Impact of winter roads on boreal peatland carbon exchange

Across Canada's boreal forest, linear disturbances, including cutlines such as seismic lines and roads, crisscross the landscape to facilitate resource exploration and extraction; many of these linear disturbances cross peatland ecosystems. Changes in tree canopy cover and the compression of the peat by heavy equipment alter local thermal, hydrological, and ecological conditions, likely changing carbon exchange on the disturbance, and possibly in the adjacent peatland. We measured bulk density, water table, soil temperature, plant cover, and CO₂ and CH₄ flux along triplicate transects crossing a winter road through a wooded fen near Peace River, Alberta, Canada. Sample plots were located 1, 5, and 10 m from the road on both sides with an additional three plots on the road. Productivity of the overstory trees, when present, was also determined. The winter road had higher bulk density, shallower water table, higher graminoid cover, and thawed earlier than the adjacent peatland. Tree productivity and CO₂ flux varied between the plots, and there was no clear pattern in relation to distance from the road. The plots on the winter road acted as a greater CO₂ sink and greater CH₄ source compared to the adjacent peatland with plots on the winter road emitting on average (standard error) 479 (138) compared to 41 (10) mg CH₄  m^-2  day^-1 in the adjacent peatland. Considering both gases, global warming potential increased from 70 to 250 g CO₂ e m^-2  year^-1 in the undisturbed area to 2100 g CO₂ e m^-2  year^-1 on the winter road. Although carbon fluxes on any given cutline through peatland will vary depending on level of compaction, line width and vegetation community shifts, the large number of linear disturbances in Canada's boreal forest and slow recovery on peatland ecosites suggest they could represent an important anthropogenic greenhouse gas source.

Evaluating carbon storage, timber harvest, and habitat possibilities for a Western Cascades (USA) forest landscape

Forest policymakers and managers have long sought ways to evaluate the capability of forest landscapes to jointly produce timber, habitat, and other ecosystem services in response to forest management. Currently, carbon is of particular interest as policies for increasing carbon storage on federal lands are being proposed. However, a challenge in joint production analysis of forest management is adequately representing ecological conditions and processes that influence joint production relationships. We used simulation models of vegetation structure, forest sector carbon, and potential wildlife habitat to characterize landscape-level joint production possibilities for carbon storage, timber harvest, and habitat for seven wildlife species across a range of forest management regimes. We sought to (1) characterize the general relationships of production possibilities for combinations of carbon storage, timber, and habitat, and (2) identify management variables that most influence joint production relationships. Our 160 000-ha study landscape featured environmental conditions typical of forests in the Western Cascade Mountains of Oregon (USA). Our results indicate that managing forests for carbon storage involves trade-offs among timber harvest and habitat for focal wildlife species, depending on the disturbance interval and utilization intensity followed. Joint production possibilities for wildlife species varied in shape, ranging from competitive to complementary to compound, reflecting niche breadth and habitat component needs of species examined. Managing Pacific Northwest forests to store forest sector carbon can be roughly complementary with habitat for Northern Spotted Owl, Olive-sided Flycatcher, and red tree vole. However, managing forests to increase carbon storage potentially can be competitive with timber production and habitat for Pacific marten, Pileated Woodpecker, and Western Bluebird, depending on the disturbance interval and harvest intensity chosen. Our analysis suggests that joint production possibilities under forest management regimes currently typical on industrial forest lands (e.g., 40- to 80-yr rotations with some tree retention for wildlife) represent but a small fraction of joint production outcomes possible in the region. Although the theoretical boundaries of the production possibilities sets we developed are probably unachievable in the current management environment, they arguably define the long-term potential of managing forests to produce multiple ecosystem services within and across multiple forest ownerships.

Carbon sources and trophic relationships of ice seals during recent environmental shifts in the Bering Sea

Dramatic multiyear fluctuations in water temperature and seasonal sea ice extent and duration across the Bering-Chukchi continental shelf have occurred in this century, raising a pressing ecological question: Do such environmental changes alter marine production processes linking primary producers to upper trophic-level predators? We examined this question by comparing the blubber fatty acid (FA) composition and stable carbon isotope ratios of individual FA (δ¹³CFA) of adult ringed seals (Pusa hispida), bearded seals (Erignathus barbatus), spotted seals (Phoca largha), and ribbon seals (Histriophoca fasciata), collectively known as "ice seals," sampled during an anomalously warm, low sea ice period in 2002-2005 in the Bering Sea and a subsequent cold, high sea ice period in 2007-2010. δ¹³C(FA) values, used to estimate the contribution to seals of carbon derived from sea ice algae (sympagic production) relative to that derived from water column phytoplankton (pelagic production), indicated that during the cold period, sympagic production accounted for 62-80% of the FA in the blubber of bearded seals, 51-62% in spotted seals, and 21-60% in ringed seals. Moreover, the δ¹³CFA values of bearded seals indicated a greater incorporation of sympagic FAs during the cold period than the warm period. This result provides the first empirical evidence of an ecosystem-scale effect of a putative change in sympagic production in the Western Arctic. The FA composition of ice seals showed clear evidence of resource partitioning among ringed, bearded, and spotted seals, and little niche separation between spotted and ribbon seals, which is consistent with previous studies. Despite interannual variability, the FA composition of ringed and bearded seals showed little evidence of differences in diet between the warm and cold periods. The findings that sympagic production contributes significantly to food webs supporting ice seals, and that the contribution apparently is less in warm years with low sea ice, raise an important concern: Will the projected warming and continuing loss of seasonal sea ice in the Arctic, and the associated decline of organic matter input from sympagic production, be compensated for by pelagic production to satisfy both pelagic and benthic carbon and energy needs?

Restoring forest structure and process stabilizes forest carbon in wildfire-prone southwestern ponderosa pine forests

Changing climate and a legacy of fire-exclusion have increased the probability of high-severity wildfire, leading to an increased risk of forest carbon loss in ponderosa pine forests in the southwestern USA. Efforts to reduce high-severity fire risk through forest thinning and prescribed burning require both the removal and emission of carbon from these forests, and any potential carbon benefits from treatment may depend on the occurrence of wildfire. We sought to determine how forest treatments alter the effects of stochastic wildfire events on the forest carbon balance. We modeled three treatments (control, thin-only, and thin and burn) with and without the occurrence of wildfire. We evaluated how two different probabilities of wildfire occurrence, 1% and 2% per year, might alter the carbon balance of treatments. In the absence of wildfire, we found that thinning and burning treatments initially reduced total ecosystem carbon (TEC) and increased net ecosystem carbon balance (NECB). In the presence of wildfire, the thin and burn treatment TEC surpassed that of the control in year 40 at 2%/yr wildfire probability, and in year 51 at 1%/yr wildfire probability. NECB in the presence of wildfire showed a similar response to the no-wildfire scenarios: both thin-only and thin and burn treatments increased the C sink. Treatments increased TEC by reducing both mean wildfire severity and its variability. While the carbon balance of treatments may differ in more productive forest types, the carbon balance benefits from restoring forest structure and fire in southwestern ponderosa pine forests are clear.

Spatial distribution and variability of carbon storage in different sympodial bamboo species in China

Selection of tree species is potentially an important management decision for increasing carbon storage in forest ecosystems. This study investigated and compared spatial distribution and variability of carbon storage in 8 sympodial bamboo species in China. The results of this study showed that average carbon densities (CDs) in the different organs decreased in the order: culms (0.4754 g g(-1)) > below-ground (0.4701 g g(-1)) > branches (0.4662 g g(-1)) > leaves (0.4420 g g(-1)). Spatial distribution of carbon storage (CS) on an area basis in the biomass of 8 sympodial bamboo species was in the order: culms (17.4-77.1%) > below-ground (10.6-71.7%) > branches (3.8-11.6%) > leaves (0.9-5.1%). Total CSs in the sympodial bamboo ecosystems ranged from 103.6 Mg C ha(-1) in Bambusa textilis McClure stand to 194.2 Mg C ha(-1) in Dendrocalamus giganteus Munro stand. Spatial distribution of CSs in 8 sympodial bamboo ecosystems decreased in the order: soil (68.0-83.5%) > vegetation (16.8-31.1%) > litter (0.3-1.7%). Total current CS and biomass carbon sequestration rate in the sympodial bamboo stands studied in China is 93.184 × 10(6) Mg C ha(-1) and 8.573 × 10(6) Mg C yr(-1), respectively. The sympodial bamboos had a greater CSs and higher carbon sequestration rates relative to other bamboo species. Sympodial bamboos can play an important role in improving climate and economy in the widely cultivated areas of the world.

