Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems.

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

Community composition and physiological plasticity control microbial carbon storage across natural and experimental soil fertility gradients.

Many microorganisms synthesise carbon (C)-rich compounds under resource deprivation. Such compounds likely serve as intracellular C-storage pools that sustain the activities of microorganisms growing on stoichiometrically imbalanced substrates, making them potentially vital to the function of ecosystems on infertile soils. We examined the dynamics and drivers of three putative C-storage compounds (neutral lipid fatty acids [NLFAs], polyhydroxybutyrate [PHB], and trehalose) across a natural gradient of soil fertility in eastern Australia. Together, NLFAs, PHB, and trehalose corresponded to 8.5-40% of microbial C and 0.06-0.6% of soil organic C. When scaled to "structural" microbial biomass (indexed by polar lipid fatty acids; PLFAs), NLFA and PHB allocation was 2-3-times greater in infertile soils derived from ironstone and sandstone than in comparatively fertile basalt- and shale-derived soils. PHB allocation was positively correlated with belowground biological phosphorus (P)-demand, while NLFA allocation was positively correlated with fungal PLFA : bacterial PLFA ratios. A complementary incubation revealed positive responses of respiration, storage, and fungal PLFAs to glucose, while bacterial PLFAs responded positively to PO43-. By comparing these results to a model of microbial C-allocation, we reason that NLFA primarily served the "reserve" storage mode for C-limited taxa (i.e., fungi), while the variable portion of PHB likely served as "surplus" C-storage for P-limited bacteria. Thus, our findings reveal a convergence of community-level processes (i.e., changes in taxonomic composition that underpin reserve-mode storage dynamics) and intracellular mechanisms (e.g., physiological plasticity of surplus-mode storage) that drives strong, predictable community-level microbial C-storage dynamics across gradients of soil fertility and substrate stoichiometry.

The contribution of PIP2-type aquaporins to photosynthetic response to increased vapour pressure deficit.

The roles of different plasma membrane aquaporins (PIPs) in leaf-level gas exchange of Arabidopsis thaliana were examined using knockout mutants. Since multiple Arabidopsis PIPs are implicated in CO2 transport across cell membranes, we focused on identifying the effects of the knockout mutations on photosynthesis, and whether they are mediated through the control of stomatal conductance of water vapour (gs), mesophyll conductance of CO2 (gm), or both. We grew Arabidopsis plants in low and high humidity environments and found that the contribution of PIPs to gs was larger under low air humidity when the evaporative demand was high, whereas any effect of a lack of PIP function was minimal under higher humidity. The pip2;4 knockout mutant had 44% higher gs than wild-type plants under low humidity, which in turn resulted in an increased net photosynthetic rate (Anet). We also observed a 23% increase in whole-plant transpiration (E) for this knockout mutant. The lack of functional plasma membrane aquaporin AtPIP2;5 did not affect gs or E, but resulted in homeostasis of gm despite changes in humidity, indicating a possible role in regulating CO2 membrane permeability. CO2 transport measurements in yeast expressing AtPIP2;5 confirmed that this aquaporin is indeed permeable to CO2.

Implications of the mesophyll conductance to CO2 for photosynthesis and water-use efficiency during long-term water stress and recovery in two contrasting Eucalyptus species.

Water stress (WS) slows growth and photosynthesis (A(n)), but most knowledge comes from short-time studies that do not account for longer term acclimation processes that are especially relevant in tree species. Using two Eucalyptus species that contrast in drought tolerance, we induced moderate and severe water deficits by withholding water until stomatal conductance (g(sw)) decreased to two pre-defined values for 24 d, WS was maintained at the target g(sw) for 29 d and then plants were re-watered. Additionally, we developed new equations to simulate the effect on mesophyll conductance (g(m)) of accounting for the resistance to refixation of CO(2). The diffusive limitations to CO(2), dominated by the stomata, were the most important constraints to A(n). Full recovery of A(n) was reached after re-watering, characterized by quick recovery of gm and even higher biochemical capacity, in contrast to the slower recovery of g(sw). The acclimation to long-term WS led to decreased mesophyll and biochemical limitations, in contrast to studies in which stress was imposed more rapidly. Finally, we provide evidence that higher gm under WS contributes to higher intrinsic water-use efficiency (iWUE) and reduces the leaf oxidative stress, highlighting the importance of gm as a target for breeding/genetic engineering.

