Revisiting the sequencing of the first tree genome: Populus trichocarpa.

Ten years ago, it was announced that the Joint Genome Institute with funds provided by the Department of Energy, Office of Science, Biological and Environmental Research would sequence the black cottonwood (Populus trichocarpa Torr. & Gray) genome. This landmark decision was the culmination of work by the forest science community to develop Populus as a model system. Since its public release in late 2006, the availability of the Populus genome has spawned research in plant biology, morphology, genetics and ecology. Here we address how the tree physiologist has used this resource. More specifically, we revisit our earlier contention that the rewards of sequencing the Populus genome would depend on how quickly scientists working with woody perennials could adopt molecular approaches to investigate the mechanistic underpinnings of basic physiological processes. Several examples illustrate the integration of functional and comparative genomics into the forest sciences, especially in areas that target improved understanding of the developmental differences between woody perennials and herbaceous annuals (e.g., phase transitions). Sequencing the Populus genome and the availability of genetic and genomic resources has also been instrumental in identifying candidate genes that underlie physiological and morphological traits of interest. Genome-enabled research has advanced our understanding of how phenotype and genotype are related and provided insights into the genetic mechanisms whereby woody perennials adapt to environmental stress. In the future, we anticipate that low-cost, high-throughput sequencing will continue to facilitate research in tree physiology and enhance our understanding at scales of individual organisms and populations. A challenge remains, however, as to how genomic resources, including the Populus genome, can be used to understand ecosystem function. Although examples are limited, progress in this area is encouraging and will undoubtedly improve as future research targets the many unique aspects of Populus as a keystone species in terrestrial ecosystems.

Timing and magnitude of C partitioning through a young loblolly pine (Pinus taeda L.) stand using 13C labeling and shade treatments.

The dynamics of rapid changes in carbon (C) partitioning within forest ecosystems are not well understood, which limits improvement of mechanistic models of C cycling. Our objective was to inform model processes by describing relationships between C partitioning and accessible environmental or physiological measurements, with a special emphasis on short-term C flux through a forest ecosystem. We exposed eight 7-year-old loblolly pine (Pinus taeda L.) trees to air enriched with (13)CO(2) and then implemented adjacent light shade (LS) and heavy shade (HS) treatments in order to manipulate C uptake and flux. The impacts of shading on photosynthesis, plant water potential, sap flow, basal area growth, root growth and soil CO(2) efflux rate (CER) were assessed for each tree over a 3-week period. The progression of the (13)C label was concurrently tracked from the atmosphere through foliage, phloem, roots and surface soil CO(2) efflux. The HS treatment significantly reduced C uptake, sap flow, stem growth and fine root standing crop, and resulted in greater residual soil water content to 1 m depth. Soil CER was strongly correlated with sap flow on the previous day, but not the current day, with no apparent treatment effect on the relationship. Although there were apparent reductions in new C flux belowground, the HS treatment did not noticeably reduce the magnitude of belowground autotrophic and heterotrophic respiration based on surface soil CER, which was overwhelmingly driven by soil temperature and moisture. The (13)C label was immediately detected in foliage on label day (half-life = 0.5 day), progressed through phloem by Day 2 (half-life = 4.7 days), roots by Days 2-4, and subsequently was evident as respiratory release from soil which peaked between Days 3 and 6. The δ(13)C of soil CO(2) efflux was strongly correlated with phloem δ(13)C on the previous day, or 2 days earlier. While the (13)C label was readily tracked through the ecosystem, the fate of root C through respiratory, mycorrhizal or exudative release pathways was not assessed. These data detail the timing and relative magnitude of C flux through various components of a young pine stand in relation to environmental conditions.

In-membrane preconcentration/membrane inlet mass spectrometry of volatile and semivolatile organic compounds.

The on-line determination of volatile and semivolatile organic compounds (SVOCs) is reported using membrane inlet mass spectrometry with in-membrane preconcentration (IMP-MIMS). Semivolatile organic compounds in aqueous samples are preconcentrated in a flow-through silicone hollow-fiber membrane inlet held in a GC oven. The sample stream is replaced with air, and the SVOCs are thermally desorbed into the mass spectrometer by rapid heating of the membrane. The method is evaluated for the on-line determination of 4-fluorobenzoic acid, 3,5-difluorobenzoic acid, 2-chlorophenol, p-tert-butylphenol, and dimethyl sulfoxide (DMSO) in water. The selectivity of the IMP-MIMS technique for SVOCs in the presence of VOCs is demonstrated. Cryotrapping and a rapid gas chromatographic separation step were added between the membrane and the mass spectrometer ion source for the determination of SVOCs in complex mixtures. The procedure is demonstrated for the determination of dimethyl sulfoxide (DMSO) in equine urine, using internal standardization with DMSO-d6. Full-scan electron ionization (EI) mass spectrometric detection showed good linearity (R = 0.998) and RSDs, relative to the internal standard, of 2.2% for desorption only and 4.6% for desorption and cryotrapping.