Alternative stable states of microbiome structure and soil ecosystem functions

Environmental Microbiome, Год журнала: 2025, Номер 20(1)

Опубликована: Март 6, 2025

Theory predicts that biological communities can have multiple stable states in terms of their species/taxonomic compositions. The presence such alternative has been examined classic ecological studies on the macro-organisms (e.g., distinction between forest and savanna vegetation types). Nonetheless, it remains an essential challenge to extend target discussion multistability from macro-organismal systems highly species-rich microbial systems. Identifying taxonomically diverse is a crucial step for predicting controlling microbiome processes light community stability. By targeting soil microbiomes, we inferred stability landscapes structure based mathematical framework statistical physics. We compiled dataset involving 11 archaeal, 332 bacterial, 240 fungal families detected > 1,500 agroecosystem samples applied energy landscape analysis estimate stability/instability observed taxonomic suggested both prokaryotic could be classified into several states. also found differed greatly associations with crop disease prevalence agroecosystems. further "tipping points", through which transitions occur. Our results suggest complex microbiomes categorized states, potentially differ ecosystem-level functioning. Such insights relationship structure, stability, functions will provide basis ecosystem restoration sustainable management

Язык: Английский

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Microbial community organization designates distinct pulmonary exacerbation types and predicts treatment outcome in cystic fibrosis

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 7, 2024

Abstract Polymicrobial infection of the airways is a hallmark obstructive lung diseases such as cystic fibrosis (CF), non-CF bronchiectasis, and chronic pulmonary disease. Pulmonary exacerbations (PEx) in these conditions are associated with accelerated function decline higher mortality rates. Understanding PEx ecology challenged by high inter-patient variability airway microbial community profiles. We analyze bacterial communities 880 CF sputum samples collected during an observational prospective cohort study develop microbiome descriptors to model reorganization prior 18 PEx. identify two dysbiosis regimes opposing dynamics. Pathogen-governed show hierarchical reduced diversity, whereas anaerobic bloom display stochasticity increased diversity. A simulation antimicrobial treatment predicts better efficacy for hierarchically organized communities. This link between PEx, organization, success advances development personalized clinical management and, potentially, other diseases.

Язык: Английский

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Alternative cliques of coexisting species in complex ecosystems

Journal of Physics Complexity, Год журнала: 2024, Номер 5(2), С. 025022 - 025022

Опубликована: Май 24, 2024

Abstract The possibility that some ecosystems can exist in alternative stable states has profound implications for ecosystem conservation and restoration. Current ecological theory on multistability mostly relies few-species dynamical models, which are intrinsically related to specific non-linear dynamics. Recent theoretical advances, however, have shown multiple ‘cliques’—small subsets of coexisting species—can be present species-rich models even under linear interactions. Yet, the mechanisms governing appearence characteristics these cliques remain largely unexplored. In work, we investigate generalized Lotka–Volterra model with mathematical computational techniques. Our findings reveal simple probabilistic constraints explain appearence, properties stability cliques. work contributes understanding complex communities.

Язык: Английский

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Modeling tumors as complex ecosystems

iScience, Год журнала: 2024, Номер 27(9), С. 110699 - 110699

Опубликована: Авг. 10, 2024

Many cancers resist therapeutic intervention. This is fundamentally related to intratumor heterogeneity: multiple cell populations, each with different phenotypic signatures, coexist within a tumor and its metastases. Like species in an ecosystem, cancer populations are intertwined complex network of ecological interactions. Most mathematical models ecology, however, cannot account for such diversity or predict consequences. Here, we propose that the generalized Lotka-Volterra model (GLV), standard tool describe species-rich communities, provides suitable framework ecology heterogeneous tumors. We develop GLV growth discuss how emerging properties provide new understanding disease. potential extensions their application plasticity, cancer-immune interactions, metastatic growth. Our work outlines set questions road map further research ecology.

