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1. Florida mangrove saltmarsh reference surface soils

   https://doi.org/10.6073/pasta/0e08cbe07c84488cb7b9dd16669946d0  

   Lewis, David Bruce ( January 2021 , Environmental Data Initiative)

   Site description. This data package consists of data obtained from sampling surface soil (the 0-7.6 cm depth profile) in black mangrove (Avicennia germinans) dominated forest and black needlerush (Juncus roemerianus) saltmarsh along the Gulf of Mexico coastline in peninsular west-central Florida, USA. This location has a subtropical climate with mean daily temperatures ranging from 15.4 °C in January to 27.8 °C in August, and annual precipitation of 1336 mm. Precipitation falls as rain primarily between June and September. Tides are semi-diurnal, with 0.57 m median amplitudes during the year preceding sampling (U.S. NOAA National Ocean Service, Clearwater Beach, Florida, station 8726724). Sea-level rise is 4.0 ± 0.6 mm per year (1973-2020 trend, mean ± 95 % confidence interval, NOAA NOS Clearwater Beach station). The A. germinans mangrove zone is either adjacent to water or fringed on the seaward side by a narrow band of red mangrove (Rhizophora mangle). A near-monoculture of J. roemerianus is often adjacent to and immediately landward of the A. germinans zone. The transition from the mangrove to the J. roemerianus zone is variable in our study area. An abrupt edge between closed-canopy mangrove and J. roemerianus monoculture may extend for up to several hundred meters in some locations, while other stretches of ecotone present a gradual transition where smaller, widely spaced trees are interspersed into the herbaceous marsh. Juncus roemerianus then extends landward to a high marsh patchwork of succulent halophytes (including Salicornia bigellovi, Sesuvium sp., and Batis maritima), scattered dwarf mangrove, and salt pans, followed in turn by upland vegetation that includes Pinus sp. and Serenoa repens. Field design and sample collection. We established three study sites spaced at approximately 5 km intervals along the western coastline of the central Florida peninsula. The sites consisted of the Salt Springs (28.3298°, -82.7274°), Energy Marine Center (28.2903°, -82.7278°), and Green Key (28.2530°, -82.7496°) sites on the Gulf of Mexico coastline in Pasco County, Florida, USA. At each site, we established three plot pairs, each consisting of one saltmarsh plot and one mangrove plot. Plots were 50 m^2 in size. Plots pairs within a site were separated by 230-1070 m, and the mangrove and saltmarsh plots composing a pair were 70-170 m apart. All plot pairs consisted of directly adjacent patches of mangrove forest and J. roemerianus saltmarsh, with the mangrove forests exhibiting a closed canopy and a tree architecture (height 4-6 m, crown width 1.5-3 m). Mangrove plots were located at approximately the midpoint between the seaward edge (water-mangrove interface) and landward edge (mangrove-marsh interface) of the mangrove zone. Saltmarsh plots were located 20-25 m away from any mangrove trees and into the J. roemerianus zone (i.e., landward from the mangrove-marsh interface). Plot pairs were coarsely similar in geomorphic setting, as all were located on the Gulf of Mexico coastline, rather than within major sheltering formations like Tampa Bay, and all plot pairs fit the tide-dominated domain of the Woodroffe classification (Woodroffe, 2002, "Coasts: Form, Process and Evolution", Cambridge University Press), given their conspicuous semi-diurnal tides. There was nevertheless some geomorphic variation, as some plot pairs were directly open to the Gulf of Mexico while others sat behind keys and spits or along small tidal creeks. Our use of a plot-pair approach is intended to control for this geomorphic variation. Plot center elevations (cm above mean sea level, NAVD 88) were estimated by overlaying the plot locations determined with a global positioning system (Garmin GPS 60, Olathe, KS, USA) on a LiDAR-derived bare-earth digital elevation model (Dewberry, Inc., 2019). The digital elevation model had a vertical accuracy of ± 10 cm (95 % CI) and a horizontal accuracy of ± 116 cm (95 % CI). Soil samples were collected via coring at low tide in June 2011. From each plot, we collected a composite soil sample consisting of three discrete 5.1 cm diameter soil cores taken at equidistant points to 7.6 cm depth. Cores were taken by tapping a sleeve into the soil until its top was flush with the soil surface, sliding a hand under the core, and lifting it up. Cores were then capped and transferred on ice to our laboratory at the University of South Florida (Tampa, Florida, USA), where they were combined in plastic zipper bags, and homogenized by hand into plot-level composite samples on the day they were collected. A damp soil subsample was immediately taken from each composite sample to initiate 1 y incubations for determination of active C and N (see below). The remainder of each composite sample was then placed in a drying oven (60 °C) for 1 week with frequent mixing of the soil to prevent aggregation and liberate water. Organic wetland soils are sometimes dried at 70 °C, however high drying temperatures can volatilize non-water liquids and oxidize and decompose organic matter, so 50 °C is also a common drying temperature for organic soils (Gardner 1986, "Methods of Soil Analysis: Part 1", Soil Science Society of America); we accordingly chose 60 °C as a compromise between sufficient water removal and avoidance of non-water mass loss. Bulk density was determined as soil dry mass per core volume (adding back the