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  http://CaliforniaAgriculture.ucop.edu ã APRIL–JUNE 2009 67 Atmosphericnitrogen (N 2 ) Industrial fixation100 Decayingorganic matterSymbioticN 2  fixersPlant & animal wastesSoilmicrobes #s = teragrams N/year Free-livingN 2  fixersGroundwaterAmmonium(NH 4+ )Nitrate(NO 3– )  Atmospheric fixation5  Ammonification NitrificationImmobilizationDenitrification193Leaching36 Biological fixation 228 Biological fixation Nitrite(NO 2– )Nitrous oxide(N 2 O)Nitric oxide(NO)Nitrous oxide(N 2 O) Nylon production Ammonia(NH 3 ) Volatili- zation100Root absorption1,200Shoot assimilation Fig. 1. Major procsss of th biogochmical nitrogn cycl. Fluxs (rd numbrs) ar in tragrams (Tg = 10 12  g) N/yar. Trrstrial organisms and soils contain organic nitrogn that is active in the cycle. Assuming that the amount of atmospheric molecular nitrogen remains constant (inputs = outputs), th man rsidnc tim of nitrogn in organic forms is about 370 yars. Sourc: Bloom 2009. RevIeW ARTICLe t As carbon dioxide rises, food quality will decline without careful nitrogen management by   Arnold J. Bloom Rising atmospheric concentrations of carbon dioxide could dramatically influence the performance of crops, but experimental results to date have been highly variable. For example, when C  3  plants are grown under car-bon dioxide enrichment, productivity increases dramatically at first. But over time, organic nitrogen in the  plants decreases and productivity diminishes in soils where nitrate is an important source of this nutrient. We have discovered a phenomenon that  provides a relatively simple explana-tion for the latter responses: in C  3   plants, elevated carbon dioxide con-centrations inhibit photorespiration, which in turn inhibits shoot nitrate assimilation. Agriculture would ben-efit from the careful management of nitrogen fertilizers, particularly those that are ammonium based. A tmospheric carbon dioxide (CO 2 )has increased about 35% since 1800 (from 280 to 380 parts per million [ppm]), and computer models predict that it will reach between 530 and 970 ppm by the end of the century (IPCC 2007). This rise in carbon dioxide could potentially be mitigated by crop plants, in which photosynthesis converts at-mospheric carbon dioxide into carbohy-drates and other organic compounds. The extent of this mitigation remains uncertain, however, due to the complex relationship between carbon and nitro-gen metabolism in plants (Finzi   et al .  2007; Johnson 2006; Reich   et al .  2006). Carbon metabolism provides the energy and carbon molecules to syn-thesize organic nitrogen compounds in plants, whereas nitrogen metabo-lism provides the amino groups for all proteins (g. 1). Proteins include all enzymes that catalyze (facilitate) bio-chemical reactions in plants, including Th ris in atmosphric carbon-dioxid lvls — about 35% sinc 1800 — changs how plants mtaboliz important nutrints, which in turn altrs food quality and nutrition, influences where plants and crops can grow, and affects pest management and other cultivation practices. Lesley Randall of the UC Davis Department of Plant Sciences attends to plants growing in hydroponic culture under elevated carbon-dioxide atmospheres, in environmental chambers at the UC Davis Controlled Environment Facility.  68 CALIFORNIA AGRICULTURE   ã VOLUME 63 , NUMBER 2 Change with CO 2  enrichment (%)  –40 0 40 80 Crop yield (28)Tree biomass (19)Grass biomass (13)Plant biomass (18)Grass nitrogen (13) High NLow N Fig. 5. Differences in yield, aboveground biomass, laf nitrogn (N) concntrations and grain protein concentrations between C 3  plants grown at lvatd (567 ppm) and ambint (366 ppm) carbon dioxid concntrations undr havy (high N) and normal N frtilization (low N). Symbols and error bars designate means ± 95% confidence intrval for crops (Ainsworth and Long 2005), trs (Curtis and Wang 1998), grasss (Wand t al. 1999), all plant spcis (d Graaff t al. 2006) and grain protin (Taub t al. 2008). Parentheses contain number of studies included in the meta-analysis. 