Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.

It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.

Focusing cells into a single stream is usually a necessary step prior to counting and separating them in microfluidic devices such as flow cytometers and cell sorters. This work presents a sheathless electrokinetic focusing of yeast cells in a planar serpentine microchannel using dc-biased ac electric fields. The concurrent pumping and focusing of yeast cells arise from the dc electrokinetic transport and the turn-induced acdc dielectrophoretic motion, respectively. The effects of electric field (including ac to dc field ratio and ac field frequency) and concentration (including buffer concentration and cell concentration) on the cell focusing performance were studied experimentally and numerically. A continuous electrokinetic filtration of E. coli cells from yeast cells was also demonstrated via their differential electrokinetic focusing in a serpentine microchannel.

We propose and demonstrate a simple, ultra sensitive radio frequency (RF) sensor to detect a single yeast cell and distinguish its viability in a microfluidic channel. On-chip interference is used to cancel background probing signals to improve sensor sensitivity. Individual viable and nonviable yeast cells (approximately 5.83 +/- 0.85 microm in diameter) are measured with clear sensing and identification of these cells.

Increased consumption of vegetables or plant food has been associated with decreased risk of developing major chronic diseases, such as cancers, diabetes, cardiovascular diseases, and age-related functional decline. Ramie leaves are rich in phenolics and flavonoids, which have been suggested for human health benefits. Phenolic contents, flavonoid contents, phenolic compounds, and anti-cancer properties in six species of ramie leaves were analyzed by Folin-reagent method, sodium borohydride/chloranil-based assay (SBC), HPLC method and antiproliferation, cytoxicity, respectively. Antioxidant activities were measured through peroxyl radical scavenging capacity (PSC) method, oxygen radical absorbance capacity (ORAC) method, and cellular antioxidant activity (CAA). Research indicated that Boehmeria penduliflora contained the highest total phenolic content (2313.7±27.28 mg GAE/100 g FW), and flavonoid content (1682.4±27.70 mg CAE/100 g FW). Boehmeria tricuspis showed the highest PSC value (9574.8±117.63 µM vit. C equiv./100 g FW), while Boehmeria penduliflora indicated the highest ORAC value (330.44±16.88 µmol Trolox equiv./g FW). The antioxidant activities were correlated with phenolic contents and flavonoid contents. Boehmeria tricuspis had the highest antiproliferative capacity with the lowest EC50 (4.11±0.19 mg/mL). The results for the analyzed ramie for CAA were significantly different from each other (p<0.05), Boehmeria tricuspis had the highest CAA value (133.63±7.10 µmol QE/100 g). Benzoic acid, 4-coumaric acid, caffeic acid, and ferulic acid were the dominant phenolic ingredients in the ramie leaves according to HPLC analysis. Our research is the first report to study the phytochemical profiles and antioxidant activities in different species of ramie leaves for their health benefit.

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Matrix-assisted pulsed-laser evaporation direct-write (MAPLE DW) has been emerging as a promising biological construct fabrication technique. The post-transfer cell viability in MAPLE DW depends on various operation conditions such as the applied laser fluence; unfortunately, the effect of laser fluence on the post-transfer cell viability has not been well elucidated. This work aims to study the effect of laser fluence on the post-transfer cell viability and the cell recovery ability in MAPLE DW of yeast cells (Saccharomyces cerevisiae). It has been observed that (1) yeast cell viability decreases as the laser fluence increases from 85 to around 1500mJ∕cm2 and (2) some of the MAPLE DW process-induced cell damage is reversible. The post-transfer yeast cell recovery is a function of laser fluence; however, this dependence relationship is not monotonic. Future work is needed to better understand the physical and chemical mechanisms of the above observations.

Microorganisms that release plant-available phosphate from natural soil phosphate stores may serve as biological alternatives to costly and environmentally damaging phosphate fertilizers. To explore this possibility, we engineered a collection of root bacteria to release plant-available orthophosphate from phytate, an abundant phosphate source in many soils. We identified 82 phylogenetically diverse phytase genes, refactored their sequences for optimal expression in Proteobacteria, and then synthesized and engineered them into the genomes of three root-colonizing bacteria. Liquid culture assays revealed 41 engineered strains with high levels of phytate hydrolysis. Among these, we identified 12 strains across three bacterial hosts that confer a growth advantage on the model plant Arabidopsis thaliana when phytate is the sole phosphate source. These data demonstrate that DNA synthesis approaches can be used to generate plant-associated strains with novel phosphate-solubilizing capabilities. IMPORTANCE Phosphate fertilizers are essential for high-yield agriculture yet are costly and environmentally damaging. Microbes that release soluble phosphate from naturally occurring sources in the soil are appealing, as they may reduce the need for such fertilizers. In this study, we used synthetic biology approaches to create a collection of engineered root-associated microbes with the ability to release phosphate from phytate. We demonstrate that these strains improve plant growth under phosphorus-limited conditions. This represents a first step in the development of phosphate-mining bacteria for future use in crop systems.