dry mass equivalent of the damp subsample removed prior to drying). Dried subsamples were obtained for determination of soil organic matter (SOM), mineral texture composition, and extractable and total carbon (C) and nitrogen (N) within the following week. Sample analyses. A dried subsample was apportioned from each composite sample to determine SOM as mass loss on ignition at 550 °C for 4 h. After organic matter was removed from soil via ignition, mineral particle size composition was determined using a combination of wet sieving and density separation in 49 mM (3 %) sodium hexametaphosphate ((NaPO_3)_6) following procedures in Kettler et al. (2001, Soil Science Society of America Journal 65, 849-852). The percentage of dry soil mass composed of silt and clay particles (hereafter, fines) was calculated as the mass lost from dispersed mineral soil after sieving (0.053 mm mesh sieve). Fines could have been slightly underestimated if any clay particles were burned off during the preceding ignition of soil. An additional subsample was taken from each composite sample to determine extractable N and organic C concentrations via 0.5 M potassium sulfate (K_2SO_4) extractions. We combined soil and extractant (ratio of 1 g dry soil:5 mL extractant) in plastic bottles, reciprocally shook the slurry for 1 h at 120 rpm, and then gravity filtered it through Fisher G6 (1.6 μm pore size) glass fiber filters, followed by colorimetric detection of nitrite (NO_2^-) + nitrate (NO_3^-) and ammonium (NH_4^+) in the filtrate (Hood Nowotny et al., 2010,Soil Science Society of America Journal 74, 1018-1027) using a microplate spectrophotometer (Biotek Epoch, Winooski, VT, USA). Filtrate was also analyzed for dissolved organic C (referred to hereafter as extractable organic C) and total dissolved N via combustion and oxidation followed by detection of the evolved CO_2 and N oxide gases on a Formacs HT TOC/TN analyzer (Skalar, Breda, The Netherlands). Extractable organic N was then computed as total dissolved N in filtrate minus extractable mineral N (itself the sum of extractable NH_4-N and NO_2-N + NO_3-N). We determined soil total C and N from dried, milled subsamples subjected to elemental analysis (ECS 4010, Costech, Inc., Valencia, CA, USA) at the University of South Florida Stable Isotope Laboratory. Median concentration of inorganic C in unvegetated surface soil at our sites is 0.5 % of soil mass (Anderson, 2019, Univ. of South Florida M.S. thesis via methods in Wang et al., 2011, Environmental Monitoring and Assessment 174, 241-257). Inorganic C concentrations are likely even lower in our samples from under vegetation, where organic matter would dilute the contribution of inorganic C to soil mass. Nevertheless, the presence of a small inorganic C pool in our soils may be counted in the total C values we report. Extractable organic C is necessarily of organic C origin given the method (sparging with HCl) used in detection. Active C and N represent the fractions of organic C and N that are mineralizable by soil microorganisms under aerobic conditions in long-term soil incubations. To quantify active C and N, 60 g of field-moist soil were apportioned from each composite sample, placed in a filtration apparatus, and incubated in the dark at 25 °C and field capacity moisture for 365 d (as in Lewis et al., 2014, Ecosphere 5, art59). Moisture levels were maintained by frequently weighing incubated soil and wetting them up to target mass. Daily CO_2 flux was quantified on 29 occasions at 0.5-3 week intervals during the incubation period (with shorter intervals earlier in the incubation), and these per day flux rates were integrated over the 365 d period to compute an estimate of active C. Observations of per day flux were made by sealing samples overnight in airtight chambers fitted with septa and quantifying headspace CO_2 accumulation by injecting headspace samples (obtained through the septa via needle and syringe) into an infrared gas analyzer (PP Systems EGM 4, Amesbury, MA, USA). To estimate active N, each incubated sample was leached with a C and N free, 35 psu solution containing micronutrients (Nadelhoffer, 1990, Soil Science Society of America Journal 54, 411-415) on 19 occasions at increasing 1-6 week intervals during the 365 d incubation, and then extracted in 0.5 M K_2SO_4 at the end of the incubation in order to remove any residual mineral N. Active N was then quantified as the total mass of mineral N leached and extracted. Mineral N in leached and extracted solutions was detected as NH_4-N and NO_2-N + NO_3-N via colorimetry as above. This incubation technique precludes new C and N inputs and persistently leaches mineral N, forcing microorganisms to meet demand by mineralizing existing pools, and thereby directly assays the potential activity of soil organic C and N pools present at the time of soil sampling. Because this analysis commences with disrupting soil physical structure, it is biased toward higher estimates of active fractions. Calculations. Non-mobile C and N fractions were computed as total C and N concentrations minus the extractable and active fractions of each element. This data package reports surface-soil constituents (moisture, fines, SOM, and C and N pools and fractions) in both gravimetric units (mass constituent / mass soil) and areal units (mass constituent / soil surface area integrated through 7.6 cm soil depth, the depth of sampling). Areal concentrations were computed as X × D × 7.6, where X is the gravimetric concentration of a soil constituent, D is soil bulk density (g dry soil / cm^3), and 7.6 is the sampling depth in cm. 

