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Leaf litter provides an important nutrient subsidy to headwater streams, but little is known about how tree genetics influence energy pathways from litter to higher trophic levels. Despite the charge to quantify carbon (C) and nitrogen (N) pathways from decomposing litter, the relationship between litter decomposition and aquatic consumers remains unresolved. We measured litter preference (attachments to litter), C and N assimilation rates, and growth rates of a shredding caddisfly (Hesperophylax magnus, Limnephilidae) in response to leaf litter of different chemical and physical phenotypes using Populus cross types (P. fremontii, P. angustifolia, and F1 hybrids) and genotypes within P. angustifolia. We combined laboratory mesocosm studies using litter from a common garden with a field study using doubly labeled litter (13C and 15N) grown in a greenhouse and incubated in Oak Creek, Arizona, USA. We found that, in the lab, shredders initially chose relatively labile (low lignin and condensed tannin concentrations, rapidly decomposing) cross type litter, but preference changed within 4 d to relatively recalcitrant (high lignin and condensed tannin concentrations, slowly decomposing) litter types. Additionally, in the lab, shredder growth rates were higher on relatively recalcitrant compared to labile cross type litter. Over the course of a three-week field experiment, shredders also assimilated more C and N from relatively recalcitrant compared to labile cross type litter. Finally, among P. angustifolia genotypes, N assimilation by shredders was positively related to litter lignin and C:N, but negatively related to condensed tannins and decomposition rate. C assimilation was likewise positively related to litter C:N, and also to litter %N. C assimilation was not associated with condensed tannins or lignin. Collectively, these findings suggest that relatively recalcitrant litter of Populus cross types provides more nutritional benefit, in terms of N fluxes and growth, than labile litter, but among P. angustifolia genotypes the specific trait of litter recalcitrance (lignin or tannins) determines effects on C or N assimilation. As shredders provide nutrients and energy to higher trophic levels, the influence of these genetically based plant decomposition pathways on shredder preference and performance may affect community and food web structure.

The species Saccharomyces uvarum and Saccharomyces kudriavzevii have gained popularity in recent decades due to their interesting oenological properties. However, although it plays a crucial role in yeast fermentation performance and compound synthesis, our understanding of nitrogen metabolism in these species remains limited. Therefore, we compared how three strains of Saccharomyces cerevisiae, Saccharomyces uvarum and Saccharomyces kudriavzevii use relevant nitrogen sources by combining quantitative analysis approaches based on isotopic tracing and modelling. The model we have developed aims to facilitate the calculation and interpretation of stable isotope data for other experiments, by providing easy visualisation of the results and predicting the kinetics of isotope incorporation beyond the sampling points. The three species exhibit significant variations in their nitrogen assimilation profile. They differ in the timing of uptake of ammonium, arginine and glutamine: Saccharomyces cerevisiae prefers glutamine, Saccharomyces kudriavzevii ammonium and Saccharomyces uvarum arginine. This contributes to a different pattern of nitrogen redistribution towards proteinogenic amino acids between strains at the start of the exponential phase, which fades on entering the stationary phase. Additionally, we found that the contribution of leucine and valine to isoamyl alcohol production varies between species; also, Saccharomyces kudriavzevii activates the synthesis of volatile compounds earlier. We compare the differences in nitrogen metabolism of S. cerevisiae, S. uvarum and S. kudriavzevii using isotopic tracing and modelling. We observed differences in ammonium, arginine and glutamine uptake, in the contribution of leucine and valine on aroma synthesis and S. kudriavzevii activates the aroma synthesis earlier.

Many invasive plant species are symbiotic N-fixers that can have strong impacts on ecosystem processes. Nitrogen-fixing plants use a diversity of strategies to regulate the degree of N-fixation, each well suited for specific environmental conditions. However, little is known about whether fixation strategies are related to invasiveness. Weed risk assessment scores were used as an index of invasiveness for eight non-native N-fixing tree species (four high-risk and four low-risk for invasiveness) in Hawaiʻi. In a shade house experiment using an isotopic tracer, we found that species varied in their growth, biomass allocation, and N-fixing traits in response to three levels of nitrogen fertilization. Species sorted into distinct fixation strategies with three species displaying a facultative strategy, four species displaying an incomplete downregulation strategy, and one species displaying either a facultative or incomplete downregulation strategy. Fixation strategies were associated with the trait plasticity of each species, but not related to risk assessment scores for invasiveness in Hawaiʻi. Facultative fixers had the highest trait plasticity and were able to regulate symbiotic nitrogen fixation with the greatest magnitude. Collectively, our results suggest that species growth traits are better predictors of N fixation strategy than weed risk assessment scores, suggesting that the link between invasiveness and N fixation strategy is tenuous.