The role of mesophyll conductance in the economics of nitrogen and water use in photosynthesis.

A recent resurgence of interest in formal optimisation theory has begun to improve our understanding of how variations in stomatal conductance and photosynthetic capacity control the response of whole plant photosynthesis and growth to the environment. However, mesophyll conductance exhibits similar variation and has similar impact on photosynthesis as stomatal conductance; yet, the role of mesophyll conductance in the economics of photosynthetic resource use has not been thoroughly explored. In this article, we first briefly summarise the knowledge of how mesophyll conductance varies in relation to environmental factors that also affect stomatal conductance and photosynthetic capacity, and then we use a simple analytical approach to begin to explore how these important controls on photosynthesis should mutually co-vary in a plant canopy in the optimum. Our analysis predicts that when either stomatal or mesophyll conductance is limited by fundamental biophysical constraints in some areas of a canopy, e.g. reduced stomatal conductance in upper canopy leaves due to reduced water potential, the other of the two conductances should increase in those leaves, while photosynthetic capacity should decrease. Our analysis also predicts that if mesophyll conductance depends on nitrogen investment in one or more proteins, then nitrogen investment should shift away from Rubisco and towards mesophyll conductance if hydraulic or other constraints cause chloroplastic CO2 concentration to decline. Thorough exploration of these issues awaits better knowledge of whether and how mesophyll conductance is itself limited by nitrogen investment, and about how these determinants of photosynthetic CO2 supply and demand co-vary among leaves in real plant canopies.

Effects of drought on mesophyll conductance and photosynthetic limitations at different tree canopy layers.

In recent years, many studies have focused on the limiting role of mesophyll conductance (gm ) to photosynthesis (An ) under water stress, but no studies have examined the effect of drought on gm through the forest canopy. We investigated limitations to An on leaves at different heights in a mixed adult stand of sessile oak (Quercus petraea) and beech (Fagus sylvatica) trees during a moderately dry summer. Moderate drought decreased An of top and lowest beech canopy leaves much more than in leaves located in the mid canopy; whereas in oak, An of the lower canopy was decreased more than in sunlit leaves. The decrease of An was probably not due to leaf-level biochemistry given that VCmax was generally unaffected by drought. The reduction in An was instead associated with reduction in stomatal and mesophyll conductances. Drought-induced increases in stomatal limitations were largest in leaves from the top canopy, whereas drought-induced increases in mesophyll limitations were largest in leaves from the lowest canopy. Sensitivity analysis highlighted the need to decompose the canopy into different leaf layers and to incorporate the limitation imposed by gm when assessing the impact of drought on the gas exchange of tree canopies.

Quaternary ammonium compounds can be abundant in some soils and are taken up as intact molecules by plants.

Studies of organic nitrogen (N) cycling and uptake by plants have focused on protein amino acids, but the soil solution includes organic N compounds from many other compound classes. The two aims of this study were to characterize the 30-50 most abundant molecules of small (< 250 Da), nonpeptide organic N in the soil solution from six soils, and to determine if two ecologically disparate species (nonmycorrhizal Banksia oblongifolia and mycorrhizal Triticum aestivum) have the ability to take up intact molecules of three quaternary ammonium compounds (betaine, carnitine and acetyl-carnitine). Protein amino acids were dominant components of the pool of small nonpeptide organic N in all soils. The most abundant other compound classes were quaternary ammonium compounds (1-28% of nonpeptide small organic N) and nonprotein amino acids (3-19% of nonpeptide small organic N). B. oblongifolia and T. aestivum took up intact quaternary ammonium compounds from dilute hydroponic solution, while T. aestivum growing in field soil took up intact quaternary ammonium compounds injected into soil. Results of this study show that the pool of organic N in soil is more diverse and plants have an even broader palate than is suggested by most of the literature on organic N.

