High-throughput microfluidic assay devices for culturing of soybean and microalgae and microfluidic electrophoretic ion nutrient sensor

In the past decade, there are significant challenges in agriculture because of the rapidly growing global population. Meanwhile, microfluidic devices or lab-on-a-chip devices, which are a set of micro-structure etch or molded into glass, silicon wafer, PDMS, or other materials, have been rapidly developed to achieve features, such as mix, separate, sort, sense, and control biochemical environment. The advantages of microfluidic technologies include high-throughput, low cost, precision control, and highly sensitive. In particular, they have offered promising potential for applications in medical diagnosis, drug discovery, and gene sequencing. However, the potential of microfluidic technologies for application in agriculture is far from being developed. This thesis focuses on the application of microfluidic technologies in agriculture. In this thesis, three different types of microfluidic systems were developed to present three approaches in agriculture investigation. Firstly, this report a high throughput approach to build a steady-state discrete relative humidity gradient using a modified multi-well plate. The customized device was applied to generate a set of humidity conditions to study the plant-pathogen interaction for two types of soybean beans, Williams and Williams 82. Next, a microfluidic microalgal bioreactor is presented to culture and screen microalgae strains growth under a set of CO2 concentration conditions. C. reinhardtii strains CC620 were cultured and screened in the customized bioreactor to validate the workability of the system. Growth rates of the cultured strain cells were analyzed under different CO2 concentrations. In addition, a multi-well-plate-based microalgal bioreactor array was also developed to do long-term culturing and screening. This work showed a promising microfluidic bioreactor for in-line screening based on microalgal culture under different CO2 concentrations. Finally, this report presents a microchip sensor system for ions separation and detection basing electrophoresis. It is a system owning high potential in various ions concentration analysis with high specificity and sensitivity. In addition, a solution sampling system was developed to extract solution from the soil. All those presented technologies not only have advantages including high-throughput, low cost, and highly sensitive but also have good extensibility and robustness. With a simple modification, those technologies can be expanded to different application areas due to experimental purposes. Thus, those presented microfluidic technologies provide new approaches and powerful tools in agriculture investigation. Furthermore, they have great potential to accelerate the development of agriculture

Towards In-situ Based Printed Sensor Systems for Real-Time Soil-Root Nutrient Monitoring and Prediction with Polynomial Regression

This dissertation explores how to increase sensor density in the agricultural framework using low-cost sensors, while also managing major bottlenecks preventing their full commercial adoption for agriculture, accuracy and drift. It also investigated whether low-cost biodegradable printed sensor sheets can result in improved stability, accuracy or drift for use in precision agriculture. In this dissertation, multiple electrode systems were investigated with much of the work focused on printed carbon graphene electrodes (with and without nanoparticles). The sensors were used in two configurations: 1) in varying soil to understand sensor degradation and the effect of environment on sensors, and 2) in plant pod systems to understand growth. It was established that 3) the sensor drift can be controlled and predicted 2) the fabricated low-cost sensors work as well as commercial sensors, and 3) these sensors were then successfully validated in the pod platform. A standardized testing system was developed to investigate soil physicochemical effects on the modified nutrient sensors through a series of controlled experiments. The construct was theoretically modeled and the sensor data was matched to the models. Supervised machine learning algorithms were used to predict sensor responses. Further models produced actionable insight which allowed us to identify a) the minimal amounts of irrigation required and b) optimal time after applying irrigation or rainfall event before achieving accurate sensor readings, both with respect to sensor depth placement within the soil matrix. The pore-scale behavior of solute transport through different depths within the sandy soil matrix was further simulated using COMSOL Multi-physics. This work leads to promising disposable printed systems for precision agriculture

Extraction of Soil Solution into a Microfluidic Chip

Collecting real-time data on physical and chemical parameters of the soil is a prerequisite for resource-efficient and environmentally sustainable agriculture. For continuous in situ measurement of soil nutrients such as nitrate or phosphate, a lab-on-chip approach combined with wireless remote readout is promising. For this purpose, the soil solution, i.e., the water in the soil with nutrients, needs to be extracted into a microfluidic chip. Here, we present a soil-solution extraction unit based on combining a porous ceramic filter with a microfluidic channel with a 12 µL volume. The microfluidic chip was fabricated from polydimethylsiloxane, had a size of 1.7 cm × 1.7 cm × 0.6 cm, and was bonded to a glass substrate. A hydrophilic aluminum oxide ceramic with approximately 37 Vol.-% porosity and an average pore size of 1 µm was integrated at the inlet. Soil water was extracted successfully from three types of soil—silt, garden soil, and sand—by creating suction with a pump at the other end of the microfluidic channel. For garden soil, the extraction rate at approximately 15 Vol.-% soil moisture was 1.4 µL/min. The amount of extracted water was investigated for 30 min pump intervals for the three soil types at different moisture levels. For garden soil and sand, water extraction started at around 10 Vol.-% soil moisture. Silt showed the highest water-holding capacity, with water extraction starting at approximately 13 Vol.-