The dynamical landscape of marine phytoplankton diversity

Observations suggest that the landscape of marine phytoplankton assemblage might be strongly heterogeneous at the dynamical mesoscale and submesoscale (10-100 km, days to months), with potential consequences in terms of global diversity and carbon export. But these variations are not well documented as synoptic taxonomic data are difficult to acquire. Here, we examine how phytoplankton assemblage and diversity vary between mesoscale eddies and submesoscale fronts. We use a multi-phytoplankton numerical model embedded in a mesoscale flow representative of the North Atlantic. Our model results suggest that the mesoscale flow dynamically distorts the niches predefined by environmental contrasts at the basin scale and that the phytoplankton diversity landscape varies over temporal and spatial scales that are one order of magnitude smaller than those of the basin-scale environmental conditions. We find that any assemblage and any level of diversity can occur in eddies and fronts. However, on a statistical level, the results suggest a tendency for larger diversity and more fast-growing types at fronts, where nutrient supplies are larger and where populations of adjacent water masses are constantly brought into contact; and lower diversity in the core of eddies, where water masses are kept isolated long enough to enable competitive exclusion.

Mechanisms of piñon pine mortality after severe drought: a retrospective study of mature trees

Conifers have incurred high mortality during recent global-change-type drought(s) in the western USA. Mechanisms of drought-related tree mortality need to be resolved to support predictions of the impacts of future increases in aridity on vegetation. Hydraulic failure, carbon starvation and lethal biotic agents are three potentially interrelated mechanisms of tree mortality during drought. Our study compared a suite of measurements related to these mechanisms between 49 mature piñon pine (Pinus edulis Engelm.) trees that survived severe drought in 2002 (live trees) and 49 trees that died during the drought (dead trees) over three sites in Arizona and New Mexico. Results were consistent over all sites indicating common mortality mechanisms over a wide region rather than site-specific mechanisms. We found evidence for an interactive role of hydraulic failure, carbon starvation and biotic agents in tree death. For the decade prior to the mortality event, dead trees had twofold greater sapwood cavitation based on frequency of aspirated tracheid pits observed with scanning electron microscopy (SEM), smaller inter-tracheid pit diameter measured by SEM, greater diffusional constraints to photosynthesis based on higher wood δ(13)C, smaller xylem resin ducts, lower radial growth and more bark beetle (Coleoptera: Curculionidae) attacks than live trees. Results suggest that sapwood cavitation, low carbon assimilation and low resin defense predispose piñon pine trees to bark beetle attacks and mortality during severe drought. Our novel approach is an important step forward to yield new insights into how trees die via retrospective analysis.

Quantifying the timescales over which exogenous and endogenous conditions affect soil respiration

Understanding how exogenous and endogenous factors and above-ground-below-ground linkages modulate carbon dynamics is difficult because of the influences of antecedent conditions. For example, there are variable lags between above-ground assimilation and below-ground efflux, and the duration of antecedent periods are often arbitrarily assigned. Nonetheless, developing models linking above- and below-ground processes is crucial for estimating current and future carbon dynamics. We collected data on leaf-level photosynthesis (Asat ) and soil respiration (Rsoil ) in different microhabitats (under shrubs vs under bunchgrasses) in the Sonoran Desert. We evaluated timescales over which endogenous and exogenous factors control Rsoil by analyzing data in the context of a semimechanistic temperature-response model of Rsoil that incorporated effects of antecedent exogenous (soil water) and endogenous (Asat ) conditions. For both microhabitats, antecedent soil water and Asat significantly affected Rsoil , but Rsoil under shrubs was more sensitive to Asat than that under bunchgrasses. Photosynthetic rates 1 and 3 d before the Rsoil measurement were most important in determining current-day Rsoil under bunchgrasses and shrubs, respectively, indicating a significant lag effect. Endogenous and exogenous controls are critical drivers of Rsoil , but the relative importance and the timescale over which each factor affects Rsoil depends on above-ground vegetation and ecosystem structure characteristics.

Night temperature and source-sink effects on overall growth, cell number and cell size in bell pepper ovaries

BACKGROUND AND AIMS

Ovary swelling, and resultant fruit malformation, in bell pepper flowers is favoured by low night temperature or a high source-sink ratio. However, the interaction between night temperature and source-sink ratio on ovary swelling and the contribution of cell size and cell number to ovary swelling are unknown. The present research examined the interactive effects of night temperature and source-sink ratio on ovary size, cell number and cell size at anthesis in bell pepper flowers.

METHODS

Bell pepper plants were grown in growth chambers at night temperatures of either 20 °C (HNT) or 12 °C (LNT). Within each temperature treatment, plants bore either 0 (non-fruiting) or two developing fruits per plant. Ovary fresh weight, cell size and cell number were measured.

KEY RESULTS

Ovary fresh weights in non-fruiting plants grown at LNT were the largest, while fresh weights were smallest in plants grown at HNT with fruits. In general, mesocarp cell size in ovaries was largest in non-fruiting plants grown at either LNT or HNT and smallest in fruiting plants at HNT. Mesocarp cell number was greater in non-fruiting plants under LNT than in the rest of the night temperature/fruiting treatments. These responses were more marked in ovaries sampled after 18 d of treatment compared with those sampled after 40 d of treatment.

CONCLUSIONS

Ovary fresh weight of flowers at anthesis increased 65 % in non-fruiting plants grown under LNT compared with fruiting plants grown under HNT. This increase was due primarily to increases in mesocarp cell number and size. These results indicate that the combined effects of LNT and high source-sink ratio on ovary swelling are additive. Furthermore, the combined effects of LNT and low source-sink ratio or HNT and high source-sink ratio can partially overcome the detrimental effects of LNT and high source-sink ratio.

Rangeomorphs, Thectardis (Porifera?) and dissolved organic carbon in the Ediacaran oceans

The mid-Ediacaran Mistaken Point biota of Newfoundland represents the first morphologically complex organisms in the fossil record. At the classic Mistaken Point localities the biota is dominated by the enigmatic group of "fractally" branching organisms called rangeomorphs. One of the few exceptions to the rangeomorph body plan is the fossil Thectardis avalonensis, which has been reconstructed as an upright, open cone with its apex in the sediment. No biological affinity has been suggested for this fossil, but here we show that its body plan is consistent with the hydrodynamics of the sponge water-canal system. Further, given the habitat of Thectardis beneath the photic zone, and the apparent absence of an archenteron, movement, or a fractally designed body plan, we suggest that it is a sponge. The recognition of sponges in the Mistaken Point biota provides some of the earliest body fossil evidence for this group, which must have ranged through the Ediacaran based on biomarkers, molecular clocks, and their position on the metazoan tree of life, in spite of their sparse macroscopic fossil record. Should our interpretation be correct, it would imply that the paleoecology of the Mistaken Point biota was dominated by sponges and rangeomorphs, organisms that are either known or hypothesized to feed in large part on dissolved organic carbon (DOC). The biology of these two clades gives insight into the structure of the Ediacaran ocean, and indicates that a non-uniformitarian mechanism delivered labile DOC to the Mistaken Point seafloor.

You can get there from here: acetone, anionic ketones and even-carbon fatty acids can provide substrates for gluconeogenesis

Although the literature contains studies published more than 30 years ago showing that acetone is not metabolically inert, it is common to find biochemistry textbooks and current research publications asserting that acetone is a 'dead-end' metabolite. In fact, acetone derived from the non-enzymatic breakdown of acetoacetate in ketotic individuals or from the oxidation of ingested isopropanol can be metabolized to D-lactate and pyruvate, and ultimately glucose. This report describes the reactions and pathways that account for the metabolism of acetone in humans.

Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests

*Here, species composition and biomass production of actively growing ectomycorrhizal (EM) mycelia were studied over the rotation period of managed Norway spruce (Picea abies) stands in south-western Sweden. *The EM mycelia were collected using ingrowth mesh bags incubated in the forest soil during one growing season. Fungal biomass was estimated by ergosterol analysis and the EM species were identified by 454 sequencing of internal transcribed spacer (ITS) amplicons. Nutrient availability and the fungal biomass in soil samples were also estimated. *Biomass production peaked in young stands (10-30 yr old) before the first thinning phase. Tylospora fibrillosa dominated the EM community, especially in these young stands, where it constituted 80% of the EM amplicons derived from the mesh bags. Species richness increased in older stands. *The establishment of EM mycelial networks in young Norway spruce stands requires large amounts of carbon, while much less is needed to sustain the EM community in older stands. The variation in EM biomass production over the rotation period has implications for carbon sequestration rates in forest soils.