Mesophyll diffusion conductance to CO2: an unappreciated central player in photosynthesis.

Mesophyll diffusion conductance to CO(2) is a key photosynthetic trait that has been studied intensively in the past years. The intention of the present review is to update knowledge of g(m), and highlight the important unknown and controversial aspects that require future work. The photosynthetic limitation imposed by mesophyll conductance is large, and under certain conditions can be the most significant photosynthetic limitation. New evidence shows that anatomical traits, such as cell wall thickness and chloroplast distribution are amongst the stronger determinants of mesophyll conductance, although rapid variations in response to environmental changes might be regulated by other factors such as aquaporin conductance. Gaps in knowledge that should be research priorities for the near future include: how different is mesophyll conductance among phylogenetically distant groups and how has it evolved? Can mesophyll conductance be uncoupled from regulation of the water path? What are the main drivers of mesophyll conductance? The need for mechanistic and phenomenological models of mesophyll conductance and its incorporation in process-based photosynthesis models is also highlighted.

Post-uptake metabolism affects quantification of amino acid uptake.

• The quantitative significance of amino acids to plant nutrition remains controversial. This experiment determined whether post-uptake metabolism and root to shoot export differ between glycine and glutamine, and examined implications for estimation of amino acid uptake. • Field soil containing a Eucalyptus pauciflora seedling was injected with uniformly (13)C- and (15)N-labelled glycine or glutamine. I quantified (15)N and (13)C excess in leaves and roots and intact labelled amino acids in leaves, roots and stem xylem sap. A tunable diode laser quantified fluxes of (12)CO(2) and (13)CO(2) from leaves and soil. • 60-360 min after addition of amino acid, intact molecules of U-(13)C,(15)N glutamine were < 5% of (15)N excess in roots, whereas U-(13)C,(15)N glycine was 30-100% of (15)N excess in roots. Intact molecules of glutamine, but not glycine, were exported from roots to shoots. • Post-uptake metabolism and transport complicate interpretation of isotope labelling such that root and shoot contents of intact amino acid, (13)C and (15)N may not reflect rates of uptake. Future experiments should focus on reconciling discrepancies between intact amino acid, (13)C and (15)N by determining the turnover of amino acids within roots. Alternatively, post-uptake metabolism and transport could be minimized by harvesting plants within minutes of isotope addition.

Is mesophyll conductance to CO2 in leaves of three Eucalyptus species sensitive to short-term changes of irradiance under ambient as well as low O2?

Mesophyll conductance to CO2 (g m) limits the diffusion of CO2 to the sites of carboxylation, and may respond rapidly (within minutes) to abiotic factors. Using three Eucalyptus species, we tested the rapid response of g m to irradiance under 21% and 1% O2. We used simultaneous measurements of leaf gas exchange and discrimination against 13CO2 with a tuneable diode laser absorption spectrometer. Measurements under 1% O2 were used to limit uncertainties due to 13C-12C fractionation occurring during photorespiration. Switching irradiance from 600 to 200µmolm-2s-1 led to a ≈60% decrease of g m within minutes in all species under both 21% O2 and 1% O2. The g m response to irradiance is unlikely to be a computation artefact since using different values for the parameters of the discrimination model changed the absolute values of g m but did not affect the relative response to irradiance. Simulations showed that possible rapid changes of any parameter were unable to explain the observed variations of g m with irradiance, except for13C-12C fractionation during carboxylation (b), which, in turn, is dependent on the fraction of leaf C assimilated by phospho-enol pyruvate carboxylase (PEPc) (ß). g m apparently increased by ≈30% when O2 was switched from 21% to 1% O2. Again, possible changes of ß with O2 could explain this apparent g m response to O2. Nevertheless, large irradiance or O2-induced changes in ß would be required to fully explain the observed changes in g m, reinforcing the hypothesis that g m is responsive to irradiance and possibly also to O2.

Mesophyll conductance to CO2, assessed from online TDL-AS records of ¹³CO2 discrimination, displays small but significant short-term responses to CO2 and irradiance in Eucalyptus seedlings.

