adaptation associated extreme can be underlain by both mutation accumulation functional interference antagonistic pleiotropy. Evidence from field studies suggests strong enough generate maintain specialists, although spatial scale over which this happens is not always clear.

Language: Английский

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