Microfluidic chips provide visual access to in situ soil ecology

Mafla-Endara, Paola Micaela; Arellano-Caicedo, Carlos; Aleklett, Kristin; Pučetaitė, Milda; Ohlsson, Pelle; Hammer, Edith C.

doi:10.1038/s42003-021-02379-5

Cited by 42 publications

(31 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These miniaturized systems have been successfully applied in specific domains of microbiology [ 83 ]. Microfluidic chips make it possible to simulate soil structure and microhabitats or to directly observe soil micropores and the dynamics of microorganisms in compartmentalized and controlled systems [ 84 , 85 ]. These devices have been used to demonstrate the movement of bacteria along fungal hyphae [ 86 ], to document the interaction between fungi and parasitic nematodes, or the mechanisms of competition between antagonistic fungi [ 61 ].…”

Section: Methods For the Study Of Bioinocula Interactions With Soil M...mentioning

confidence: 99%

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Ptaszek

Canfora²,

Pugliese

et al. 2023

Microorganisms

View full text Add to dashboard Cite

Microbial-based products (either as biopesticide or biofertilizers) have a long history of application, though their use is still limited, mainly due to a perceived low and inconsistent efficacy under field conditions. However, their efficacy has always been compared to chemical products, which have a completely different mechanism of action and production process, following the chemical paradigm of agricultural production. This paradigm has also been applied to regulatory processes, particularly for biopesticides, making the marketing of microbial-based formulations difficult. Increased knowledge about bioinocula behavior after application to the soil and their impact on soil microbiome should foster better exploitation of microbial-based products in a complex environment such as the soil. Moreover, the multifunctional capacity of microbial strains with regard to plant growth promotion and protection should also be considered in this respect. Therefore, the methods utilized for these studies are key to improving the knowledge and understanding of microbial-based product activity and improving their efficacy, which, from farmers’ point of view, is the parameter to assess the usefulness of a treatment. In this review, we are thus addressing aspects related to the production and formulation process, highlighting the methods that can be used to evaluate the functioning and impact of microbial-based products on soil microbiome, as tools supporting their use and marketing.

show abstract

Section: Methods For the Study Of Bioinocula Interactions With Soil M...mentioning

confidence: 99%

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Ptaszek

Canfora²,

Pugliese

et al. 2023

Microorganisms

View full text Add to dashboard Cite

show abstract

“…To this end, new technology may help probe the nexus between phototrophic organisms and MFCs. One promising direction involves microuidic lab-on-a-chip systems, which enable growth and real-time monitoring of living organisms such as soil bacteria, [184][185][186][187] biolms, 188,189 and even plant roots under highly controlled conditions. [190][191][192] For example, there are an increasing number of studies using microuidics to study naturally uorescent photosynthetic bacteria, sometimes…”

Section: Future Perspectives and Conclusionmentioning

confidence: 99%

Phototrophic microbial fuel cells: a greener approach to sustainable power generation and wastewater treatment

Sonawane¹,

Vijay²,

Deng³

et al. 2023

Sustainable Energy Fuels

View full text Add to dashboard Cite

show abstract

“…Although significant improvements have been made in culturing so-far unculturable microorganisms, finding an appropriate culture medium remains difficult. High-throughput culturing platforms have emerged to isolate and screen a large number of microbial cells ( Mafla-Endara et al, 2021 ; Trivedi et al, 2021 ). The ability to isolate single cells using microfluidics coupled with technologies amplifying genomic DNA from single cells will revolutionize the study of unculturable species and of microheterogeneity within species ( Chen et al, 2021 ).…”

Section: Ongoing and Future Developmentsmentioning

confidence: 99%

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

et al. 2022

View full text Add to dashboard Cite

Soils are fundamental resources for agricultural production and play an essential role in food security. They represent the keystone of the food value chain because they harbor a large fraction of biodiversity—the backbone of the regulation of ecosystem services and “soil health” maintenance. In the face of the numerous causes of soil degradation such as unsustainable soil management practices, pollution, waste disposal, or the increasing number of extreme weather events, it has become clear that (i) preserving the soil biodiversity is key to food security, and (ii) biodiversity-based solutions for environmental monitoring have to be developed. Within the soil biodiversity reservoir, microbial diversity including Archaea, Bacteria, Fungi and protists is essential for ecosystem functioning and resilience. Microbial communities are also sensitive to various environmental drivers and to management practices; as a result, they are ideal candidates for monitoring soil quality assessment. The emergence of meta-omics approaches based on recent advances in high-throughput sequencing and bioinformatics has remarkably improved our ability to characterize microbial diversity and its potential functions. This revolution has substantially filled the knowledge gap about soil microbial diversity regulation and ecology, but also provided new and robust indicators of agricultural soil quality. We reviewed how meta-omics approaches replaced traditional methods and allowed developing modern microbial indicators of the soil biological quality. Each meta-omics approach is described in its general principles, methodologies, specificities, strengths and drawbacks, and illustrated with concrete applications for soil monitoring. The development of metabarcoding approaches in the last 20 years has led to a collection of microbial indicators that are now operational and available for the farming sector. Our review shows that despite the recent huge advances, some meta-omics approaches (e.g., metatranscriptomics or meta-proteomics) still need developments to be operational for environmental bio-monitoring. As regards prospects, we outline the importance of building up repositories of soil quality indicators. These are essential for objective and robust diagnosis, to help actors and stakeholders improve soil management, with a view to or to contribute to combining the food and environmental quality of next-generation farming systems in the context of the agroecological transition.

show abstract

Microfluidic chips provide visual access to in situ soil ecology

Cited by 42 publications

References 56 publications

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Microbial-Based Products to Control Soil-Borne Pathogens: Methods to Improve Efficacy and to Assess Impacts on Microbiome

Phototrophic microbial fuel cells: a greener approach to sustainable power generation and wastewater treatment

Potential of Meta-Omics to Provide Modern Microbial Indicators for Monitoring Soil Quality and Securing Food Production

Contact Info

Product

Resources

About