Unraveling plant–microbe interactions: can integrated omics approaches offer concrete answers? DOI Creative Commons

Roy Njoroge Kimotho,

Solomon Maina

Journal of Experimental Botany, Journal Year: 2023, Volume and Issue: 75(5), P. 1289 - 1313

Published: Nov. 9, 2023

Abstract Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help deeper insights into plant–microbe interactions a concerted way. Integrating multi-omics datasets transform our understanding of the microbiome from unspecified genetic influences interacting species specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies crop research review key aspects integration host microbial omics-based be used comprehensive outline complex crop–microbe We describe these technological advances have helped unravel crucial genes pathways that control beneficial, pathogenic, commensal identify knowledge gaps synthesize current limitations approaches. studies which multi-omics-based approaches led improved models community structure function. Finally, recommend holistic integrating achieve precision efficiency data analysis, for biotic abiotic stress contribution microbiota shaping fitness.

Language: Английский

Machine learning and deep learning applications in microbiome research DOI Creative Commons
Ricardo Hernández Medina, Svetlana Kutuzova, K Nielsen

et al.

ISME Communications, Journal Year: 2022, Volume and Issue: 2(1)

Published: Oct. 6, 2022

Abstract The many microbial communities around us form interactive and dynamic ecosystems called microbiomes. Though concealed from the naked eye, microbiomes govern influence macroscopic systems including human health, plant resilience, biogeochemical cycling. Such feats have attracted interest scientific community, which has recently turned to machine learning deep methods interrogate microbiome elucidate relationships between its composition function. Here, we provide an overview of how latest studies harness inductive prowess artificial intelligence methods. We start by highlighting that data – being compositional, sparse, high-dimensional necessitates special treatment. then introduce traditional novel discuss their strengths applications. Finally, outlook pipelines, focusing on bottlenecks considerations address them.

Language: Английский

Citations

145
Microbes to support plant health: understanding bioinoculant success in complex conditions DOI Creative Commons
Sanne WM Poppeliers, Juan J. Sánchez-Gil, Ronnie de Jonge

et al.

Current Opinion in Microbiology, Journal Year: 2023, Volume and Issue: 73, P. 102286 - 102286

Published: March 4, 2023

A promising, sustainable way to enhance plant health and productivity is by leveraging beneficial microbes. Beneficial microbes are natural soil residents with proven benefits for performance health. When applied in agriculture improve crop yield performance, these commonly referred as bioinoculants. Yet, despite their promising properties, bioinoculant efficacy can vary dramatically the field, hampering applicability. Invasion of rhizosphere microbiome a critical determinant success. complex phenomenon that shaped interactions local, resident host plant. Here, we explore all dimensions cross-cutting ecological theory molecular biology microbial invasion rhizosphere. We refer famous Chinese philosopher strategist Sun Tzu, who believed solutions problems require deep understanding themselves, review major biotic factors determining effectiveness.

Language: Английский

Citations

60
Harnessing biological nitrogen fixation in plant leaves DOI Open Access
Yong‐Guan Zhu, Jingjing Peng, Cai Chen

et al.

Trends in Plant Science, Journal Year: 2023, Volume and Issue: 28(12), P. 1391 - 1405

Published: June 1, 2023

Language: Английский

Citations

59
Harnessing the plant microbiome for sustainable crop production DOI
Stéphane Compant, Fabricio Cassán, Tanja Kostić

et al.

Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 15, 2024

Language: Английский

Citations

46
Unlocking bacterial potential to reduce farmland N2O emissions DOI Creative Commons
Elisabeth Gautefall Hiis, Silas H. W. Vick, Lars Molstad

et al.

Nature, Journal Year: 2024, Volume and Issue: 630(8016), P. 421 - 428

Published: May 29, 2024

Abstract Farmed soils contribute substantially to global warming by emitting N 2 O (ref. 1 ), and mitigation has proved difficult . Several microbial nitrogen transformations produce O, but the only biological sink for is enzyme NosZ, catalysing reduction of 3 ). Although strengthening NosZ activity in would reduce emissions, such bioengineering soil microbiota considered challenging 4,5 However, we have developed a technology achieve this, using organic waste as substrate vector O-respiring bacteria selected their capacity thrive 6–8 Here analysed biokinetics our most promising bacterium, Cloacibacterium sp. CB-01, its survival effect on emissions field experiments. Fertilization with from biogas production, which CB-01 had grown aerobically about 6 × 10 9 cells per millilitre, reduced 50–95%, depending type. The strong long-lasting ascribed tenacity soil, rather than biokinetic parameters, were inferior those other strains bacteria. Scaling data up European level, find that national anthropogenic could be 5–20%, more if including wastes. This opens an avenue cost-effective options are lacking at present.

