Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism.

RATIONALE: Position-specific 13 C/12 C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids. METHODS: Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The 13 C/12 C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ13 C values relative to a working standard. RESULTS: This methodology constrains position-specific δ13 C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ13 C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7-5‰ for each carbon position. Position-specific δ13 C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO2 , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline. CONCLUSIONS: This study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

Plant growth chamber design for subambient pCO2 and δ13 C studies.

RATIONALE: Subambient pCO2 has persisted across the major Phanerozoic ice ages, including the entire late Cenozoic (ca 30 Ma to present). Stable isotope analysis of plant-derived organic matter is used to infer changes in pCO2 and climate in the geologic past, but a growth chamber that can precisely control environmental conditions, including pCO2 and δ13 C value of CO2 (δ13 CCO2 ) at subambient pCO2 , is lacking. METHODS: We designed and built five identical chambers specifically for plant growth under stable subambient pCO2 (ca 100 to 400 ppm) and δ13 CCO2 conditions. We tested the pCO2 and δ13 CCO2 stability of the chambers both with and without plants, across two 12-hour daytime experiments and two extended 9-day experiments. We also compared the temperature and relative humidity conditions among the chambers. RESULTS: The average δ13 CCO2 value within the five chambers ranged from -18.76 to -19.10‰; the standard deviation never exceeded 0.14‰ across any experiment. This represents better δ13 CCO2 stability than that achieved by all previous chamber designs, including superambient pCO2 chambers. Every pCO2 measurement (n = 1225) was within 5% of mean chamber values. The temperature and relative humidity conditions differed by no more than 0.4°C and 1.6%, respectively, across all chambers within each growth experiment. CONCLUSIONS: This growth chamber design extends the range of pCO2 conditions for which plants can be grown for δ13 C analysis of their tissues at subambient levels. This new capability allows for careful isolation of environmental effects on plant 13 C discrimination across the entire range of pCO2 experienced by terrestrial land plants.

Temperature-induced water stress in high-latitude forests in response to natural and anthropogenic warming.

The Arctic is particularly sensitive to climate change, but the independent effects of increasing atmospheric CO2 concentration (pCO2 ) and temperature on high-latitude forests are poorly understood. Here, we present a new, annually resolved record of stable carbon isotope (δ(13) C) data determined from Larix cajanderi tree cores collected from far northeastern Siberia in order to investigate the physiological response of these trees to regional warming. The tree-ring record, which extends from 1912 through 1961 (50 years), targets early twentieth-century warming (ETCW), a natural warming event in the 1920s to 1940s that was limited to Northern hemisphere high latitudes. Our data show that net carbon isotope fractionation (Δ(13) C), decreased by 1.7‰ across the ETCW, which is consistent with increased water stress in response to climate warming and dryer soils. To investigate whether this signal is present across the northern boreal forest, we compiled published carbon isotope data from 14 high-latitude sites within Europe, Asia, and North America. The resulting dataset covered the entire twentieth century and spanned both natural ETCW and anthropogenic Late Twentieth-Century Warming (~0.7 °C per decade). After correcting for a ~1‰ increase in Δ(13) C in response to twentieth century pCO2 rise, a significant negative relationship (r = -0.53, P < 0.0001) between the average, annual Δ(13) C values and regional annual temperature anomalies is observed, suggesting a strong control of temperature on the Δ(13) C value of trees growing at high latitudes. We calculate a 17% increase in intrinsic water-use efficiency within these forests across the twentieth century, of which approximately half is attributed to a decrease in stomatal conductance in order to conserve water in response to drying conditions, with the other half being attributed to increasing pCO2 . We conclude that annual tree-ring records from northern high-latitude forests record the effects of climate warming and pCO2 rise across the twentieth century.

Large-scale plant growth chamber design for elevated pCO2 and δ13C studies.