Mesophyll conductance (g(m)) is now recognized as an important limiting process for photosynthesis, as it results in a significant decrease of CO(2) diffusion from substomatal cavities where water evaporation occurs, to chloroplast stroma. Over the past decade, an increasing number of studies proposed that g(m) can vary in the short term (e.g. minutes), but these variations are still controversial, especially those potentially induced by changing CO(2) and irradiance. In this study, g(m) data estimated with online (13)C discrimination recorded with a tunable diode laser absorption spectrometer (TDL-AS) during leaf gas exchange measurements, and based on the single point method, are presented. The data were obtained with three Eucalyptus species. A 50% decrease in g(m) was observed when the CO(2) mole fraction was increased from 300 µmol mol(-1) to 900 µmol mol(-1), and a 60% increase when irradiance was increased from 200 µmol mol(-1) to 1100 µmol mol(-1) photosynthetic photon flux density (PPFD). The relative contribution of respiration and photorespiration to overall (13)C discrimination was also estimated. Not taking this contribution into account may lead to a 50% underestimation of g(m) but had little effect on the CO(2)- and irradiance-induced changes. In conclusion, (i) the observed responses of g(m) to CO(2) and irradiance were not artefactual; (ii) the respiratory term is important to assess absolute values of g(m) but has no impact on the responses to CO(2) and PPFD; and (iii) increasing irradiance and reducing the CO(2) mole fraction results in rapid increases in g(m) in Eucalyptus seedlings.

How does P affect photosynthesis and metabolite profiles of Eucalyptus globulus?

Phosphorus (P) has multiple effects on plant metabolism, but there are many unresolved questions especially for evergreen trees. For example, we do not know the general effects of P on metabolism, or if P affects photosynthesis via the internal conductance to CO(2) transfer from sub-stomatal cavities to chloroplast or amounts of Rubisco. This study investigates how P deficiency affects seedlings of the evergreen tree Eucalyptus globulus grown for 2.5 months with four nutrient solutions differing in P concentration. To determine why photosynthesis was affected by P supply, Rubisco was quantified by capillary electrophoresis, internal conductance was quantified from gas exchange and carbon isotope discrimination, and biochemical parameters of photosynthesis were estimated from A/C(c) responses. Additional insights into the effect of P on metabolism were provided by gas chromatography-mass spectrometry (GC-MS) metabolite profiling. Larger concentrations of P in the nutrient solution led to significantly faster rates of photosynthesis. There was no evidence that stomatal or internal conductances contributed to the effect of P supply on photosynthesis. The increase in photosynthesis with P supply was correlated with V(cmax), and amounts of P, phosphate and fructose 6-phosphate (6-P). Phosphorous supply affected approximately one-third of the 90 aqueous metabolites quantified by GC-MS, but the effect size was generally smaller than reported for experiments on herbaceous species. Phosphorus deficiency decreased concentrations of phosphate, glucose 6-P and fructose 6-P more than it decreased photosynthesis, suggesting faster turnover of smaller pools of phosphate and phosphorylated intermediates. The effect of P supply on most amino acids was small, with the exception of arginine and glutamine, which increased dramatically under P deficiency. P deficiency had small or non-significant effects on carbohydrates and organic acids of the tricarboxylic acid (TCA) cycle. The small effect of P on carbohydrates, organic acids and (most) amino acids likely reflects a functional homeostasis among C metabolism (glycolysis, TCA and pentose P cycles), rates of photosynthesis and growth. The strong functional homeostasis in E. globulus may reflect a conservative, long-term growth and metabolic strategy of evergreen trees.

Responses to water stress of gas exchange and metabolites in Eucalyptus and Acacia spp.

