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Modern microbial and ecosystem sciences require diverse interdisciplinary teams that are often challenged in “speaking” to one another due to different languages and data product types. Here we introduce the IsoGenie Database (IsoGenieDB; https://isogenie-db.asc.Ohio-state.edu/), a de novo developed data management and exploration platform, as a solution to this challenge of accurately representing and integrating heterogenous environmental and microbial data across ecosystem scales. The IsoGenieDB is a public and private data infrastructure designed to store and query data generated by the IsoGenie Project, a ~10 year DOE-funded project focused on discovering ecosystem climate feedbacks in a thawing permafrost landscape. The IsoGenieDB provides (i) a platform for IsoGenie Project members to explore the project's interdisciplinary datasets across scales through the inherent relationships among data entities, (ii) a framework to consolidate and harmonize the datasets needed by the team's modelers, and (iii) a public venue that leverages the same spatially explicit, disciplinarily integrated data structure to share published datasets. The IsoGenieDB is also being expanded to cover the NASA-funded Archaea to Atmosphere (A2A) project, which scales the findings of IsoGenie to a broader suite of Arctic peatlands, via the umbrella A2A Database (A2A-DB). The IsoGenieDB's expandability and flexible architecture allow it to serve as an example ecosystems database.

For the past decade, observations of carbonyl sulfide (OCS or COS) have been investigated as a proxy for carbon uptake by plants. OCS is destroyed by enzymes that interact with CO2 during photosynthesis, namely carbonic anhydrase (CA) and RuBisCO, where CA is the more important one. The majority of sources of OCS to the atmosphere are geographically separated from this large plant sink, whereas the sources and sinks of CO2 are co-located in ecosystems. The drawdown of OCS can therefore be related to the uptake of CO2 without the added complication of co-located emissions comparable in magnitude. Here we review the state of our understanding of the global OCS cycle and its applications to ecosystem carbon cycle science. OCS uptake is correlated well to plant carbon uptake, especially at the regional scale. OCS can be used in conjunction with other independent measures of ecosystem function, like solar-induced fluorescence and carbon and water isotope studies. More work needs to be done to generate global coverage for OCS observations and to link this powerful atmospheric tracer to systems where fundamental questions concerning the carbon and water cycle remain.

Systematic biases in eddy covariance measurements of net ecosystem-atmosphere carbon dioxide exchange (NEE) are ubiquitous in forests when turbulence is low at night. We propose an alternative to the conventional bias correction, the friction velocity (u*) filter, by hypothesizing that these biases have two separate, concurrent causes: (1) a subcanopy CO2 storage pool that eludes typical storage measurements, creating a turbulence-dependent bias, and (2) advective divergence loss of CO2, creating a turbulence-independent bias. We correct for (1) using a simple parametric model of missing storage (MS). Prior experiments have inferred (2) directly from atmospheric measurements (DRAINO). For sites at which DRAINO experiments have not been performed or are infeasible, we estimate (2) empirically using a PAR-extrapolated advective respiration loss (PEARL) approach. We compare u* filter estimates of advection and NEE to MS-PEARL estimates at one temperate forest and two tropical forest sites. We find that for tropical forests, u* filters can produce a range of extreme NEE estimates, from long-term forest carbon emission to sequestration, that diverge from independent assessments and are not physically sustainable. Our MS model eliminates the dependence of nighttime NEE on u*, consistent with findings from DRAINO studies that nighttime advective losses of CO2 are often not dependent on the strength of turbulence. Our PEARL estimates of mean advective loss agree with available DRAINO measurements. The MS-PEARL correction to long-term NEE produces better agreement with forest inventories at all three sites. Moreover, the correction retains all nighttime eddy covariance data and is therefore more widely applicable than the u* filter approach, which rejects substantial nighttime data—up to 93% at one of the tropical sites. The full MS-PEARL NEE correction is therefore an equally defensible and more practical alternative to the u* filter, but leads to different conclusions about the resulting carbon balance. Our results therefore highlight the need to investigate which approach's underlying hypotheses are more physically realistic.