Re-assessment of plant carbon dynamics at the Duke free-air CO(2) enrichment site: interactions of atmospheric [CO(2)] with nitrogen and water availability over stand development

*The potential for elevated [CO(2)]-induced changes to plant carbon (C) storage, through modifications in plant production and allocation of C among plant pools, is an important source of uncertainty when predicting future forest function. Utilizing 10 yr of data from the Duke free-air CO(2) enrichment site, we evaluated the dynamics and distribution of plant C. *Discrepancy between heights measured for this study and previously calculated heights required revision of earlier allometrically based biomass determinations, resulting in higher (up to 50%) estimates of standing biomass and net primary productivity than previous assessments. *Generally, elevated [CO(2)] caused sustained increases in plant biomass production and in standing C, but did not affect the partitioning of C among plant biomass pools. Spatial variation in net primary productivity and its [CO(2)]-induced enhancement was controlled primarily by N availability, with the difference between precipitation and potential evapotranspiration explaining most interannual variability. Consequently, [CO(2)]-induced net primary productivity enhancement ranged from 22 to 30% in different plots and years. *Through quantifying the effects of nutrient and water availability on the forest productivity response to elevated [CO(2)], we show that net primary productivity enhancement by elevated [CO(2)] is not uniform, but rather highly dependent on the availability of other growth resources.

Role of transitory carbon reserves during adjustment to climate variability and source-sink imbalances in oil palm (Elaeis guineensis)

Oil palm (Elaeis guineensis Jacq.) is a perennial, tropical, monocotyledonous plant characterized by simple architecture and low phenotypic plasticity, but marked by long development cycles of individual phytomers (a pair of one leaf and one inflorescence at its axil). Environmental effects on vegetative or reproductive sinks occur with various time lags depending on the process affected, causing source-sink imbalances. This study investigated how the two instantaneous sources of carbon assimilates, CO(2) assimilation and mobilization of transitory non-structural carbohydrate (NSC) reserves, may buffer such imbalances. An experiment was conducted in Indonesia during a 22-month period (from July 2006 to May 2008) at two contrasting locations (Kandista and Batu Mulia) using two treatments (control and complete fruit pruning treatment) in Kandista. Measurements included leaf gas exchange, dynamics of NSC reserves and dynamics of structural aboveground vegetative growth (SVG) and reproductive growth. Drought was estimated from a simulated fraction of transpirable soil water. The main sources of variation in source-sink relationships were (i) short-term reductions in light-saturated leaf CO(2) assimilation rate (A(max)) during seasonal drought periods, particularly in Batu Mulia; (ii) rapid responses of SVG rate to drought; and (iii) marked lag periods between 16 and 29 months of environmental effects on the development of reproductive sinks. The resulting source-sink imbalances were buffered by fluctuations in NSC reserves in the stem, which mainly consisted of glucose and starch. Starch was the main buffer for sink variations, whereas glucose dynamics remained unexplained. Even under strong sink limitation, no negative feedback on A(max) was observed. In conclusion, the different lag periods for environmental effects on assimilate sources and sinks in oil palm are mainly buffered by NSC accumulation in the stem, which can attain 50% (dw:dw) in stem tops. The resulting dynamics of growth and production are complex because several dozen phytomers of different phenological ages develop at any given time and interact with a common pool of reserves.

Fog interception by Sequoia sempervirens (D. Don) crowns decouples physiology from soil water deficit

Although crown wetting events can increase plant water status, leaf wetting is thought to negatively affect plant carbon balance by depressing photosynthesis and growth. We investigated the influence of crown fog interception on the water and carbon relations of juvenile and mature Sequoia sempervirens trees. Field observations of mature trees indicated that fog interception increased leaf water potential above that of leaves sheltered from fog. Furthermore, observed increases in leaf water potential exceeded the maximum water potential predicted if soil water was the only available water source. Because field observations were limited to two mature trees, we conducted a greenhouse experiment to investigate how fog interception influences plant water status and photosynthesis. Pre-dawn and midday branchlet water potential, leaf gas exchange and chlorophyll fluorescence were measured on S. sempervirens saplings exposed to increasing soil water deficit, with and without overnight canopy fog interception. Sapling fog interception increased leaf water potential and photosynthesis above the control and soil water deficit treatments despite similar dark-acclimated leaf chlorophyll fluorescence. The field observations and greenhouse experiment show that fog interception represents an overlooked flux into the soil-plant-atmosphere continuum that temporarily, but significantly, decouples leaf-level water and carbon relations from soil water availability.

Coppicing shifts CO2 stimulation of poplar productivity to above-ground pools: a synthesis of leaf to stand level results from the POP/EUROFACE experiment

A poplar short rotation coppice (SRC) grown for the production of bioenergy can combine carbon (C) storage with fossil fuel substitution. Here, we summarize the responses of a poplar (Populus) plantation to 6 yr of free air CO(2) enrichment (POP/EUROFACE consisting of two rotation cycles). We show that a poplar plantation growing in nonlimiting light, nutrient and water conditions will significantly increase its productivity in elevated CO(2) concentrations ([CO(2)]). Increased biomass yield resulted from an early growth enhancement and photosynthesis did not acclimate to elevated [CO(2)]. Sufficient nutrient availability, increased nitrogen use efficiency (NUE) and the large sink capacity of poplars contributed to the sustained increase in C uptake over 6 yr. Additional C taken up in high [CO(2)] was mainly invested into woody biomass pools. Coppicing increased yield by 66% and partly shifted the extra C uptake in elevated [CO(2)] to above-ground pools, as fine root biomass declined and its [CO(2)] stimulation disappeared. Mineral soil C increased equally in ambient and elevated [CO(2)] during the 6 yr experiment. However, elevated [CO(2)] increased the stabilization of C in the mineral soil. Increased productivity of a poplar SRC in elevated [CO(2)] may allow shorter rotation cycles, enhancing the viability of SRC for biofuel production.

Plant species, atmospheric CO2 and soil N interactively or additively control C allocation within plant-soil systems

Two plant species, Medicago truncatula (legume) and Avena sativa (non-legume), were grown in low- or high-N soils under two CO2 concentrations to test the hypothesis whether C allocation within plant-soil system is interactively or additively controlled by soil N and atmospheric CO2 is dependent upon plant species. The results showed the interaction between plant species and soil N had a significant impact on microbial activity and plant growth. The interaction between CO2 and soil N had a significant impact on soil soluble C and soil microbial biomass C under Madicago but not under Avena. Although both CO2 and soil N affected plant growth significantly, there was no interaction between CO2 and soil N on plant growth. In other words, the effects of CO2 and soil N on plant growth were additive. We considered that the interaction between N2 fixation trait of legume plant and elevated CO2 might have obscured the interaction between soil N and elevated CO2 on the growth of legume plant. In low-N soil, the shoot-to-root ratio of Avena dropped from 2.63 +/- 0.20 in the early growth stage to 1.47 +/- 0.03 in the late growth stage, indicating that Avena plant allocated more energy to roots to optimize nutrient uptake (i.e. N) when soil N was limiting. In high-N soil, the shoot-to-root ratio of Medicago increased significantly over time (from 2.45 +/- 0.30 to 5.43 +/- 0.10), suggesting that Medicago plants allocated more energy to shoots to optimize photosynthesis when N was not limiting. The shoot-to-root ratios were not significantly different between two CO2 levels.

Terrestrial carbon and intraspecific size-variation shape lake ecosystems

Conceptual models of lake ecosystem structure and function have generally assumed that energy in pelagic systems is derived from in situ photosynthesis and that its use by higher trophic levels depends on the average properties of individuals in consumer populations. These views are challenged by evidence that allochthonous subsidies of organic carbon greatly influence energy mobilization and transfer and the trophic structure of pelagic food webs, and that size variation within consumer species has major ramifications for lake community dynamics and structure. These discoveries represent conceptual shifts that have yet to be integrated into current views on lake ecosystems. Here, we assess key aspects of energy mobilization and size-structured community dynamics, and show how these processes are intertwined in pelagic food webs.

Effects of Carbohydrate Accumulation on Photosynthesis Differ between Sink and Source Leaves of Phaseolus vulgaris L

Accumulation of non-structural carbohydrate in leaves represses photosynthesis. However, the extent of repression should be different between sink leaves (sugar consumers) and source leaves (sugar exporters). We investigated the effects of carbohydrate accumulation on photosynthesis in the primary leaves of bean (Phaseolus vulgaris L.) during leaf expansion. To increase the carbohydrate content of the leaves, we supplied 20 mM sucrose solution to the roots for 5 d (sugar treatment). Plants supplied only with water and nutrients were used as controls. The carbohydrate contents, which are the sum of glucose, sucrose and starch, of the sugar-treated leaves were 1.5-3 times of those of the control leaves at all developmental stages. In the young sink leaves, the photosynthetic rate at saturating light and at an ambient CO2 concentration (A360) did not differ between the sugar-treated and control leaves. The A360 of sugar-treated source leaves gradually decreased relative to the control source leaves with leaf expansion. The initial slope of the A-Ci (CO2 concentration in the intercellular space) curve, and the Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) content per leaf area showed trends similar to that of A360. Differences in Amax between the treatments were slightly smaller than those in A360. These results indicate that the effect of carbohydrate accumulation on photosynthesis is significant in the source leaves, but not in the young sink leaves, and that the decrease in Rubisco content was the main cause of the carbohydrate repression of photosynthesis.

