Algae drive convergent bacterial community assembly at low dilution frequency

iScience, Год журнала: 2023, Номер 26(6), С. 106879 - 106879

Опубликована: Май 17, 2023

Microbial community assembly is a complex dynamical process that determines structure and function. The interdependence of inter-species interactions nutrient availability presents challenge for understanding assembly. We sought to understand how external supply rate modulated affect the process. A statistical decomposition taxonomic structures bacterial communities assembled with without algae at varying dilution frequencies allowed separation effects biotic (presence algae) abiotic (dilution frequency) factors on For infrequent dilutions, strongly impact assembly, driving initially diverse consortia converge common structure. Analyzing sequencing data revealed this convergence largely mediated by decline in relative abundance specific taxa presence algae. This study shows phototroph-heterotroph can be powerful model systems processes relevant global ecosystem functioning.

Язык: Английский

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Searching for Principles of Microbial Ecology Across Levels of Biological Organization

Integrative and Comparative Biology, Год журнала: 2023, Номер 63(6), С. 1520 - 1531

Опубликована: Июнь 6, 2023

Synopsis Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at levels biological organization, individual species, interactions, communities, is a major challenge. To what extent are these organization governed by separate principles, how can we connect develop predictive models for function communities? Here, will discuss recent advances point towards rooted various disciplines physics, biochemistry, dynamical systems. By considering marine carbon cycle as concrete example, demonstrate integration offer deeper insights into impact increasing temperatures, such those associated with climate change, on ecosystem-scale processes. We argue focusing transcend specific microbiomes, pave way comprehensive understanding community development diverse ecosystems.

Язык: Английский

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Interfacial morphodynamics of proliferating microbial communities

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 24, 2023

In microbial communities, various cell types often coexist by occupying distinct spatial domains. What determines the shape of interface between such domains—which in turn influences interactions cells and overall community function? Here, we address this question developing a continuum model 2D spatially-structured with two types. We find that, depending on balance different proliferation rates substrate friction coefficients, domains is either stable smooth, or unstable develops finger-like protrusions. establish quantitative principles describing when these interfacial behaviors arise, good agreement both results previous experimental reports as well new experiments performed here. Our work thus helps to provide biophysical basis for understanding morphodynamics proliferating broader range active systems.

Язык: Английский

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The Architecture of Theory and Data in Microbiome Design: towards an S-matrix for microbiomes

Опубликована: Авг. 9, 2024

Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used range mathematical models understand, predict, control microbiomes, ranging from mechanistic models, putting populations their interactions as focus, purely statistical approaches, searching patterns empirical experimental data. We review success limitations these modeling approaches when designing novel especially guided by (inevitably) incomplete Although successful at predicting generic assembly, phenomenological tend fall short precision needed design implement specific functionality microbiome. argue that effectively with optimal functions diverse environments, should combine data-driven techniques models---a middle, third way using theory inform design.

Язык: Английский

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Response of wild aquatic insect communities to thermal variation through comparative landscape transcriptomics

Archives of Insect Biochemistry and Physiology, Год журнала: 2024, Номер 116(4)

Опубликована: Авг. 1, 2024

Abstract Fluctuations in temperature are recognized as a potent driver of selection pressure, fostering genomic variations that crucial for the adaptation and survival organisms under selection. Notably, water is pivotal factor influencing aquatic organism persistence. By comprehending how respond to shifts temperature, we can understand their potential physiological adaptations environmental change one or multiple species. This, turn, contributes formulation biologically relevant guidelines landscape scale transcriptome profile lotic systems. Here, investigated distinct responses seven stream stonefly species, collected from four geographical regions across Japan, including atmospheric temperatures. We achieved this by assessing differences gene expression through RNA‐sequencing within individual species exploring patterns community‐genes among different identified 735 genes exhibited differential expressions gradient. Remarkably, community displayed levels respiration metabolic genes. Additionally, diversity molecular functions appeared be linked spatial variation, with potentially contributing overall functional found 22 consistent response variations. These related respiration, metabolism development clear gradient providing robust evidence divergent adaptive temperature. Our findings underscore local conditions, suggesting shared may occur similar conditions. This study emphasizes significance considering various when impacts changes on insect communities understanding mechanisms cope such changes.