Studies of water stress commonly examine either gas exchange or leaf metabolites, and many fail to quantify the concentration of CO2 in the chloroplasts (C(c)). We redress these limitations by quantifying C(c) from discrimination against ¹³CO2 and using gas chromatography-mass spectrometry (GC-MS) for leaf metabolite profiling. Five Eucalyptus and two Acacia species from semi-arid to mesic habitats were subjected to a 2 month water stress treatment (Ψ(pre-dawn) = -1.7 to -2.3 MPa). Carbohydrates dominated the leaf metabolite profiles of species from dry areas, whereas organic acids dominated the metabolite profiles of species from wet areas. Water stress caused large decreases in photosynthesis and C(c), increases in 17-33 metabolites and decreases in 0-9 metabolites. In most species, fructose, glucose and sucrose made major contributions to osmotic adjustment. In Acacia, significant osmotic adjustment was also caused by increases in pinitol, pipecolic acid and trans-4-hydroxypipecolic acid. There were also increases in low-abundance metabolites (e.g. proline and erythritol), and metabolites that are indicative of stress-induced changes in metabolism [e.g. γ-aminobutyric acid (GABA) shunt, photorespiration, phenylpropanoid pathway]. The response of gas exchange to water stress and rewatering is rather consistent among species originating from mesic to semi-arid habitats, and the general response of metabolites to water stress is rather similar, although the specific metabolites involved may vary.

Determination of the site of CO2 sensing in poplar: is the area-based N content and anatomy of new leaves determined by their immediate CO2 environment or by the CO2 environment of mature leaves?

Exposure to an elevated CO(2) concentration ([CO(2)]) generally decreases leaf N content per unit area (N(area)) and stomatal density, and increases leaf thickness. Mature leaves can 'sense' elevated [CO(2)] and this regulates stomatal development of expanding leaves (systemic regulation). It is unclear if systemic regulation is involved in determination of leaf thickness and N(area)-traits that are significantly correlated with photosynthetic capacity. A cuvette system was used whereby [CO(2)] around mature leaves was controlled separately from that around expanding leaves. Expanding leaves of poplar (Populus trichocarpa×P. deltoides) seedlings were exposed to elevated [CO(2)] (720 µmol mol(-1)) while the remaining mature leaves inside the cuvette were under ambient [CO(2)] of 360 µmol mol(-1). Reverse treatments were performed. Exposure of newly developing leaves to elevated [CO(2)] increased their thickness, but when mature leaves were exposed to elevated [CO(2)] the increase in thickness of new leaves was less pronounced. The largest response to [CO(2)] was reflected in the palisade tissue thickness (as opposed to the spongy tissue) of new leaves. The N(area) of new leaves was unaffected by the local [CO(2)] where the new leaves developed, but decreased following the exposure of mature leaves to elevated [CO(2)]. The volume fraction of mesophyll cells compared with total leaf and the mesophyll cell density changed in a manner similar to the response of N(area). These results suggest that N(area) is controlled independently of the leaf thickness, and suggest that N(area) is under systemic regulation by [CO(2)] signals from mature leaves that control mesophyll cell division.

Variability in mesophyll conductance between barley genotypes, and effects on transpiration efficiency and carbon isotope discrimination.

Leaf internal, or mesophyll, conductance to CO(2) (g(m)) is a significant and variable limitation of photosynthesis that also affects leaf transpiration efficiency (TE). Genotypic variation in g(m) and the effect of g(m) on TE were assessed in six barley genotypes (four Hordeum vulgare and two H. bulbosum). Significant variation in g(m) was found between genotypes, and was correlated with photosynthetic rate. The genotype with the highest g(m) also had the highest TE and the lowest carbon isotope discrimination as recorded in leaf tissue (Delta(p)). These results suggest g(m) has unexplored potential to provide TE improvement within crop breeding programmes.

Phloem sap and leaf delta13C, carbohydrates, and amino acid concentrations in Eucalyptus globulus change systematically according to flooding and water deficit treatment.

Phloem is a central conduit for the distribution of photoassimilate, nutrients, and signals among plant organs. A revised technique was used to collect phloem sap from small woody plants in order to assess changes in composition induced by water deficit and flooding. Bled phloem sap delta(13)C and sugar concentrations were compared to delta(13)C of bulk material, soluble carbon extracts, and the neutral sugar fraction from leaves. Amino acid composition and inorganic ions of the phloem sap was also analysed. Quantitative, systematic changes were detected in phloem sap composition and delta(13)C in response to altered water availability. Phloem sap delta(13)C was more sensitive to changes of water availability than the delta(13)C of bulk leaf, the soluble carbon fraction, and the neutral soluble fraction of leaves. Changes in water availability also resulted in significant changes in phloem sugar (sucrose and raffinose), inorganic nutrient (potassium), and amino acid (phenylalanine) concentrations with important implications for the maintenance of phloem function and biomass partitioning. The differences in carbohydrate and amino acid composition as well as the delta(13)C in the phloem, along with a new model system for phloem research, offer an improved understanding of the phloem-mediated signal, nutrient, and photoassimilate transduction in relation to water availability.

