Environment-organism feedbacks drive changes in ecological interactions DOI Creative Commons
Oliver J. Meacock, Sara Mitri

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

Опубликована: Ноя. 2, 2023

Abstract Ecological interactions, the impact of one organism on growth and death another, underpin our understanding long-term composition functional properties communities. In recent years, context-dependency interactions – their tendency to change values in different environments, locations at times has become an increasingly important theme ecological research. However, overarching theoretical assumption been that external environmental factors are responsible for driving these changes. Here, we derive a interaction framework which teases apart separate roles played by extrinsic inputs intrinsic changes driven organisms within environment itself. At heart theory is ‘instantaneous interaction’, quantity captures feedback between it. limit intrinsic, organismdriven dominates over drivers, find this can give rise temporal spatial context-dependencies as modify time and/or space. We use small synthetic microbial communities model ecosystems demonstrate power framework, using it predict time-dependent intra-specific toxin degradation system relate dependencies crossfeeding Our helps explain ubiquity systems where population such placing equal footing inhabit

Язык: Английский

Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology DOI Creative Commons

Óscar Adrián Gallardo-Navarro,

Bernardo Aguilar-Salinas,

Jorge Gustavo Rocha

и другие.

Heliyon, Год журнала: 2024, Номер 10(14), С. e33896 - e33896

Опубликована: Июль 1, 2024

Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts health, while the soil rhizosphere microbiomes influence productivity of crops. However, complexity diversity make them challenging study difficult develop into applications, as they often exhibit emergence unpredictable higher-order phenomena. Synthetic ecology aims at simplifying by constituting synthetic or semi-natural with reduced that become easier analyze. This strategy combines methodologies simplify existing complex systems (top-down approach) build system from its constituent components (bottom-up approach). Simplified are studied understand how interactions among populations shape behavior community model predict their response external stimuli. By harnessing potential through a multidisciplinary approach, we can advance knowledge ecological concepts address critical public agricultural, environmental issues more effectively.

Язык: Английский

Процитировано

6
Quantifying microbial interactions: concepts, caveats, and applications DOI
Nittay Meroz,

Tal Livny,

Jonathan Friedman

и другие.

Current Opinion in Microbiology, Год журнала: 2024, Номер 80, С. 102511 - 102511

Опубликована: Июль 13, 2024

Язык: Английский

Процитировано

6
Effect of Selective Substrates on Germination of Pomegranate (Punica granatum) and Trifoliate Orange (Poncirus trifoliata) Seeds with and Without the Presence of Plant-Beneficial Microorganisms DOI Creative Commons
H. Kalorizou,

Dimitra Stefanopoulou,

Paschalis Giannoulis

и другие.

Seeds, Год журнала: 2025, Номер 4(1), С. 12 - 12

Опубликована: Март 6, 2025

Insect-based (silkworm cocoons) and plant-based (cotton wool pads gauzes) fiber substrates were used to support ameliorate seed germination originating from trifoliate orange (Poncirus trifoliata) pomegranate (Punica granatum) trees. Three different commercial formulations of beneficial microorganisms (Bacillus spp.-Azotobacter spp., Saccharomyces boulardii, cerevisiae) administered seeds in order evaluate their contribution growth. The silkworm cocoons provided better rates for P. trifoliata (83.33%) among the tested media without any microbial supplementation. These increased towards absolute maximum (100%) when Bacillus S. boulardii cerevisiae applied. Furthermore, inoculums spp. 2 mL 3 g raised ability by 30–33.33% 50–67.7%, respectively, on cocoon compared plant-derived, cellulosic under same biotic exposure. On increasing size applied inoculums, moved optimum suboptimum all media. Examination multipartite pH compatibility (between seeds, microorganisms, media) was functional value. In conclusion, both tree species can be using bacterial yeast supplementation, including medical-grade environmentally friendly materials such as insect- substrates.

Язык: Английский

Процитировано

0
Differential effects of environmentally relevant concentrations of ibuprofen on denitrification and nitrous oxide emissions in river sediments DOI

Tongyue Zhuo,

Sibo Zhang, Zhong Zhang

и другие.

Journal of Hazardous Materials, Год журнала: 2025, Номер 493, С. 138326 - 138326

Опубликована: Апрель 17, 2025

Язык: Английский

Процитировано

0
Competition and cooperation: The plasticity of bacteria interactions across environments DOI
Josephine Solowiej-Wedderburn, Jennifer T. Pentz, Ludvig Lizana

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июль 3, 2024

Bacteria live in diverse communities, forming complex networks of interacting species. A central question bacterial ecology is why some species engage cooperative interactions, whereas others compete. But this often neglects the role environment. Here, we use genome-scale metabolic from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions microbes varying environmental conditions (provision compounds). By scanning thousands environments for 10,000 pairs bacteria each collection, found that most were able both compete cooperate depending on availability resources. This approach allowed us determine commonalities between could facilitate potential cooperation or competition a pair Namely, especially obligate, common less environments. Further, as compounds removed environment, tended degrade towards obligacy. However, also average at least one compound be an environment switch interaction facultative vice versa. Together our indicates high degree plasticity microbial

