Genetic and species rearrangements in microbial consortia impact biodegradation potential

The ISME Journal, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Language: Английский

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Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 14, 2025

Language: Английский

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Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation

Biotechnology for Biofuels and Bioproducts, Journal Year: 2025, Volume and Issue: 18(1)

Published: Jan. 18, 2025

Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role lignin degradation coastal wetlands, where turnover rates likely underestimated. However, the metabolic potentials of these remain elusive. This greatly hinders our understanding global carbon cycle and "bottom-up" design synthetic to enhance conversion. Here, we developed two groups degrading consortia, L6 L18, through 6- 18-month situ enrichments East China Sea, respectively. Lignin by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon metagenomic sequencing suggested possessed varied taxonomic compositions, yet similar functional traits. Further comparative based on assembly, revealed harbored abundant metagenome-assembled genomes (MAGs) encoded diverse unique gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched highlighting degradation. Furthermore, generalist taxa, which possess flexibility, increased during extended enrichment period, indicating advantage generalists adapting heterogenous resources. study advances strategies prokaryotic lays foundation for communities sustainable lignocellulose biorefining.

Language: Английский

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Microbial functional guilds respond cohesively to rapidly fluctuating environments

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 30, 2025

Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal climactic variations. Understanding how microbial populations respond these is critical for predicting the impact of perturbations, interventions, and climate change on communities. Since typically harbor tens hundreds distinct taxa, response abundances perturbations potentially complex. However, while taxonomic diversity high, many taxa can be grouped into functional guilds strains with similar metabolic traits. These effectively reduce complexity system by providing a physiologically motivated coarse-graining. Here, using combination simulations, theory, experiments, we show that nutrient depends timescale those fluctuations. Rapid drive cohesive, positively correlated abundance dynamics within guilds. For slower variation, members guild begin compete due resource preferences, driving negative correlations between same guild. Our results provide route understanding relationship community changing environments, as well an experimental approach discovering via designed

Language: Английский

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Metabolic synergy and complementarity in the Ips typographus holobiont

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

Microbial symbiosis plays a central role in shaping ecological and evolutionary processes, driving the adaptation of host organisms to challenging environments. However, mechanisms underlying functional integration metabolic cooperation within holobionts remain poorly understood. Current research often emphasizes taxonomic composition microbiomes, but interactions that sustain these associations are less explored, especially nutrient-poor ecosystems. This study addresses this knowledge gap by investigating interdependencies gut microbiome European spruce bark beetle (Ips typographus, ESBB). Using meta-transcriptomic analyses, we reveal critical contributions bacterial fungal symbionts facilitating survival. Our findings show microbial partners compensate for deficiencies, with cross-kingdom enabling biosynthesis essential nutrients such as amino acids vitamins. Furthermore, division labor among taxa is evident, bacteria primarily degrading plant polymers xylan pectin, fungi specializing glucan degradation. Functional redundancy key pathways suggests an adaptive mechanism ensure nutrient availability under fluctuating community composition. In addition, identify previously unappreciated pathway nitrogen acquisition via oxidation inorganic nitrogen. highlight importance their success symbiotic associations. results provide framework exploring cycling resource use.

Language: Английский

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Universal Niche Geometry Governs the Response of Ecosystems to Environmental Perturbations

PRX Life, Journal Year: 2025, Volume and Issue: 3(1)

Published: Feb. 13, 2025

How ecosystems respond to environmental perturbations is a fundamental question in ecology, made especially challenging due the strong coupling between species and their environment. Here, we introduce theoretical framework for calculating steady-state response of generalized consumer-resource models. Our construction applicable wide class systems, including models with nonreciprocal interactions, cross-feeding, nonlinear growth/consumption rates. Within our framework, all ecological variables are embedded into four distinct vector spaces, interactions represented by geometric transformations these spaces. We show that, near steady state, such directly map perturbations—in resource availability mortality rates—to shifts niche structure. illustrate ideas variety settings minimal model pH-induced toxicity bacterial denitrification. end discussing biological implications framework. that it extremely difficult distinguish cooperative competitive measuring responses external perturbations. Published American Physical Society 2025

Language: Английский

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Towards synthetic ecology: strategies for the optimization of microbial community functions

Frontiers in Synthetic Biology, Journal Year: 2025, Volume and Issue: 3

Published: March 18, 2025

Microbial communities are able to carry out myriad functions of biotechnological interest, ranging from the degradation industrial waste synthesis valuable chemical products. Over past years, several strategies have emerged for design microbial and optimization their functions. Here we provide an accessible overview these strategies. We highlight how principles synthetic biology, originally devised engineering individual organisms sub-organismal units (e.g., enzymes), influenced development field ecology. With this, aim encourage readers critically evaluate insights biology should guide our approach community-level engineering.

Language: Английский

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The State-of-the-Art on Exploring Polysaccharide-Protein Interactions and Its Mechanisms, Stability, and Their Role in Food Systems

Food Reviews International, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 36

Published: April 3, 2025

Language: Английский

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Hydrogen Production, Storage, and Decarbonization via Heterogenous Catalytic CO2 Hydrogenation

Korean Journal of Chemical Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: April 3, 2025

Language: Английский

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Dynamic coexistence driven by physiological transitions in microbial communities

Proceedings of the National Academy of Sciences, Journal Year: 2025, Volume and Issue: 122(16)

Published: April 17, 2025

Microbial ecosystems are commonly modeled by fixed interactions between species in steady exponential growth states. However, microbes often modify their environments so strongly that they forced out of the state into stressed, nongrowing Such dynamics typical ecological succession nature and serial-dilution cycles laboratory. Here, we introduce a phenomenological model, Community State Model, to gain insight dynamic coexistence due changes physiological states during cyclic succession. Our model specifies preference each along global coordinate, taken be biomass density community, but is otherwise agnostic specific (e.g., nutrient starvation, stress, aggregation), order focus on self-consistency conditions combinations states, “community states,” stable ecosystem. We identify three key features such dynamical communities contrast starkly with steady-state communities: enhanced community stability through staggered dominance different increased tolerance diversity fast growing dominating distinct requirement late-growing species. These features, derived explicitly for simplified models, proposed here as principles aiding understanding complex communities. shifts ecosystem from bottom–up studies based fixed, idealized interspecies interaction top–down accessible macroscopic observables rates total density, enabling quantitative examination community-wide characteristics.

Language: Английский

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