Open Access Publications

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Open access publications by faculty, postdocs, and graduate students in the Department of Plant and Soil Sciences.


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    FLUXNET-CH4: a global, multi-ecosystem dataset and analysis of methane seasonality from freshwater wetlands
    (Earth System Science Data, 2021-07-29) Delwiche, Kyle B.; Knox, Sara Helen; Malhotra, Avni; Fluet-Chouinard, Etienne; et al.
    Methane (CH4) emissions from natural landscapes constitute roughly half of global CH4 contributions to the atmosphere, yet large uncertainties remain in the absolute magnitude and the seasonality of emission quantities and drivers. Eddy covariance (EC) measurements of CH4 flux are ideal for constraining ecosystem-scale CH4 emissions due to quasi-continuous and high-temporal-resolution CH4 flux measurements, coincident carbon dioxide, water, and energy flux measurements, lack of ecosystem disturbance, and increased availability of datasets over the last decade. Here, we (1) describe the newly published dataset, FLUXNET-CH4 Version 1.0, the first open-source global dataset of CH4 EC measurements (available at, last access: 7 April 2021). FLUXNET-CH4 includes half-hourly and daily gap-filled and non-gap-filled aggregated CH4 fluxes and meteorological data from 79 sites globally: 42 freshwater wetlands, 6 brackish and saline wetlands, 7 formerly drained ecosystems, 7 rice paddy sites, 2 lakes, and 15 uplands. Then, we (2) evaluate FLUXNET-CH4 representativeness for freshwater wetland coverage globally because the majority of sites in FLUXNET-CH4 Version 1.0 are freshwater wetlands which are a substantial source of total atmospheric CH4 emissions; and (3) we provide the first global estimates of the seasonal variability and seasonality predictors of freshwater wetland CH4 fluxes. Our representativeness analysis suggests that the freshwater wetland sites in the dataset cover global wetland bioclimatic attributes (encompassing energy, moisture, and vegetation-related parameters) in arctic, boreal, and temperate regions but only sparsely cover humid tropical regions. Seasonality metrics of wetland CH4 emissions vary considerably across latitudinal bands. In freshwater wetlands (except those between 20∘ S to 20∘ N) the spring onset of elevated CH4 emissions starts 3 d earlier, and the CH4 emission season lasts 4 d longer, for each degree Celsius increase in mean annual air temperature. On average, the spring onset of increasing CH4 emissions lags behind soil warming by 1 month, with very few sites experiencing increased CH4 emissions prior to the onset of soil warming. In contrast, roughly half of these sites experience the spring onset of rising CH4 emissions prior to the spring increase in gross primary productivity (GPP). The timing of peak summer CH4 emissions does not correlate with the timing for either peak summer temperature or peak GPP. Our results provide seasonality parameters for CH4 modeling and highlight seasonality metrics that cannot be predicted by temperature or GPP (i.e., seasonality of CH4 peak). FLUXNET-CH4 is a powerful new resource for diagnosing and understanding the role of terrestrial ecosystems and climate drivers in the global CH4 cycle, and future additions of sites in tropical ecosystems and site years of data collection will provide added value to this database. All seasonality parameters are available at (Delwiche et al., 2021). Additionally, raw FLUXNET-CH4 data used to extract seasonality parameters can be downloaded from (last access: 7 April 2021), and a complete list of the 79 individual site data DOIs is provided in Table 2 of this paper.