Role of mesophyll diffusion conductance in constraining potential photosynthetic productivity in the field.

Limited mesophyll diffusion conductance to CO(2) (g(m)) can significantly constrain plant photosynthesis, but the extent of g(m)-limitation is still imperfectly known. As g(m) scales positively with foliage photosynthetic capacity (A), the CO(2) drawdown from substomatal cavities (C(i)) to chloroplasts (C(C), C(i)-C(C)=A/g(m)) rather than g(m) alone characterizes the mesophyll diffusion limitations of photosynthesis. The dependencies of g(m) on A, foliage structure (leaf dry mass per unit area, M(A)), and the resulting drawdowns across a dataset of 81 species of contrasting foliage structure and photosynthetic potentials measured under non-stressed conditions were analysed to describe the structure-driven potential photosynthetic limitations due to g(m). Further the effects of key environmental stress factors and leaf and plant developmental alterations on g(m) and CO(2) drawdown were evaluated and the implications of varying g(m) on foliage photosynthesis in the field were simulated. The meta-analysis demonstrated that g(m) of non-stressed leaves was negatively correlated with M(A), and despite the positive relationship between g(m) and A, the CO(2) drawdown was larger in leaves with more robust structure. The correlations were stronger with mass-based g(m) and A, probably reflecting the circumstance that mesophyll diffusion is a complex three-dimensional process that scales better with mesophyll volume-weighted than with leaf area-weighted traits. The analysis of key environmental stress effects on g(m) and CO(2) drawdowns demonstrated that the effect of individual stresses on CO(2) drawdowns varies depending on the stress effects on foliage structure and assimilation rates. Leaf diffusion limitations are larger in non-senescent older leaves and also in senescent leaves, again reflecting more robust leaf structure and/or non-co-ordinated alterations in leaf photosynthesis and g(m). According to simulation analyses, in plants with a larger part of the overall diffusion conductance from the ambient atmosphere to the chloroplasts in the mesophyll, photosynthesis is less sensitive to changes in stomatal conductance. Accordingly, in harsher environments that support vegetation with tougher long-living stress-tolerant leaves with lower g(m), reductions in stomatal conductance that are common during stress periods are expected to alter photosynthesis less than in species where a larger part of the total diffusion limitation is determined by stomata. While structural robustness improves plant performance under environmental stress, low g(m) and inherently large CO(2) drawdown in robust leaves limits the photosynthesis of these plants more severely under favourable conditions when stomatal conductance is high. The differences in overall responsiveness to environmental modifications of plants with varying g(m) need consideration in current large-scale ecosystem productivity models.

Role of corticular photosynthesis following defoliation in Eucalyptus globulus.

Defoliation can reduce net fixation of atmospheric CO(2) by the canopy, but increase the intensity and duration of photosynthetically active radiation on stems. Stem CO(2) flux and leaf gas exchange in young Eucalyptus globulus seedlings were measured to assess the impact of defoliation on these processes and to determine the potential contribution of re-fixation by photosynthetic inner bark in offsetting the effects of defoliation in a woody species. Pot and field trials examined how artificial defoliation of the canopy affected the photosynthetic characteristics of main stems of young Eucalyptus globulus seedlings. Defoliated potted seedlings were characterized by transient increases in foliar photosynthetic rates and concomitant decreases in stem CO(2) fluxes (both in the dark and light). Defoliated field-grown seedlings showed similar stem CO(2) flux responses, but of reduced magnitude. Despite demonstrating increased re-fixation capability, defoliated potted-seedlings had slowed stem growth. The green stem of seedlings exhibited largely shade-adapted characteristics. Defoliation reduced stem chlorophyll a/b ratio and increased carotenoid concentration. An increased capacity to re-fix internally respired CO(2) (up to 96%) suggested that stem re-fixation represents a previously unexplored mechanism to minimize the impact of foliar loss by maximizing the contribution of all photosynthetic tissues, particularly for young seedlings.