Nutritional requirements of mycelial growth of Cordyceps sinensis in submerged culture

AIMS

The nutritional requirements for mycelial growth of Cordyceps sinensis in semi-synthetic liquid media were investigated. The results provide a basis for further physiological study and industrial fermentation of the fungus.

METHODS AND RESULTS

Nutritional requirements, including 17 carbohydrates, 16 nitrogen compounds, nine vitamins, four macro-elements, four trace-elements and eight ratios of carbon to nitrogen, were studied for their effects on the mycelial growth in submerged cultures of C. sinensis by using one-factor-at-a-time and orthogonal matrix methods. Among these variables, sucrose, peptone, folic acid, calcium, zinc and a carbon to nitrogen ratio 12 : 1 were identified as the requirements for the optimum mycelial growth. The concentrations of sucrose, peptone and yeast extract were optimized and the effects of medium composition on mycelial growth were found to be in the order sucrose > yeast extract > peptone. The optimal concentration for mycelial growth was determined as 50 g l(-1) sucrose, 10 g l(-1) peptone and 3 g l(-1) yeast extract.

CONCLUSIONS

Under optimal culture conditions, over 22 g l(-1) of mycelial biomass could be obtained after 40 days in submerged cultures.

SIGNIFICANCE AND IMPACT OF THE STUDY

Cordyceps sinensis, one of the most valued medicinal fungi, is shown to grow in axenic culture. This is the first report on nutritional requirements and design of a simplified semi-synthetic medium for mycelial growth of this psychrophilic species, which grows slowly below 20 degrees C. The results of this study will facilitate research on mass production of the fungus under defined culture conditions.

Woody debris contribution to the carbon budget of selectively logged and maturing mid-latitude forests

Woody debris (WD) is an important component of forest C budgets, both as a C reservoir and source of CO2 to the atmosphere. We used an infrared gas analyzer and closed dynamic chamber to measure CO(2) efflux from downed coarse WD (CWD; diameter>or=7.5 cm) and fine WD (FWD; 7.5 cm>diameter>or=2 cm) to assess respiration in a selectively logged forest and a maturing forest (control site) in the northeastern USA. We developed two linear regression models to predict WD respiration: one based on WD temperature, moisture, and size (R2=0.57), and the other on decay class and air temperature (R2=0.32). WD respiration (0.28+/-0.09 Mg C ha-1 year-1) contributed only approximately 2% of total ecosystem respiration (12.3+/-0.7 Mg C ha-1 year-1, 1999-2003), but net C flux from CWD accounted for up to 30% of net ecosystem exchange in the maturing forest. C flux from CWD on the logged site increased modestly, from 0.61+/-0.29 Mg C ha-1 year-1 prior to logging to 0.77+/-0.23 Mg C ha-1 year-1 after logging, reflecting increased CWD stocks. FWD biomass and associated respiration flux were approximately 7 times and approximately 5 times greater, respectively, in the logged site than the control site. The net C flux associated with CWD, including inputs and respiratory outputs, was 0.35+/-0.19 Mg C ha-1 year-1 (net C sink) in the control site and -0.30+/-0.30 Mg C ha-1 year-1 (net C source) in the logged site. We infer that accumulation of WD may represent a small net C sink in maturing northern hardwood forests. Disturbance, such as selective logging, can enlarge the WD pool, increasing the net C flux from the WD pool to the atmosphere and potentially causing it to become a net C source.

Intra-annual radial growth and water relations of trees: implications towards a growth mechanism

There is a missing link between tree physiological and wood-anatomical knowledge which makes it impossible mechanistically to explain and predict the radial growth of individual trees from climate data. Empirical data of microclimatic factors, intra-annual growth rates, and tree-specific ratios between actual and potential transpiration (T PET(-1)) of trees of three species (Quercus pubescens, Pinus sylvestris, and Picea abies) at two dry sites in the central Wallis, Switzerland, were recorded from 2002 to 2004 at a 10 min resolution. This included the exceptionally hot and dry summer of 2003. These data were analysed in terms of direct (current conditions) and indirect impacts (predispositions of the past year) on growth. Rain was found to be the only factor which, to a large extent, consistently explained the radial increment for all three tree species at both sites and in the short term as well. Other factors had some explanatory power on the seasonal time-scale only. Quercus pubescens built up much of its tree ring before bud break. Pinus sylvestris and Picea abies started radial growth 1-2 weeks after Quercus pubescens and this was despite the fact that they had a high T PET(-1) before budburst and radial growth started. A high T PET(-1) was assumed to be related to open stomata, a very high net CO2 assimilation rate, and thus a potential carbon (C)-income for the tree. The main period of radial growth covered about 30-70% of the productive days of a year. In terms of C-allocation, these results mean that Quercus pubescens depended entirely on internal C-stores in the early phase of radial growth and that for all three species there was a long time period of C-assimilation which was not used for radial growth in above-ground wood. The results further suggest a strong dependence of radial growth on the current tree water relations and only secondarily on the C-balance. A concept is discussed which links radial growth over a feedback loop to actual tree water-relations and long-term affected C-storage to microclimate.

TEMPERATURE INFLUENCES CARBON ACCUMULATION IN MOIST TROPICAL FORESTS

Evergreen broad-leaved tropical forests can have high rates of productivity and large accumulations of carbon in plant biomass and soils. They can therefore play an important role in the global carbon cycle, influencing atmospheric CO2 concentrations if climate warms. We applied meta-analyses to published data to evaluate the apparent effects of temperature on carbon fluxes and storages in mature, moist tropical evergreen forest ecosystems. Among forests, litter production, tree growth, and belowground carbon allocation all increased significantly with site mean annual temperature (MAT); total net primary productivity (NPP) increased by an estimated 0.2-0.7 Mg C x ha(-1) x yr(-1) x degrees C(-1). Temperature had no discernible effect on the turnover rate of aboveground forest biomass, which averaged 0.014 yr(-1) among sites. Consistent with these findings, forest biomass increased with site MAT at a rate of 5-13 Mg C x ha(-1) x degrees C(-1). Despite greater productivity in warmer forests, soil organic matter accumulations decreased with site MAT, with a slope of -8 Mg C x ha(-1) x degrees C(-1), indicating that decomposition rates of soil organic matter increased with MAT faster than did rates of NPP. Turnover rates of surface litter also increased with temperature among forests. We found no detectable effect of temperature on total carbon storage among moist-tropical evergreen forests, but rather a shift in ecosystem structure, from low-biomass forests with relatively large accumulations of detritus in cooler sites, to large-biomass forests with relatively smaller detrital stocks in warmer locations. These results imply that, in a warmer climate, conservation of forest biomass will be critical to the maintenance of carbon stocks in moist tropical forests.

Genome-wide analysis of differentially expressed genes from Penicillium chrysogenum grown with a repressing or a non-repressing carbon source

Penicillium chrysogenum is an economically important ascomycete used as industrial producer of penicillin. However, with the exception of penicillin biosynthesis genes, little attention has been paid to the genetics of other aspects of the metabolism of this fungus. In this article we describe the first attempt of systematic analysis of expressed genes in P. chrysogenum, using a suppression subtractive hybridization approach to clone and identify sequences of genes differentially expressed in media with glucose or lactose as carbon source (penicillin-repressing or non-repressing conditions). A total of 167 clones were analysed, 95 from the glucose condition and 72 from the lactose condition. Genes differentially expressed in the glucose condition encode mainly proteins involved in the mitochondrial electron transport chain and primary metabolism. Genes expressed differentially in lactose-containing medium include genes for secondary metabolism (pcbC, isopenicillin N synthase), different hydrolases and a gene encoding a putative hexose transporter or sensor. The results provided information on how the metabolism of this fungus adapts to different carbon sources. The expression patterns of some of the genes support the hypothesis that glucose induces higher rates of respiration in P. chrysogenum while repressing secondary metabolism.

Sex allocation of a cosexual wind-pollinated tree, Quercus dentata, in terms of four currencies

Sex allocation of a cosexual wind-pollinated species, Quercus dentata (Fagaceae), was analyzed using biomass, carbon, nitrogen and phosphorus as currencies based on data accumulated for 61 individuals from 1997-2004. Strongly female-biased sex allocation was indicated when measured in terms of biomass and carbon, but no significant bias was detected when measured in terms of nitrogen or phosphorus. From an adaptive viewpoint, there is little support for strong female-biased sex allocation, suggesting that sex allocation in terms of nitrogen or phosphorus is closer to the real picture. The relative sex allocation considerably varied from year to year, but the relative femaleness of individuals in the population was rather constant across years. No significant correlation was observed between relative sex allocation and fecundity or tree height, but individuals that showed very low fecundity tended to produce only acorns.

