Microbial role in N2O-NO2 production and CH4 oxidation under active hypogenic settings

The hydrothermal caves linked to active faulting have subterranean atmospheres with a distinctive gaseous composition containing deep endogenous gases, such as carbon dioxide, methane and nitrogen oxides (NOx). Ascending fluids through associated near-surface hydrothermal processes can mobilize endogenous gases into the Critical Zone and, ultimately, to the lower troposphere. Nitrogen oxides are polluting gases and can have adverse effects on human health, especially inhaled NO2. They also catalyse ozone (O3) production in the lower layers of the atmosphere and the greenhouse effect, when they react with volatile organic compounds. The largest source of NOx emissions is anthropogenic. The rest is produced naturally by microbial processes in soil and water, by lightning, volcanic activity, storms, etc. Production of N2O and NO2 is associated with soil and other active-geothermal ecosystems, far less is known about the sources and sinks of these gases within subterranean locations. Here, we report high N2O and NO2 concentrations detected along a hypogenic system associated with an active faulting (Vapour Cave, southern Spain), which enables direct gas exchange with the low-atmosphere. These anomalous concentrations of N2O and, NO2 are about ten and five times higher than the typical atmospheric background, respectively. Gaseous composition analyses of subterranean atmosphere were conducted by high precision field-deployable CRDS and FTIR spectrometers for measuring in situ the target tracer gases (NO2, N2O, CH4, CO2) and &#948;13C of both carbon-GHGs. DNA extraction, sequencing and phylogenetic analyses were conducted to characterize the microbial community of cave sediments. The results showed that N2O and NO2 emission depends on the activity of nitrification by ammonia oxidizing microorganisms (such as members of the family Nitrosomonadaceae and phylum Thaumarchaeota) and/or as a result of incomplete denitrification by heterotrophic denitrifying bacteria (such as Bacillus, Acinetobacter and Cupriavidus) from this hydrothermal and hypoxic ecosystem. On the other hand, CH4 concentrations and &#948;13CH4 vary along the cave (with the deep), in deepest cave locations CH4 values are higher with lighter &#948;13C values in comparison with the more superficial areas, which indicates a deep endogenous origin of methane. However, in areas near the entrance we observe lower concentrations of methane and heavier &#948;13C values (CH4<1 ppm and &#948;13C close to &#8722;30&#8240;), as a result of methane oxidation by denitrifying methanotrophs of the NC10 phylum during gas migration from the deepest areas to the surface.These new findings reveal the sourcing of these nitrogenous gases into the upper vadose zone of a hypogenic/geothermal ecosystem, and its potential release to the lower troposphere. A better understanding of biogeochemical processes controlling the production of nitrogenous gases in subterranean environments will be useful to identify and characterize new possible sources, reservoirs and sinks of greenhouse gases (CO2, CH4, N2O and NOx) in order to calculate more accurately the budgets and for the design of new mitigation strategies of these gases.

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Cyclonic and anticyclonic contributions to atmospheric energetics

Scientific Reports ◽

10.1038/s41598-021-92548-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Satoru Okajima ◽

Hisashi Nakamura ◽

Yohai Kaspi

Keyword(s):

Storm Track ◽

Mean Flow ◽

Weather Variability ◽

Jet Streams ◽

Near Surface ◽

Westerly Jet ◽

Track Dynamics ◽

New Findings ◽

Atmospheric Energetics ◽

Thermally Driven

AbstractMigratory cyclones and anticyclones account for most of the day-to-day weather variability in the extratropics. These transient eddies act to maintain the midlatitude jet streams by systematically transporting westerly momentum and heat. Yet, little is known about the separate contributions of cyclones and anticyclones to their interaction with the westerlies. Here, using a novel methodology for identifying cyclonic and anticyclonic vortices based on curvature, we quantify their separate contributions to atmospheric energetics and their feedback on the westerly jet streams as represented in Eulerian statistics. We show that climatological westerly acceleration by cyclonic vortices acts to dominantly reinforce the wintertime eddy-driven near-surface westerlies and associated cyclonic shear. Though less baroclinic and energetic, anticyclones still play an important role in transporting westerly momentum toward midlatitudes from the upper-tropospheric thermally driven jet core and carrying eddy energy downstream. These new findings have uncovered essential characteristics of atmospheric energetics, storm track dynamics and eddy-mean flow interaction.