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    Substantial hysteresis in emergent temperature sensitivity of global wetland CH4 emissions
    (Nature Communications, 2021-04-15) Chang, Kuang-Yu; Riley, William J.; Knox, Sara H.; Jackson, Robert B.; McNicol, Gavin; Poulter, Benjamin; Aurela, Mika; Baldocchi, Dennis; Bansal, Sheel; Bohrer, Gil; Campbell, David I.; Cescatti, Alessandro; Chu, Housen; Delwiche, Kyle B.; Desai, Ankur R.; Euskirchen, Eugenie; Friborg, Thomas; Goeckede, Mathias; Helbig, Manuel; Hemes, Kyle S.; Hirano, Takashi; Iwata, Hiroki; Kang, Minseok; Keenan, Trevor; Krauss, Ken W.; Lohila, Annalea; Mammarella, Ivan; Mitra, Bhaskar; Miyata, Akira; Nilsson, Mats B.; Noormets, Asko; Oechel, Walter C.; Papale, Dario; Peichl, Matthias; Reba, Michele L.; Rinne, Janne; Runkle, Benjamin R. K.; Ryu, Youngryel; Sachs, Torsten; Schäfer, Karina V. R.; Schmid, Hans Peter; Shurpali, Narasinha; Sonnentag, Oliver; Tang, Angela C. I.; Torn, Margaret S.; Trotta, Carlo; Tuittila, Eeva-Stiina; Ueyama, Masahito; Vargas, Rodrigo; Vesala, Timo; Windham-Myers, Lisamarie; Zhang, Zhen; Zona, Donatella
    Wetland methane (CH4) emissions (FCH4) are important in global carbon budgets and climate change assessments. Currently, FCH4 projections rely on prescribed static temperature sensitivity that varies among biogeochemical models. Meta-analyses have proposed a consistent FCH4 temperature dependence across spatial scales for use in models; however, site-level studies demonstrate that FCH4 are often controlled by factors beyond temperature. Here, we evaluate the relationship between FCH4 and temperature using observations from the FLUXNET-CH4 database. Measurements collected across the globe show substantial seasonal hysteresis between FCH4 and temperature, suggesting larger FCH4 sensitivity to temperature later in the frost-free season (about 77% of site-years). Results derived from a machine-learning model and several regression models highlight the importance of representing the large spatial and temporal variability within site-years and ecosystem types. Mechanistic advancements in biogeochemical model parameterization and detailed measurements in factors modulating CH4 production are thus needed to improve global CH4 budget assessments.
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    Distribution of urban green spaces: Comparative analysis between cities in different countries
    (Ornamental Horticulture, 2020-11-04) Garcia, Cecília Souza Gontijo; Paiva, Patrícia Duarte de Oliveira; Bruck, Jules; Sousa, Rafael de Brito
    The presence of urban green spaces (UGS) increases the human’s contact with nature and provides numerous benefits to the society and the local environment. In this way, analyzing, planning and stimulating the implementation of UGS in cities is a fundamental action to improve the life quality of urban society. In this context, the aim was to analyze the situation and distribution of the green spaces of the universities cities of Lavras, Minas Gerais State (Brazil) and Newark, Delaware (USA). For data collection, researches performed field visits and used aerial photography to survey and analysis before calculating indicators including green area index (GAI) and green space ratio (GSR). The city of Lavras has a GAI of 0.54 m2 inh-1. The GSR value was 0.29%, not meeting the minimum of 5% required by local municipal law. Furthermore, there is a bad distribution of UGSs in the urban framework. However, in Newark, the distribution of UGSs is homogeneous and covers all regions of the city. The calculated GAI was 50.2 m² inh-1 and the GSR has met the 7% minimum required by its Newark Municipal Law. When comparing the two cities, in different countries and conditions it is concluded that Newark (DE) presents UGS indicators, GAI (m² inh-1) and GSR (%), higher than the values obtained in Lavras (MG), indicating the need for Government actions to increase these values. Resumo As áreas verdes públicas urbanas (AVPs) concebem um importante tema, pois sua presença nas cidades, ampliando o contato do homem com a natureza, além dos efeitos ambientais geram inúmeros benefícios. Dessa maneira, analisar, planejar e estimular a implantação das AVPs nas cidades é ação fundamental para a melhoria da qualidade de vida da sociedade urbana. Nesse contexto objetivou-se analisar a situação e distribuição das áreas verdes das cidades universitárias de Lavras, estado de Minas Gerais, Brasil e Newark, estado de Delaware, EUA. Para a coleta de dados foram realizadas visitas a campo e o levantamento de áreas das AVPs por meio da análise de imagens de satélite utilizando o software ArcGIS e calculados os indicadores, índice de áreas verdes (IAV) e percentual de áreas verdes (PAV). A cidade de Lavras possui um IAV de 0,54m² hab-1. O valor de PAV foi de 0,29%, não cumprindo o mínimo de 5% exigido pela lei municipal local. Além disto, existe uma má distribuição das AVPs na malha urbana. Já em Newark, a distribuição das AVPs é homogênea abrangendo todas as regiões da cidade. O IAV calculado foi de 50,2m² hab-1 e o PAV cumpriu o mínimo de 7% exigido pela sua Lei municipal de Newark. Ao comparar as duas cidades, conclui-se que Newark (DE) apresenta indicadores sobre as áreas verdes públicas, IAV (m² hab-1) e PAV (%) superiores em comparação aos valores obtidos em Lavras (MG), indicando a necessidade de ações governamentais para ampliar esses valores.