Язык: Английский

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Environmental modulators of algae-bacteria interactions at scale

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Март 24, 2023

Abstract Photosynthetic microbes associated with non-photosynthetic, heterotrophic, bacteria play a key role in the global primary production. Understanding these phototroph-heterotroph associations is therefore important, but remains challenging because they reside chemically complex aquatic and terrestrial environments. We do not understand how myriad of environmental parameters from nutrient availability to pH impact interactions between phototrophs their heterotrophic partners. Here, we leverage massively parallel droplet microfluidic platform that enables us interrogate algae-bacteria > 100,000 communities across ∼525 conditions varying pH, carbon phosphorous availability. By developing statistical framework dissect this dataset, reveal dependance on strongly modulated by buffering capacity. Furthermore, show chemical identity available organic source controls capacity, modulate interactions. leveraging high-throughput platform, our study reveals previously underappreciated modulating

Язык: Английский

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Species’ functional traits and interactions drive nitrate-mediated sulfur-oxidizing community structure and functioning

mBio, Год журнала: 2023, Номер 14(5)

Опубликована: Сен. 13, 2023

Understanding the processes and mechanisms governing microbial community assembly their linkages to ecosystem functioning has long been a core issue in ecology. An in-depth insight still requires combining with analyses of species' functional traits interactions. Our study showed how interactions determined structure functions by well-controlled laboratory experiment nitrate-mediated sulfur oxidation systems using high-throughput sequencing culture-dependent technologies. The results provided solid evidences that were intrinsic factors determining function. More importantly, our established quantitative links between function based on interactions, which would have important implications for design synthesis microbiomes expected functions.

Язык: Английский

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Distribution of denitrifiers predicted by correlative niche modeling of changing environmental conditions and future climatic scenarios across the Baltic Sea

Ecological Informatics, Год журнала: 2023, Номер 78, С. 102346 - 102346

Опубликована: Окт. 22, 2023

Denitrifying microbial communities provide an important ecosystem function in aquatic systems. Yet, knowledge on predictive and modeling of these complex changing is limited. The emergently challenging question how the geographical distribution denitrifiers responds to ongoing future environmental change not yet fully understood. In our study we use metadata-based correlative niche analyze selected putative genus Sphingomonas, Mycoplana, Shewanella, Alteromonas at different predicted conditions climatic scenarios across Baltic Sea. Using power ensemble approach eight machine-learning algorithms, habitat suitability were evaluated using geophysical bioclimatic variables, benthic conditions, four Representative Concentration Pathway (RCP) trajectories global warming increase scenarios. All algorithms provided successful prediction capabilities both for variable importance, with Area Under Curve (AUC) values between 0.89 1.00. Model findings revealed that salinity nitrate concentrations significantly explained variation denitrifiers. Rising temperatures 0.8 1.8 °C RCP60–2050 hence are diminish or eliminate suitable habitats denitrifier distributions Multi-collated terrestrial marine variables contributed within area. high AUC presented allowed accurate projections can be used improve understanding changes may affect organisms denitrification capacity

Язык: Английский

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Data-driven prediction of colonization outcomes for complex microbial communities

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Апрель 21, 2023

Abstract Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the species complex communities remains a fundamental challenge ecology, mainly due our limited knowledge diverse physical, biochemical, and ecological processes governing dynamics. Here, we proposed data-driven approach independent any dynamics model predict from baseline compositions communities. We systematically validated this using synthetic data, finding that machine learning models (including Random Forest neural ODE) not only binary outcome but also post-invasion steady-state abundance invading species. Then conducted experiments for two commensal gut bacteria Enterococcus faecium Akkermansia muciniphila hundreds human stool-derived vitro communities, confirming successfully outcomes. Furthermore, found while most resident were predicted have weak negative impact on strongly interacting could significantly alter outcomes, e.g., presence faecalis inhibits invasion E. . The presented results suggest is powerful tool inform ecology management

Язык: Английский

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Data-driven prediction of colonization outcomes for complex microbial communities

Research Square (Research Square), Год журнала: 2023, Номер unknown

Опубликована: Авг. 24, 2023

Abstract Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the species complex communities remains a fundamental challenge ecology, mainly due our limited knowledge diverse physical, biochemical, and ecological processes governing dynamics. Here, we proposed data-driven approach independent any dynamics model predict from baseline compositions communities. We systematically validated this using synthetic data, finding that machine learning models (including Random Forest neural ODE) not only binary outcome but also post-invasion steady-state abundance invading species. Then conducted experiments for two commensal gut bacteria Enterococcus faecium Akkermansia muciniphila hundreds human stool-derived vitro communities, confirming successfully outcomes. Furthermore, found while most resident were predicted have weak negative impact on strongly interacting could significantly alter outcomes, e.g., presence faecalis inhibits invasion E. faecium. The presented results suggest is powerful tool inform ecology management

Язык: Английский

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