Zoe G. Cardon

The magnitude of hydraulic redistribution by plant roots: a review and synthesis of empirical and modeling studies

Hydraulic redistribution (HR) - the movement of water from moist to dry soil through plant roots - occurs worldwide within a range of different ecosystems and plant species. The proposed ecological and hydrologic impacts of HR include increasing dry-season transpiration and photosynthetic rates, prolonging the life span of fine roots and maintaining root-soil contact in dry soils, and moving rainwater down into deeper soil layers where it does not evaporate. In this review, we compile estimates of the magnitude of HR from ecosystems around the world, using representative empirical and modeling studies from which we could extract amounts of water redistributed by plant root systems. The reported average magnitude of HR varies by nearly two orders of magnitude across ecosystems, from 0.04 to 1.3 mm H(2)O d(-1) in the empirical literature, and from 0.1 to 3.23 mm H(2)O d(-1) in the modeling literature. Using these synthesized data, along with other published studies, we examine this variation in the magnitude of upward and downward HR, considering effects of plant, soil and ecosystem characteristics, as well as effects of methodological details (in both empirical and modeling studies) on estimates of HR. We take both ecological and hydrologic perspectives.

Contrasting effects of elevated CO2 on old and new soil carbon pools

Soil organic carbon (SOC) is the largest reservoir of organic carbon in the terrestrial biosphere. Though the influence of increasing atmospheric CO2 on net primary productivity, on the flow of newly fixed carbon belowground, and on the quality of new plant litter in ecosystems has been examined, indirect effects of increased CO2 on breakdown of large SOC pools already in ecosystems are not well understood. We found that exposure of California grassland communities to elevated CO2 retarded decomposition of older SOC when mineral nutrients were abundant, thus increasing the turnover time of SOC already in the system. Under elevated CO2, soil microorganisms appeared to shift from consuming older SOC to utilizing easily degraded rhizodeposits derived from increased root biomass. In contrast to this increased retention of stabilized older SOC under elevated CO2, movement of newly fixed carbon from roots to stabilized SOC pools was retarded; though root biomass increased under elevated CO2, new carbon in mineral-bound pools decreased. These contrasting effects of elevated CO2 on dynamics of old and new soil carbon pools contribute to a new soil carbon equilibrium that could profoundly affect long-term net carbon movement between terrestrial ecosystems and the atmosphere.

Galactosides in the rhizosphere: Utilization by Sinorhizobium meliloti and development of a biosensor

Identifying the types and distributions of organic substrates that support microbial activities around plant roots is essential for a full understanding of plant–microbe interactions and rhizosphere ecology. We have constructed a strain of the soil bacterium Sinorhizobium meliloti containing a gfp gene fused to the melA promoter which is induced on exposure to galactose and galactosides. We used the fusion strain as a biosensor to determine that galactosides are released from the seeds of several different legume species during germination and are also released from roots of alfalfa seedlings growing on artificial medium. Galactoside presence in seed wash and sterile root washes was confirmed by HPLC. Experiments examining microbial growth on α-galactosides in seed wash suggested that α-galactoside utilization could play an important role in supporting growth of S. meliloti near germinating seeds of alfalfa. When inoculated into microcosms containing legumes or grasses, the biosensor allowed us to visualize the localized presence of galactosides on and around roots in unsterilized soil, as well as the grazing of fluorescent bacteria by protozoa. Galactosides were present in patches around zones of lateral root initiation and around roots hairs, but not around root tips. Such biosensors can reveal intriguing aspects of the environment and the physiology of the free-living soil S. meliloti before and during the establishment of nodulation, and they provide a nondestructive, spatially explicit method for examining rhizosphere soil chemical composition.

Carbon cycling in soil

As yet, nobody knows what effects climate change will have on soil carbon reserves, or how those changes will affect the global carbon cycle. Soils are the primary terrestrial repository for carbon, so minor changes in the balance between belowground carbon storage and release could have major impacts on greenhouse gases. Soil fauna, roots, fungi, and microbes interact with mineral and organic matter to process soil carbon. Studies have been hampered by the difficulty of observing processes beneath the earths surface, but advances in science and technology are improving our ability to understand belowground ecosystems.

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

BackgroundThe increasing availability of time series microbial community data from metagenomics and other molecular biological studies has enabled the analysis of large-scale microbial co-occurrence and association networks. Among the many analytical techniques available, the Local Similarity Analysis (LSA) method is unique in that it captures local and potentially time-delayed co-occurrence and association patterns in time series data that cannot otherwise be identified by ordinary correlation analysis. However LSA, as originally developed, does not consider time series data with replicates, which hinders the full exploitation of available information. With replicates, it is possible to understand the variability of local similarity (LS) score and to obtain its confidence interval.ResultsWe extended our LSA technique to time series data with replicates and termed it extended LSA, or eLSA. Simulations showed the capability of eLSA to capture subinterval and time-delayed associations. We implemented the eLSA technique into an easy-to-use analytic software package. The software pipeline integrates data normalization, statistical correlation calculation, statistical significance evaluation, and association network construction steps. We applied the eLSA technique to microbial community and gene expression datasets, where unique time-dependent associations were identified.ConclusionsThe extended LSA analysis technique was demonstrated to reveal statistically significant local and potentially time-delayed association patterns in replicated time series data beyond that of ordinary correlation analysis. These statistically significant associations can provide insights to the real dynamics of biological systems. The newly designed eLSA software efficiently streamlines the analysis and is freely available from the eLSA homepage, which can be accessed at http://meta.usc.edu/softs/lsa.

