First draft reference genome and annotation of the alternative oil species Physaria fendleri.

In the wake of increasing demand for renewable energy sources, plant-based sources including alternative oilseeds have come to the forefront of interest. Hydroxy fatty acids (HFAs), produced in a few oilseed species, are important chemical feedstocks for industrial applications. An integrated approach was taken to assemble the first draft genome of the alternative HFA producer Physaria fendleri (n = 6), an outcrossing species with high heterozygosity. Both de novo transcriptome assemblies and genome assemblies were produced with public and generated sequencing reads. Resulting intermediate assemblies were then scaffolded and patched with multiple data sources, followed by super-scaffolding onto a masked genome of Camelina laxa (n = 6). Despite a current lack of available resources for the physical mapping of genomic scaffolds of Physaria fendleri, topography of the genome with respect to repeat and gene content was preserved at the scaffold level and not significantly lost via super-scaffolding. Read representation, gene and genome completion statistics, and annotation results illustrated the creation of a functional draft genome and a tool for future research on alternative oil species.

Optimising mechanical separation of anaerobic digestate for total solids and nutrient removal.

Mechanical separation of anaerobic digestate has been identified as a method to reduce pollution risk to waterways by partitioning phosphorus in the solid fraction and reducing its application to land. Separators have adjustable parameters which affect separation efficiency, and hence the degree of phosphorous partitioning, but information on how these parameters affect separation performance is limited in the literature. Two well known technologies were investigated, decanter centrifuge and screw press, to determine the most efficient method of separation. Counterweight load and the use of an oscillator were adjusted for the screw press, while bowl speed, auger differential speed, feed rate and polymer addition were modified for the decanter centrifuge. Separation efficiency was determined for total solids, phosphorus, nitrogen, potassium, and carbon, and the total solids content of resulting fractions was measured. The decanter centrifuge had higher separation efficiency for phosphorus in all cases, ranging from 51% to 71.5%, while the screw press had a phosphorus separation efficiency ranging from 8.5% to 10.9% for digestate of ∼5% solids (slurry/grass silage mix). Separation by decanter centrifuge partitioned up to 56% of nitrogen in the solid fraction leaving a reduced nitrogen content in the liquid fraction available for land spreading; this nitrogen would most likely need to be replaced by chemical fertiliser which would add to the cost of the system. The decanter centrifuge is better suited to cases where phosphorus recovery is the most important factor, while the screw press could be advantageous in cases where cost is a limiting factor.

Investigation of physiological and molecular mechanisms conferring diurnal variation in auxinic herbicide efficacy.

The efficacy of auxinic herbicides, a valuable weed control tool for growers worldwide, has been shown to vary with the time of day in which applications are made. However, little is known about the mechanisms causing this phenomenon. Investigating the differential in planta behavior of these herbicides across different times of application may grant an ability to advise which properties of auxinic herbicides are desirable when applications must be made around the clock. Radiolabeled herbicide experiments demonstrated a likely increase in ATP-binding cassette subfamily B (ABCB)-mediated 2,4-D and dicamba transport in Palmer amaranth (Amaranthus palmeri S. Watson) at simulated dawn compared to mid-day, as dose response models indicated that many orders of magnitude higher concentrations of N-1-naphthylphthalamic acid (NPA) and verapamil, respectively, are required to inhibit translocation by 50% at simulated sunrise compared to mid-day. Gas chromatographic analysis displayed that ethylene evolution in A. palmeri was higher when dicamba was applied during mid-day compared to sunrise. Furthermore, it was found that inhibition of translocation via 2,3,5-triiodobenzoic acid (TIBA) resulted in an increased amount of 2,4-D-induced ethylene evolution at sunrise, and the inhibition of dicamba translocation via NPA reversed the difference in ethylene evolution across time of application. Dawn applications of these herbicides were associated with increased expression of a putative 9-cis-epoxycarotenoid dioxygenase biosynthesis gene NCED1, while there was a notable lack of trends observed across times of day and across herbicides with ACS1, encoding 1-aminocyclopropane-1-carboxylic acid synthase. Overall, this research indicates that translocation is differentially regulated via specific protein-level mechanisms across times of application, and that ethylene release, a chief phytotoxic process involved in the response to auxinic herbicides, is related to translocation. Furthermore, transcriptional regulation of abscisic acid involvement in phytotoxicity and/or translocation are suggested.

Seed Priming with Polyethylene Glycol Induces Physiological Changes in Sorghum (Sorghum bicolor L. Moench) Seedlings under Suboptimal Soil Moisture Environments.

Osmopriming with PEG has potential to improve seed germination, seedling emergence, and establishment, especially under stress conditions. This research investigated germination performance, seedling establishment, and effects of osmopriming with PEG on physiology in sorghum seedlings and their association with post-priming stress tolerance under various soil moisture stress conditions. Results showed that seed priming increased the environmental range suitable for sorghum germination and has potential to provide more uniform and synchronous emergence. Physiologically, seed priming strengthened the antioxidant activities of APX, CAT, POD, and SOD, as well as compatible solutes including free amino acid, reducing sugar, proline, soluble sugar, and soluble protein contents. As a result, seed priming reduced lipid peroxidation and stabilized the cell membrane, resulting in increased stress tolerance under drought or excessive soil moisture environments. Overall, results suggested that seed priming with PEG was effective in improving seed germination and seedling establishment of sorghum under adverse soil moisture conditions. Osmopriming effectively strengthened the antioxidant system and increased osmotic adjustment, likely resulting in increased stress tolerance.

Salinity and sodicity of weathered minesoils in northwestern new Mexico and northeastern Arizona.

Evolving relationships between electrical conductivity (EC) and sodium adsorption ratio (SAR) in reconstructed soils at surface mines have been insufficiently documented in the literature. Some minesoils (i.e., rootzone material) are classified as saline, sodic, or saline-sodic and are considered unsuitable for revegetation. Weatherable minerals such as calcite and gypsum are common in alkaline minesoils and on dissolution tend to mitigate elevated SAR levels by maintaining or increasing electrolytes in the soil and providing sources of exchangeable calcium and magnesium. Topsoils (i.e., coversoils) contribute to mitigation of sodic conditions when soluble cations are translocated from coversoils into the underlying minesoils. This study evaluated the weathering characteristics of minesoils sites from three surface coal mines in northwestern New Mexico and northeastern Arizona. Minesoils were grouped into 11 classes based on EC and SAR. After 6 to 14 yr, differences between upper and lower halves of the coversoils suggest general increases occurred with EC, SAR, chloride (Cl(-)), and sulfate (SO(4)(2-)) with depth. Within the reclaimed minesoils, there were several significant (P < 0.05 or < 0.10) relationships among EC and SAR that related to Minesoil Class. Lower SAR levels with corresponding increases in EC compared to baseline minesoils were more apparent in upper minesoil depths (0-5 and 5-15 cm). Minesoil anion concentrations suggested coversoil leachates and gypsum dissolution influenced EC and SAR chemistry. Over time, chemical changes have increased the apparent stability of the saline and sodic reclaimed minesoils studied thereby reducing risks associated with potential aggregate slaking and clay particle dispersion.