Bacteriovorax are unique predatory bacteria with potential roles and benefits as antibacterial agents to mitigate certain bacterial diseases in plants and animals, controlling bacterial populations and recycling nutrients in the environment. These bacteria may also be an important unexploited source of new novel therapeutic compounds. To realize the full potential of Bacteriovorax, it is necessary to better understand their genome structure and to bring order to the system of classifying and naming them. The purpose of this study is to use whole-genomic sequences to identify the best-performing genes in order to advance the classification and systematics of Bacteriovorax bacteria. The construction of a more accurate phylogenetic tree of Bacteriovorax will provide a framework to define novel isolates in future studies.
This information and resulting classification scheme will be disseminated to the scientific community through publications, sequence databases and a website. Florida A&M is a historically black college and university with few applicants submitting DDIG proposals. The student Co-PI will share her experiences in planning and writing the proposal through presentations to inspire others and thus potentially increasing future numbers of proposals from minority students.
It is challenging yet fascinating to study the predator-prey interactions of microbes which are often the dominant factors driving energy flow, nutrient recycling and structural and functional changes in aquatic environments. Bdellovibrio and like Organisms (BALOs) are a unique group of predatory bacteria that have potential roles and benefits as antibacterial agents controlling bacterial populations in nature, re-cycling nutrients in the environment and may be an important unexploited source for novel therapeutic compounds. BALOs are the only known predatory bacteria that possess a life cycle alternating between an extracellular free-living phase and an intracellular growth and multiplication phase, which results in the death and lysis of the prey and release of new progenies. Based on their small size, about 1/5th that of a typical bacterium cell, BALOs have been called "the world’s smallest hunters". Despite the uniqueness, and increasing understanding, of the potential of these organisms in various applications, their taxonomy, classification and phylogeny are ill-defined. This gap in knowledge has limited interest and research on these predatory bacteria. The intent of this project is to close this knowledge gap. The primary aim of this Doctoral Dissertation Improvement Grant (DDIG) award was to provide an opportunity for Huan Chen, a doctoral student, to expand and improve upon her dissertation research project to advance the ecology and systematics of the BALOs. The principal objective was to fill major gaps in knowledge on the systematics of BALOs using genomic approaches, which will increase the capacity to investigate the predator activities including gene function and products of specific BALO strains. Bacteriovorax is a special group of BALOs found exclusively in salt-water environments. Until recently, little was known about the classification and taxonomy of the Bacteriovorax and how to define and distinguish one isolate from another. To realize the full potential of the Bacteriovorax, it is necessary to have knowledge of the structure of their genome, particularly which genes are important in predation and to bring order to the system of classification and naming of the organisms. This is necessary to avoid confusion and be able to detect, identify and classify the various isolates so that those isolates that are useful can be distinguish from those that are not. The approach used whole genomic sequences as a guide to identify functional genes to further classify Bacteriovorax. The major outcomes of this project was that Huan Chen and other members of the project team successfully assembled, annotated and analyzed 454 pyrosequencing reads and Illumina reads of four Bacteriovorax strains isolated from diverse salt water environments. By comparing their genome sequences with Bdellovbiro bacteriovorus HD100 and other delta-proteobacteiroa, 594 genes were identified that may be responsible for the predators’ predatory life style. The unique genomic features of Bacteriovorax that are essential for their ecological function were also reported in Chen’s dissertation. The phylogeny based on whole genome sequences were constructed and was found to not conform to the phylogenetic tree based solely on 16S rRNA genes. The results collectively advance the genomics, ecology and systematics of Bacteriovorax, and therefore allow greater considerations for the practical applications of these fascinating predators. Reconstruction of a more accurate phylogenetic tree of closely related Bacteriovorax groups will facilitate the investigation of predator activities in nature and serve as a standard to define novel BALO isolates in future studies. The knowledge generated from this research will subsequently supplement the inventory and systematics of the earth’s biota. The sequence and resulting classification scheme will be disseminated to the scientific community through publications, sequence data bases and a website. This award provided an excellent opportunity for Ms. Chen to integrate her training into an important multi-disciplinary area including systematics, phylogeny, bioinformatics and microbial ecology. Through the DDIG, Ms. Chen was able to visit on several occasions one of the world’s foremost research centers, the J. Craig Venter Institute (JCVI), to receive training to improve the taxonomic uncertainty of the Bacteriovorax under the supervision of Dr. Jonathan Badger, an expert in the evolution and phylogeny of microbes. This was an important addition to Ms. Chen’s dissertation project. To broaden participation of others in science, Ms. Chen shared her experiences in planning, writing and implementing the DDIG proposal through seminar presentations at Florida A&M University, one of the nations’ Historically Black College and Universities. Ms. Chen has served as a resource person encouraging other students to apply, thus potentially increasing the number of DDIG proposals submitted by students from underrepresented groups. She also presented lectures to demonstrate basic phylogenetic concepts and simple analysis learned at JCVI to undergraduate students and high school students participating in the School of the Environment ’s Summer school.