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2. Experimental study of metamorphic reactions and dehydration processes at the blueschist–eclogite transition during warm subduction

   https://doi.org/10.1111/jmg.12560  

   Cheng, Nanfei ; Jenkins, David M. ( August 2020 , Journal of Metamorphic Geology)

   The transition between blueschist and eclogite plays an important role in subduction zones via dehydration and densification processes in descending oceanic slabs. There are a number of previous petrological studies describing potential mineral reactions taking place at the transition. An experimental determination of such reactions could help constrain the pressure–temperature conditions of the transition as well as the processes of dehydration. However, previous experimental contributions have focused on the stability of spontaneously formed hydrous minerals in basaltic compositions rather than on reactions among already formed blueschist facies minerals. Therefore, this study conducted three groups of experiments to explore the metamorphic reactions among blueschist facies minerals at conditions corresponding to warm subduction, where faster reaction rates are possible on the time scale of laboratory experiments. The first group of experiments was to establish experimental reversals of the reaction glaucophane+paragonite to jadeite+pyrope+quartz+H₂O over the range of 2.2–3.5 GPa and 650–820°C. This reaction has long been treated as key to the blueschist–eclogite transition. However, only the growth of glaucophane+paragonite was observed at the intersectional stability field of both paragonite and jadeite+quartz, confirming thermodynamic calculations that the reaction is not stable in the system Na₂O–MgO–Al₂O₃–SiO₂–H₂O. The second set of experiments involved unreversed experiments using glaucophane+zoisite ±quartz in low‐Fe and Ca‐rich systems and were run at 1.8–2.4 GPa and 600–780°C. These produced omphacite+paragonite/kyanite+H₂O accompanied by compositional shifts in the sodium amphibole, glaucophane, towards sodium–calcium amphiboles such as winchite (☐(CaNa)(Mg₄Al)Si₈O₂₂(OH)₂) and barroisite (☐(CaNa)(Mg₃Al₂)(AlSi₇)O₂₂(OH)₂). This suggests that a two‐step dehydration occurs, first involving the breakdown of glaucophane+zoisite towards a paragonite‐bearing assemblage, then the breakdown of paragonite to release H₂O. It also indicates that sodium–calcium amphibole can coexist with eclogite phases, thereby extending the thermal stability of amphibole to greater subduction zone depths. The third set of experiments was an experimental investigation at 2.0–2.4 GPa and 630–850°C involving a high‐Fe (Fe#=Fe_total/(Fe_total+Mg)≈0.36) natural glaucophane, synthetic paragonite and their eclogite‐forming reaction products. The results indicated that garnet and omphacite grew over most of these pressure–temperature conditions, which demonstrates the importance of Fe‐rich glaucophane in forming the key eclogite assemblage of garnet+omphacite, even under warm subduction zone conditions. Based on the experiments of this study, reaction between glaucophane+zoisite is instrumental in controlling dehydration processes at the blueschist–eclogite transition during warm subduction.