Identification and expression analysis of two inorganic C- and N-responsive genes encoding novel and distinct molecular forms of eukaryotic phosphoenolpyruvate carboxylase in the green microalga Chlamydomonas reinhardtii

Phosphoenolpyruvate carboxylase (PEPC [Ppc]) has been previously purified and characterized in biochemical and immunological terms from two green microalgae, Chlamydomonas reinhardtii and Selenastrum minutum. The findings indicate that these algae possess at least two distinct PEPC enzyme-forms, homotetrameric Class-1 and heteromeric Class-2, that differ significantly from each other and their plant and prokaryotic counterparts. Surprisingly, however, green-algal PEPC has been unexplored to date in molecular terms. This study reports the molecular cloning of the two Ppc genes in C. reinhardtii (CrPpc1, CrPpc2), each of which is transcribed in vivo and encodes a fully active, recombinant PEPC that lacks the regulatory, N-terminal seryl-phosphorylation domain that typifies the vascular-plant enzyme. These distinct catalytic subunit-types differ with respect to their (i) predicted molecular mass ( approximately 108.9 [CrPpc1] versus approximately 131.2 kDa [CrPpc2]) and critical C-terminal tetrapeptide; and (ii) immunoreactivity with antisera against the p102 and p130 polypeptides of S. minutum PEPC1/PEPC2 and PEPC2, respectively. Only the Ppc1 transcript encodes the p102 catalytic subunits common to both Class-1 and Class-2 enzyme-forms in C. reinhardtii. The steady-state transcript levels of both CrPpc1/2 are coordinately up-/down-regulated by changes in [CO2] or [NH] during growth, and generally mirror the response of cytoplasmic glutamine synthetase (Gs1) transcript abundance to changes in inorganic [N] at 5% CO2. These collective findings provide key molecular insight into the Ppc genes and corresponding PEPC catalytic subunits in the eukaryotic algae.

The role of alternative oxidase in modulating carbon use efficiency and growth during macronutrient stress in tobacco cells

When wild-type (wt) tobacco (Nicotiana tabacum cv. Petit Havana SR1) cells are grown under macronutrient (P or N) limitation, they induce large amounts of alternative oxidase (AOX), which constitutes a non-energy-conserving branch of the respiratory electron transport chain. To investigate the significance of AOX induction, wt cells were compared with transgenic (AS8) cells lacking AOX. Under nutrient limitation, growth of wt cell cultures was dramatically reduced and carbon use efficiency (g cell dry weight gain g(-1) sugar consumed) decreased by 42-63%. However, the growth of AS8 was only moderately reduced by the nutrient deficiencies and carbon use efficiency values remained the same as under nutrient-sufficient conditions. As a result, the nutrient limitations more severely compromised the tissue nutrient status (P or N) of AS8 than wt cells. Northern analyses and a comparison of the mitochondrial protein profiles of wt and AS8 cells indicated that the lack of AOX in AS8 under P limitation was associated with increased levels of proteins commonly associated with oxidative stress and/or stress injury. Also, the level of electron transport chain components was consistently reduced in AS8 while tricarboxylic acid cycle enzymes did not show a universal trend in abundance in comparison to the wt. Alternatively, the lack of AOX in AS8 cells under N limitation resulted in enhanced carbohydrate accumulation. It is concluded that AOX respiration provides an important general mechanism by which plant cells can modulate their growth in response to nutrient availability and that AOX also has nutrient-specific roles in maintaining cellular redox and carbon balance.

The gene NCE103 (YNL036w) from Saccharomyces cerevisiae encodes a functional carbonic anhydrase and its transcription is regulated by the concentration of inorganic carbon in the medium

Carbonic anhydrase (CA) catalyses the rapid interconversion between CO(2) and HCO(3) (-). Despite its wide distribution among living organisms, the presence of CA in fungi has been controversially discussed. Using mass spectrometric analysis of (18)O exchange from doubly labelled CO(2), we were able to measure CA activity in intact cells of Saccharomyces cerevisiae. Intracellular CA activity was lacking in the Deltance103 mutant, indicating that NCE103 encodes a functional CA. This was proven by overexpressing and purification of the NCE103 gene product showing a specific activity of around 6900 units per mg protein. Interestingly, the in vivo CA activity was 10-20 times higher in cells grown on low inorganic carbon (Ci; air containing 0.035% CO(2)) than in high-Ci cells (grown on 5% CO(2)). The enhanced CA activity of low-Ci cells was inducible after transferring high-Ci cells to air. Northern blot analysis revealed that that expression of NCE103 is transcriptionally regulated by low Ci which was also demonstrated by fusing the NCE103 promoter to beta-galactosidase as a reporter gene. Inactivation of NCE103 results in a high CO(2) requiring mutant indicating that a functional CA is an important prerequisite for S. cerevisiae to grow under low-Ci conditions.

Nutrient and temperature limitation of bacterioplankton growth in temperate lakes

Limitation of bacterioplankton production by nutrients and temperature was investigated in eight temperate lakes in summer. Six of the lakes were resampled in autumn. The lakes differ in nutrient content, water color, and concentration of dissolved organic carbon. Nutrients (phosphorus, nitrogen, and organic carbon) were added alone and in all possible combinations to filtered lake water inoculated with bacteria from the lake. After incubation for 36-40 h at in situ temperatures (ranging from 7 to 20 degrees C), the response in bacterioplankton production was determined. The effect of increased temperature on bacterioplankton growth was also tested. Bacterioplankton production was often limited by phosphorus alone, organic carbon alone, or the two in combination. Phosphorus limitation of bacterioplankton production was more common in the summer, whereas limitation by organic carbon was more frequently observed in the autumn. There was a close balance between limitation by phosphorus and organic carbon in the epilimnion in the summer. In the hypolimnion in the summer, bacterioplankton growth was primarily phosphorus-limited. The effect of phosphorus additions decreased with increasing phosphorus concentrations in the lakes. However, there were no correlations between the effect of added organic carbon and water color, dissolved organic carbon concentration, or phosphorus concentration. When temperature was low (in the hypolimnion in the summer, and throughout the water column in the autumn) temperature also limited bacterioplankton production. Thus, temperature and inorganic nutrients or organic compounds can limit bacterioplankton growth both alone and simultaneously. However, at low temperatures, temperature is the most important factor influencing bacterioplankton growth.

Analysis of the tomato fruit growth response to temperature and plant fruit load in relation to cell division, cell expansion and DNA endoreduplication

BACKGROUND AND AIMS

To better understand the regulation of fruit growth in response to environmental factors, the effects of temperature and plant fruit load on cell number, cell size and DNA endoreduplication were analysed.

METHODS

Plants were grown at 20/20 degrees C, 25/25 degrees C and 25/20 degrees C day/night temperatures, and inflorescences were pruned to two ('2F') or five ('5F') flowers.

KEY RESULTS AND CONCLUSIONS

Despite a lower fruit growth rate at 20/20 degrees C, temperature did not affect final fruit size because of the compensation between cell number and size. The higher cell number at 20/20 degrees C (9.0 x 10(6) against 7.9 x 10(6) at 25/25 degrees C and 7.7 x 10(6) at 25/20 degrees C) resulted from an extended period of cell division, and the smaller cell size was due to a shorter period of expansion rather than a lower expansion rate. By contrast, the lower fruit growth rate and size of 5F fruits compared with 2F fruits resulted from the slow down of cell expansion, whereas the number of cells was hardly affected in the proximal fruit. However, within the inflorescence the decreasing gradient of fruit size from proximal to distal fruits was due to a decrease in cell number with similar cell size. Fruit size variations within each treatment were always positively correlated to variations in cell number, but not in cell size. Negative correlations between cell size and cell number suggested that cells of tomato pericarp can be seen as a population of competing sinks. Mean ploidy was slightly delayed and reduced in 5F fruits compared with 2F fruits. It was highest at 25/25 degrees C and lowest at 25/20 degrees C. Treatments did not affect ploidy and cell size in similar ways, but within each treatment, positive correlations existed between mean ploidy and cell size, though significant only in the 2F-25/20 treatment.

