Urban trees face a myriad of complex challenges growing in the built environment. The most common environmental conditions influencing urban tree mortality are water availability, nutrient deficiency and soil compaction. Long-term survival of recently installed trees has been directly attributed to site conditions, planting technique, and posttransplant maintenance. Tree survival is also dependent on selection of healthy, suitable plant material. Production methods for woody plants include traditional plastic containers (CG), pot-in-pot containers (PIP), and in-ground fabric containers (IGF). Alternatively, field grown trees may be produced as bare-root (BR) or root ball-excavated and burlapwrapped (B&B) trees. Each of these methods offers unique advantages in relation to production and installation. Many of the studies reviewed reveal varying post-transplant establishment and survival responses to production methods at a species-specific level.

Plant xylem colonization is the hallmark of vascular wilt diseases caused by phytopathogens within the Fusarium oxysporum species complex. Recently, xylem colonization has also been reported among endophytic F. oxysporum strains, resulting in some uncertainty. This study compares xylem colonization processes by pathogenic versus endophytic strains in Arabidopsis thaliana and Solanum lycopersicum using Arabidopsis pathogen Fo5176, tomato pathogen Fol4287, and the endophyte Fo47 that can colonize both plant hosts. We observed that all strains were able to advance from epidermis to endodermis within 3 days post-inoculation (dpi) and reached the root xylem at 4 dpi. However, this shared progression was restricted to lateral roots and the elongation zone of the primary root. Only pathogens reached the xylem above the primary-root maturation zone (PMZ). Related to the distinct colonization patterns, we also observed stronger induction of callose at the PMZ and lignin deposition at primary-lateral roots junctions by the endophyte in both plants. This observation was further supported by stronger induction of Arabidopsis genes involved in callose and lignin biosynthesis during the endophytic colonization (Fo47) comparing to the pathogenic interaction (Fo5176). Moreover, both pathogens encode more plant cell wall degrading enzymes than the endophyte Fo47. Therefore, observed differences in callose and lignin deposition could be the combination of host production and the subsequent fungal degradation. In summary, this study demonstrates spatial differences between endophytic and pathogenic colonization, strongly suggesting that further investigations of molecular arm-races are needed to understand how plants differentiate friend from foe.

Current and emerging plant diseases caused by obligate parasitic microbes such as rusts, downy mildews, and powdery mildews threaten worldwide crop production and food safety. These obligate parasites are typically unculturable in the laboratory, posing technical challenges to characterize them at the genetic and genomic level. Here we have developed a data analysis pipeline integrating several bioinformatic software programs. This pipeline facilitates rapid gene discovery and expression analysis of a plant host and its obligate parasite simultaneously by next generation sequencing of mixed host and pathogen RNA (i.e., metatranscriptomics). We applied this pipeline to metatranscriptomic sequencing data of sweet basil (Ocimum basilicum) and its obligate downy mildew parasite Peronospora belbahrii, both lacking a sequenced genome. Even with a single data point, we were able to identify both candidate host defense genes and pathogen virulence genes that are highly expressed during infection. This demonstrates the power of this pipeline for identifying genes important in host–pathogen interactions without prior genomic information for either the plant host or the obligate biotrophic pathogen. The simplicity of this pipeline makes it accessible to researchers with limited computational skills and applicable to metatranscriptomic data analysis in a wide range of plant-obligate-parasite systems.

Course-based Undergraduate Research Experiences (CUREs) integrate active, discovery-based learning into undergraduate curriculums, adding tremendous value to Biochemistry and Molecular Biology (BMB) education. There are multiple challenges in transforming a research project into a CURE, such as the readiness of students, the time commitment of the instructor, and the productivity of the research. In this article, we report a CURE course developed and offered in the University of Massachusetts Amherst BMB Department since 2018 that addresses these challenges. Our CURE focuses on fungal effectors which are proteins secreted by a destructive pathogenic fungus Fusarium oxysporum, one of the top five most devastating plant pathogens. By studying this group of proteins, students are connected to real-world problems and participate in the search for potential solutions. A three-week "standard Bootcamp" is implemented to help students familiarize themselves with all basic techniques and boost their confidence. Next, molecular cloning, a versatile technique with modularity and repeatability, is used as the bedrock of the course. Our past five years of experience have confirmed that we have developed a novel and feasible CURE protocol. Measurable progress documented by students who took this course includes stimulated active learning and increased career trajectory to pursue hypothesis-based research to address societal needs. In addition, data generated through the course advance ongoing lab research. Collectively, we encourage the implementation of CURE among research-intensive faculty to provide a more inclusive research experience to all students, an important element in predicting career success.

Basil downy mildew (BDM), caused by the oomycete pathogen Peronospora belbahrii, is the most significant disease threatening sweet basil production across the world. A downy mildew resistant sweet basil cultivar Mrihani (MRI) was identified in a germplasm screen, and fertile progeny were produced through a breeding program with BDM-susceptible commercial sweet basil cultivar Newton (SB22). However, the specific genes and molecular mechanisms which confer the resistance in MRI and selected progeny remain unknown. This study was designed to identify candidate resistance genes and the potential mechanisms that enable BDM resistance through a comparative transcriptomic approach. RNA samples from BDM-infected MRI and SB22 plants were harvested at 4 time points during the first 3 days of infection to capture genes, pathways, and biological processes involved in disease resistance. This global transcription expression profile confirmed the continuous growth of the pathogen only in the susceptible cultivar SB22, consistent with the infection phenotype. Three categories of genes uniquely induced in the MRI cultivar upon pathogen challenge were identified: the plant pathogen recognition nucleotide-binding leucine rich repeat proteins (NLRs), the multi-functional receptor-like kinases, and secondary metabolic enzymes. Validation of the top resistance candidate NLR gene confirmed its unique presence in the MRI cultivar as well as two out of four resistant MRIxSB22 F2 progeny. Additionally, unique upregulation of the salicylic acid synthesis pathway genes in MRI suggests the importance of this hormone signaling pathway in BDM resistance. This study demonstrates the feasibility of using comparative transcriptomics to identify resistance genes in non-model crops for rapid improvement in marker-assisted breeding approaches.