    

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3. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography

   https://doi.org/10.7554/eLife.07574  

   Keedy, Daniel A ; Kenner, Lillian R ; Warkentin, Matthew ; Woldeyes, Rahel A ; Hopkins, Jesse B ; Thompson, Michael C ; Brewster, Aaron S ; Van Benschoten, Andrew H ; Baxter, Elizabeth L ; Uervirojnangkoorn, Monarin ; et al ( September 2015 , eLife)

   Proteins are the workhorses of the cell. The shape that a protein molecule adopts enables it to carry out its role. However, a protein’s shape, or 'conformation', is not static. Instead, a protein can shift between different conformations. This is particularly true for enzymes – the proteins that catalyze chemical reactions. The region of an enzyme where the chemical reaction happens, known as the active site, often has to change its conformation to allow catalysis to proceed. Changes in temperature can also make a protein shift between alternative conformations. Understanding how a protein shifts between conformations gives insight into how it works. A common method for studying protein conformation is X-ray crystallography. This technique uses a beam of X-rays to figure out where the atoms of the protein are inside a crystal made of millions of copies of that protein. At room temperature or biological temperature, X-rays can rapidly damage the protein. Because of this, most crystal structures are determined at very low temperatures to minimize damage. But cooling to low temperatures changes the conformations that the protein adopts, and usually causes fewer conformations to be present. Keedy, Kenner, Warkentin, Woldeyes et al. have used X-ray crystallography from a very low temperature (-173°C or 100 K) to above room temperature (up to 27°C or 300 K) to explore the alternative conformations of an enzyme called cyclophilin A. These alternative conformations include those that have previously been linked to this enzyme’s activity. Starting at a low temperature, parts of the enzyme were seen to shift from having a single conformation to many conformations above a threshold temperature. Unexpectedly, different parts of the enzyme have different threshold temperatures, suggesting that there isn’t a single transition across the whole protein. Instead, it appears the way a protein’s conformation changes in response to temperature is more complex than was previously realized. This result suggests that conformations in different parts of a protein are coupled to each other in complex ways. Keedy, Kenner, Warkentin, Woldeyes et al. then performed X-ray crystallography at room temperature using an X-ray free-electron laser (XFEL). This technique can capture the protein’s structure before radiation damage occurs, and confirmed that the alternative conformations observed were not affected by radiation damage. The combination of X-ray crystallography at multiple temperatures, new analysis methods for identifying and measuring alternative conformations, and XFEL crystallography should help future studies to characterize conformational changes in other proteins. 