The influence of soil structure on microbial processes in microfluidic models

The way microbes behave in nature can vary widely depending on the spatial characteristics of the habitats they are located in. The spatial structure of the microbial environment can determine whether and to which extent processes such as organic matter degradation, and synergistic or antagonistic microbial processes occur. Investigating how the different spatial characteristics of microhabitats influence microbes has been challenging due to methodological limitations. In the case of soil sciences, attempts to describe the inner structure of the soil pore space, and to connect it to microbial processes, such as to determine the access of nutrient limited soil microorganisms to soil organic matter pools, has been one of the main goals of the field in the last years. The present work aimed at answering the question of how spatial complexity affects microbial dispersal, growth, and the degradation of a dissolved organic substrate. Using microfluidic devices, designed to mimic the inner soil pore physical structures, we first followed the dispersal and growth of soil microbes in the devices, using soil inocula or burying the microfluidic devices in the top layer of a soil (Paper I). We found that inter-kingdom interactions can play an important role for the dispersal of water-dwelling organisms and that these physically modified their environment. To reveal the effect of the different structures on microbes in more detail we tested the influence of increasing spatial complexity in a porespace on the growth and substrate degradation of bacterial and fungal laboratory strains. The parameters we used to manipulate the pore space’s complexity were two: via the turning angle and turning order of pore channels (Paper II), and via the fractal order of a pore maze (Paper III). When we tested the effect of an increase in turning angle sharpness on microbial growth, we found that as angles became sharper, bacterial and fungal growth decreased, but fungi were more affected than bacteria. We also found that their substrate degradation was only affected when bacteria and fungi grew together, being lower as the angles were sharper. Our next series of experiments, testing the effect of maze fractal complexity, however, showed a different picture. The increase in maze complexity reduced fungal growh, similar to the previous experiments, but increased bacterial growth and substrate consumption, at least until a certain depth into the mazes, contrary to our initial hypothesis. To increase the relevance of our studies, we performed experiments in both microfluidic device designs inoculated with a soil microbial extract and followed the substrate degradation patterns over time (Paper IV). We found that as complexity increased, both in terms of angle sharpness and fractal order, substrate consumption also increased. Our results, specially in mazes, might be caused by a reduced competition among bacterial communities and individuals in complex habitats, allowing co-existence of different metabolic strategies and the onset of bacterial biofilm formation leading to a higher degradation efficiency, but further studies are required to confirm this. Our results show that the spatial characteristic of microhabitats is an important factor providing microbes with conditions for a wide variety of ecological interactions that determine their growth and their organic matter turnover

Bio- und Umweltsensorik basierend auf organischer Optoelektronik

The integration of organic light emitting diodes (OLEDs) and organic photodetectors (OPDs) promises compact and low-cost hybrid integrated sensors for optical detection. The thermal evaporation-based device fabrication technique allows for all optical sensing elements being permanently aligned with a high degree of miniaturization, creating more portable, energy-efficient and multiplexing-capable devices; these may be easily combined with microfluidic units resulting in a minimal sample and reagent volume demand of the sensor. This dissertation deals in particular with the system design, development, characterization and deployment of a monolithic integrated sensor unit with 8 OLED and 8 OPD pixel pairs for different applications. The following work provides an extensive study of the system efficiency via ray tracing simulations, investigating crucial boundary conditions for efficient analyte detection. The proposed sensing unit contains OLED and OPD devices with an individual pixel size of 0.5mm × 0.5mm fabricated on a 12.5mm × 12.5mm glass substrate. The developed sensor system was successfully characterized and applied in a biosensing application by detecting fluorescence labelled single-stranded DNA (ssDNA) after forming the Förster resonance energy transfer (FRET) upon the hybridization of two ssDNA strands. This optoelectronic sensor has the potential to enable compact and low-cost fluorescence point-of-care (POC) devices for decentralised multiplex biomedical testing. Additionally, this sensing platform was deployed in environmental and agricultural applications to detect nutrients such as nitrite and nitrate. In this colorimetric application the popular Griess reaction was utilized to form the nitrite concentration dependent amount of azo dye, which absorbs light around 540nm