50403020100  0 200 400 600 800 C i  (ppm)    N  e   t   C   O    2   a  s  s   i  m   i   l  a   t   i  o  n   (  µ  m  o   l   /  m    2     /  s  e  c   ) 365 ppm CO 2 567 ppm CO 2 Fig. 3. Nt carbon dioxid assimilation (photosynthsis) as a function of carbon dioxid concntrations within a laf (C i ) for C 3  plants grown at either ambient (365 parts pr million [ppm]) or lvatd (567 ppm) atmosphric carbon dioxid concntrations, in fr air CO 2  enrichment (FACe) plots, whr plants growing in soil undr th opn sky ar xposd to lvatd carbon dioxid. Man of 285 studis (Ainsworth and Rogrs 2007). carbon metabolism. Any environmental perturbation that interferes with nitro-gen metabolism sooner or later inhibits carbon metabolism. Carbon dioxide acclimation The focal point of crop responses to rising carbon dioxide levels is the enzyme rubisco (ribulose-1,5-bisphos-phate carboxylase/oxygenase). Rubisco is the most prevalent protein on Earth and contains as much as half of the nitrogen in plant leaves. It catalyzes two different chemical reactions: one reaction combines a 5-carbon sugar RuBP (ribulose-1,5-bisphosphate) with carbon dioxide, and the other reaction combines this same sugar with oxygen.The reaction of RuBP with carbon dioxide produces a 6-carbon com-pound that immediately divides into two molecules of a 3-carbon compound (3-phosphoglycerate), hence the name C 3  carbon xation (g. 2). These prod- ucts pass through an elaborate bio-chemical cycle (Calvin-Benson cycle) that eventually forms one molecule of a 6-carbon sugar (fructose-6-phos-phate) and regenerates RuBP.The reaction of RuBP with oxygen oxidizes the RuBP, splits it into one mol-ecule of a 3-carbon compound (3-phos-phoglycerate) and one molecule of a Rubisco ATPNADPHCO 2 O 2 Photorespiration CO 2 PG + PGAPGARuBPCO 2 C 3  carbon fixation CH 2 OATP2 PGAATPNADPHATPNADPHRuBP Fig. 2. C 3  carbon xation and photorspiration pathways in which th nzym rubisco (ribbon modl in cntr) catalyzs ractions btwn a 5-carbon sugar, RuBP (ribulos-1,5-biphosphat) and ithr CO 2  or O 2 . The first stable products of C 3  carbon fixation are two molecules of PGA (a 3-carbon compound, 3-phosphoglycrat); th rst stabl products of photorspiration ar on molcul of PGA and on molcul of PG (a 2-carbon compound, 2-phosphoglycolat). High-energy compounds ATP and NADPH, generated from photosynthesis, drive these ractions. As atmosphric CO 2  increases, there is an initial increase in C 3  carbon fixation (and sugar productivity), whil photorspiration is inhibitd. W hav shown that inhibiting photorespiration diminishes nitrate assimilation. In plants that depend on nitrate as a nitrogen source, this eventually inhibits plant productivity and lowers protein content. Nitrogen is part of th amino groups ssntial to all protins, and protins includ th nzyms that facilitat biochmical ractions. Sourc: Bloom 2009. Fig. 4. Each line shows change in biomass over tim for spcic plants grown at lvatd (567 ppm) and ambint (365 ppm) carbon dioxid atmosphrs, in fr air CO 2  enrichment (FACe) plots (Duks t al. 2005; Kornr 2006) and opn-top chambrs (Rass t al. 2005; Kimball t al. 2007). Year of treatment 0 2 4 6 8 10 12100806040200–20    B   i  o  m  a  s  s  c   h  a  n  g  e  w   i   t   h   C   O    2   e  n  r   i  c   h  m  e  n   t   (   %   ) Phoenix, sour orangeChesapeake Bay, Scirpus Duke, Pinus Oak Ridge, Liquidambar  Swiss, mixed deciduousJasper Ridge, grassland At elevated carbon dioxide concentrations, C 3  plants that rely on nitrate as a nitrogen source suffer severe deprivation of organic nitrogen.    M   o    l   e   c   u    l   e   :   I   n   g   e   r   A   n    d   e   r   s   s   o   n  http://CaliforniaAgriculture.ucop.edu ã APRIL–JUNE 2009 69 2-carbon compound (2-phosphoglyco-late), and subsequently releases carbon dioxide, hence the names C 2  pathway or, more commonly, photorespiration. In total, photorespiration consumes bio-chemical energy, but does not result in any net production of sugar (Foyer et al. 2009). Thus, photorespiration has been viewed as a wasteful process, a vestige of the high carbon dioxide atmospheres (over 1,000 ppm) under which plants evolved (Wingler et al. 2000).The balance between C 3  carbon xa -tion and photorespiration depends on the relative amounts of carbon dioxide and oxygen entering the active site of rubisco (i.e., portion of the enzyme involved in the primary chemical reac- tions) and the afnity of the enzyme