Soil nutrition-dependent dynamics of the root-associated microbiome in paddy rice DOI Open Access
Asahi Adachi, Yuniar Devi Utami,

John Jewish Dominguez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 2, 2024

Summary Plants accommodate diverse microbial communities (microbiomes), which can change dynamically during plant adaptation to varying environmental conditions. However, the direction of these changes and underlying mechanisms driving them, particularly in crops adapting field conditions, remain poorly understood. We investigate root-associated microbiome rice ( Oryza sativa L.) using 16S rRNA gene amplicon metagenome sequencing, across four consecutive cultivation seasons a high-yield, non-fertilized, pesticide-free paddy field, compared neighboring fertilized pesticide-treated field. Our findings reveal that root community shifts diverges based on soil fertilization status developmental stages. Notably, nitrogen-fixing bacteria such as Telmatospirillum, Bradyrhizobium Rhizomicrobium were over-represented grown non-fertilized implying assembly microbes supports nutrient-deficient environments. A machine learning model trained data successfully predicted status, highlighting potential analysis forecasting nutrition levels. Additionally, we observed significant ccamk mutants, lack master regulator mycorrhizal symbiosis, under laboratory conditions but not suggesting condition-dependent role for CCaMK establishing microbiomes rice.

Language: Английский

Strategies for tailoring functional microbial synthetic communities DOI Creative Commons
Jiayi Jing, Paolina Garbeva, Jos M. Raaijmakers

et al.

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

Published: Jan. 1, 2024

Abstract Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity soil microorganisms their complex interactions make it challenging to pinpoint the main players life support functions can provide plants, including enhanced tolerance (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity unravel molecular chemical basis interplay specific microbiome functions. While SynComs have been successfully employed dissect or reproduce microbiome-associated phenotypes, assembly reconstitution these often based on generic abundance patterns taxonomic identities co-occurrences but only rarely informed by functional traits. Here, we review recent studies designing reveal common principles discuss multidimensional approaches community design. We propose strategy tailoring design integration high-throughput experimental assays with strains computational genomic analyses capabilities.

Language: Английский

Citations

26
Engineering agricultural soil microbiomes and predicting plant phenotypes DOI
Chiara A. Berruto, Gözde S. Demirer

Trends in Microbiology, Journal Year: 2024, Volume and Issue: 32(9), P. 858 - 873

Published: Feb. 29, 2024

Language: Английский

Citations

14
A systematic discussion and comparison of the construction methods of synthetic microbial community DOI Creative Commons
Chenglong Li, Yanfeng Han,

Xiao Zou

et al.

Synthetic and Systems Biotechnology, Journal Year: 2024, Volume and Issue: 9(4), P. 775 - 783

Published: June 20, 2024

Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over past few years. However, there is little consensus on method to synthetic from construction functional verification. Here, we review concept, characteristics, history applications community, summarizing several methods for construction, such as isolation culture, core microbiome mining, automated design, gene editing. In addition, also systematically summarized design concepts, technological thresholds, applicable scenarios various methods, highlighted their advantages limitations. Ultimately, this provides four efficient, detailed, easy-to-understand -follow steps with major implications agricultural practices, production, environmental governance.

Language: Английский

Citations

7
Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology DOI Creative Commons

Óscar Adrián Gallardo-Navarro,

Bernardo Aguilar-Salinas,

Jorge Gustavo Rocha

et al.

Heliyon, Journal Year: 2024, Volume and Issue: 10(14), P. e33896 - e33896

Published: July 1, 2024

Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts health, while the soil rhizosphere microbiomes influence productivity of crops. However, complexity diversity make them challenging study difficult develop into applications, as they often exhibit emergence unpredictable higher-order phenomena. Synthetic ecology aims at simplifying by constituting synthetic or semi-natural with reduced that become easier analyze. This strategy combines methodologies simplify existing complex systems (top-down approach) build system from its constituent components (bottom-up approach). Simplified are studied understand how interactions among populations shape behavior community model predict their response external stimuli. By harnessing potential through a multidisciplinary approach, we can advance knowledge ecological concepts address critical public agricultural, environmental issues more effectively.

Language: Английский

Citations

6
Connecting microbial community assembly and function DOI
Leonora Bittleston

Current Opinion in Microbiology, Journal Year: 2024, Volume and Issue: 80, P. 102512 - 102512

Published: July 16, 2024

Language: Английский

Citations

5
Microbiome-mediated plant disease resistance: recent advances and future directions DOI Creative Commons
Yulin Du,

Xiaowei Han,

Kenichi Tsuda

et al.

Journal of General Plant Pathology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 17, 2024

Abstract Plant pathogens cause plant diseases that significantly decrease crop yields, posing a serious threat to global food security. While disease resistance has traditionally been understood as the trait determined by innate immune system and pathogen virulence system, recent research underscores pivotal role of microbiome in resistance. Plant-associated microbiomes confer protection against through direct inhibition, resource competition, activation responses. Agricultural practices such rotation, intercropping, disease-resistant breeding, biocontrol, organic farming modulate microbiomes, thereby influencing This review synthesizes latest advancements understanding intricate interactions among plants, pathogens, microbiomes. We emphasize need for in-depth mechanistic studies linking agricultural dynamics propose future directions leverage sustainable agriculture.

Language: Английский

Citations

5
A cross-systems primer for synthetic microbial communities DOI
Elijah C. Mehlferber, Gontran Arnault, Bishnu Joshi

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(11), P. 2765 - 2773

Published: Oct. 30, 2024

Language: Английский

Citations

5
Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms DOI
Adriel M. Sierra, Omayra Meléndez,

Rita Bethancourt

et al.

Journal of Chemical Ecology, Journal Year: 2024, Volume and Issue: 50(11), P. 815 - 829

Published: May 29, 2024

Language: Английский

Citations

4
Roots of synthetic ecology: microbes that foster plant resilience in the changing climate DOI
Ekaterina Kozaeva, Abdul Aziz Eida, Ella F Gunady

et al.

Current Opinion in Biotechnology, Journal Year: 2024, Volume and Issue: 88, P. 103172 - 103172

Published: July 18, 2024

Language: Английский

Citations

4
Embracing complexity in plant–microbiome systems DOI Creative Commons
María Josefina Poupin, Bernardo González

Environmental Microbiology Reports, Journal Year: 2024, Volume and Issue: 16(4)

Published: Aug. 1, 2024

Abstract Despite recent advances in understanding the role of microorganisms plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, sustainable agriculture. This article explores some these discusses emerging research areas microbiomes. Firstly, it emphasizes need move beyond taxonomic characterization towards microbial functions within ecosystems. Secondly, controlling methodological biases enhancing OMICS technologies' standardization is imperative a deeper comprehension plant–microbiota interactions. Furthermore, while microbiota has primarily centred on bacteria fungi, other players such as archaea, viruses, microeukaryotes have been largely overlooked. Emerging evidence highlights their presence potential roles, underscoring thorough assessments. Future should aim elucidate ecological interactions, impact performance, how context shapes community dynamics. Finally, discussion provided multiple layers abiotic biotic factors influencing spatiotemporal dynamics plant–microbiome systems require in‐depth attention. Examples illustrate synthetic communities computational methods machine learning artificial intelligence provide alternatives tackle challenges analyse complex system.

Language: Английский

Citations

4