Photosynthetic Electron Transport in Single Guard Cells as Measured by Scanning Electrochemical Microscopy

Scanning electrochemical microscopy (SECM) is a powerful new tool for studying chemical and biological processes. It records changes in faradaic current as a microelectrode ([less than equal]7 [mu]m in diameter) is moved across the surface of a sample. The current varies as a function of both distance from the surface and the surfaces chemical and electrical properties. We used SECM to examine in vivo topography and photosynthetic electron transport of individual guard cells in Tradescantia fluminensis, to our knowledge the first such analysis for an intact plant. We measured surface topography at the micrometer level and concentration profiles of O2 evolved in photosynthetic electron transport. Comparison of topography and oxygen profiles above single stomatal complexes clearly showed photosynthetic electron transport in guard cells, as indicated by induction of O2 evolution by photosynthetically active radiation. SECM is unique in its ability to measure topography and chemical fluxes, combining some of the attributes of patch clamping with scanning tunneling microscopy. In this paper we suggest several questions in plant physiology that it might address.

Influence of rhizodeposition under elevated CO2 on plant nutrition and soil organic matter

Atmospheric CO2 concentrations can influence ecosystem carbon storage through net primary production (NPP), soil carbon storage, or both. In assessing the potential for carbon storage in terrestrial ecosystems under elevated CO2, both NPP and processing of soil organic matter (SOM), as well as the multiple links between them, must be examined. Within this context, both the quantity and quality of carbon flux from roots to soil are important, since roots produce specialized compounds that enhance nutrient acquisition (affecting NPP), and since the flux of organic compounds from roots to soil fuels soil microbial activity (affecting processing of SOM).From the perspective of root physiology, a technique is described which uses genetically engineered bacteria to detect the distribution and amount of flux of particular compounds from single roots to non-sterile soils. Other experiments from several labs are noted which explore effects of elevated CO2 on root acid phosphatase, phosphomonoesterase, and citrate production, all associated with phosphorus nutrition. From a soil perspective, effects of elevated CO2 on the processing of SOM developed under a C4 grassland but planted with C3 California grassland species were examined under low (unamended) and high (amended with 20 g m−2 NPK) nutrients; measurements of soil atmosphere δ13C combined with soil respiration rates show that during vegetative growth in February, elevated CO2 decreased respiration of carbon from C4 SOM in high nutrient soils but not in unamended soils.This emphasis on the impacts of carbon loss from roots on both NPP and SOM processing will be essential to understanding terrestrial ecosystem carbon storage under changing atmospheric CO2 concentrations.

Tools for the Microbiome: Nano and Beyond

The microbiome presents great opportunities for understanding and improving the world around us and elucidating the interactions that compose it. The microbiome also poses tremendous challenges for mapping and manipulating the entangled networks of interactions among myriad diverse organisms. Here, we describe the opportunities, technical needs, and potential approaches to address these challenges, based on recent and upcoming advances in measurement and control at the nanoscale and beyond. These technical needs will provide the basis for advancing the largely descriptive studies of the microbiome to the theoretical and mechanistic understandings that will underpin the discipline of microbiome engineering. We anticipate that the new tools and methods developed will also be more broadly useful in environmental monitoring, medicine, forensics, and other areas.

Corrected calculations for soil and ecosystem measurements of CO 2 flux using the LI-COR 6200 portable photosynthesis system

Abstract. The LI-COR 6200 portable photosynthesis system (LI-6200) is commonly used in combination with large chambers to measure ecosystem level CO2 flux in ecosystems with small-statured canopies (agriculture, tundra, grasslands, forest understory, etc.). Two problems with the methodology lead to artifactually low estimates of rates of net ecosystem assimilation of CO2 (or overestimates of ecosystem respiration). The first is that accuracy of the equations used by the LI-6200 to calculate photosynthesis depends on a constant vapor pressure in the chamber. This assumption is commonly violated with large ecosystem chambers when evapotranspiration rates are high. We provide equations that correct this problem and permit recalculation of the LI-COR fluxes. The second problem is that of boundary layer formation under still conditions, such as at night. As high concentrations of CO2 close to the ground surface become mixed by chamber fans, exceptionally high values of net ecosystem respiration result. Substantial mixing time is necessary for rates to stabilize. As ecologists attempt to understand how global change might affect whole-ecosystem carbon balance, both of these technical problems must be addressed to get accurate results.

Dependence of the extent and direction of average stomatal response in Zea mays L. and Phaseolus vulgaris L. on the frequency of fluctuations in environmental stimuli

Stomatal responses to fluctuating light and CO2 were investigated in Zea mays and Phaseolus vulgaris. Slow-moving stomata can affect carbon gain and water loss by plants during light flecks, under dynamic cloud cover, during alternating windy and calm air conditions (which influence CO2 concentrations and humidity immediately around leaves in plant canopies), at natural CO2 vents, or in growth chambers with imperfect CO2 control. It was found that the frequency of constant-amplitude fluctuations in light and CO2 dramatically affected the time-averaged stomatal conductance in both Zea and Phaseolus. During oscillations in light, average stomatal conductance was driven either above or below that observed at steady state at the average light level, depending on the frequency of the oscillations. Under oscillating CO2, the departure of average stomatal conductance away from that observed at steady state at the average CO2 level was also frequency dependent in both species. Upon cessation of oscillations and return of light or CO2 to the stable median level, stomatal conductance also returned to a steady state, matching that before oscillations were initiated. This work shows that fluctuations in light and CO2, and equally important, their frequency, can be critical in determining time-averaged stomatal conductance under unstable environmental conditions.