Dynamic light use and protection from excess light in upper canopy and coppice leaves of Nothofagus cunninghamii in an old growth, cool temperate rainforest in Victoria, Australia

Responses to simulated sunflecks were examined in upper canopy and coppice leaves of Nothofagus cunninghamii growing in an old-growth rainforest gully in Victoria, Australia. Shaded leaves were exposed to a sudden increase in irradiance from 20 to 1500 micromol m(-2) s(-1). Gas exchange and chlorophyll fluorescence were measured during a 10 min simulated sunfleck and, in the ensuing dark treatment, we examined the recovery of PS II efficiency and the conversion state of xanthophyll cycle pigments. Photosynthetic induction was rapid compared with tropical and northern hemisphere species. Stomatal conductance was relatively high in the shade and stomata did not directly control photosynthetic induction under these conditions. During simulated sunflecks, zeaxanthin was formed rapidly and photochemical efficiency was reduced. These processes were reversed within 30 min in coppice leaves, but this took longer in upper canopy leaves. Poor drought tolerance and achieving a positive carbon balance in a shaded canopy may be functionally related to high stomatal conductance in the shade in N. cunninghamii. The more persistent reduction in photochemical efficiency of upper canopy leaves, which means less efficient light use in subsequent shade periods, but stronger protection from high light, may be related to the generally higher irradiance and longer duration of sunflecks in the upper canopy, but potentially reduces carbon gain during shade periods by 30%.

Experimental analysis of the role of water and carbon in tree stem diameter variations

The variations of stem diameter as they can be accurately measured by Linear Variable Differential Transformer (LVDT) reflect the addition of four components: irreversible radial growth, reversible living-cell dehydration/rehydration, thermal expansion and contraction, and expansion of dead conducting elements due to the increase and relaxation of internal tensions. The correct interpretation of LVDT signals, with respect to the practical applications, should make an exact distinction between these four components. This paper describes a set of two experiments with potted hybrid walnut trees. Double girdling, water stress, and duration of the day versus night periods were used in the phytotron as experimental factors to induce variations of the carbon and water status of plant tissues. The latter were assessed, respectively, by water potential and transpiration, and by local stem respiration and carbohydrate content. The results are interpreted in terms of carbon or water limitation effects on stem diameter variations where radial growth and tissue elasticity could be distinguished. Moreover, they suggest no or very low involvement of CO2 originating from a distance, i.e. carried by the transpirational flux of xylem sap, in the total stem CO2 efflux rate.

The sources of carbon and nitrogen supplying leaf growth. Assessment of the role of stores with compartmental models

Patterns of synthesis and breakdown of carbon (C) and nitrogen (N) stores are relatively well known. But the role of mobilized stores as substrates for growth remains less clear. In this article, a novel approach to estimate C and N import into leaf growth zones was coupled with steady-state labeling of photosynthesis ((13)CO(2)/(12)CO(2)) and N uptake ((15)NO(3)(-)/(14)NO(3)(-)) and compartmental modeling of tracer fluxes. The contributions of current C assimilation/N uptake and mobilization from stores to the substrate pool supplying leaf growth were then quantified in plants of a C(3) (Lolium perenne) and C(4) grass (Paspalum dilatatum Poir.) manipulated thus to have contrasting C assimilation and N uptake rates. In all cases, leaf growth relied largely on photoassimilates delivered either directly after fixation or short-term storage (turnover rate = 1.6-3.3 d(-1)). Long-term C stores (turnover rate < 0.09 d(-1)) were generally of limited relevance. Hence, no link was found between the role of stores and C acquisition rate. Short-term (turnover rate = 0.29-0.90 d(-1)) and long-term (turnover rate < 0.04 d(-1)) stores supplied most N used in leaf growth. Compared to dominant (well-lit) plants, subordinate (shaded) plants relied more on mobilization from long-term N stores to support leaf growth. These differences correlated well with the C-to-N ratio of growth substrates and were associated with responses in N uptake. Based on this, we argue that internal regulation of N uptake acts as a main determinant of the importance of mobilized long-term stores as a source of N for leaf growth.

Influence of carbon and nitrogen sources and temperature on hyperproduction of a thermotolerant beta-glucosidase from synthetic medium by Kluyveromyces marxianus

The effect of carbon source and its concentration, inoculum size, yeast extract concentration, nitrogen source, pH of the fermentation medium, and fermentation temperature on beta-glucosidase production by Kluyveromyces marxianus in shake-flask culture was investigated. These were the independent variables that directly regulated the specific growth and beta-glucosidase production rate. The highest product yield, specific product yield, and productivity of beta-glucosidase occurred in the medium (pH 5.5) inoculated with 10% (v/v) inoculum of the culture. Cellobiose (20 g/L) significantly improved beta-glucosidase production measured as product yield (YP/S) and volumetric productivity (QP) followed by sucrose, lactose, and xylose. The highest levels of productivity (144 IU/[L.h]) of beta-glucosidase occurred on cellobiose in the presence of CSL at 35 degrees C and are significantly higher than the values reported by other researchers on almost all other organisms. The thermodynamics and kinetics of beta-glucosidase production and its deactivation are also reported. The enzyme was substantially stable at 60 degrees C and may find application in some industrial processes.

[Contact phase activation can occur with certain types of activated carbon]

HFR is an integrated hemodiafiltration system that utilizes a double chamber filter to separate convection from diffusion. The ultrafiltrate is regenerated by passage through a sorbent cartridge made up of resin and activated carbon. A small percentage of patients using this technique had gastrointestinal symptoms that included nausea/vomiting, diarrhea and/or stomach cramps approximately 1-2 hours after the start of HFR. We undertook a series of investigations to try and elucidate the cause of these reactions. Since the majority of the patients were taking ACE inhibitors, attention was focused on contact phase activation. Healthy and uremic plasma were incubated with different components of the HFR circuit. The activated carbon caused a moderate activation of factor XII and production of kallikrein, while there was no activation for the lines, double filter or resin. Patients taking ACE inhibitors may be at risk for treatments involved with contact phase activation as ACE inhibitors also block the degradation of bradykinin. A new sorbent cartridge has now been developed that contains only resin.

Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants

Microarray analysis and the 'InterAct class' method were used to study interactions between carbon and nitrogen signaling in Arabidopsis.

Background

Carbon and nitrogen are two signals that influence plant growth and development. It is known that carbon- and nitrogen-signaling pathways influence one another to affect gene expression, but little is known about which genes are regulated by interactions between carbon and nitrogen signaling or the mechanisms by which the different pathways interact.

Results

Microarray analysis was used to study global changes in mRNA levels due to carbon and nitrogen in Arabidopsis thaliana. An informatic analysis using InterAct Class enabled us to classify genes on the basis of their responses to carbon or nitrogen treatments. This analysis provides in vivo evidence supporting the hypothesis that plants have a carbon/nitrogen (CN)-sensing/regulatory mechanism, as we have identified over 300 genes whose response to combined CN treatment is different from that expected from expression values due to carbon and nitrogen treatments separately. Metabolism, energy and protein synthesis were found to be significantly affected by interactions between carbon and nitrogen signaling. Identified putative cis-acting regulatory elements involved in mediating CN-responsive gene expression suggest multiple mechanisms for CN responsiveness. One mechanism invokes the existence of a single CN-responsive cis element, while another invokes the existence of cis elements that promote nitrogen-responsive gene expression only when present in combination with a carbon-responsive cis element.

Conclusion

This study has allowed us to identify genes and processes regulated by interactions between carbon and nitrogen signaling and take a first step in uncovering how carbon- and nitrogen-signaling pathways interact to regulate transcription.

Soil water content and organic carbon availability are major determinants of soil microbial community composition

Exploration of environmental factors governing soil microbial community composition is long overdue and now possible with improved methods for characterizing microbial communities. Previously, we observed that rice soil microbial communities were distinctly different from tomato soil microbial communities, despite management and seasonal variations within soil type. Potential contributing factors included types and amounts of organic inputs, organic carbon content, and timing and amounts of water inputs. Of these, both soil water content and organic carbon availability were highly correlated with observed differences in composition. We examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of phospholipid fatty acid data, we determined flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Although flooding without organic carbon addition influenced composition some, organic carbon addition was necessary to substantially alter community composition. Organic carbon availability had the same general effects on microbial communities regardless of whether it was compost or vetch in origin. In addition, flooded samples, regardless of organic carbon inputs, had significantly lower ratios of fungal to bacterial biomarkers, whereas under drier conditions and increased organic carbon availability the microbial communities had higher proportions of fungal biomass. When comparing field and microcosm soil, flooded +C microcosm samples were most similar to field-collected rice soil, whereas all other treatments were more similar to field-collected tomato soil. Overall, manipulating water and carbon content selected for microbial communities similar to those observed when the same factors were manipulated at the field scale.