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Multi-model subseasonal forecasts of spring cold spells: potential value for the hazelnut agribusiness

10.5194/egusphere-egu2020-20707 ◽

2020 ◽

Author(s):

Paolo Ruggieri ◽

Stefano Materia ◽

Angel G. Muñoz ◽

M.Carmen Alvarez Castro ◽

Simon J. Mason ◽

...

Keyword(s):

Black Sea ◽

Extreme Event ◽

Global Scale ◽

Mitigation Strategies ◽

Added Value ◽

Economic Sectors ◽

Near Surface ◽

Black Sea Region ◽

Probabilistic Forecasts ◽

Spring Frosts

Producing probabilistic subseasonal forecasts of extreme events up to six weeks in advance is crucial for many economic sectors. In agribusiness, this time-scale is particularly critical because it allows for mitigation strategies to be adopted for counteracting weather hazards and taking advantage of opportunities. For example, spring frosts are detrimental for many nut trees, resulting in dramatic losses at harvest time. To explore subseasonal forecast quality in boreal spring, identified as one of the most sensitive times of the year by agribusiness end-users, we build a multi-system ensemble using four models involved in the Subseasonal-to-Seasonal (S2S) Prediction Project. Two-meter temperature forecasts are used to analyze cold spell predictions in the coastal Black Sea region, an area that is a global leader in the production of hazelnuts. When analyzed at global scale, the multi-system ensemble probabilistic forecasts for near-surface temperature is better than climatological values for several regions, especially the Tropics, even many weeks in advance; however, in coastal Black Sea skill is low after the second forecast week. When cold spells are predicted instead of near-surface temperatures, skill improves for the region, and the forecasts prove to contain potentially useful information to stakeholders willing to put mitigation plans into effect. Using a cost-loss model approach for the first time in this context, we show that there is added value of having such a forecast system instead of a business-as-usual strategy, not only for predictions released one to two weeks ahead of the extreme event, but also at longer lead-times.

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Impact of land–water sensitivity contrast on MOPITT retrievals and trends over a coastal city

Atmospheric Measurement Techniques ◽

10.5194/amt-13-3521-2020 ◽

2020 ◽

Vol 13 (7) ◽

pp. 3521-3542

Author(s):

Ian Ashpole ◽

Aldona Wiacek

Keyword(s):