The seasonal pattern of the carbon isotope content (δ13C) of atmospheric CO2 depends on local and nonlocal land-atmosphere exchange and atmospheric transport. Previous studies suggested that the δ13C of the net land-atmosphere CO2 flux (δsource) varies seasonally as stomatal conductance of plants responds to vapor pressure deficit of air (VPD). We studied the variation of δsource at seven sites across the United States representing forests, grasslands, and an urban center. Using a two-part mixing model, we calculated the seasonal δsource for each site after removing background influence and, when possible, removing δ13C variation of nonlocal sources. Compared to previous analyses, we found a reduced seasonal (March–September) variation in δsource at the forest sites (0.5‰ variation). We did not find a consistent seasonal relationship between VPD and δsource across forest (or other) sites, providing evidence that stomatal response to VPD was not the cause of the global, coherent seasonal pattern in δsource. In contrast to the forest sites, grassland and urban sites had a larger seasonal variation in δsource (5‰) dominated by seasonal transitions in C3/C4 grass productivity and in fossil fuel emissions, respectively. Our findings were sensitive to the location used to account for atmospheric background variation within the mixing model method that determined δsource. Special consideration should be given to background location depending on whether the intent is to understand site level dynamics or regional scale impacts of land-atmosphere exchange. The seasonal amplitude in δ13C of land-atmosphere CO2 exchange (δsource) varied across land cover types and was not driven by seasonal changes in vapor pressure deficit. The largest seasonal amplitudes of δsource were at grassland and urban sites, driven by changes in C3/C4 grass productivity and fossil fuel emissions, respectively. Mixing model approaches may incorrectly calculate δsource when background atmospheric observations are remote and/or prone to anthropogenic influence.

Climate models require an understanding of ecosystem-scale respiration and photosynthesis, yet there is no way of measuring these two fluxes directly; here, new instrumentation is used to determine these fluxes in a temperate forest, showing, for instance, that respiration is less during the day than at night. Seasonal variation in forest productivity Much of the carbon dioxide emitted into the atmosphere is taken up by forest ecosystems. Forest carbon sink estimates are based on the idea that ecosystem respiration is greater during the day than at night and that the efficiency of photosynthetic light use declines after spring. Rick Wehr et al. determine ecosystem photosynthesis and daytime respiration in a temperate deciduous forest over a three-year period on the basis of the isotopic composition of net ecosystem exchange. The work reveals that ecosystem respiration is in fact lower during the day than at night -- evidence of the inhibition of leaf respiration by light (the Kok effect) at the ecosystem scale. The authors argue that current approaches for estimating photosynthesis and daytime respiration do not take this effect into account and therefore overestimate ecosystem photosynthesis and daytime respiration at their forest site, and portray ecosystem photosynthetic light-use efficiency as declining when it is in fact stable. The findings may have implications for estimates of biospheric productivity and carbon cycle-climate interactions. Terrestrial ecosystems currently offset one-quarter of anthropogenic carbon dioxide (CO.sub.2) emissions because of a slight imbalance between global terrestrial photosynthesis and respiration.sup.1. Understanding what controls these two biological fluxes is therefore crucial to predicting climate change.sup.2. Yet there is no way of directly measuring the photosynthesis or daytime respiration of a whole ecosystem of interacting organisms; instead, these fluxes are generally inferred from measurements of net ecosystem-atmosphere CO.sub.2 exchange (NEE), in a way that is based on assumed ecosystem-scale responses to the environment. The consequent view of temperate deciduous forests (an important CO.sub.2 sink) is that, first, ecosystem respiration is greater during the day than at night; and second, ecosystem photosynthetic light-use efficiency peaks after leaf expansion in spring and then declines.sup.3, presumably because of leaf ageing or water stress. This view has underlain the development of terrestrial biosphere models used in climate prediction.sup.4,5 and of remote sensing indices of global biosphere productivity.sup.5,6. Here, we use new isotopic instrumentation.sup.7 to determine ecosystem photosynthesis and daytime respiration.sup.8 in a temperate deciduous forest over a three-year period. We find that ecosystem respiration is lower during the day than at night--the first robust evidence of the inhibition of leaf respiration by light.sup.9,10,11 at the ecosystem scale. Because they do not capture this effect, standard approaches.sup.12,13 overestimate ecosystem photosynthesis and daytime respiration in the first half of the growing season at our site, and inaccurately portray ecosystem photosynthetic light-use efficiency. These findings revise our understanding of forest-atmosphere carbon exchange, and provide a basis for investigating how leaf-level physiological dynamics manifest at the canopy scale in other ecosystems., Author(s): R. Wehr [sup.1] , J. W. Munger [sup.2] , J. B. McManus [sup.3] , D. D. Nelson [sup.3] , M. S. Zahniser [sup.3] , E. A. Davidson [sup.4] , [...]