Importance of mesophyll diffusion conductance in estimation of plant photosynthesis in the field.

Mesophyll diffusion conductance to CO(2) (g(m)) is an important leaf characteristic determining the drawdown of CO(2) from substomatal cavities (C(i)) to chloroplasts (C(C)). Finite g(m) results in modifications in the shape of the net assimilation (A) versus C(i) response curves, with the final outcome of reduced maximal carboxylase activity of Rubisco (V(cmax)), and a greater ratio of the capacity for photosynthetic electron transport to V(cmax) (J(max)/V(cmax)) and alterations in mitochondrial respiration rate (R(d)) when estimated from A/C(i) responses without considering g(m). The influence of different Farquhar et al. model parameterizations on daily photosynthesis under non-stressed (C(i) kept constant throughout the day) and stressed conditions (mid-day reduction in C(i)) was compared. The model was parameterized on the basis of A/C(C) curves and A/C(i) curves using both the conventional fitting procedure (V(cmax) and R(d) fitted separately to the linear part of the response curve and J(max) to the saturating part) and a procedure that fitted all parameters simultaneously. The analyses demonstrated that A/C(i) parameterizations overestimated daily assimilation by 6-8% for high g(m) values, while they underestimated if by up to 70% for low g(m) values. Qualitative differences between the A/C(i) and A/C(C) parameterizations were observed under stressed conditions, when underestimated V(cmax) and overestimated R(d) of A/C(i) parameterizations resulted in excessive mid-day depression of photosynthesis. Comparison with measured diurnal assimilation rates in the Mediterranean sclerophyll species Quercus ilex under drought further supported this bias of A/C(i) parameterizations. While A/C(i) parameterization predicted negative carbon balance at mid-day, actual measurements and simulations with the A/C(C) approach yielded positive carbon gain under these conditions. In addition, overall variation captured by the best A/C(i) parameterization was poor compared with the A/C(C) approach. This analysis strongly suggests that for correct parameterization of daily time-courses of photosynthesis under realistic field conditions, g(m) must be included in photosynthesis models.

Uptake of inorganic and amino acid nitrogen from soil by Eucalyptus regnans and Eucalyptus pauciflora seedlings.

This study examined whether two species of Eucalyptus can take up the amino acid glycine from soil and compared the uptake rate of glycine with the uptake rates of nitrate and ammonium. Ectomycorrhizal seedlings of two ecologically disparate species were studied: Eucalyptus regnans F. Muell., a fast-growing forest tree from low altitudes; and Eucalyptus pauciflora Sieber ex Spreng., a slow-growing tree that forms the alpine treeline. Seedlings were grown from seeds in field soil. When seedlings were 4-5 months old, soils were injected with equimolar mixtures of isotope-labeled glycine, ammonium and nitrate. Seedlings and soil were harvested 4 and 48 h later. Isotope ratio mass spectrometry analysis of (13)C and (15)N enrichment in plants receiving glycine indicated uptake of 1.5 (13)C for every (15)N at the 4-h harvest (versus 2:1 (13)C:(15)N in labeled glycine), suggesting intact uptake of around 75% of glycine. Gas chromatography-mass spectrometry analysis detected intact (13)C(2),(15)N-glycine in roots, but the pool of (13)C(2),(15)N-glycine was 10-500 times smaller than (13)C and (15)N excess, and no (13)C(2),(15)N-glycine was detected in shoots. This is consistent with glycine being taken up as an intact molecule that is subsequently metabolized rapidly. Both species took up more nitrate than ammonium, and glycine was the least preferred form of nitrogen (N). Microbes took up more N than seedlings, and their preference for N forms was the mirror image of the plant preferences. These data suggest that patterns of microbial uptake may determine plant preference for forms of N.