Transport Model ◽

Weighted Least Squares ◽

Temporal Trends ◽

Lower Troposphere ◽

Near Surface ◽

Surface Level ◽

Coastal City ◽

Water Sensitivity ◽

Land Water ◽

Co Concentrations

Abstract. We compare MOPITT Version 7 (V7) Level 2 (L2) and Level 3 (L3) carbon monoxide (CO) products for the 1∘×1∘ L3 grid box containing the coastal city of Halifax, Canada (longitude −63.58∘, latitude 44.65∘), with a focus on the seasons DJF and JJA, and highlight a limitation in the L3 products that has significant consequences for the temporal trends in near-surface CO identified using those data. Because this grid box straddles the coastline, the MOPITT L3 products are created from the finer spatial resolution L2 products that are retrieved over both land and water, with a greater contribution from retrievals over water because more of the grid box lies over water than land. We create alternative L3 products for this grid box by separately averaging the bounded L2 retrievals over land (L3L) and water (L3W) and demonstrate that profile and total column CO (TCO) concentrations, retrieved at the same time, differ depending on whether the retrieval took place over land or water. These differences (ΔRET) are greatest in the lower troposphere (LT), where mean retrieved volume mixing ratios (VMRs) are greater in L3W than L3L, with maximum mean differences of 11.6 % (14.3 ppbv, p=0.001) at the surface level in JJA. Retrieved CO concentrations are more similar, on average, in the middle and upper troposphere (MT and UT), although large differences (in excess of 40 %) do infrequently occur. TCO is also greater in L3W than L3L in both seasons. By analysing L3L and L3W retrieval averaging kernels and simulations of these retrievals, we demonstrate that, in JJA, ΔRET is strongly influenced by differences in retrieval sensitivity over land and water, especially close to the surface where L3L has significantly greater information content than L3W. In DJF, land–water differences in retrieval sensitivity are much less pronounced and appear to have less of an impact on ΔRET, which analysis of wind directions suggests is more likely to reflect differences in true profile concentrations (i.e. real differences). The original L3 time series for the 1∘×1∘ grid box containing Halifax (L3O) corresponds much more closely to L3W than L3L, owing to the greater contribution from L2 retrievals over water than land. Thus, in JJA, variability in retrieved CO concentrations close to the surface in L3O is suppressed compared to L3L, and a declining trend detected using weighted least squares (WLS) regression analysis is significantly slower in L3O (strongest surface level trend identifiable is −1.35 (±0.35) ppbv yr−1) than L3L (−2.85 (±0.60) ppbv yr−1). This is because contributing L2 retrievals over water are closely tied to a priori CO concentrations used in the retrieval, owing to their lack of near-surface sensitivity in JJA, and these are based on monthly climatological CO profiles from a chemical transport model and therefore have no yearly change (surface level trend in L3W is −0.60 (±0.33) ppbv yr−1). Although our analysis focuses on DJF and JJA, we demonstrate that the findings also apply to MAM and SON. The results that we report here suggest that similar analyses be performed for other coastal cities before using MOPITT surface CO.

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Dominant Anomaly Patterns in the Near-Surface Baroclinicity and Accompanying Anomalies in the Atmosphere and Oceans. Part II: North Pacific Basin

Journal of Climate ◽

10.1175/2010jcli3017.1 ◽

2010 ◽

Vol 23 (24) ◽

pp. 6445-6467 ◽

Cited By ~ 26

Author(s):

Mototaka Nakamura ◽

Shozo Yamane

Keyword(s):

Heat Flux ◽

North Pacific ◽

Spatial Scales ◽

Baroclinic Instability ◽

Lower Troposphere ◽

Pacific Basin ◽

Mean Flow ◽

Near Surface ◽

Eddy Heat Flux ◽

North Pacific Basin

Abstract Variability in the monthly-mean flow and storm track in the North Pacific basin is examined with a focus on the near-surface baroclinicity. Dominant patterns of anomalous near-surface baroclinicity found from empirical orthogonal function (EOF) analyses generally show mixed patterns of shift and changes in the strength of near-surface baroclinicity. Composited anomalies in the monthly-mean wind at various pressure levels based on the signals in the EOFs show accompanying anomalies in the mean flow up to 50 hPa in the winter and up to 100 hPa in other seasons. Anomalous eddy fields accompanying the anomalous near-surface baroclinicity patterns exhibit, broadly speaking, structures anticipated from simple linear theories of baroclinic instability, and suggest a tendency for anomalous wave fluxes to accelerate–decelerate the surface westerly accordingly. However, the relationship between anomalous eddy fields and anomalous near-surface baroclinicity in the midwinter is not consistent with the simple linear baroclinic instability theories. Composited anomalous sea surface temperature (SST) accompanying anomalous near-surface baroclinicity often exhibits moderate values and large spatial scales in the basin, rather than large values concentrated near the oceanic fronts. In the midsummer and in some cases in cold months, however, large SST anomalies are found around the Kuroshio–Oyashio Extensions. Accompanying anomalies in the net surface heat flux, SST in the preceding and following months, and meridional eddy heat flux in the lower troposphere suggest active roles played by the ocean in generating the concomitant anomalous large-scale atmospheric state in some of these cases.