Language: Английский

Citations

41
The emerging role of the gut microbiota and its application in inflammatory bowel disease DOI Open Access
Wang Xiu, Jianhua Peng,

Pei-Pei Cai

et al.

Biomedicine & Pharmacotherapy, Journal Year: 2024, Volume and Issue: 179, P. 117302 - 117302

Published: Aug. 19, 2024

Inflammatory bowel disease (IBD), including Crohn's and ulcerative colitis, is a complex disorder with an unknown cause. However, the dysbiosis of gut microbiome has been found to play role in IBD etiology, exacerbated immune responses defective intestinal barrier integrity. The can also be potential biomarker for several diseases, IBD. Currently, conventional treatments targeting pro-inflammatory cytokines pathways IBD-associated do not yield effective results. Other therapies that directly target dysbiotic outcomes are emerging. We review health its as diagnostic, prognostic, therapeutic This explores emerging advancements microbiome-associated alterations IBD, such nanoparticle or encapsulation delivery, fecal microbiota transplantation, nutritional therapies, microbiome/probiotic engineering, phage therapy, mesenchymal stem cells (MSCs), proteins, herbal formulas.

Language: Английский

Citations

16
Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience DOI Creative Commons

Israt Jahan Misu,

Md. Omar Kayess, Md. Nurealam Siddiqui

et al.

Microorganisms, Journal Year: 2025, Volume and Issue: 13(2), P. 233 - 233

Published: Jan. 22, 2025

The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, overall health of plants. This review aims to update our knowledge critically discuss diversity functional roles rice as well microbiome engineering strategies enhance biofertilization resilience. Rice hosts various microorganisms that affect cycling, growth promotion, resistance stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone metabolite production, enhanced solubilization uptake, regulation host gene expression. Recent research on molecular biology has elucidated complex interactions within microbiomes signalling mechanisms establish beneficial microbial communities, which are crucial sustainable production environmental health. Crucial factors successful commercialization agents include soil properties, practical field conditions, genotype. Advances engineering, from traditional inoculants synthetic biology, optimize availability resilience abiotic stresses like drought. Climate change intensifies challenges, but innovations microbiome-shaping genes (M genes) offer promising solutions crop also discusses agronomic implications emphasizing need further exploration M breeding disease traits. Ultimately, we provide an current findings rice, highlighting pathways productivity sustainably while minimizing impacts.

Language: Английский

Citations

2
The potential of tailoring the gut microbiome to prevent and treat cardiometabolic disease DOI
Rima Chakaroun, Lisa Olsson, Fredrik Bäckhed

et al.

Nature Reviews Cardiology, Journal Year: 2022, Volume and Issue: 20(4), P. 217 - 235

Published: Oct. 14, 2022

Language: Английский

Citations

69
Plant Microbiome Engineering: Hopes or Hypes DOI Creative Commons
Muhammad Siddique Afridi, Sher Ali, Abdus Salam

et al.

Biology, Journal Year: 2022, Volume and Issue: 11(12), P. 1782 - 1782

Published: Dec. 7, 2022

Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This plant-associated community, usually regarded as the plant’s second genome, plays crucial role in plant health. It unquestioned that collectively contributes to growth fitness. also provides safeguard from pathogens, induces tolerance host against abiotic stressors. The revolution omics, gene-editing sequencing tools have somehow led unravel compositions latent interactions between plants microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical ecological methods been proposed. Such platforms solely dedicated engineer by untangling potential barriers, achieve better agriculture output. Yet, several limitations, for example, biological obstacles, constraints molecular capably impact engineering functionality, remained unaddressed problems. In this review, we provide holistic overview composition, complexities, major challenges engineering. Then, unearthed all inevitable factors serve bottlenecks discouraging functionality. Lastly, exploring inherent micro/macrofauna, propose economic eco-friendly strategies could be harnessed sustainably biotechnologically resilient

Language: Английский

Citations

68
Ecological and Evolutionary Implications of Microbial Dispersal DOI Creative Commons
Gordon Custer,

Luana Bresciani,

Francisco Dini‐Andreote

et al.

Frontiers in Microbiology, Journal Year: 2022, Volume and Issue: 13

Published: April 6, 2022

Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal an essential process with direct ecological evolutionary implications that modulate community assembly turnover. Seminal studies have shown environmental context (e.g., local edaphic properties, resident community), timing frequency, traits, collectively account for patterns distribution resulting in either their persistence or unsuccessful establishment within communities. key importance process, relatively little known about how operates microbiomes divergent systems types. Here, we discuss parallels macro- micro-organismal ecology a focus on idiosyncrasies may lead to novel mechanisms by which affects structure function microbiomes. Within implications, revise short- long-distance microbial through active passive mechanisms, coalescence, these align recent advances metacommunity theory. Conversely, enumerate can affect diversification rates promoting gene influxes communities and/or shifting genes allele frequencies

Language: Английский

Citations

64