Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress DOI Open Access
Kun Yan,

Shuqi Ma,

Qiliang Zhu

et al.

Plant Cell & Environment, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

How different stress responses by male and female plants are influenced interactions with rhizosphere microbes remains unclear. In this study, we employed poplar as a dioecious model plant quantified biotic associations between microorganisms to explore the relationship microbial adaptation. We propose health index (HI) comprehensively characterize physiological characteristics adaptive capacity of under stress. It was found that poplars demonstrated higher salt tolerance than females, root-secreted citric acid significantly in rhizospheres poplars. Positive association among bacteria increased HI stress, while fungal cross-domain (bacteria-fungi) did not. further identified keystone bacterial taxon regulating association, ASV_22706, which itself regulated positively correlated host HI. The abundance taxa negatively Compared poplars, enriched more prebiotics probiotics This work primarily reveals adaptation differences plants, suggests approach improve adaptability conditions.

Language: Английский

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling DOI Creative Commons
Zhepu Ruan, Kai Chen,

Weimiao Cao

et al.

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

Published: June 1, 2024

Abstract Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within are largely unknown, and practical principles tools microbiome engineering still lacking. Here, we present a combinatory top-down bottom-up framework to engineer the construction of function-enhanced synthetic microbiomes. We show that application herbicide herbicide-degrader inoculation drives convergent succession different toward functional (e.g., enhanced bioremediation herbicide-contaminated soils). develop modeling pipeline, SuperCC, can be used document simulate performances Using construct bioremediation-enhanced based on 18 keystone species identified from Our results highlight importance in shaping functions provide guidance

Language: Английский

Citations

44
A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities DOI Creative Commons
Huadong Peng, Alexander P. S. Darlington, Eric J. South

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(3), P. 848 - 863

Published: Feb. 7, 2024

Engineered microbial consortia often have enhanced system performance and robustness compared with single-strain biomanufacturing production platforms. However, few tools are available for generating co-cultures of the model key industrial host Saccharomyces cerevisiae. Here we engineer auxotrophic overexpression yeast strains that can be used to create through exchange essential metabolites. Using these as modules, engineered two- three-member using different cross-feeding architectures. Through a combination ensemble modelling experimentation, explored how cellular (for example, metabolite strength) environmental initial population ratio, density extracellular supplementation) factors govern dynamics in systems. We tested use toolkit division labour case study show it enables tuneable antioxidant resveratrol production. expect this become useful resource variety applications synthetic ecology biomanufacturing.

Language: Английский

Citations

21
Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome DOI
Grégoire Michoud, Hannes Peter, Susheel Bhanu Busi

et al.

Nature Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Language: Английский

Citations

2
Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks DOI Creative Commons
Xi Peng,

Shang Wang,

Miaoxiao Wang

et al.

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

Published: Sept. 17, 2024

Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and complementarity networks. We apply this approach temperature gradient hot spring, unraveling the interplay between thermal stress cooperation. Our analysis reveals an increase in frequency of with rising temperatures. Amino acids, coenzyme A derivatives, carbohydrates emerge as key exchange metabolites, forming foundation for syntrophic which commensalistic take greater proportion than mutualistic ones. These exchanges are most prevalent phylogenetically distant species, especially archaea-bacteria collaborations, crucial adaptation harsh environments. Furthermore, identify significant positive correlation basal metabolite genome size disparity, potentially signifying means streamlined leverage cooperation metabolically richer partners. This phenomenon is also confirmed another composting system has similar wide range fluctuations. provides feasible way decipher mechanisms underlying microbial interactions, our findings suggested environmental regulates cooperative strategies thermophiles, while dependencies have been hardwired into their during co-evolutions.