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    Social media analysis reveals environmental injustices in Philadelphia urban parks
    (Scientific Reports, 2023-08-03) Walter, Matthew; Bagozzi, Benjamin E.; Ajibade, Idowu; Mondal, Pinki
    The United Nations Sustainable Development Goal (SDG) target 11.7 calls for access to safe and inclusive green spaces for all communities. Yet, historical residential segregation in the USA has resulted in poor quality urban parks near neighborhoods with primarily disadvantaged socioeconomic status groups, and an extensive park system that addresses the needs of primarily White middle-class residents. Here we center the voices of historically marginalized urban residents by using Natural Language Processing and Geographic Information Science to analyze a large dataset (n = 143,913) of Google Map reviews from 2011 to 2022 across 285 parks in the City of Philadelphia, USA. We find that parks in neighborhoods with a high number of residents from historically disadvantaged demographic groups are likely to receive lower scores on Google Maps. Physical characteristics of these parks based on aerial and satellite images and ancillary data corroborate the public perception of park quality. Topic modeling of park reviews reveal that the diverse environmental justice needs of historically marginalized communities must be met to reduce the uneven park quality—a goal in line with achieving SDG 11 by 2030.
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    Plant growth-promoting rhizobacteria mediate soil hydro-physical properties: An investigation with Bacillus subtilis and its mutants
    (Vadose Zone Journal, 2023-07-31) Kaniz, Fatema; Zheng, Wenjuan; Bais, Harsh; Jin,Yan
    Plant growth-promoting rhizobacteria and other soil bacteria have the potential to improve soil hydro-physical properties and processes through the production of extracellular polymeric substances (EPS). However, the mechanisms by which EPS mediates changes in soil properties and processes remain incompletely understood, partly due to variations in EPS composition produced under different environmental conditions. In this study, we investigated the influence of different bacterial traits on intrinsic soil properties and processes of evaporation and infiltration using sand treated with the wild-type Bacillus subtilis variant (UD1022) and its two mutant variants, – and srf. The – mutant suppresses EPS production through alterations in the eps and tasA genes, while the srf mutant lacks the gene for surfactin production. Experimental results confirmed that the solution viscosity of the – mutant was the lowest and the solution surface tension of the srf mutant was the highest among the three tested bacteria strains. The distinct intrinsic properties of EPS produced by these bacterial strains resulted in varied hydro-physical responses in the treated sand. Key influences included modifications in wettability, hydraulic decoupling (or mixed wettability), and aggregation, which collectively led to reduced evaporation rates and heterogeneous water distribution during infiltration in the bacteria-treated sands. Our findings advance the understanding of the role bacterial EPS play in vadose zone hydrology and offer insights for the development of sustainable strategies for increasing water retention, supporting crop production in arid regions, and facilitating land restoration. Abbreviations CHO carbohydrate EPS extracellular polymeric substances PGPR plant growth-promoting rhizobacteria
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    Characterization of integration sites and transfer DNA structures in Agrobacterium-mediated transgenic events of maize inbred B104
    (G3: Genes | Genomes | Genetics, 2023-07-31) Neelakandan, Anjanasree K.; Kabahuma, Mercy; Yang, Qin; Lopez, Miriam; Wisser, Randall J.; Balint-Kurti, Peter; Lauter, Nick
    In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest.
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    Potential for carbon sequestration after biochar-P fertilizer application: A biological and chemical assessment
    (European Journal of Soil Science, 2023-07-17) Borges, Bernardo M. M. N.; Barreto, Matheus Sampaio C.; Pavinato, Paulo S.; Franco, Henrique C. J.; Carvalho, João Luís Nunes; Strauss, Mathias; Sohi, Saran
    Innovation is required on many fronts in agriculture, not only to improve nutrient use efficiency but also to mitigate the effects of climate change. Our previous studies presented the high agronomic efficiency of an experimental phosphate fertilizer using a biochar-matrix, called ‘BioFert’. However, the efficiency of BioFert for soil carbon sequestration goals has not yet been evaluated. We incubated BioFert and initial raw sugarcane-biochar over 56 days in two soils (i.e., Ferralsol and Alisol) and measured the total CO2 and δ13C-CO2 to quantify the contribution of native soil organic matter, sugarcane-biochar, or BioFert to carbon mineralization. There was no significant difference in cumulative CO2 release between BioFert and the control (without carbon addition), and BioFert was less mineralized than carbon from sugarcane-biochar regardless of soil type. In addition, accelerated aging by thermal oxidation of these carbon sources revealed that more than 80% of BioFert-carbon was prevented from accelerated mineralization, while sugarcane-biochar achieved ~80% of carbon mineralization. The residual solids after oxidation were analysed by X-ray photoelectron spectroscopy and indicated aliphatic/aromatic and carboxylic chemical bonds on the BioFert surface, which might offer new cation exchange sites over time. We conclude that BioFert is not only a phosphate fertilizer with high phosphorus use efficiency but also a stable source of carbon for soil carbon sequestration purposes. Highlights - Similar CO2 cumulative release between BioFert and the control. - BioFert had more than 80% of its C stable against accelerated mineralization. - BioFert is a promising stable C source for soil C sequestration.