Among the three major global carbon cycle components, the terrestrial one has been the most uncertain because of the complexity of the soil organic carbon (SOC) dynamics. Previous tracer studies, however, have shown that SOC consists of labile and resistant pools. Labile pools turn over in decades, and resistant pools turn over in hundreds or thousands of years. Labile pools are active in carbon and nutrient cycles and responsive to land-use management changes, whereas resistant pools are less so. Very few studies have actually quantified labile and resistant SOC pools because the isotopic tracer methods, such as the paired-plot bulk-carbon (PPBC) method, can only be applied to a few special cases. I found a study of SOC in the North America Great Plains, in which some of the data are suitable for the PPBC method. The results revealed that the turnover times of the labile SOC pools ranged from 17 years to 93 years, and the sizes ranged from 1.2 g kg−1 to 17.6 g kg−1. The turnover times of the resistant pools ranged from 899 years to 5138 years, and the sizes ranged from 5.0 g kg−1 to 12.4 g kg−1. Land management practices changed the sizes of the labile pools but not their turnover times. This study also pointed out a possibility that allows the application of the PPBC method to a set of much broader cases.

Amino acid nitrogen isotopic analysis is a relatively new method for estimating trophic position. It uses the isotopic difference between an individual’s ‘trophic’ and ‘source’ amino acids to determine its trophic position. So far, there is no accepted explanation for the mechanism by which the isotopic signals in ‘trophic’ and ‘source’ amino acids arise. Yet without a metabolic understanding, the utility of nitrogen isotopic analyses as a method for probing trophic relations, at either bulk tissue or amino acid level, is limited. I draw on isotopic tracer studies of protein metabolism, together with a consideration of amino acid metabolic pathways, to suggest that the ‘trophic’/‘source’ groupings have a fundamental metabolic origin, to do with the cycling of amino-nitrogen between amino acids. ‘Trophic’ amino acids are those whose amino-nitrogens are interchangeable, part of a metabolic amino-nitrogen pool, and ‘source’ amino acids are those whose amino-nitrogens are not interchangeable with the metabolic pool. Nitrogen isotopic values of ‘trophic’ amino acids will reflect an averaged isotopic signal of all such dietary amino acids, offset by the integrated effect of isotopic fractionation from nitrogen cycling, and modulated by metabolic and physiological effects. Isotopic values of ‘source’ amino acids will be more closely linked to those of equivalent dietary amino acids, but also modulated by metabolism and physiology. The complexity of nitrogen cycling suggests that a single identifiable value for ‘trophic discrimination factors’ is unlikely to exist. Greater consideration of physiology and metabolism should help in better understanding observed patterns in nitrogen isotopic values.

Environmental heterogeneity is ubiquitous, but environmental systems are often analyzed as if they were homogeneous instead, resulting in aggregation errors that are rarely explored and almost never quantified. Here I use simple benchmark tests to explore this general problem in one specific context: the use of seasonal cycles in chemical or isotopic tracers (such as Cl−, δ18O, or δ2H) to estimate timescales of storage in catchments. Timescales of catchment storage are typically quantified by the mean transit time, meaning the average time that elapses between parcels of water entering as precipitation and leaving again as streamflow. Longer mean transit times imply greater damping of seasonal tracer cycles. Thus, the amplitudes of tracer cycles in precipitation and streamflow are commonly used to calculate catchment mean transit times. Here I show that these calculations will typically be wrong by several hundred percent, when applied to catchments with realistic degrees of spatial heterogeneity. This aggregation bias arises from the strong nonlinearity in the relationship between tracer cycle amplitude and mean travel time. I propose an alternative storage metric, the young water fraction in streamflow, defined as the fraction of runoff with transit times of less than roughly 0.2 years. I show that this young water fraction (not to be confused with event-based \"new water\" in hydrograph separations) is accurately predicted by seasonal tracer cycles within a precision of a few percent, across the entire range of mean transit times from almost zero to almost infinity. Importantly, this relationship is also virtually free from aggregation error. That is, seasonal tracer cycles also accurately predict the young water fraction in runoff from highly heterogeneous mixtures of subcatchments with strongly contrasting transit-time distributions. Thus, although tracer cycle amplitudes yield biased and unreliable estimates of catchment mean travel times in heterogeneous catchments, they can be used to reliably estimate the fraction of young water in runoff.

Climate change is expected to pose a global threat to forest health by intensifying extreme events like drought and insect attacks. Carbon allocation is a fundamental process that determines the adaptive responses of long-lived late-maturing organisms like trees to such stresses. However, our mechanistic understanding of how trees coordinate and set allocation priorities among different sinks (e.g., growth and storage) under severe source limitation remains limited. Using flux measurements, isotopic tracing, targeted metabolomics, and transcriptomics, we investigated how limitation of source supply influences sink activity, particularly growth and carbon storage, and their relative regulation in Norway spruce (Picea abies) clones. During photosynthetic deprivation, absolute rates of respiration, growth, and allocation to storage all decline. When trees approach neutral carbon balance, i.e., daytime net carbon gain equals nighttime carbon loss, genes encoding major enzymes of metabolic pathways remain relatively unaffected. However, under negative carbon balance, photosynthesis and growth are down-regulated while sucrose and starch biosynthesis pathways are up-regulated, indicating that trees prioritize carbon allocation to storage over growth. Moreover, trees under negative carbon balance actively increase the turnover rate of starch, lipids, and amino acids, most likely to support respiration and mitigate stress. Our study provides molecular evidence that trees faced with severe photosynthetic limitation strategically regulate storage allocation and consumption at the expense of growth. Understanding such allocation strategies is crucial for predicting how trees may respond to extreme events involving steep declines in photosynthesis, like severe drought, or defoliation by heat waves, late frost, or insect attack.

