Abstract:An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity ( C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas… Show more
“…A highly useful starting point would be to delve into dynamic variation in microbial genes involved in carbon metabolism and nitrogen cycling in the rhizosphere, in combination with root exudate metabolomics and measurements of root N uptake. Stable isotope labeling and in situ visualization methods [69–73] could further complement our understanding of how management, plant roots, and their interactive effects shape rhizosphere processes.…”
BackgroundRhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.ResultsHost selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.ConclusionsPlant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.
“…A highly useful starting point would be to delve into dynamic variation in microbial genes involved in carbon metabolism and nitrogen cycling in the rhizosphere, in combination with root exudate metabolomics and measurements of root N uptake. Stable isotope labeling and in situ visualization methods [69–73] could further complement our understanding of how management, plant roots, and their interactive effects shape rhizosphere processes.…”
BackgroundRhizosphere microbial communities are key regulators of plant performance, yet few studies have assessed the impact of different management approaches on the rhizosphere microbiomes of major crops. Rhizosphere microbial communities are shaped by interactions between agricultural management and host selection processes, but studies often consider these factors individually rather than in combination. We tested the impacts of management (M) and rhizosphere effects (R) on microbial community structure and co-occurrence networks of maize roots collected from long-term conventionally and organically managed maize-tomato agroecosystems. We also explored the interaction between these factors (M × R) and how it impacts rhizosphere microbial diversity and composition, differential abundance, indicator taxa, co-occurrence network structure, and microbial nitrogen-cycling processes.ResultsHost selection processes moderate the influence of agricultural management on rhizosphere microbial communities, although bacteria and fungi respond differently to plant selection and agricultural management. We found that plants recruit management-system-specific taxa and shift N-cycling pathways in the rhizosphere, distinguishing this soil compartment from bulk soil. Rhizosphere microbiomes from conventional and organic systems were more similar in diversity and network structure than communities from their respective bulk soils, and community composition was affected by both M and R effects. In contrast, fungal community composition was affected only by management, and network structure only by plant selection. Quantification of six nitrogen-cycling genes (nifH, amoA [bacterial and archaeal], nirK, nrfA, and nosZ) revealed that only nosZ abundance was affected by management and was higher in the organic system.ConclusionsPlant selection interacts with conventional and organic management practices to shape rhizosphere microbial community composition, co-occurrence patterns, and at least one nitrogen-cycling process. Reframing research priorities to better understand adaptive plant-microbe feedbacks and include roots as a significant moderating influence of management outcomes could help guide plant-oriented strategies to improve productivity and agroecosystem sustainability.
“…Thus, stochastic average masked signals of heterogeneous populations can be avoided. Consequently, the level of biological noises could be controlled and clear correlations could be established [ 123 , 124 , 125 , 126 , 127 ].…”
Flow cytometry and its technological possibilities have greatly advanced in the past decade as analysis tool for single cell properties and population distributions of different cell types in bioreactors. Along the way, some solutions for automated real‐time flow cytometry (ART‐FCM) were developed for monitoring of bioreactor processes without operator interference over extended periods with variable sampling frequency. However, there is still great potential for ART‐FCM to evolve and possibly become a standard application in bioprocess monitoring and process control. This review first addresses different components of an ART‐FCM, including the sampling device, the sample‐processing unit, the unit for sample delivery to the flow cytometer and the settings for measurement of pre‐processed samples. Also, available algorithms are presented for automated data analysis of multi‐parameter fluorescence datasets derived from ART‐FCM experiments. Furthermore, challenges are discussed for integration of fluorescence‐activated cell sorting into an ART‐FCM setup for isolation and separation of interesting subpopulations that can be further characterized by for instance omics‐methods. As the application of ART‐FCM is especially of interest for bioreactor process monitoring, including investigation of population heterogeneity and automated process control, a summary of already existing setups for these purposes is given. Additionally, the general future potential of ART‐FCM is addressed.
“…The processes of selective detection and rapid manipulation of particles can be done through direct contact and contactless manipulation of targeted particles. The former includes techniques such as the pressure-driven membrane filtration using micro membrane or nano membrane (Chung et al, 2017), micro-gripper (Bolopion et al, 2010), colour label techniques such as epithelial cell adhesion molecule (EpCAM) (Torrico et al, 2018), fluorescence activated cell sorting (Verma et al, 2018;(Gougoulias et al, 2018) and mixing of magnetic materials including magnetic activated cell sorting (MACS) (Suzuki et al, 2007). Overall, these techniques have negative impacts on particles and their medium because of the nature of direct contact and contaminating of materials owing to the dye marker colour and magnetic beads.…”
Section: Introductionmentioning
confidence: 99%
“…Therefore, in this work, a DEP MEMS consist of microelectrode arrays with tapered profile, have been studied as a tool for highly efficient detection and manipulation of particles and its performance has been compared with those of conventional designs (Chen et al, 2014;Srivastava et al, 2008;Han et al, 2011). The proposed DEP MEMS microelectrodes can selectively detect and manipulate according to the lateral and vertical forces and can be implemented for development of lab-on-a-chip application.…”
Purpose
This paper aims to present the dielectrophoresis (DEP) force (FDEP), defined as microelectrofluidics mechanism capabilities in performing selective detection and rapid manipulation of blood components such as red blood cells (RBC) and platelets. The purpose of this investigation is to understand FDEP correlation to the variation of dynamic dielectric properties of cells under an applied voltage bias.
Design/methodology/approach
In this paper, tapered design DEP microelectrodes are used and explained. To perform the characterization and optimization by analysing the DEP polarization factor, the change in dynamic dielectric properties of blood components are observed according to the crossover frequency (fxo) and adjustment frequency (fadj) variation for selective detection and rapid manipulation.
Findings
Experimental observation of dynamic dielectric properties change shows clear correlation to DEP polarization factor when performing selective detection and rapid manipulation. These tapered DEP microelectrodes demonstrate an in situ DEP patterning efficiency more than 95%.
Research limitations/implications
The capabilities of tapered DEP microelectrode devices are introduced in this paper. However, they are not yet mature in medical research studies for various purposes such as identifying cells and bio-molecules for detection, isolation and manipulation application. This is because of biological property variations that require further DEP characterization and optimization.
Practical implications
The introduction of microelectrofluidics using DEP microelectrodes operate by selective detecting and rapid manipulating via lateral and vertical forces. This can be implemented on precision health-care development for lab-on-a-chip application in microfluidic diagnostic and prognostic devices.
Originality/value
This study introduces a new concept to understand the dynamic dielectric properties change. This is useful for rapid, label free and precise methods to conduct selective detection and rapid manipulation of mixtures of RBC and platelets. Further, potential applications that can be considered are for protein, toxin, cancer cell and bacteria detections and manipulation. Implementation of tapered DEP microelectrodes can be used based on the understanding of dynamic dielectric properties of polarization factor analysis.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.