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Evaluation of a Regional Reanalysis and ERA-Interim over East Asia Using In Situ Observations during 2013–14

Journal of Applied Meteorology and Climatology ◽

10.1175/jamc-d-16-0227.1 ◽

2017 ◽

Vol 56 (10) ◽

pp. 2821-2844 ◽

Cited By ~ 7

Author(s):

Eun-Gyeong Yang ◽

Hyun Mee Kim

Keyword(s):

Relative Humidity ◽

East Asia ◽

Geopotential Height ◽

Spatial Scales ◽

Weather Prediction ◽

Surface Wind ◽

Lower Troposphere ◽

Near Surface ◽

Skill Scores ◽

Regional Reanalysis

AbstractIn this study, the East Asia Regional Reanalysis (EARR) is developed for the period 2013–14 and characteristics of the EARR are examined in comparison with ERA-Interim (ERA-I) reanalysis. The EARR is based on the Unified Model with 12-km horizontal resolution, which has been an operational numerical weather prediction model at the Korea Meteorological Administration since being adopted from the Met Office in 2011. Relative to the ERA-I, in terms of skill scores, the EARR performance for wind, temperature, relative humidity, and geopotential height improves except for mean sea level pressure, the lower-troposphere geopotential height, and the upper-air relative humidity. In a similar way, RMSEs of the EARR are smaller than those of ERA-I for wind, temperature, and relative humidity, except for the upper-air meridional wind and the upper-air relative humidity in January. With respect to the near-surface variables, the triple collocation analysis and the correlation coefficients confirm that EARR provides a much improved representation when compared with ERA-I. In addition, EARR reproduces the finescale features of near-surface variables in greater detail than ERA-I does, and the kinetic energy (KE) spectra of EARR agree more with the canonical atmospheric KE spectra than do the ERA-I KE spectra. On the basis of the fractions skill score, the near-surface wind of EARR is statistically significantly better simulated than that of ERA-I for all thresholds, except for the higher threshold at smaller spatial scales. Therefore, although special care needs to be taken when using the upper-air relative humidity from EARR, the near-surface variables of the EARR that were developed are found to be more accurate than those of ERA-I.

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Measuring the Vertical Profiles of Aerosol Extinction in the Lower Troposphere by MAX-DOAS at a Rural Site in the North China Plain

Atmosphere ◽

10.3390/atmos11101037 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1037

Author(s):

Siyang Cheng ◽

Junli Jin ◽

Jianzhong Ma ◽

Xiaobin Xu ◽

Liang Ran ◽

...

Keyword(s):

North China Plain ◽

North China ◽

Lower Troposphere ◽

Temporal Variations ◽

Rural Site ◽

Optical Absorption Spectroscopy ◽

Aerosol Extinction ◽

Vertical Profiles ◽

Near Surface ◽

The North

Ground-based multi-axis differential optical absorption spectroscopy (MAX-DOAS) measurements were performed during the summer (13 June–20 August) of 2014 at a rural site in North China Plain. The vertical profiles of aerosol extinction (AE) in the lower troposphere were retrieved to analyze the temporal variations of AE profiles, near-surface AE, and aerosol optical depth (AOD). The average AOD and near-surface AE over the period of study were 0.51 ± 0.26 and 0.33 ± 0.18 km−1 during the effective observation period, respectively. High AE events and elevated AE layers were identified based on the time series of hourly AE profiles, near-surface AEs and AODs. It is found that in addition to the planetary boundary layer height (PBLH) and relative humidity (RH), the variations in the wind field have large impacts on the near-surface AE, AOD, and AE profile. Among 16 wind sectors, higher AOD or AE occur mostly in the directions of the cities upstream. The diurnal variations of the AE profiles, AODs and near-surface AEs are significant and influenced mainly by the source emissions, PBLH, and RH. The AE profile shape from MAX-DOAS measurement is generally in agreement with that from light detection and ranging (lidar) observations, although the AE absolute levels are different. Overall, ground-based MAX-DOAS can serve as a supplement to measure the AE vertical profiles in the lower troposphere.