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4. Compressional Behavior of Hydrous Orthoenstatite: Insight into the Nature of LVZ under Continental Plate

   https://doi.org/10.3390/min10010071  

   Hua, Florian Tian-Siang ; Dera, Przemyslaw ; Kung, Jennifer ( January 2020 , Minerals)

   A suite of hydrous orthoenstatite crystals were synthesized at 5–7 GPa and 1100–1300 °C, corresponding to the mid upper mantle conditions in continental regions. The synthetic crystals presented a clear, inclusion-free, and euhedral form with a size range from 100 to a few hundred microns. The Al- and water content of crystals were less than 2 wt. % and ranging from ~500 ppm to 1000 ppm, respectively, characterized by Raman and IR spectroscopy, electron microscopy, and SIMS. The analysis shows that the capability of water incorporation for this suite of hydrous orthoenstatite is correlated to the Al-content in the crystal structure. To understand how the detailed crystal structure reflects the influence of water and Al, single crystal X ray diffraction analysis was performed for this suite of hydrous orthoenstatite. By comparing the results obtained at ambient conditions, we find that for low-level of Al-content, <2 wt. %, the Al3+ cation tends to occupy one of tetrahedral sites (TB) only. Analysis of the X ray diffraction results under high pressure indicates that the elasticity of orthoenstatites is insensitive to the presence of low-level water and Al. We use this finding to evaluate the velocity profile at the mid upper mantle of continental regions to compare with seismic observation. The comparison indicates that the cause of the low velocity zone in continental regions originates from the geotherm profile rather than the effect of water on the elasticity of mantle phases. 

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5. Alkaline magmatism on Neo‐Tethyan extensional domains: Evidences from the Gejiu complex in Yunnan, China

   https://doi.org/10.1002/gj.4165  

   Wang, Yu‐Fei ; Dong, Guo‐Chen ; Santosh, M. ; Liu, Chang ; Chen, Wei ; Liang, Jing‐Li ; Zhang, Yin‐Chu ( May 2021 , Geological Journal)

   The Gejiu alkaline complex (GAC) within the western part of the Youjiang Basin provides a window to investigate the evolution in the junction of Cathaysia, Yangtze and Indochina blocks. Here, we investigate the GAC in terms of their petrology, zircon U–Pb geochronology, whole‐rock geochemistry, and Sr–Nd isotopic data to gain insights into the origin and evolution of the alkaline magma. The GAC is lithologically composed of alkali syenites and feldspathoid syenites, in which some were altered into sericite syenites. Zircon U–Pb dating of the alkali syenites yielded an age of 85.03 ± 0.47 Ma, which is slightly older than the feldspathoid syenites. The alkali syenites and feldspathoid syenites are silica‐saturated and silica‐undersaturated, respectively, and are characterized by high alkalinity with K₂O + Na₂O of 11.55–17.08 wt% and Al₂O₃of 18.57–22.49 wt%, low MgO of 0.11–1.39 wt%, weakly negative Eu anomalies, enrichments of LILEs such as Th and U, HFSEs like Zr and Hf but depletion of Ba, Sr, Nb, Ta, P, Ti, strongly fractionated LREEs to HREEs. Their uniform Sr–Nd isotope composition with initial⁸⁷Sr/⁸⁶Sr = 0.708802–0.710571 andε_Nd(t) = −7.1 to −6.6 indicates that they were products of a homologous magma. They crystallized atc. 810–956°C and have a relatively high magmatic oxygen fugacity. Our geochemical and isotopic data proved that the GAC magma was derived from the low‐degree partial melting (<10%) of a phlogopite‐bearing‐enriched mantle that was metasomatized by subducting sediments and originated possibly from the spinel and garnet transition zone at a depth of 60–80 km and a pressure of about 1.8–2.4 Gpa. The primary magma experienced protracted two‐stage crystal fractionation of clinopyroxene+amphibole and biotite+K‐feldspar, forming alkali syenites and feldspathoid syenites. Crustal contamination plays a negligible role in their formation. Considering previous tectonic studies, it was therefore proposed that the GAC formed in an extensional tectonic setting related to the Neo‐Tethyan tectonic regions during the Late Cretaceous.

    

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