The rise of high-throughput phenotyping (HTP) has led to a dramatic increase in the ability to rapidly – and accurately – phenotype various organisms including plants. However, methods for efficiently managing, processing, analyzing, and sharing HTP data have not caught up to this new-found ability to collect big data which in turn introduces a whole host of new challenges. To address these, we have architected and implemented a multi-faceted infrastructure of webservices to further unify and automate the entire data collection process. We have integrated CyVerse and Slack into our IoHTP, two commonly used tools within plant science labs. CyVerse is a cloud-based data storage & management solution and Slack allows for bilateral instant-message communication with the HTP machines to keep researchers in touch with their autonomous experiments. Next, we are also developing our own website for administering jobs remotely to any number of (possibly geographically distributed) HTP machines. This innovative open-source approach has the potential to further advance high-throughput phenotyping worldwide by allowing interdisciplinary experts, namely in the plant and computer sciences, to collaborate more effectively and efficiently.

Anthropogenic factors such as climate change, harsh agricultural practices, and mining have contributed to increases in soil salinization and heavy metal contamination. Highly saline environments drastically lower yield for crop species and elevated levels of toxic metals like cadmium are carcinogenic in the environment. Some plants that have evolved in high-salinity habitats or in soils with heavy metals could be used to remediate contaminated soils. Halophytes are plants with various adaptations that allow them to survive and reproduce in saline conditions. General mechanisms for salt tolerance/uptake in halophytes are hypothesized to help deal with other stresses like heavy metals. Plants with these traits could be utilized to extract salt and heavy metals from affected soils in a process called phytoremediation. We plan to develop Sea Rocket (Cakile maritima) in the Mustard family as a model system to understand mechanisms of salt (NaCl) and cadmium uptake and tolerance, as it has been shown to accumulate both. As part of this study, we will hydroponically grow C. maritima in different stress treatments using salt and cadmium. As the plants uptake the pollutants, the conductivity of the solution will change. We will develop an automated pipeline to track these changes in real-time using conductivity sensors. In addition, we will sample root and leaf tissues at various time points to measure salt and cadmium uptake using ICP-OES elemental analysis. This data will provide insights into salt and cadmium uptake/tolerance and paves a path toward efficient and viable solutions improving phytoremediation approaches.

Generating data has become cheaper and easier, but alone is not sufficient to answer biological questions – data must be analyzed and interpreted. However, many algorithms can create or exacerbate biases (e.g., facial-recognition, ancestry, and disease risk). This necessitates incorporating diverse perspectives to confront both the moral and technical “big data challenges”. To move to a future where this is possible, it is necessary for researchers to develop skills in data management, processing, and analytics. Specifically, the field of plant phenotyping has moved from time consuming hand measurements to the use and development of high-throughput phenotyping. These systems require data-enabled/fluent users, yet academic programs in biology do not provide sufficient data science training. Here we present the Bioinformatics in Plant Science (BIPS) program at the University of Missouri (MU) as a model for training the next generation of data-enabled/fluent scientists. BIPS aims to mentor undergraduate students to build foundational skills in plant biology, research, and computational science. Our program pairs biology and computer science students to address biological questions through computational methods, with many focusing on plant phenotyping methods. The students learn to tackle problems using multidisciplinary approaches, alongside learning how to work in teams while building science communication skills (e.g., professional conferences, research forums, presenting to lawmakers). Through peer learning, BIPS students can understand and incorporate diverse perspectives from both the biological and computational side to address one of NSF’s 10 big ideas: harnessing the data revolution.

(250 words) Micronutrients, such as iron, zinc, and sulfur, play a vital role in both plant and human development. Understanding how plants sense and allocate nutrients within their tissues may offer different venues to develop plants with high nutritional value. Despite decades of intensive research, more than 40% of genes in Arabidopsis remain uncharacterized or have no assigned function. While several resources such as mutant populations or diversity panels offer the possibility to identify genes critical for plant nutrition, the ability to consistently track and assess plant growth in an automated, unbiased way is still a major limitation. High-throughput phenotyping (HTP) is the new standard in plant biology but few HTP systems are open source and user friendly. Therefore, we developed OPEN Leaf, an open source HTP for hydroponic experiments. OPEN Leaf is capable of tracking changes in both size and color of the whole plant and specific regions of the rosette. We have also integrated communication platforms (Slack) and cloud services (CyVerse) to facilitate user communication, collaboration, data storage, and analysis in real time. As a proof-of-concept, we report the ability of OPEN Leaf to track changes in size and color when plants are growing hydroponically with different levels of nutrients. We expect that the availability of open source HTP platforms, together with standardized experimental conditions agreed by the scientific community, will advance the identification of genes and networks mediating nutrient uptake and allocation in plants.

Anthropogenic factors such as climate change, harsh agricultural practices, and mining have contributed to increases in soil salinization and heavy metal contamination. Highly saline environments drastically lower yield for crop species and elevated levels of toxic metals like cadmium are carcinogenic in the environment. Some plants that have evolved in high-salinity habitats or in soils with heavy metals could be used to remediate contaminated soils. Halophytes are plants with various adaptations that allow them to survive and reproduce in saline conditions. General mechanisms for salt tolerance/uptake in halophytes are hypothesized to help deal with other stresses like heavy metals. Plants with these traits could be utilized to extract salt and heavy metals from affected soils in a process called phytoremediation. We plan to develop Sea Rocket (Cakile maritima) in the Mustard family as a model system to understand mechanisms of salt (NaCl) and cadmium uptake and tolerance, as it has been shown to accumulate both. As part of this study, we will hydroponically grow C. maritima in different stress treatments using salt and cadmium. As the plants uptake the pollutants, the conductivity of the solution will change. We will develop an automated pipeline to track these changes in real-time using conductivity sensors. In addition, we will sample root and leaf tissues at various time points to measure salt and cadmium uptake using ICP-OES elemental analysis. This data will provide insights into salt and cadmium uptake/tolerance and paves a path toward efficient and viable solutions improving phytoremediation approaches.