Language: Английский

Citations

11
Metabolic complexity drives divergence in microbial communities DOI
Michael Silverstein, Jennifer Bhatnagar, Daniel Segrè

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(8), P. 1493 - 1504

Published: July 2, 2024

Language: Английский

Citations

10
Interspecific interactions facilitate keystone species in a multispecies biofilm that promotes plant growth DOI Creative Commons
Nan Yang,

Henriette Lyng Røder,

Wisnu Adi Wicaksono

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Microorganisms colonizing plant roots co-exist in complex, spatially structured multispecies biofilm communities. However, little is known about microbial interactions and the underlying spatial organization within communities established on roots. Here, a well-established four-species model (Stenotrophomonas rhizophila, Paenibacillus amylolyticus, Microbacterium oxydans, Xanthomonas retroflexus, termed as SPMX) was applied to Arabidopsis study impact of growth community dynamics SPMX co-culture notably promoted root development biomass. Co-cultured increased colonization formed biofilms, structurally different from those by monocultures. By combining 16S rRNA gene amplicon sequencing fluorescence situ hybridization with confocal laser scanning microscopy, we found that composition significantly changed over time. Monoculture P. amylolyticus colonized poorly, but its population were highly enhanced when residing biofilm. Exclusion reduced overall production three species, resulting loss growth-promoting effects. Combined analysis, this led identification keystone species. Our findings highlight weak colonizers may benefit mutualistic complex hereby become important species impacting function. This work expands knowledge uncovering interspecific roots, beneficial for harnessing mutualism promoting growth.

Language: Английский

Citations

9
Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria DOI Creative Commons
Junbo Tang, Wenlong Zuo,

Lizhen Guo

et al.

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

Published: Aug. 13, 2024

The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro vivo, provides complementary demethylation service to promote growth on methylated homogalacturonan, an enriched polysaccharide pectin. In exchange, shares digestive products with Bifidobacterium, through which positive established. This vanishes when not required non-methylated diet. Results from biochemical gene expression analyses combined model simulation further suggest that ratio change major homogalacturonan breakdown products, galacturonic acid (GalA) di-GalA, determines bacterial interaction. study unravels glycan metabolism may shape Microbial honey bee are incompletely understood. authors report reciprocal core genera: aids pectin backbone enabling its by Gilliamella; return, digestion products.

Language: Английский

Citations

9
Unveiling the deterministic dynamics of microbial meta-metabolism: a multi-omics investigation of anaerobic biodegradation DOI Creative Commons
Xingsheng Yang, Kai Feng, Shang Wang

et al.

Microbiome, Journal Year: 2024, Volume and Issue: 12(1)

Published: Sept. 7, 2024

Language: Английский

Citations

9
Dynamically induced spatial segregation in multispecies bacterial bioconvection DOI Creative Commons

Óscar Adrián Gallardo-Navarro,

Rinat Arbel‐Goren, Elias August

et al.

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

Published: Jan. 22, 2025

Active matter, from motile bacteria to animals, can exhibit striking collective and coherent behavior. Despite significant advances in understanding the behavior of homogeneous systems, little is known about self-organization dynamics heterogeneous active such as complex diverse bacterial communities. Under oxygen gradients, many species swim towards air-liquid interfaces auto-organized, directional bioconvective flows, whose spatial scales exceed cell size by orders magnitude. Here we show that multispecies suspensions undergoing oxytactic-driven bioconvection dynamically driven segregation, despite enhanced mixing fact these coexist their natural habitat. Segregation observed patterns spatially interlocked domains, with local dominance one constituent suspension. Our findings suggest segregation mechanisms are species-specific behaviors under conditions hydrodynamic flow, rather than biochemical repulsion. Thus, different characteristics same ecological context enhance access limiting resources. This work provides novel insights on role heterogeneity well microbial communities, organization Heterogeneous including often forms environmental yet remain poorly understood. study reveals enhancing resource coexistence shared habitats.

Language: Английский

Citations

1
Harnessing microbial co-culture to increase the production of known secondary metabolites DOI
Yuzhen Li, Wanqi Zhang, Pengfei Hu

et al.

Natural Product Reports, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Co-culturing may provoke the biosynthesis of novel natural products. However, various microbial co-culture techniques also boost fermentation titer, yield and rate known products – we review current progress towards such a goal.

Language: Английский

Citations

1