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    Physiochemical Controls on the Horizontal Exchange of Blue Carbon Across the Salt Marsh-Tidal Channel Interface
    (Journal of Geophysical Research: Biogeosciences, 2023-06-06) Fettrow, Sean; Jeppi, Virginia; Wozniak, Andrew; Vargas, Rodrigo; Michael, Holly; Seyfferth, Angelia L.
    Tidal channels are biogeochemical hotspots that horizontally exchange carbon (C) with marsh platforms, but the physiochemical drivers controlling these dynamics are poorly understood. We hypothesized that C-bearing iron (Fe) oxides precipitate and immobilize dissolved organic carbon (DOC) during ebb tide as the soils oxygenate, and dissolve into the porewater during flood tide, promoting transport to the channel. The hydraulic gradient physically controls how these solutes are horizontally exchanged across the marsh platform-tidal channel interface; we hypothesized that this gradient alters the concentration and source of C being exchanged. We further hypothesized that trace soil gases (i.e., CO2, CH4, dimethyl sulfide) are pushed out of the channel bank as the groundwater rises. To test these hypotheses, we measured porewater, surface water, and soil trace gases over two 24-hr monitoring campaigns (i.e., summer and spring) in a mesohaline tidal marsh. We found that Fe2+ and DOC were positively related during flood tide but not during ebb tide in spring when soils were more oxidized. This finding shows evidence for the formation and dissolution of C-bearing Fe oxides across a tidal cycle. In addition, the tidal channel contained significantly (p < 0.05) more terrestrial-like DOC when the hydraulic gradient was driving flow toward the channel. In comparison, the channel water was saltier and contained significantly (p < 0.05) more marine-like DOC when the hydraulic gradient reversed direction. Trace gas fluxes increased with rising groundwater levels, particularly dimethyl sulfide. These findings suggest multiple physiochemical mechanisms controlling the horizontal exchange of C at the marsh platform-tidal channel interface. Plain Language Summary Tidal salt marshes store large amounts of carbon belowground in soils, but there is also a significant amount of carbon flowing into and out of these ecosystems via tidal channels. We investigated the carbon flowing between the channel bank and surface water in a salt marsh in Delaware. We found that soil minerals (i.e., iron oxides) control the mobility of carbon as iron oxides retain carbon during ebb tides and release carbon during flood tides as the minerals dissolve. The gradient between the groundwater and surface water elevation (i.e., hydraulic gradient) controls the flow direction for dissolved carbon, altering the concentration and source of carbon found in the tidal channel across tidal cycles. In addition, gases trapped in channel banks are pushed out of the soils as the tide rises. These findings will improve our understanding of carbon cycles in these critical carbon sinks. Key Points - Physiochemical mechanisms control horizontal exchange of carbon across marsh-tidal channel interfaces, affecting lateral carbon flux - Dissolution and reprecipitation of carbon-bearing Fe oxides during flood and ebb tides control the horizontal mobility of carbon - Hydraulic gradients control the carbon character in the tidal channel, and rising tides push greenhouse gases out of the channel bank
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    Hydrothermal Leaching of Amylose from Native, Oxidized and Heat-Treated Starches
    (Processes, 2023-05-11) Nikolenko, Mykola V.; Myrhorodska-Terentieva, Viktoriia D.; Sakhno, Yuriy; Jaisi, Deb P.; Likozar, Blaž; Kostyniuk, Andrii
    The kinetics of amylose leaching in hot, excess water from native, oxidized-by-potassium permanganate and heat-treated potato starch at temperatures of 62–90 °C was investigated in isothermal conditions. For the first time, it was proposed to describe the kinetic data by the Kroger–Ziegler equation. It was found that for native starch in the range of 62–70 °C, the activation energy of the amylose leaching process is 192.3 kJ/mol, and at a temperature of 80–90 °C, it decreases to 22 kJ/mol. Similar patterns were established for modified starches. In the kinetic mode, the activation energy was 102.5 kJ/mol for oxidized starch and 44.7 and 82.5 kJ/mol for heat-treated starches at a temperature of 135 °C for 2.5 and 5 h. In the diffusion mode, it was: 18.7 kJ/mol for oxidized and 16.2 and 18.9 kJ/mol for heat-treated starches for 2.5 and 5 h, respectively. It is shown that the consideration of amylose leaching as a heterogeneous pseudochemical process makes it possible to explain the change in the activation energy with increasing temperature by the transition of the leaching process from the kinetic to the diffusion mode. As such a pseudochemical process, it is proposed to consider the breaking of multiple hydrogen bonds between amylose macromolecules. The change in the activation energies of amylose extraction from modified starches is explained by the change in the degree of amylose polymerization. Thin-layer chromatography was used to compare the molecular weight distributions of the resulting modified amylose samples. FTIR spectroscopy and thermal methods of analysis were used to study the transformations of starch during heat treatment.