Язык: Английский

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The development of ecological systems along paths of least resistance

Current Biology, Год журнала: 2024, Номер 34(20), С. 4813 - 4823.e14

Опубликована: Сен. 26, 2024

Язык: Английский

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Assembly Graph as the Rosetta Stone of Ecological Assembly

Environmental Microbiology, Год журнала: 2025, Номер 27(1)

Опубликована: Янв. 1, 2025

Ecological assembly-the process of ecological community formation through species introductions-has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non-theoreticians, they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool connect emerging theories. The visually represents dynamics, where nodes symbolise combinations edges represent transitions driven by introductions. Through lens graphs, review how processes reduce uncertainty in random arrivals (informational approach), identify graphical properties that guarantee coexistence examine class dynamical models constrain topology graphs (dynamical quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, also methods decompose complex into smaller, measurable components, well computational tools for deriving graphs. In sum, this math-light progress aims catalyse research towards predictive understanding assembly.

Язык: Английский

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Modeling tumors as species-rich ecological communities

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

Опубликована: Апрель 26, 2024

Many advanced cancers resist therapeutic intervention. This process is fundamentally related to intra-tumor heterogeneity: multiple cell populations, each with different mutational and phenotypic signatures, coexist within a tumor its metastatic nodes. Like species in an ecosystem, many cancer populations are intertwined complex network of ecological interactions. Most mathematical models ecology, however, cannot account for such diversity nor able predict consequences. Here we propose that the Generalized Lotka-Volterra model (GLV), standard tool describe complex, species-rich communities, provides suitable framework ecology heterogeneous tumors. We develop GLV growth discuss how emerging properties, as outgrowth multistability, provide new understanding disease. Additionally, potential extensions their application three active areas research, namely plasticity, cancer-immune interplay resistance tumors treatment. Our work outlines set questions tentative road map further research ecology.

Язык: Английский

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Assembly Graph as the Rosetta Stone of Ecological Assembly

Опубликована: Авг. 2, 2024

Ecological assembly---the process of ecological community formation through species introductions---has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non-theoreticians, they lack a unifying lens. Here, I introduce the assembly graph as an integrative tool connect emerging theories. The visually represents dynamics, where nodes symbolize combinations edges represent transitions driven by introductions. Through lens graphs, review how processes reduce uncertainty in random arrivals (informational approach), identify graphical properties that guarantee coexistence examine class dynamical models constrain topology graphs (dynamical quantify transition probabilities with incomplete information (probabilistic approach). To facilitate empirical testing, also methods decompose complex into smaller, measurable components, well computational tools for deriving graphs. In sum, this math-light progress aims catalyze research towards predictive understanding assembly.

Язык: Английский

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Fundamental Constraints to the Logic of Living Systems

Опубликована: Июнь 13, 2024

It has been argued that the historical nature of evolution makes it a highly path-dependent process. Under this view, outcome evolutionary dynamics could have resulted in organisms with different forms and functions. At same time, there is ample evidence convergence constraints strongly limit domain potential design principles can achieve. Are these limitations relevant shaping fabric possible? Here, we argue fundamental are associated logic living matter. We illustrate idea by considering thermodynamic properties systems, linear molecular information, cellular building blocks life, multicellularity development, threshold computations cognitive discrete architecture ecosystems. In all examples, present available suggest avenues towards well-defined theoretical formulation.

Язык: Английский

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The development of ecological systems along paths of least resistance

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

Опубликована: Июнь 28, 2024

Abstract A long-standing question in biology is whether there are common principles that characterize the development of ecological systems (the appearance a group taxa), regardless organismal diversity and environmental context. Classic theory holds these develop following sequenced orderly process generally proceeds from fast-growing to slow-growing taxa depends on life-history trade-offs. However, it also possible this developmental order simply path with least resistance for survival component species hence favored by probability alone. Here, we use data show fast-to most likely diverse when local taxon interactions self-organize minimize resistance. First, demonstrate theoretically more than simultaneous one, at until number iterations becomes so large as be ecologically implausible. We then greater life histories improves likelihood taxa. Using bacterial metazoan systems, present empirical evidence moves along paths The capacity simple explain trend paves way an enhanced understanding collective features characterizing life.

Язык: Английский

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