RATIONALE: Throughout at least the next century, CO(2) fertilization and environmental stresses (e.g. nutrient, moisture, insect herbivory) are predicted to affect yields of economically important crop species. Stable isotopes of carbon are used to study plant stresses, which affect yields, but a growth chamber design that can be used to isolate the effects of environmental stresses on crop-sized species through precise maintenance of pCO(2) levels and the δ(13)C values of atmospheric CO(2) (δ(13) C(CO2)) is lacking. METHODS: We designed and built low-cost plant growth chambers for growing staple crop species under precise pCO(2) and δ(13) C(CO2) conditions. Over the course of 14 hours, we assessed for pCO(2) stability at two targeted levels (ambient, ~400 ppm; and 2×, ~800 ppm) and measured the δ(13) C(CO2) value within the two chambers using a stable isotope ratio mass spectrometer. We also compared the temperature and relative humidity conditions within the two growth chambers, and in the ambient, outside air. RESULTS: Across our experimental period, we achieved δ(13) C(CO2) stability (ambient: -8.05 ± 0.17‰; elevated: -12.99 ± 0.29‰) that showed nearly half the variability of any previously reported values for other chamber designs. The stability of the pCO(2) conditions (ambient: 406 ± 3 ppm; elevated: 793 ± 54 ppm) was comparable with that in previous studies, but our design provided ~8 times more growing space than previous chamber designs. We also measured nearly identical temperature and relative humidity conditions for the two chambers throughout the experiment. CONCLUSIONS: Our growth chamber design marks a significant improvement in our ability to test for plant stress across a range of future pCO(2) scenarios. Through significant improvement in δ(13) C(CO2) stability and increased chamber size, small changes in carbon isotope fractionation can be used to assess stress in crop species under specific environmental (temperature, relative humidity, pCO(2)) conditions.

Characterization of ancient DNA supports long-term survival of Haloarchaea.

Bacteria and archaea isolated from crystals of halite 10(4) to 10(8) years old suggest long-term survival of halophilic microorganisms, but the results are controversial. Independent verification of the authenticity of reputed living prokaryotes in ancient salt is required because of the high potential for environmental and laboratory contamination. Low success rates of prokaryote cultivation from ancient halite, however, hamper direct replication experiments. In such cases, culture-independent approaches that use the polymerase chain reaction (PCR) and sequencing of 16S ribosomal DNA are a robust alternative. Here, we use amplification, cloning, and sequencing of 16S ribosomal DNA to investigate the authenticity of halophilic archaea cultured from subsurface halite, Death Valley, California, 22,000 to 34,000 years old. We recovered 16S ribosomal DNA sequences that are identical, or nearly so (>99%), to two strains, Natronomonas DV462A and Halorubrum DV427, which were previously isolated from the same halite interval. These results provide the best independent support to date for the long-term survival of halophilic archaea in ancient halite. PCR-based approaches are sensitive to small amounts of DNA and could allow investigation of even older halites, 10(6) to 10(8) years old, from which microbial cultures have been reported. Such studies of microbial life in ancient salt are particularly important as we search for microbial signatures in similar deposits on Mars and elsewhere in the Solar System.

Reconciliation of marine and terrestrial carbon isotope excursions based on changing atmospheric CO2 levels.

Negative carbon isotope excursions measured in marine and terrestrial substrates indicate large-scale changes in the global carbon cycle, yet terrestrial substrates characteristically record a larger-amplitude carbon isotope excursion than marine substrates for a single event. Here we reconcile this difference by accounting for the fundamental increase in carbon isotope fractionation by land plants in response to increasing atmospheric CO2 concentration (pCO2). We show that for any change in pCO2 concentration (ΔpCO2), terrestrial and marine records can be used together to reconstruct background and maximum pCO2 levels across the carbon isotope excursion. When applied to the carbon isotope excursion at the Palaeocene-Eocene boundary, we calculate pCO2=674-1,034 p.p.m.v. during the Late Palaeocene and 1,384-3,342 p.p.m.v. during the height of the carbon isotope excursion across all sources postulated for the carbon release. This analysis demonstrates the need to account for changing pCO2 concentration when analysing large-scale changes in the carbon isotope composition of terrestrial substrates.

Practical considerations for the use of pollen δ13C value as a paleoclimate indicator.

RATIONALE: Workers have shown a correlation between temperature and the pollen δ(13)C value, and therefore suggested using pollen δ(13)C values to reconstruct paleotemperature. To evaluate the potential for pollen δ(13)C values to be used as a paleotemperature proxy, it is essential to quantify the variability in pollen δ(13)C values and to evaluate the effect of temperature on pollen δ(13)C values, in isolation, under controlled environmental conditions. METHODS: Pollen was isolated from 146 Hibiscus flowers from 26 plants within a single climate environment to evaluate isotopic variability in pollen δ(13)C values. The nearest leaf (n = 82) and flower phloem (n = 30) were also sampled to measure the δ(13)C variability in carbon providing the raw material for new growth. To evaluate the correlation between temperature and pollen δ(13)C values, we isolated pollen from 89 Brassica rapa plants grown in controlled growth chambers with temperatures ranging from 17 to 32°C. RESULTS: The range in pollen δ(13)C values collected from different flowers on the same Hibiscus plant was large (average = 1.6‰), and could be as much as 3.2‰. This amount of variability was similar to that seen between flower-adjacent leaves, and phloem extracted from styles of individual flowers. In controlled growth chamber experiments, we saw no correlation between temperature and the pollen (R(2) = 0.005) or leaf (R(2) = 0.10) δ(13)C values. CONCLUSIONS: We measured large variability in pollen δ(13)C values. When temperature was isolated from other environmental parameters, temperature did not correlate with the pollen δ(13)C value. These results complicate the supposed relationship between temperature and pollen δ(13)C values and caution against using nanogram isotope analytical techniques for characterizing whole-plant individuals.