for each gas (i.e., degree to which it attracts carbon dioxide or oxygen). At current atmospheric levels of carbon dioxide and oxygen (about 380 and 209,700 ppm, respectively), photorespiration in most crops (C 3  plants including wheat, rice, barley, oats, legumes, vegetables, and fruit and nut trees) dissipates over a quarter of the organic carbon produced during carbon dioxide as-similation (conversion from inorganic to organic form) (Sharkey 1988). In contrast, C 4  crops (such as corn, sorghum and sugar cane), which have a metabolic carbon dioxide pump that increases the concentration of this com-pound at the catalytic site of rubisco, minimize photorespiration at the ex-pense of the additional energy required for pumping.Elevated levels of atmospheric car- bon dioxide inhibit photorespiration in C 3  plants, making photosynthesis more efcient. Initially, this accelerates both their photosynthetic carbon dioxide assimilation and their growth by about a third. After a few days or weeks, however, carbon dioxide assimilation and growth both slow down until they are accelerated in the long term by only about 12% and 8%, respectively (gs. 3 and 4). Moreover, leaf nitrogen and protein concentrations ultimately decrease more than 12% under carbon dioxide enrichment (g. 5). Such a loss of nitrogen and protein signicantly diminishes the value of this plant ma-terial as food for animals and humans. Fig. 6. Diffrncs in laf carbon xation capacity (photosynthsis [PS]) vrsus total nitrogn concntration (N) btwn C 3  plants grown at lvatd (567 ppm) and ambint (366 ppm) carbon dioxid concntrations. Each symbol designates the mean ratio for a species. Shown are the regression line (solid, slop = 0.815, r   = 0.71) and 1:1 lin (dottd). This data suggsts that changs in photosynthesis from carbon dioxide enrichment derive from changes in plant nitrogen levels under carbon dioxide nrichmnt (ellsworth t al. 2004). 40200–20–40–40 –20 0 20 40 HerbsTreesShrubsChange in N with CO 2  enrichment (%)    C   h  a  n  g  e   i  n   P   S  w   i   t   h   C   O    2   e  n  r   i  c   h  m  e  n   t   (   %   ) Together these trends are known as carbon dioxide acclimation. CO 2  acclimation hypotheses Several hypotheses have been put forward to explain carbon dioxide ac-climation. Carbohydrat sink limitation. Ac-cording to this hypothesis, plants under carbon dioxide enrichment initially as-similate more carbon dioxide into carbo-hydrates than they can incorporate into their growing tissues. In response, they diminish carbon dioxide assimilation by decreasing their rubisco levels (Long et al. 2004). This change in rubisco levels, however, is not necessarily selective; the decrease may instead just be part of the overall decline in protein and nitrogen concentrations (Ainsworth and Long 2005; Makino and Mae 1999). Progressive nitrogen limitation. An-other hypothesis for carbon dioxide acclimation is that shoots accumulate carbohydrates faster than roots can absorb nitrogen from soils, making leaf nitrogen concentrations decrease (Hungate et al. 2003; Luo et al. 2004; Norby et al. 2001; Reich et al. 2006). As these leaves senesce and drop to the ground, (1) plant litter quality declines, (2) microbial immobilization of soil nitrogen increases because of the high carbon-to-nitrogen ratios in the litter, (3) soil nitrogen availability to plants further diminishes because more soil nitrogen is tied up in microorganisms, (4) plants become even more nitrogen limited, (5) plant protein levels decline What was grown in a controlld nvironmntal chambr at lvatd carbon dioxid (700 ppm). Plants in th thr containrs on th lft rcivd ammonium (NH 4+ ) as th sol nitrogn sourc, whras thos on th right rcivd nitrat (NO 3 – ). Plants grown at ambint carbon dioxid undr ammonium and nitrat nutrition wr indistinguishabl (not shown).  