3D Printing Biomimetic and Hierarchical Wood Structure for Endosphere Microbiome Study
Plants are regarded as superorganisms that rely on microbiomes for functions and traits. On the other side, plants feed the microbial community and influence their composition and activities. Nowadays, nanomaterials have been widely used in scientific research and everyday usage. The research about the influence of nanomaterials to the human-related microbiome has been intensively conducted, however limited attention has been paid to the plant based microbiome. Cellulose is the major composition of plant matter, and the most abundant organic and bio-degradable polymer on Earth. This research will focus on preparing cellulose/nanomaterials, including nanoparticles, carbon nanotubes, and aerogels, in order to study their effect on various bacteria. The cellulose/nanomaterials will be mixed and then subjected to freeze casting suspension. The materials will then be processed using the decomposition method to study their interaction with decomposed bacteria.
Quantifying the Impact of Weather Whiplash on Roots and Hyphae with an Automated Minirhizotron Camera System
Root exudation and turnover are primary soil carbon and energy sources for the rhizosphere microbiome. Plants are the interface between the atmosphere and the soil. Thus, plant stress from weather and climate events drive rhizosphere microbiome responses to stress. Current imaging technologies impede high-temporal-resolution root dynamics data. Minirhizotrons are commonly used for in situ monitoring of roots, and allow non-destructive tracking of root metrics overtime. However, high minirhizotron camera cost ($18,000+) and poor root-soil contrast prevent automated imaging and analysis. I propose to develop an inexpensive minirhizotron camera system using off-the-shelf computers (Raspberry Pi) and components to facilitate permanent camera deployment, high-temporal-resolution imaging, and automated image analysis using machine visioning. Experiments will complement work described in section 4.3.c.1.1 of the MAPS research proposal. Primary goals are to i) examine how weather whiplash impacts short-term (hours) and long-term (months) root dynamics, and ii) assess how root dynamics affect carbon inputs.
Smart adaptation of enriched microbiomes in Recovered Nutrient Products (bio‐fertilizers) from anaerobic wastewater treatment to the native soil
Anaerobic Membrane Bioreactors (AnMBRs) are emerging as a viable option for municipalities and agro-businesses for energy positive wastewater treatment with simultaneous recovery of valuable nutrients (Nitrogen, Phosphorus) and water for indirect potable reuse. A pilot scale Anaerobic Membrane Bioreactor (AnMBR) operated by the team including me at Ft. Riley, KS treating 1000 gallons per day of wastewater has consistently achieved these goals. More specifically, anaerobic microbial communities have been shown to vary in predominance with time and season, in the organic biosolids and inorganic nutrient product fractions from AnMBRs. The central hypothesis of the proposed research is that wastewater enriched microbial communities present in land applied nutrient products from the AnMBR will integrate with the soil microbiome to beneficially regulate the N and P release rates as well as the transformations of these two nutrients in the top soil layers. Understanding the transport and proliferation of these microbiomes can be achieved through plant uptake studies and field plot experiments. This research is very relevant to the current Kansas NSF EPSCoR program on microbiomes with a strong focus on the unexplored topic of microbiome interactions between the engineered/built environment such as wastewater treatment based bioreactors and the natural soil microbiome.
A Study of DNA Mutations through Error Control
Coding Theory
Living beings, in particular, microorganisms, rely on DNA mutations for their evolution. Changes in the DNA sequence could be a result of random events such as DNA replication errors, or a result of intentional alterations introduced by genetic engineering. A similar phenomenon occurs in telecommunications when sequences of information are transmitted over a noisy channel, introducing multiple random errors. To overcome this problem, communication engineers “encode” each sequence before transmission, giving them the ability to correct errors later in the receiver. This is called “Error Control Coding”, a well-established area in communications, which started in 1948 and has been perfected over time. There are immense functional similarities between the DNA correction mechanisms in microorganisms and the error control techniques used in telecommunications. This research exploits these similarities and combines statistical methods with the powerful toolbox of algebraic error control coding to understand the behavior and evolution of microorganisms.
Transforming Metagenomic Sequencing Data
Analysis with Scalable Assembly and Comprehensive Annotation
The proposed research seeks to develop a series of computational methods and software for the analyses of metagenomic sequencing data. The proposed methods include de novo assembly methods with reduced computational requirement and enhanced parallelism, which facilitate the reconstruction of the metagenomes from huge-volume metagenomic datasets such as those collected form soil. They also include a series of annotation methods that improve the gene-calling, non-coding RNA discovery, gene cluster finding, and functional categorization of metagenomic data. Finally, novel phylogenetic reconstruction methods are also proposed to take advantage from the drastically improved annotation sensitivity and accuracy. The proposed methods can be directly applied on metagenomic and/or metatranscriptomic sequencing data generated from microbiome samples that are collected from environments such as aquatic, plant and/or soil systems.
Workforce Development, Education and Outreach funding is provided by the Kansas NSF EPSCoR RII Track-1 Award OIA-1656006 titled: "Microbiomes of Aquatic, Plant, and Soil Systems across Kansas." The grant's workforce development and educational objectives are designed to enhance STEM education in Kansas by supporting activities that will lead to an expanded STEM workforce or prepare a new generation for STEM careers in the areas of aquatic, plant and soil microbiome environments and ecological systems.