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Phyllodistomum kupermani n. sp. from the European perch, Perca fluviatilis L. (Perciformes: Percidae), and redescription of Phyllodistomum macrocotyle (Lühe, 1909) with notes on the species diversity and host specificity in the European Phyllodistomum spp. (Trematoda: Gorgoderidae)

Parasites & Vectors ◽

10.1186/s13071-020-04434-2 ◽

2020 ◽

Vol 13 (1) ◽

Author(s):

Romualda Petkevičiūtė ◽

Alexander E. Zhokhov ◽

Virmantas Stunžėnas ◽

Larisa G. Poddubnaya ◽

Gražina Stanevičiūtė

Keyword(s):

Urinary Bladder ◽

Surface Topography ◽

Phylogenetic Analyses ◽

Perca Fluviatilis ◽

Species Differentiation ◽

Freshwater Species ◽

European Perch ◽

Volga River ◽

Tegumental Surface ◽

New Findings

Abstract Background European species of the large genus Phyllodistomum Braun, 1899 had historically been erected based solely on morphological characters. Unfortunately, many of them are still poorly known and inadequately described. Molecular approaches are critical to delineate species which were impossible to differentiate based on morphology alone. Methods New samples of adult Phyllodistomum spp. were collected from the urinary bladder and/or ureters of European freshwater fishes and fixed to conduct a light and scanning electron microscopy study, and to obtain sequences of nuclear (ITS2 spacer and 28S rRNA gene), to be analysed in the context of a molecular phylogeny. Results Based on new findings, a new species of Phyllodistomum from the urinary bladder of the European perch, Perca fluviatilis, in Volga River basin, Russia, is described. Additionally, new data on the morphology and tegumental surface topography of P. macrocotyle (Lühe, 1909) Odhner, 1911 from ureters of the common rudd, Scardinius erythrophthalmus, is presented. The host range of P. folium, confirmed by DNA analysis, is extended to other cyprinid fish species. Conclusions The present study has again shown that species of the genus Phyllodistomum are in dire need of revision based on both molecular analysis and detailed morphological redescriptions of the forms attributed to the genus. Morphologically, P. kupermani n. sp. most closely resembles P. pseudofolium, a highly host-specific parasite of Gymnocephalus cernuus (L.), but molecular phylogenetic analyses based on ITS2 and 28S rDNA sequences showed that these species are distantly related. Phyllodistomum kupermani n. sp. was found to be phylogenetically most closely related to the type-species of Phyllodistomum, P. folium. Phylogenetic analyses revealed that Phyllodistomum kupermani n. sp. and P. folium formed a clade with other freshwater species for which cystocercous cercariae develop in bivalves of the family Sphaeriidae. The micromorphology and tegumental surface topography of P. macrocotyle revealed in the present study provide a valuable taxonomic criterion for congeneric species differentiation.

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New findings of Coprinellus species (Psathyrellaceae, Agaricales) in China

Phytotaxa ◽

10.11646/phytotaxa.374.2.3 ◽

2018 ◽

Vol 374 (2) ◽

pp. 119 ◽

Cited By ~ 2

Author(s):

MEI HUANG ◽

TOLGOR BAU

Keyword(s):

New Species ◽

Maximum Likelihood ◽

Bayesian Methods ◽

Phylogenetic Analyses ◽

Morphological Features ◽

Its Sequences ◽

New Findings ◽

A New Species

Two taxa of Coprinellus from China are described on the basis of morphological features and phylogeny. Coprinellus pseudodisseminatus is described as a new species in Coprinellus section Setulosi due to its milky-white to pale-grey pileus, lageniform caulocystidia, the presence of pileocystidia and cheilocystidia, and ellipsoid basidiospores. Coprinellus aureogranulatus, belonging to section Micacei, is new to China. Phylogenetic analyses based on ITS sequences by the Maximum Likelihood and Bayesian methods showed that C. pseudodisseminatus and C. aureogranulatus are a new and newly recorded species, respectively. Illustrations, photographs, and detailed descriptions of the two species are provided.