An overview of the binary collision impact theory of spectral line shapes has been given to provide a unified statistical mechanical approach to line-shape theory, laser theory, nonlinear optics, and transport phenomena in dilute gases. The computation of spectral line profiles corresponding to those obtained from ultra-high-resolution spectral line-shape measurements requires numerical ab initio calculation of scattering amplitudes directly from the underlying dynamics of collisions between radiatively active molecules and their perturbers. The Wigner distribution function-density matrix is utilized to describe the kinetic theory of spectral line shapes and to discuss the various collisional processes that contribute to the kernel of kinetic equations. The influence of features of the potential energy surface on spectral parameters is also discussed, and the importance of comparing experimental line profiles directly with numerically computed line shapes obtained from reliable interaction potentials is emphasized. This contrasts sharply with the universal practice of comparing experimental line widths and shifts using some average or approximate theoretical scattering cross- sections and it contrasts sharply with fitting experimental profiles to some convenient analytical line-shape model; hence the phrase 'a paradigm shift' in the title of this work. PACS Nos.: 32.70.Jz, 33.20.-t, 33.70.Gj, 34.50.-s. Nous avons presente une revue de la theorie du profile de raies spectrales suite a des collisions binaires, de facon a developper une approche unifiee de mecanique statistique pour la theorie du profile de raie, l'optique non lineaire, la theorie des lasers et les phenomenes de transport dans les gaz dilues. Le calcul du profil des raies spectrales qui correspondent a ces mecanismes exige un calcul ab initio des amplitudes de diffusion directement a partir de la dynamique des collisions entre des molecules a impact radiatif et les mecanismes perturbateurs. Nous couplons la fonction de distribution de Wigner et la matrice de densite pour decrire la theorie cinetique du profile de raie spectrale et discuter les differents mecanismes de collision qui contribuent au noyau des equations cinetiques. Nous analysons egalement l'influence des particularites de la surface d'energie sur les parametres spectraux et nous insistons sur l'importance de comparer les profiles experimentaux de raie directement avec les profiles de raie calcules a partir de potentiels fiables. Ceci contraste nettement avec la pratique universelle ou on compare les valeurs experimentales des largeurs et deplacements de raie en utilisant des sections efficaces approximatives quelconques, theoriques ou moyennes et contraste nettement avec l'ajustement des profiles de raie experimentaux a une forme analytique commode; d'ou l'expression << un changement de paradigm >> dans le titre. [Traduit par la Redaction], 1. Introduction The impact theory of spectral line shapes has been around for about a century, beginning with the classical theory of Lorentz [1], and was essentially completed with the [...]

An infrared laser spectrometer based on difference-frequency generation in LiI[O.sub.3] is described. The spectrometer has a frequency uncertainty of less than 1 MHz and a signal-to-noise ratio between 3000:1 and 10,000:1. These properties allow the spectrometer to be used for studies of the non-Lorentzian and non-Voigt character of absorption line shapes in atmospheric trace gases. OCIS codes: 300.1030, 300.6190, 300.6320, 300.6340, 300.6360, 300.6390.