The long-term cooling, decline in the partial pressure of carbon dioxide, and the establishment of permanent polar ice sheets during the Neogene period 1 , 2 have frequently been attributed to increased uplift and erosion of mountains and consequent increases in silicate weathering, which removes atmospheric carbon dioxide 3 , 4 . However, geological records of erosion rates are potentially subject to averaging biases 5 , 6 , and the magnitude of the increase in weathering fluxes—and even its existence—remain debated 7 – 9 . Moreover, an increase in weathering scaled to the proposed erosional increase would have removed nearly all carbon from the atmosphere 10 , which has led to suggestions of compensatory carbon fluxes 11 – 13 in order to preserve mass balance in the carbon cycle. Alternatively, an increase in land surface reactivity—resulting from greater fresh-mineral surface area or an increase in the supply of reactive minerals—rather than an increase in the weathering flux, has been proposed to reconcile these disparate views 8 , 9 . Here we use a parsimonious carbon cycle model that tracks two weathering-sensitive isotopic tracers (stable 7 Li/ 6 Li and cosmogenic 10 Be/ 9 Be) to show that an increase in land surface reactivity is necessary to simultaneously decrease atmospheric carbon dioxide, increase seawater 7 Li/ 6 Li and retain constant seawater 10 Be/ 9 Be over the past 16 million years. We find that the global silicate weathering flux remained constant, even as the global silicate weathering intensity—the fraction of the total denudation flux that is derived from silicate weathering—decreased, sustained by an increase in erosion. Long-term cooling during the Neogene thus reflects a change in the partitioning of denudation into weathering and erosion. Variable partitioning of denudation and consequent changes in silicate weathering intensity reconcile marine isotope and erosion records with the need to maintain mass balance in the carbon cycle and without requiring increases in the silicate weathering flux. A carbon cycle model constrained by weathering-sensitive isotopic tracers reveals that long-term cooling in the Neogene period reflects a change in how surface denudation is partitioned into weathering and erosion.

Horizontal drilling and hydraulic fracturing have enhanced energy production but raised concerns about drinking-water contamination and other environmental impacts. Identifying the sources and mechanisms of contamination can help improve the environmental and economic sustainability of shale-gas extraction. We analyzed 113 and 20 samples from drinking-water wells overlying the Marcellus and Barnett Shales, respectively, examining hydrocarbon abundance and isotopie compositions (e.g.,C₂H₆/CH₄, δ¹³C-CH₄) and providing, to our knowledge, the first comprehensive analyses of noble gases and their isotopes (e.g., ⁴He, ²⁰Ne, ³⁶Ar) in ground water near shale-gas wells. We addressed two questions. (i) Are elevated levels of hydrocarbon gases in drinking-water aquifers near gas wells natural or anthropogenic? (ii) If fugitive gas contamination exists, what mechanisms cause it? Against a backdrop of naturally occurring salt- and gas-rich groundwater, we identified eight discrete clusters of fugitive gas contamination, seven in Pennsylvania and one in Texas that showed increased contamination through time. Where fugitive gas contamination occurred, the relative proportions of thermogenic hydrocarbon gas (e.g., CH₄, ⁴He) were significantly higher (P < 0.01) and the proportions of atmospheric gases (air-saturated water e.g., N₂, ³⁶Ar) were significantly lower (P < 0.01) relative to background groundwater. Noble gas isotope and hydrocarbon data link four contamination clusters to gas leakage from intermediate-depth strata through failures of annulus cement, three to target production gases that seem to implicate faulty production casings, and one to an underground gas well failure. Noble gas data appear to rule out gas contamination by upward migration from depth through overlying geological strata triggered by horizontal drilling or hydraulic fracturing.

Methanol is a liquid with high energy storage capacity that holds promise as an alternative substrate to replace sugars in the biotechnology industry. It can be produced from CO 2 or methane and its use does not compete with food and animal feed production. However, there are currently only limited biotechnological options for the valorization of methanol, which hinders its widespread adoption. Here, we report the conversion of the industrial platform organism Escherichia coli into a synthetic methylotroph that assimilates methanol via the energy efficient ribulose monophosphate cycle. Methylotrophy is achieved after evolution of a methanol-dependent E . coli strain over 250 generations in continuous chemostat culture. We demonstrate growth on methanol and biomass formation exclusively from the one-carbon source by 13 C isotopic tracer analysis. In line with computational modeling, the methylotrophic E. coli strain optimizes methanol oxidation by upregulation of an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway and downregulating tricarboxylic acid cycle enzymes. En route towards sustainable bioproduction processes, our work lays the foundation for the efficient utilization of methanol as the dominant carbon and energy resource. Using one carbon compounds as feedstock is a promising approach in abating climate change. Here, the authors report the conversion of E. coli into a synthetic methylotroph that assimilates methanol via the ribulose monophosphate cycle and a set of distinctive mutations.