Precipitation pulses and carbon fluxes in semiarid and arid ecosystems

In the arid and semiarid regions of North America, discrete precipitation pulses are important triggers for biological activity. The timing and magnitude of these pulses may differentially affect the activity of plants and microbes, combining to influence the C balance of desert ecosystems. Here, we evaluate how a "pulse" of water influences physiological activity in plants, soils and ecosystems, and how characteristics, such as precipitation pulse size and frequency are important controllers of biological and physical processes in arid land ecosystems. We show that pulse size regulates C balance by determining the temporal duration of activity for different components of the biota. Microbial respiration responds to very small events, but the relationship between pulse size and duration of activity likely saturates at moderate event sizes. Photosynthetic activity of vascular plants generally increases following relatively larger pulses or a series of small pulses. In this case, the duration of physiological activity is an increasing function of pulse size up to events that are infrequent in these hydroclimatological regions. This differential responsiveness of photosynthesis and respiration results in arid ecosystems acting as immediate C sources to the atmosphere following rainfall, with subsequent periods of C accumulation should pulse size be sufficient to initiate vascular plant activity. Using the average pulse size distributions in the North American deserts, a simple modeling exercise shows that net ecosystem exchange of CO2 is sensitive to changes in the event size distribution representative of wet and dry years. An important regulator of the pulse response is initial soil and canopy conditions and the physical structuring of bare soil and beneath canopy patches on the landscape. Initial condition influences responses to pulses of varying magnitude, while bare soil/beneath canopy patches interact to introduce nonlinearity in the relationship between pulse size and soil water response. Building on this conceptual framework and developing a greater understanding of the complexities of these eco-hydrologic systems may enhance our ability to describe the ecology of desert ecosystems and their sensitivity to global change.

Enrichment and identification of bacteria capable of reducing chemical oxygen demand of anaerobically treated molasses spent wash

AIMS

The aim of this study was to isolate and identify bacterial strains capable of using recalcitrant compounds of molasses spent wash as sole carbon source from the soils of abandoned sites of distillery effluent discharge and characterize their ability of reducing the chemical oxygen demand (COD) of the spent wash.

METHODS AND RESULTS

The isolates were grouped into six haplotypes by amplified ribosomal DNA restriction analysis (ARDRA) and BOX-PCR. The phylogenetic position of the representatives of the six main haplotypes strains was determined by 16S rDNA sequencing. They showed maximum similarity to six genera viz. Pseudomonas, Enterobacter, Stenotrophomonas, Aeromonas, Acinetobacter and Klebsiella. The extent of COD (44%) reduced collectively by the six strains was equal to that reduced individually by Aeromonas, Acinetobacter, Pseudomonas and Enterobacter. With spent wash as sole carbon source, the COD reducing strains grew faster at 37 degrees C than 30 degrees C.

CONCLUSIONS

Bacterial strains capable of degrading some of the recalcitrant compounds of anaerobically digested molasses spent wash can be isolated from the soils of abandoned sites of distillery effluent discharge. Biostimulation of these bacteria, which can degrade 44% of the carbon compounds of anaerobically digested molasses spent wash can be achieved by nitrogen fertilization and relatively higher temperature.

SIGNIFICANCE AND IMPACT OF THE STUDY

Supplementation of nitrogen source and controlling the temperature can be used in evolving strategies for in situ bioremediation of anaerobically digested spent wash from distilleries.

Belowground carbon cycling in a humid tropical forest decreases with fertilization

Only a small fraction of the carbon (C) allocated belowground by trees is retained by soils in long-lived, decay-resistant forms, yet because of the large magnitude of terrestrial primary productivity, even small changes in C allocation or retention can alter terrestrial C storage. The humid tropics exert a disproportionately large influence over terrestrial C storage, but C allocation and belowground retention in these ecosystems remain poorly quantified. Using mass balance and 13C isotope methods, we examined the effects of afforestation and fertilization, two land-use changes of large-scale importance, on belowground C cycling at a humid tropical site in Hawaii. Here we report that in unfertilized plots, 80% of the C allocated belowground by trees to roots and mycorrhizae was returned to the atmosphere within 1 year; 9% of the belowground C flux was retained in coarse roots and 11% was retained as new soil C. The gains in new soil C were offset entirely by losses of old soil C. Further, while fertilization early in stand development increased C storage in the litter layer and in coarse roots, it reduced by 22% the flux of C moving through roots and mycorrhizae into mineral soils. Because soil C formation rates related strongly to rhizosphere C flux, fertilization may reduce an already limited capacity of these forests to sequester decay-resistant soil C.

Seasonal and Artificially Elevated Temperatures Influence Bioenergetic Allocation Patterns in the Common Pond Snail,Physella virgata

Allocation of organic carbon (OC) to primary energetic pathways was estimated under seasonal and artificially elevated ambient temperatures for a field population of a freshwater pulmonate snail, Physella virgata. Allocation to respiration increased with temperature. Snails allocated most assimilated OC to reproduction within their natural temperature range (15 degrees -35 degrees C), where assimilation efficiencies remained relatively stable at 25%-35%. However, in artificially heated waters exceeding 35 degrees C, declining assimilation rates and increasing respiratory demands inhibited allocation to reproduction and growth. At the species' 40 degrees C upper thermal limit, assimilation efficiencies fell below 10%, while average consumption levels more than doubled relative to snails unaffected by the thermal effluent. Ambient temperature substantially influenced OC allocation over P. virgata's natural temperature range and negatively affected growth and reproduction at temperatures approaching or exceeding maximum natural levels.

Effect of different starvation conditions on the flocculation of Saccharomyces cerevisiae

AIMS

To study the effect of different starvation conditions on the flocculation of an ale brewing yeast of Saccharomyces cerevisiae NCYC 1195.

METHODS AND RESULTS

Flocculation was assessed by a micro-flocculation technique (Soares and Mota 1997). Carbon-starved cells of a NewFlo phenotype strain did not lose flocculation during a 48 h period. Cells incubated only in the presence of fermentable carbon sources (glucose, galactose and maltose at 2%, w/v), showed a progressive flocculation loss. The incubation of cells in 4% (v/v) ethanol did not induce a flocculation loss. The simultaneous incubation of cells in the presence of 2% (w/v) glucose and 15 microg ml(-1) cycloheximide hindered flocculation loss. The presence of 0.1 mmol l(-1) PMSF or 10 mmol l-1 EDTA prevented partially or completely, respectively, the loss of flocculation in the presence of glucose.

CONCLUSIONS

Fermentable sugars induced a flocculation loss, which seems to require de novo protein synthesis and the involvement of different proteases.

SIGNIFICANCE AND IMPACT OF THE STUDY

The findings reported here contribute to the elucidation of the role of nutrients on the physiological control of yeast flocculation.

Distinct molecular mechanisms involved in carbon catabolite repression of the arabinose regulon in Bacillus subtilis

The Bacillus subtilis proteins involved in the utilization of L-arabinose are encoded by the araABDLMNPQ-abfA metabolic operon and by the araE/araR divergent unit. Transcription from the ara operon, araE transport gene and araR regulatory gene is induced by L-arabinose and negatively controlled by AraR. Additionally, expression of both the ara operon and the araE gene is regulated at the transcriptional level by glucose repression. Here, by transcriptional fusion analysis in different mutant backgrounds, it is shown that CcpA most probably complexed with HPr-Ser46-P plays the major role in carbon catabolite repression of the ara regulon by glucose and glycerol. Site-directed mutagenesis and deletion analysis indicate that two catabolite responsive elements (cres) present in the ara operon (cre araA and cre araB) and one cre in the araE gene (cre araE) are implicated in this mechanism. Furthermore, cre araA located between the promoter region of the ara operon and the araA gene, and cre araB placed 2 kb downstream within the araB gene are independently functional and both contribute to glucose repression. In Northern blot analysis, in the presence of glucose, a CcpA-dependent transcript consistent with a message stopping at cre araB was detected, suggesting that transcription 'roadblocking' of RNA polymerase elongation is the most likely mechanism operating in this system. Glucose exerts an additional repression of the ara regulon, which requires a functional araR.

Carbon sequestration in Synechococcus Sp.: from molecular machines to hierarchical modeling

The U.S. Department of Energy recently announced the first five grants for the Genomes to Life (GTL) Program. The goal of this program is to "achieve the most far-reaching of all biological goals: a fundamental, comprehensive, and systematic understanding of life." While more information about the program can be found at the GTL website (www.doegenomestolife.org), this paper provides an overview of one of the five GTL projects funded, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling." This project is a combined experimental and computational effort emphasizing developing, prototyping, and applying new computational tools and methods to elucidate the biochemical mechanisms of the carbon sequestration of Synechococcus Sp., an abundant marine cyanobacteria known to play an important role in the global carbon cycle. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO(2) are important terms in the global environmental response to anthropogenic atmospheric inputs of CO(2) and that oceanic microorganisms play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. The project includes five subprojects: an experimental investigation, three computational biology efforts, and a fifth which deals with addressing computational infrastructure challenges of relevance to this project and the Genomes to Life program as a whole. Our experimental effort is designed to provide biology and data to drive the computational efforts and includes significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Our computational efforts include coupling molecular simulation methods with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes and developing a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. Furthermore, given that the ultimate goal of this effort is to develop a systems-level of understanding of how the Synechococcus genome affects carbon fixation at the global scale, we will develop and apply a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, because the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats, we have also established a companion computational infrastructure to support this effort as well as the Genomes to Life program as a whole.