Язык: Английский

Процитировано

2
Environment‐Organism Feedbacks Drive Changes in Ecological Interactions DOI Creative Commons
Oliver J. Meacock, Sara Mitri

Ecology Letters, Год журнала: 2024, Номер 28(1)

Опубликована: Дек. 31, 2024

Ecological interactions are foundational to our understanding of community composition and function. While known change depending on the environmental context, it has generally been assumed that external factors responsible for driving these dependencies. Here, we derive a theoretical framework which instead focuses how intrinsic changes caused by organisms themselves alter interaction values. Our central concept is 'instantaneous interaction', captures feedback between current state organismal growth, generating spatiotemporal context-dependencies as modify their environment over time and/or space. We use small microbial communities illustrate this can predict time-dependencies in toxin degradation system, relate time- spatial-dependencies crossfeeding communities. By re-centring relationship environment, predicts variations wherever intrinsic, organism-driven dominates drivers.

Язык: Английский

Процитировано

1
Collective peroxide detoxification determines microbial mutation rate plasticity in E. coli DOI Creative Commons
Rowan Green, Hejie Wang,

Carol Botchey

и другие.

PLoS Biology, Год журнала: 2024, Номер 22(7), С. e3002711 - e3002711

Опубликована: Июль 15, 2024

Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining variation available a population. One such dependency inverse relationship between mutation rates and population density microbial species. Here, we determine mechanism responsible this rate plasticity. Using dynamical computational modelling culture estimation, show that negative arises from collective ability of populations control concentrations hydrogen peroxide. We demonstrate loss density-associated plasticity (DAMP) when Escherichia coli are deficient degradation further reduction denser restored peroxide degradation-deficient cells by presence wild-type mixed Together, these model-guided experiments provide mechanistic explanation DAMP, applicable across all domains life, frames as dynamic trait shaped community composition.

Язык: Английский

Процитировано

0
Modelling interactions that determine core gut microbiome stability to predict microbiome perturbation by opportunistic pathogens DOI Creative Commons
Pim J. van Leeuwen, Stanley Brul, Jurgen Seppen

и другие.

Опубликована: Июль 15, 2024

The gut microbiome plays a crucial role in host homeostasis, with implications for nutrition, immune development, metabolism, and protection against pathogens. Changes composition are associated health after microbial shifts, opportunistic pathogens have unique chance to invade overgrow the However, complexity of inhibits understanding cause consequence. This study describes species interaction model predict stability. method aids perturbation by Escherichia coli Bacteroides ovatus validate predictions co-culture growth experiments. Despite their inherent differences rates commensals, both E. B. can successfully an established consortium. mechanisms invasion differ; replaces original consortium bacterium, whereas integrates into microbiome. research enhances our processes stability health.

Язык: Английский

Процитировано

0
Environment-mediated interactions cause an externalized and collective memory in microbes DOI

Shubham Gajrani,

Xiaozhou Ye, Christoph Ratzke

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 14, 2024

Abstract Microbes usually live in complex communities interacting with many other microbial species. These interactions determine who can persist a community and how the overall forms functions. often exert by chemically changing environment, like taking up nutrients or producing toxins. environmental changes over time. We show here that such lasting cause memory effect where current growth conditions alter interaction outcomes future. Importantly, this is only stored environment not inside bacterial cells. Only collective effort of bacteria build memory, making it an emergent property populations. This “population memory” also impact assembly more lead to different final depending on system’s past. Overall, we understand fully, have consider species abiotic but history.

Язык: Английский

Процитировано

0
Environment-organism feedbacks drive changes in ecological interactions DOI Creative Commons
Oliver J. Meacock, Sara Mitri

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

Опубликована: Ноя. 2, 2023

Abstract Ecological interactions, the impact of one organism on growth and death another, underpin our understanding long-term composition functional properties communities. In recent years, context-dependency interactions – their tendency to change values in different environments, locations at times has become an increasingly important theme ecological research. However, overarching theoretical assumption been that external environmental factors are responsible for driving these changes. Here, we derive a interaction framework which teases apart separate roles played by extrinsic inputs intrinsic changes driven organisms within environment itself. At heart theory is ‘instantaneous interaction’, quantity captures feedback between it. limit intrinsic, organismdriven dominates over drivers, find this can give rise temporal spatial context-dependencies as modify time and/or space. We use small synthetic microbial communities model ecosystems demonstrate power framework, using it predict time-dependent intra-specific toxin degradation system relate dependencies crossfeeding Our helps explain ubiquity systems where population such placing equal footing inhabit

Язык: Английский

Процитировано

1