70 CALIFORNIA AGRICULTURE   ã VOLUME 63 , NUMBER 2 and (6) plant processes including pho- tosynthesis slow down (g. 6). This hypothesis, however, has difculty in explaining the variation in carbon di-oxide acclimation among sites (Finzi et al. 2007) and among methods of carbon dioxide enrichment (Ainsworth and Long 2005). Role of photorespiration We have discovered another explana-tion for carbon dioxide acclimation: in C 3  plants, shoot assimilation of nitrate into organic nitrogen compounds depends on photorespiration, so any condition that inhibits photorespiration (elevated carbon dioxide or low oxygen concentra-tions) also inhibits shoot nitrate assimi- lation (gs. 7 and 8). Thus, at elevated carbon dioxide concentrations, C 3  plants that rely on nitrate as a nitrogen source suffer severe deprivation of organic nitrogen compounds such as proteins. The resulting decline in organic nitrogen compounds reduces the plants’ yield and biomass production. While high applications of nitrogen fertilizer may partially compensate for this, the plants’ nitrogen and protein concentrations still diminish (g. 5). Ammonium and nitrate are the two main sources of nitrogen that are ac-cessible to plants from the soil. Plants show a wide range of responses to carbon dioxide enrichment because the  balance between nitrate and ammo-nium availability varies over seasons, years, locations and plant species. In an annual California grassland where nitrate was the predominant nitro-gen source, net primary productivity diminished under carbon dioxide enrichment (g. 4) (Dukes et al. 2005). This was presumably because elevated carbon dioxide inhibited plant nitrate assimilation (by both shoots and roots), and the grasses became deprived of organic nitrogen. In contrast, ammo-nium is the major form of nitrogen available to plants in marshes because wet, anaerobic soils promote denitri- cation (the conversion of nitrate into nitrous oxide and dinitrogen gas) and nitrate leaching (the removal of dis- Fig. 7. Rspons of nitrat (NO 3 – ) assimilation in C 3  and C 4  plants as a function of carbon dioxid concntrations insid a laf (C i ). Rlativ NO 3 – assimilation was assessed from changs in CO 2 -O 2  fluxes with a shift from NH 4 +  to NO 3 –  nutrition ( ∆ AQ). Th C 3  species includd barly (Bloom t al. 1989), what (Bloom t al. 2002), tomato (Sarls and Bloom 2003), Arabidopsis (Rachmilvitch t al. 2004) and Flaveria pringlei   and giant redwood (Bloom, unpublishd data). Th C 4  species includd maiz (Cousins and Bloom 2003, 2004) and Flaveria bidentis  and  Amaranthus retroflexus  (Bloom, unpublishd data). 0 200 400 600 800 1,0000.30.20.10.0 C i  (ppm)     R  e   l  a   t   i  v  e  n   i   t  r  a   t  e  a  s  s   i  m   i   l  a   t   i  o  n C 3  plantsC 4  plants    R  a   t  e   (  µ  m  o   l  n   i   t  r  a   t  e   /  p   l  a  n   t  g  r  a  m   /  m   i  n .   ) AssimilationUptakeAssimilationUptake B (wheat) sssxxwmnnmaba A (Arabidopsis) 0.60.40.20.0 360 ppm CO 2  and 21% O 2 720 ppm CO 2  and 21% O 2 360 ppm CO 2  and 2% O 2 Fig. 8. Nitrat (NO 3 – ) uptak as th amount of NO 3 –  depleted from a medium, and nitrate assimilation as th diffrnc btwn th rats of nt NO 3 –  uptak and nt accumulation of fr NO 3 –  in plant tissus: (A) 36-day-old Arabidopsis or (B) 10-day-old what wr xposd to 360 ppm carbon dioxid (CO 2 ) and 21% O 2  , 720 ppm carbon dioxide and 21% O 2 , or 360 ppm CO 2  and 2% O 2 . Shown are the mean ±  Se (n = 13–16). Tratmnts labld with diffrnt lttrs diffr signicantly ( P    ≤  0.05). Light lvls wr 500 and 1,000 micromoles of quanta per meter squared per second for Arabidopsis and wheat, respectively (Rachmilvitch t al. 2004). solved nitrate into deep groundwater or surface water). For example, the dominant C 3  plant in the Chesapeake Bay marsh ( Scirpus olneyi ) showed little carbon dioxide acclimation (g. 4); even after a decade of treatment, photosynthesis and growth remained about 35% greater under carbon diox-ide enrichment (Rasse et al. 2005), with little change in nitrogen concentrations (Erickson et al. 2007). In wheat, an-other C 3  plant, elevated carbon dioxide atmospheres stimulated less growth under nitrate than under ammonium nutrition (g. 9; see photo, page 69). Physiological mechanisms Several physiological mechanisms appear to be responsible for the depen-dency of nitrate assimilation on photo-respiration.First, the initial biochemical step of nitrate assimilation is the conversion of nitrate to nitrite in leaves. This step is powered by the high-energy com-pound NADH (reduced nicotinamide adenine dinucleotide), and photorespi-
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