Corn content of French fry oil from national chain vs. small business restaurants.

Several issues, ranging from sustainability to health, may interest the consumers in the corn content of their food. However, because restaurants are excluded from the Nutrition Labeling and Education Act of 1990, national chain restaurants provide nonspecific ingredient information and small businesses supply none. We measured the carbon isotope composition of fry oil in French fries purchased from 68 (67%) of the 101 national chain fast food restaurants on Oahu (i.e., McDonald's, Burger King, Wendy's, Arby's, and Jack in the Box), and paired this with a similar number of small businesses (n = 66) to calculate minimum percent contribution of corn to total fry oil. We found that the majority (69%) of the national chain restaurants served fries containing corn oil, whereas this was true for only a minority (20%) of the small businesses. Corn oil is more expensive than soybean oil (for example) when purchased from a small business supplier, suggesting that large-scale corporate agreements are necessary to make corn oil frying cost-effective. When considering French fry oil along with corn-fed beef and chicken, as well as high-fructose corn syrup-sweetened soda, we see the pervasive influence of corn as an ingredient in national chain fast food.

Halophilic Archaea cultured from ancient halite, Death Valley, California.

Halophilic Archaea cultured from ancient fluid inclusions in a 90-m-long (0- to 100,000-year-old) salt core from Death Valley, California, demonstrate survival of bacterial cells in subsurface halite for up to 34,000 years. Five enrichment cultures, representing three genera of halophilic Archaea (Halorubrum, Natronomonas and Haloterrigena), were obtained from five surface-sterilized halite crystals exclusively in one section of the core (13.0-17.8 m; 22,000-34,000 years old) containing perennial saline lake deposits. Prokaryote cells were observed microscopically in situ within fluid inclusions from every layer that produced culturable cells. Another 876 crystals analysed from depths of 8.1-86.7 m (10,000-100,000 years old) failed to yield live halophilic Archaea. Considering the number of halite crystals tested (culturing success of 0.6%), microbial survival in fluid inclusions in halite is rare and related to the paleoenvironment, which controls the distribution and abundance of trapped microorganisms. Two cultures from two crystals at 17.8 m that yielded identical 16S rRNA sequences (genus: Haloterrigena) demonstrate intra-laboratory reproducibility. Inter-laboratory reproducibility is shown by two halophilic Archaea (genus: Natronomonas), with 99.3% similarity of 16S rRNA sequences, cultured from the same core interval, but at separate laboratories.

Microscopic identification of prokaryotes in modern and ancient halite, Saline Valley and Death Valley, California.

Primary fluid inclusions in halite crystallized in Saline Valley, California, in 1980, 2004-2005, and 2007, contain rod- and coccoid-shaped microparticles the same size and morphology as archaea and bacteria living in modern brines. Primary fluid inclusions from a well-dated (0-100,000 years), 90 m long salt core from Badwater Basin, Death Valley, California, also contain microparticles, here interpreted as halophilic and halotolerant prokaryotes. Prokaryotes are distinguished from crystals on the basis of morphology, optical properties (birefringence), and uniformity of size. Electron micrographs of microparticles from filtered modern brine (Saline Valley), dissolved modern halite crystals (Saline Valley), and dissolved ancient halite crystals (Death Valley) support in situ microscopic observations that prokaryotes are present in fluid inclusions in ancient halite. In the Death Valley salt core, prokaryotes in fluid inclusions occur almost exclusively in halite precipitated in perennial saline lakes 10,000 to 35,000 years ago. This suggests that trapping and preservation of prokaryotes in fluid inclusions is influenced by the surface environment in which the halite originally precipitated. In all cases, prokaryotes in fluid inclusions in halite from the Death Valley salt core are miniaturized (<1 microm diameter cocci, <2.5 microm long, very rare rod shapes), which supports interpretations that the prokaryotes are indigenous to the halite and starvation survival may be the normal response of some prokaryotes to entrapment in fluid inclusions for millennia. These results reinforce the view that fluid inclusions in halite and possibly other evaporites are important repositories of microbial life and should be carefully examined in the search for ancient microorganisms on Earth, Mars, and elsewhere in the Solar System.