Environmental modulators of algae-bacteria interactions at scale

Gopalakrishnappa, Chandana; Li, Zeqian; Kuehn, Seppe

doi:10.1101/2023.03.23.534036

Cited by 3 publications

(1 citation statement)

References 45 publications

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“…This complexity is perhaps most apparent in soils, which possess immense taxonomic diversity [4], spatial heterogeneity [5], and chemically diverse environments [6]. As a result, environmental perturbations can modify collective metabolic activity in many ways, from direct changes in microbial composition, physiology [7], and ecological interactions [8, 9] to indirect modification of nutrient availability [10–12] and spatial organization [5, 13]. Thus, a key question arises: which mechanisms are important for determining the metabolic response of complex microbiomes to environmental change?…”

Section: Introductionmentioning

confidence: 99%

Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

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A major challenge in microbiome research is understanding how natural communities respond to environmental change. The ecological, spatial, and chemical complexity of soils makes understanding how these communities respond metabolically to perturbations particularly challenging. Here we measure the dynamics of respiratory nitrate utilization in >1,500 soil microcosms from 20 soil samples subjected to pH perturbations. Despite the complexity of the soil microbiome a minimal mathematical model with two parameters, the quantity of active biomass and the availability of a limiting nutrient, quantifies observed nitrate utilization dynamics across soils and pH perturbations. The model reveals three distinct functional phases that encode the low-dimensional dynamics of nitrate utilization in response to short and long-term pH perturbations: a phase where acidic perturbations induce cell death that limits metabolic activity, a nutrient-limiting phase where nitrate utilization is performed by dominant taxa that utilize nutrients released from the soil matrix, and a resurgent growth phase in basic conditions, where nutrients are in excess and rare taxa rapidly outgrow dominant populations. The underlying functional mechanism of each phase is revealed by our interpretable model and tested via amendment experiments, nutrient measurements, and sequencing. The long-term pH of the soil determines the size of pH changes necessary to drive transitions between functional phases. Our results unify decades of previous studies on nitrogen utilization and pH in soils under a single quantitative framework. A minimal mathematical formalism reveals the existence of a few qualitative phases that capture the mechanisms and dynamics of a community responding to environmental change.

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Section: Introductionmentioning

confidence: 99%

Functional regimes define the response of the soil microbiome to environmental change

Lee,

Liu,

Crocker

et al. 2024

Preprint

Self Cite

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Environmentally dependent interactions shape patterns in gene content across natural microbiomes

Crocker,

Lee,

Chakraverti-Wuerthwein

et al. 2024

Nat Microbiol

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Synthetic microbial ecology: engineering habitats for modular consortia

Chen,

Destouches,

Cook

et al. 2024

Journal of Applied Microbiology

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Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.

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Environmental modulators of algae-bacteria interactions at scale

Cited by 3 publications

References 45 publications

Functional regimes define the response of the soil microbiome to environmental change

Functional regimes define the response of the soil microbiome to environmental change

Environmentally dependent interactions shape patterns in gene content across natural microbiomes

Synthetic microbial ecology: engineering habitats for modular consortia

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