Distributed environmental monitoring

With increasingly ubiquitous use of web-based technologies in society today, autonomous sensor networks represent the future in large-scale information acquisition for applications ranging from environmental monitoring to in vivo sensing. This chapter presents a range of on-going projects with an emphasis on environmental sensing; relevant literature pertaining to sensor networks is reviewed, validated sensing applications are described and the contribution of high-resolution temporal data to better decision-making is discussed

Distributed chemical sensor networks for environmental sensing

Society is increasingly accustomed to instant access to real-time information, due to the ubiquitous use of the internet and web-based access tools. Intelligent search engines enable huge data repositories to be searched, and highly relevant information returned in real time. These repositories increasingly include environmental information related to the environment, such as distributed air and water quality. However, while this information at present is typically historical, for example, through agency reports, there is increasing demand for real-time environmental data. In this paper, the issues involved in obtaining data from autonomous chemical sensors are discussed, and examples of current deployments presented. Strategies for achieving large-scale deployments are discussed

Analysis of relevant technical issues and deficiencies of the existing sensors and related initiatives currently set and working in marine environment. New generation technologies for cost-effective sensors

The last decade has seen significant growth in the field of sensor networks, which are currently collecting large amounts of environmental data. This data needs to be collected, processed, stored and made available for analysis and interpretation in a manner which is meaningful and accessible to end users and stakeholders with a range of requirements, including government agencies, environmental agencies, the research community, industry users and the public. The COMMONSENSE project aims to develop and provide cost-effective, multi-functional innovative sensors to perform reliable in-situ measurements in the marine environment. The sensors will be easily usable across several platforms, and will focus on key parameters including eutrophication, heavy metal contaminants, marine litter (microplastics) and underwater noise descriptors of the MSFD. The aims of Tasks 2.1 and 2.2 which comprise the work of this deliverable are: • To obtain a comprehensive understanding and an up-to-date state of the art of existing sensors. • To provide a working basis on “new generation” technologies in order to develop cost-effective sensors suitable for large-scale production. This deliverable will consist of an analysis of state-of-the-art solutions for the different sensors and data platforms related with COMMONSENSE project. An analysis of relevant technical issues and deficiencies of existing sensors and related initiatives currently set and working in marine environment will be performed. Existing solutions will be studied to determine the main limitations to be considered during novel sensor developments in further WP’s. Objectives & Rationale The objectives of deliverable 2.1 are: • To create a solid and robust basis for finding cheaper and innovative ways of gathering data. This is preparatory for the activities in other WPs: for WP4 (Transversal Sensor development and Sensor Integration), for WP(5-8) (Novel Sensors) to develop cost-effective sensors suitable for large-scale production, reducing costs of data collection (compared to commercially available sensors), increasing data access availability for WP9 (Field testing) when the deployment of new sensors will be drawn and then realized

Microfluidics Expanding the Frontiers of Microbial Ecology

Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.National Science Foundation (U.S.) (Grant OCE-0744641-CAREER)National Science Foundation (U.S.) (Grant IOS-1120200)National Science Foundation (U.S.) (Grant CBET-1066566)National Science Foundation (U.S.) (Grant CBET-0966000)National Institutes of Health (U.S.) (NIH grant 1R01GM100473-0)Human Frontier Science Program (Strasbourg, France)Human Frontier Science Program (Strasbourg, France) (award RGY0089)Gordon and Betty Moore Foundation (Microbial Initiative Investigator Award

Custom-engineered micro-habitats for characterizing rhizosphere interactions

The interactions amongst plants and microorganisms within the rhizosphere have a profound influence on global biogeochemical cycles, and a better understanding of these interactions will benefit society through improved climate change prediction, increased food security, and enhanced bioenergy production. However, the rhizosphere is one of the most complex and bio-diverse ecosystems on earth, making it difficult to parse apart specific interactions between species. This difficulty is compounded by the inability to directly visualize rhizosphere interactions through the soil. Additionally, conventional laboratory techniques do not offer real-time, high-resolution visualization or the proper environmental control to isolate and probe these interactions. A knowledge gap persists in how to design appropriate culturing platforms that allow researchers to collect spatially and temporally sensitive information about physical and chemical interactions in the rhizosphere. This dissertation addresses that gap by demonstrating the design and use of several custom-engineered micro-habitats in characterizing plant-microbe interactions. Specifically this thesis introduces novel protocols for culturing plants and microorganisms together in microfluidic platforms, pairing platforms to multi-modal imaging techniques with organelle scale resolution, and recreating the structural complexity of the rhizosphere in a microfluidic habitat. Not only does this thesis introduce novel engineered systems, but the work contained herein also goes beyond proof-of-concept experiments and demonstrates the ability of these platforms to generate hypotheses and answer outstanding biological questions