We present measurements of the shifts and widths of the rovibrational lines of the fundamental band of CO highly diluted in He and Ar at 296 K. The shifts are decomposed into parts odd and even in the line number, m. These are then compared with close coupled calculations carried out with the best known interaction potentials. There is general agreement between the calculated and measured values of the broadening and shifting. Furthermore, the results illustrate that the decomposition of the shifts into parts, odd and even in m, is a powerful tool for separating out the relative contributions of the isotropic and anisotropic part of the interaction to the shifts and which part needs to be corrected if there is a discrepancy. Thus, shift measurements can be added to the list of experiments that may be used to determine reliable interaction potentials. The results also show, given a potential, that close coupled calculations are accurate and could be used to confirm or establish empirical models of the temperature dependence of the broadening or shifting, etc. Such modeling is important at atmospheric physics. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Spatiotemporal variability in ozone dry deposition is often overlooked despite its implications for interpreting and modeling tropospheric ozone concentrations accurately. Understanding the influences of stomatal versus nonstomatal deposition processes on ozone deposition velocity is important for attributing observed changes in the ozone depositional sink and associated damage to ecosystems. Here, we aim to identify the stomatal versus nonstomatal deposition processes driving observed variability in ozone deposition velocity over the northeastern United States during June–September. We use ozone eddy covariance measurements from Harvard Forest in Massachusetts, which span a decade, and from Kane Experimental Forest in Pennsylvania and Sand Flats State Forest in New York, which span one growing season each, along with observation‐driven modeling. Using a cumulative precipitation indicator of soil wetness, we infer that high soil uptake during dry years and low soil uptake during wet years may contribute to the twofold interannual variability in ozone deposition velocity at Harvard Forest. We link stomatal deposition and humidity to variability in ozone deposition velocity on daily timescales. The humidity dependence may reflect higher uptake by leaf cuticles under humid conditions, noted in previous work. Previous work also suggests that uptake by leaf cuticles may be enhanced after rain, but we find that increases in ozone deposition velocity on rainy days are instead mostly associated with increases in stomatal conductance. Our analysis highlights a need for constraints on subseasonal variability in ozone dry deposition to soil and fast in‐canopy chemistry during ecosystem stress. Key Points: Stomatal and cuticular deposition are inferred as drivers of day‐to‐day variability in deposition velocityHigher stomatal uptake increases deposition velocity on rainy daysObserved interannual variability at Harvard Forest may reflect enhanced ozone deposition to dry soil [ABSTRACT FROM AUTHOR]

The seasonal pattern of the carbon isotope content (δ13C) of atmospheric CO2 depends on local and nonlocal land-atmosphere exchange and atmospheric transport. Previous studies suggested that the δ13C of the net land-atmosphere CO2 flux ( δsource) varies seasonally as stomatal conductance of plants responds to vapor pressure deficit of air (VPD). We studied the variation of δsource at seven sites across the United States representing forests, grasslands, and an urban center. Using a two-part mixing model, we calculated the seasonal δsource for each site after removing background influence and, when possible, removing δ13C variation of nonlocal sources. Compared to previous analyses, we found a reduced seasonal (March-September) variation in δsource at the forest sites (0.5‰ variation). We did not find a consistent seasonal relationship between VPD and δsource across forest (or other) sites, providing evidence that stomatal response to VPD was not the cause of the global, coherent seasonal pattern in δsource. In contrast to the forest sites, grassland and urban sites had a larger seasonal variation in δsource (5‰) dominated by seasonal transitions in C3/C4 grass productivity and in fossil fuel emissions, respectively. Our findings were sensitive to the location used to account for atmospheric background variation within the mixing model method that determined δsource . Special consideration should be given to background location depending on whether the intent is to understand site level dynamics or regional scale impacts of land-atmosphere exchange. The seasonal amplitude in δ13C of land-atmosphere CO2 exchange ( δsource ) varied across land cover types and was not driven by seasonal changes in vapor pressure deficit. The largest seasonal amplitudes of δsource were at grassland and urban sites, driven by changes in C3/C4 grass productivity and fossil fuel emissions, respectively. Mixing model approaches may incorrectly calculate δsource when background atmospheric observations are remote and/or prone to anthropogenic influence. [ABSTRACT FROM AUTHOR]