Evolutionary repeatability of emergent properties of ecological communities DOI Creative Commons
Sandeep Venkataram, Sergey Kryazhimskiy

Published: Dec. 10, 2022

Most species belong to ecological communities where their interactions give rise emergent community-level properties, such as diversity and productivity. Understanding predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability human health. Less attention paid the fact that can also because member evolve. Yet, our ability predict long-term eco-evolutionary dynamics hinges on repeatably result of evolution. Here, we review studies evolution both natural experimental make case at least sometimes evolve repeatably. We discuss challenges faced investigations evolutionary repeatability. In particular, only handful enable us quantify argue quantifying repeatability community level is critical approaching what see three open questions field: (1) Is observed degree surprising? (2) How related traits species? (3) What factors affect repeatability? outline some theoretical empirical approaches addressing questions. Advances directions will not enrich basic understanding ecology but help dynamics.

Language: Английский

The community-function landscape of microbial consortia DOI Creative Commons

Álvaro Sánchez,

Djordje Bajić, Juan Díaz‐Colunga

et al.

Cell Systems, Journal Year: 2023, Volume and Issue: 14(2), P. 122 - 134

Published: Feb. 1, 2023

Language: Английский

Citations

60
Plants and endophytes interaction: a “secret wedlock” for sustainable biosynthesis of pharmaceutically important secondary metabolites DOI Creative Commons
Poonam Kumari,

Nikky Deepa,

Prabodh Kumar Trivedi

et al.

Microbial Cell Factories, Journal Year: 2023, Volume and Issue: 22(1)

Published: Nov. 4, 2023

Abstract Many plants possess immense pharmacological properties because of the presence various therapeutic bioactive secondary metabolites that are great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal being cultivated on large scale. However, enhance yield simultaneously manage pest infestations, agrochemicals routinely used have detrimental impact whole ecosystem, ranging from biodiversity loss water pollution, soil degradation, nutrient imbalance enormous health hazards both consumers agricultural workers. To address challenges, biological eco-friendly alternatives looked upon with high hopes where endophytes pitch as key players due their tight association host plants. The intricate interplay endophytic microorganisms has emerged captivating subject scientific investigation, profound implications for sustainable biosynthesis pharmaceutically important metabolites. This review delves into hidden world "secret wedlock" endophytes, elucidating multifaceted interactions underpin synthesis compounds significance plant hosts. Here, we briefly diversity highlight potential role core endomicrobiome. We also propose successful implementation situ microbiome manipulation through high-end techniques can pave way towards more enriched future.

Language: Английский

Citations

28
Data-driven prediction of colonization outcomes for complex microbial communities DOI Creative Commons
Lu Wu, Xu‐Wen Wang,

Zining Tao

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: March 16, 2024

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 microbial ecology, mainly due our limited knowledge diverse mechanisms governing dynamics. Here, we propose data-driven approach independent any dynamics model predict from baseline compositions communities. We systematically validate this using synthetic data, finding that machine learning models not only binary outcome but also post-invasion steady-state abundance invading species. Then conduct experiments for commensal gut bacteria Enterococcus faecium and Akkermansia muciniphila hundreds human stool-derived vitro communities, confirming approaches experiments. Furthermore, find while most resident are predicted have weak negative impact on strongly interacting could significantly alter outcomes, e.g., faecalis inhibits invasion E. invasion. The presented results suggest powerful tools inform ecology management

Language: Английский

Citations

10
Dynamic responses in Pseudomonas stutzeri M3 bioaugmentation of crude-oil-contaminated soil: Hydrocarbons, microbial community structures, and functional genes DOI
Lin Li,

Yizhan Liu,

Ying Zhang

et al.

Journal of environmental chemical engineering, Journal Year: 2024, Volume and Issue: 12(1), P. 111863 - 111863

Published: Jan. 4, 2024

Language: Английский

Citations

5
Ecological landscapes guide the assembly of optimal microbial communities DOI Creative Commons
Ashish B. George, Kirill S. Korolev

PLoS Computational Biology, Journal Year: 2023, Volume and Issue: 19(1), P. e1010570 - e1010570

Published: Jan. 10, 2023

Assembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the community challenging because number of possible grows exponentially with species, so an exhaustive search cannot be performed even a dozen species. A heuristic that improves function by adding or removing one species at time more practical, but it unknown whether this strategy can discover nearly community. Using consumer-resource models without cross-feeding, we investigate how efficacy depends on distribution resources, niche overlap, other aspects ecology. We show determined ruggedness appropriately-defined ecological landscape. identify specific measures are both predictive performance robust to noise low sampling density. The feasibility our approach demonstrated using experimental data from soil Overall, results establish conditions necessary success provide concrete design principles building high-performing consortia.

Language: Английский

Citations

12
The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes DOI
Shreya Arya, Ashish B. George, James P. O’Dwyer

et al.

Current Opinion in Microbiology, Journal Year: 2025, Volume and Issue: 83, P. 102580 - 102580

Published: Jan. 22, 2025

Language: Английский

Citations

0
Interfacial Morphodynamics of Proliferating Microbial Communities DOI Creative Commons
Alejandro Martínez-Calvo, Carolina Trenado-Yuste, Hyunseok Lee

et al.

Physical Review X, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 29, 2025

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 fingerlike 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 communities broader range active systems. Published American Physical Society 2025

Language: Английский

Citations

0
Environmental modulators of algae-bacteria interactions at scale DOI

Chandana Gopalakrishnappa,

Zeqian Li, Seppe Kuehn

et al.

Cell Systems, Journal Year: 2024, Volume and Issue: 15(9), P. 838 - 853.e13

Published: Sept. 1, 2024

Language: Английский

Citations

3
Robustness of microbiome function DOI Creative Commons
Kiseok Keith Lee, Yeonwoo Park, Seppe Kuehn

et al.

Current Opinion in Systems Biology, Journal Year: 2023, Volume and Issue: 36, P. 100479 - 100479

Published: Sept. 15, 2023

Language: Английский

Citations

8
Evolutionary repeatability of emergent properties of ecological communities DOI
Sandeep Venkataram, Sergey Kryazhimskiy

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 378(1877)

Published: April 2, 2023

Most species belong to ecological communities where their interactions give rise emergent community-level properties, such as diversity and productivity. Understanding predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability human health. Less attention paid the fact that can also because member evolve. Yet, our ability predict long-term eco-evolutionary dynamics hinges on repeatably result of evolution. Here, we review studies evolution both natural experimental make case at least sometimes evolve repeatably. We discuss challenges faced investigations evolutionary repeatability. In particular, only handful enable us quantify argue quantifying repeatability community level is critical approaching what see three open questions field: (i) Is observed degree surprising? (ii) How related traits species? (iii) What factors affect repeatability? outline some theoretical empirical approaches addressing questions. Advances directions will not enrich basic understanding ecology but help dynamics. This article part theme issue 'Interdisciplinary biology'.

Language: Английский

Citations

6