People
Primary Investigators
Assistant Professor, Department of Plant, Soil, and Microbial Science
Gregory is an assistant professor in the Department of Plant Soil and Microbial Sciences at Michigan State University. His research focuses on (1) phylogenetic and functional diversity of plant-associated fungi; (2) environmental and genetic factors that structure microbiome communities; (3) the evolution and functional relevance of bacterial symbionts of fungi.
His lab leverages a diverse array of tools and a strong multidisciplinary approach, including comparative genomics, transcriptomics, and systems biology, to investigate gene family dynamics and the evolution of gene-gene interactions following gene and genome duplications. In this NSF Dimensions of Biodiversity project, we will perform comparative co-expression network analyses aimed at identifying key gene modules underlying symbioses between fungi, bacteria and plants including those that permitted early evolution and adaptation of land plants.
The Liu lab creates new computational methodologies for efficient and accurate comparative genomic analyses – especially in the context of complex evolutionary scenarios – and then connects the resulting insights to phenotype and function. The end goal of our big-data-driven approach is to generate hypotheses that result in new biological and biomedical discoveries.
Lab Technicians & Post-docs
Alessandro is studying the diversity, evolution and functions of endobacteria living in Mucoromycota fungi, systematics and taxonomy of Endogonales and Mortierellomycotina, and interactions of these fungi with plants.
I study molecular mechanisms underlying fungal-algal mutualisms, and is particularly interested in biotechnological applications utilizing fungal-algal consortia for biofuel and other high-value biomaterials. I also research lipid metabolism of plant, algae, and fungi.
I am responsible for the management of the lab, including ordering and maintaining inventory, equipment, establishing and maintaining of lab databases and software licenses. The acquisition, cultivation and maintenance of our extensive plant inventory in the greenhouse and the growing facilities is also part of my work. As a researcher I am specialized in molecular biology techniques, especially RNA and gDNA extraction for transcriptome and genome sequencing of various plant tissues and I assist with the culturing and transformation of the Physcomitrella patens cultures and the generation of a toolbox for terpene synthases and related biosynthetic genes.
Graduate Students
Julian is a Master’s student studying bacterial-fungal interactions in the plant microbiome, isolating and describing the diversity of Mortierellomycotina, and Mortierella-microalgae symbiosis, using techniques including computational image analysis and genomics, microscopy, and nucleic acid techniques. Julian has been working in the Bonito Lab since January 2017.
Davis is working to classify the model moss species, Physcomitrella patens, interaction with various fungal species. Current efforts are looking at transcriptomic differences and alternative gene expression in the presence and absence of fungal symbionts to elucidate possible communication pathways involved. Additionally, tools for a large scale phenomic approach are being developed using Raspberry Pi microcomputers and automated cameras to quantify growth rate, temporal changes, and overall plant health. In the future Davis intends to further study the evolutionary implications of moss/fungal symbioses as a possible mechanism for initial plant terrestrial colonization and study plant stress response with the predicted fitness advantages that are gained from the interaction.
My research focus is on the mechanisms of plant association by fungi in the Mortierellaceae. To further development of Mortierella elongata as a model system, I am working to establish a transformation system for this fungus. My career interests include science education and outreach, curriculum development, and creating distance learning resources. My favorite hobbies are hiking, cooking, and dancing.
I am broadly interested in plant regulatory evolution. To this end, I plan to utilize bioinformatic tools to resolve the dynamics of plant Conserved Non-coding Sequences (CNSs). Advances in sequencing technology allow for both intra- and inter-specific comparisons at higher resolutions than ever before. Studying these CNSs may reveal potential short-term adaptive mechanisms as well as early steps of creating genetic novelty. Outside of the lab, I enjoy running and playing ultimate frisbee. At home, I am lucky to have the company of my fiance, Jess, and dog, Brooks.
Undergraduate Students
Abby graduated undergrad from MSU, working with Gregory Bonito for three years. Recently, she has been working on developing a phenomics system for fungal-moss interactions. She will continue to be a Spartan because she is attending graduate school at MSU.
Not Pictured: Balindile Mosta, Peyen Kuopei