Modeling effects of hydrological changes on the carbon and nitrogen balance of oak in floodplains

We extended the applicability of the ecosystem model BIOME-BGC to floodplain ecosystems to study effects of hydrological changes on Quercus robur L. stands. The extended model assesses floodplain peculiarities, i.e., seasonal flooding and water infiltration from the groundwater table. Our interest was the tradeoff between (a). maintaining regional applicability with respect to available model input information, (b). incorporating the necessary mechanistic detail and (c). keeping the computational effort at an acceptable level. An evaluation based on observed transpiration, timber volume, soil carbon and soil nitrogen content showed that the extended model produced unbiased results. We also investigated the impact of hydrological changes on our oak stands as a result of the completion of an artificial canal network in 1971, which has stopped regular springtime flooding. A comparison of the 11 years before versus the 11 years after 1971 demonstrated that the hydrological changes affected mainly the annual variation across years in leaf area index (LAI) and soil carbon and nitrogen sequestration, leading to stagnation of carbon and nitrogen stocks, but to an increase in the variance across years. However, carbon sequestration to timber was unaffected and exhibited no significant change in cross-year variation. Finally, we investigated how drawdown of the water table, a general problem in the region, affects modeled ecosystem behavior. We found a further amplification of cross-year LAI fluctuations, but the variance in soil carbon and nitrogen stocks decreased. Volume increment was unaffected, suggesting a stabilization of the ecosystem two decades after implementation of water management measures.

Carbon acquisition and water use in a Northern Utah Juniperus osteosperma (Utah juniper) population

Water use and carbon acquisition were examined in a northern Utah population of Juniperus osteosperma (Torr.) Little. Leaf-level carbon assimilation, which was greatest in the spring and autumn, was limited by soil water availability. Gas exchange, plant water potential and tissue hydrogen stable isotopic ratio (deltaD) data suggested that plants responded rapidly to summer rain events. Based on a leaf area index of 1.4, leaf-level water use and carbon acquisition scaled to canopy-level means of 0.59 mm day(-1) and 0.13 mol m(-2) ground surface day(-1), respectively. Patterns of soil water potential indicated that J. osteosperma dries the soil from the surface downward to a depth of about 1 m. Hydraulic redistribution is a significant process in soil water dynamics. Eddy covariance data indicated a mean evapotranspiration rate of 0.85 mm day(-1) from March to October 2001, during which period the juniper population at the eddy flux site was a net source of CO2 (3.9 mol m(-2) ground area). We discuss these results in relation to the rapid range expansion of juniper species during the past century.

Formation of protoplasts from cultured tobacco cells and Arabidopsis thaliana by the action of cellulosomes and pectate lyase from Clostridium cellulovorans

The crude culture supernatants from Clostridium cellulovorans were tested for their ability to convert plant cells to protoplasts. The supernatants readily released protoplasts from cultured tobacco cells and Arabidopsis thaliana. The crude culture supernatant from pectin-grown cells was more active than supernatants from glucose-, cellobiose-, xylan-, and locust bean gum-grown cells. After removal of cellulosomes, the crude culture supernatant lost its protoplast formation activity. The protoplast formation activity of the crude culture supernatant from C. cellulovorans was more effective than those of commercial enzymes based on protein content.

Water limitations to carbon exchange in old-growth and young ponderosa pine stands

We investigated the impact of seasonal soil water deficit on the processes driving net ecosystem exchange of carbon (NEE) in old-growth and recently regenerating ponderosa pine (Pinus ponderosa Doug. ex Laws.) stands in Oregon. We measured seasonal patterns of transpiration, canopy conductance and NEE, as well as soil water, soil temperature and soil respiration. The old-growth stand (O) included two primary age classes (50 and 250 years), had a leaf area index (LAI) of 2.1 and had never been logged. The recently regenerating stand (Y) consisted predominantly of 14-year-old ponderosa pine with an LAI of 1.0. Both stands experienced similar meteorological conditions with moderately cold wet winters and hot dry summers. By August, soil volumetric water content within the upper 30 cm had declined to a seasonal minimum of 0.07 at both sites. Between April and June, both stands showed similar rates of transpiration peaking at 0.96 mm day(-1); thereafter, trees at the Y site showed increasing drought stress with canopy stomatal resistance increasing 6-fold by mid-August relative to values for trees at the O site. Over the same period, predawn water potential (psi(pd)) of trees at the Y site declined from -0.54 to -1.24 MPa, whereas psi(pd) of trees at the O site remained greater than -0.8 MPa throughout the season. Soil respiration at the O site showed a strong seasonal correlation with soil temperature with no discernible constraints imposed by declining soil water. In contrast, soil respiration at the Y site peaked before seasonal maximal soil temperatures and declined thereafter with declining soil water. No pronounced seasonal pattern in daytime NEE was observed at either site between April and September. At the Y site this behavior was driven by concurrent soil water limitations on soil respiration and assimilation, whereas there was no evidence of seasonal soil water limitations on either process at the O site.

Use of a physiological process model with forestry yield tables to set limits on annual carbon balances

We present an approach that sets limits on annual carbon fluxes for different aged forests by using a simple process-based model (3-PG) and information derived from yield tables and local weather stations. Given a measure of height-growth potential, model predictions are constrained to match stand dynamics described in yield tables. Thus constrained, the model can provide reasonable annual estimates of gross photosynthesis under a specified climate, even with inexact knowledge of soil properties. If we assume that leaf litterfall and fine-root turnover approach equilibrium at canopy closure, maximum net annual ecosystem exchange can also be predicted from modeled estimates of these two detrital components and estimates of foliage, branch, stem and coarse-root production. The latter four components of production are predicted from allometric relationships with mean stem diameter. The approach is demonstrated for Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) stands between Ages 20 and 150 years growing under conditions typical of those at Wind River, Washington, USA. Gross photosynthesis (Pg) by Douglas-fir at Ages 20, 70 and 150 years with leaf area indices (L) of 8.1, 6.9 and 4.0 was predicted at 1630, 1580 and 1160 g C m-2 year(1, respectively. Maximum net ecosystem production (Pe) for the same range in age classes was predicted to average 275, 294 and 207 g C m-2 year-1, respectively. The predicted reductions in L for older stands do not occur because other species fill the canopy gaps created by natural mortality of Douglas-fir. As a result of the development of an understory, total Pg is predicted to decrease only slightly with the aging of the overstory. Estimates of Pe exclude respiration from coarse woody debris, although additions of this component are provided annually by the model. The process-based modeling approach, constrained by yield table estimates of stand properties, sets reasonable limits on annual carbon exchange and suggests which environmental variables deserve careful monitoring to refine estimates of carbon fluxes.

Belowground carbon pools and processes in different age stands of Douglas-fir

Forest floor material and soil organic matter may act as both a source and a sink in global CO2 cycles. Thus, the ecosystem processes controlling these pools are central to understanding the transfers of carbon (C) between the atmosphere and terrestrial systems. To examine these ecosystem processes, the effect of stand age on temporal carbon source-sink relationships was examined in 20-year-old, 40-year-old and old-growth stands of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) in the Cascade Mountains of south-central Washington State. Belowground C and nitrogen (N) storage and soil respiration were measured. In addition, nylon mesh bags containing homogenized soils from each site were buried at the respective sites to quantify root ingrowth and potential C sequestration and loss. The sites supporting the 20- and 40-year-old stands had soil C stores reflecting the C contributions from logging residue, coarse woody debris and stumps left after harvest. Because the N-fixer red alder (Alnus rubra Bong.) comprised 33% of the 40-year-old stand, this site had significantly greater concentrations and pools of N in the forest floor than sites without red alder. This N-rich site had consistently lower soil CO2 efflux rates during the growing season than the sites supporting the 20-year-old and old-growth stands. Estimated annual soil C efflux was 1367, 883 and 1194 g m-2 for the sites supporting the 20-, 40- and old-growth stands, respectively. These values are higher than previously reported values. Root ingrowth was significantly less in the 40-year-old stand than in the 20-year-old stand, and both young stands showed markedly less fine root growth than the old-growth stand. At the sites supporting the young stands, C and N were lost from the soil bags, whereas there was an increase in C and N in the soil bags at the site supporting the old-growth stand. The fine root growth and soil respiration data support the hypothesis that belowground C allocation decreases with increasing fertility. Quantification of the source-sink relationship of soil C at the three stands based on litterfall, relative root ingrowth and soil respiration measurements was compromised because of significant CO2 flux from decaying organic matter in the young stands.