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Dynamics of Lower-Tropospheric Vorticity in Idealized Simulations of Tropical Cyclone Formation

Journal of the Atmospheric Sciences ◽

10.1175/jas-d-18-0219.1 ◽

2019 ◽

Vol 76 (3) ◽

pp. 707-727 ◽

Cited By ~ 3

Author(s):

Yaping Wang ◽

Christopher A. Davis ◽

Yongjie Huang

Keyword(s):

Boundary Layer ◽

Tropical Cyclone ◽

Mass Flux ◽

Cloud Model ◽

Vertical Wind Shear ◽

Lower Troposphere ◽

Cold Pool ◽

Surface Drag ◽

Near Surface ◽

Cold Pools

Abstract Idealized simulations are conducted using the Cloud Model version 1 (CM1) to explore the mechanism of tropical cyclone (TC) genesis from a preexisting midtropospheric vortex that forms in radiative–convective equilibrium. With lower-tropospheric air approaching near saturation during TC genesis, convective cells become stronger, along with the intensifying updrafts and downdrafts and the larger area coverage of updrafts relative to downdrafts. Consequently, the low-level vertical mass flux increases, inducing vorticity amplification above the boundary layer. Of interest is that while surface cold pools help organize lower-tropospheric updrafts, genesis still proceeds, only slightly delayed, if subcloud evaporation cooling and cold pool intensity are drastically reduced. More detrimental is the disruption of near saturation through the introduction of weak vertical wind shear. The lower-tropospheric dry air suppresses the strengthening of convection, leading to weaker upward mass flux and much slower near-surface vortex spinup. We also find that surface spinup is similarly inhibited by decreasing surface drag despite the existence of a nearly saturated column, whereas larger drag accelerates spinup. Increased vorticity above the boundary layer is followed by the emergence of a horizontal pressure gradient through the depth of the boundary layer. Then the corresponding convergence resulting from the gradient imbalance in the frictional boundary layer causes vorticity amplification near the surface. It is suggested that near saturation in the lower troposphere is critical for increasing the mass flux and vorticity just above the boundary layer, but it is necessary yet insufficient because the spinup is strongly governed by boundary layer dynamics.

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Geochemical Fingerprinting of Rising Deep Endogenous Gases in an Active Hypogenic Karst System

Geofluids ◽

10.1155/2018/4934520 ◽

2018 ◽

Vol 2018 ◽

pp. 1-19 ◽

Cited By ~ 3

Author(s):

A. Fernandez-Cortes ◽

R. Perez-Lopez ◽

S. Cuezva ◽

J. M. Calaforra ◽

J. C. Cañaveras ◽

...

Keyword(s):

Pooled Analysis ◽

Microbial Reduction ◽

Karst System ◽

Microbial Oxidation ◽

Active Faulting ◽

Measured Concentration ◽

Geochemical Fingerprinting ◽

Gas Formation ◽

Gaseous Composition ◽

Cave Environment

The hydrothermal caves linked to active faulting can potentially harbour subterranean atmospheres with a distinctive gaseous composition with deep endogenous gases, such as carbon dioxide (CO2) and methane (CH4). In this study, we provide insight into the sourcing, mixing, and biogeochemical processes involved in the dynamic of deep endogenous gas formation in an exceptionally dynamic hypogenic karst system (Vapour Cave, southern Spain) associated with active faulting. The cave environment is characterized by a prevailing combination of rising warm air with large CO2 outgassing (>1%) and highly diluted CH4 with an endogenous origin. The δ13CCO2 data, which ranges from −4.5 to −7.5‰, point to a mantle-rooted CO2 that is likely generated by the thermal decarbonation of underlying marine carbonates, combined with degassing from CO2-rich groundwater. A pooled analysis of δ13CCO2 data from exterior, cave, and soil indicates that the upwelling of geogenic CO2 has a clear influence on soil air, which further suggests a potential for the release of CO2 along fractured carbonates. CH4 molar fractions and their δD and δ13C values (ranging from −77 to −48‰ and from −52 to −30‰, respectively) suggest that the methane reaching Vapour Cave is the remnant of a larger source of CH4, which was likely generated by microbial reduction of carbonates. This CH4 has been affected by a postgenetic microbial oxidation, such that the gas samples have changed in both molecular and isotopic composition after formation and during migration through the cave environment. Yet, in the deepest cave locations (i.e., 30 m below the surface), measured concentration values of deep endogenous CH4 are higher than in atmospheric with lighter δ13C values with respect to those found in the local atmosphere, which indicates that Vapour Cave may occasionally act as a net source of CH4 to the open atmosphere.

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