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    Scanning X-ray fluorescence spectroscopy and micro-X-ray absorption near-edge structure analysis as a guiding tool for the conservation treatment of two eighteenth-century Philadelphian portraits
    (X-Ray Spectrometry, 2023-04-02) Porell, Mina; Cushman, Matthew; Fischel, Jason S. T.; Fischel, Matthew H. H.; Sparks, Donald L.; Grayburn, Rosie
    An in-depth technical examination and conservation treatment of paintings by William Williams (Bristol 1727–1791 Bristol) has shed light on the artist's materials and technique. This investigation centered primarily on Williams's two 1766 portraits of William and David Hall. The paintings are considered the earliest life-sized, full-length portraits executed in the Philadelphia area. The analysis of the artist's palette indicated deliberate choices in the use of orpiment (As2S3). The mineral's tendency to oxidize to colorless and water-soluble arsenic oxides likely caused color changes and degraded organic binder in the orpiment-rich areas. μ-XANES revealed orpiment photodegradation to arsenate species at the paint surface, with migration to the ground layers. Just below the paint surface, arsenic remains bound primarily as arsenite, with some associated with sulfur as orpiment. This As distribution suggests that the paint is liable to further degradation by photooxidation and use of moisture would be detrimental. Given this treatment-critical degradation phenomenon, it was important to identify all arsenic-containing areas of both portraits. Scanning XRF allowed rapid and accurate collection of maps from both portraits. Elemental maps of arsenic identified the orpiment-rich areas of the painting, which would be susceptible to further degradation upon exposure to water during treatment. An aqueous adhesive was necessary to consolidate the cupped paint of the glue-paste lined paintings. The arsenic maps guided the use of two different consolidants–BEVA 371 for the water-sensitive orpiment-rich paint and sturgeon glue for all other areas, striking a compromise between esthetic improvement and long term preservation.
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    Effect of core cultivation, fertility, and plant growth regulators on recovery of voided creeping bentgrass greens canopies following annual bluegrass control via methiozolin
    (Weed Technology, 2023-04-13) Venner, Katelyn A.; Ervin, Erik; Koo, Suk-Jin; Peppers, John M.; Askew, Shawn D.
    Methiozolin is commonly used for the safe and selective removal of annual bluegrass from creeping bentgrass golf greens. Studies were conducted in 2013 and 2014 with the objective of assessing fertility programs consisting of synthetic fertilizers and biostimulants, with and without the plant growth regulator trinexapac-ethyl, to aid putting green canopy recovery following annual bluegrass removal via methiozolin. Additional studies were conducted to compare recovery of creeping bentgrass following an aggressive core aerification event with fertility programs with and without methiozolin. In all cases, the addition of 7 kg ha−1 of N-P-K from fertilizer or biostimulant biweekly to greens increased turfgrass recovery time by 1 to 3 wk compared to a standard green’s fertility program alone. Creeping bentgrass treated with biostimulants recovered equivalent to or quicker than creeping bentgrass treated with synthetic fertilizer (SF) in all cases. In the presence of methiozolin treatments, trinexapac-ethyl reduced time to 90% recovery (T90) by 0.25 to 0.5 wk at two locations, and increased T90 recovery time by 0.1 wk at one location. Otherwise, plots treated with SF plus trinexapac-ethyl were equivalent to plots treated with SF only. Methiozolin slowed turfgrass recovery time at one location where severe drought stress occurred but not at the other location that did not experience drought stress. These results suggest that turf managers should increase fertilizer treatments but will not need to discontinue trinexapac-ethyl use to maximize creeping bentgrass recovery following annual bluegrass control with methiozolin. These data also suggest that methiozolin has the potential to negatively affect creeping bentgrass recovery when drought stress is experienced.
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    Rice husk and charred husk amendments increase porewater and plant Si but water management determines grain As and Cd concentration
    (Plant and Soil, 2022-03-09) Linam, Franklin; Limmer, Matt A.; Tappero, Ryan; Seyfferth, Angelia L.
    Purpose Rice is a staple crop worldwide and a silicon (Si) hyperaccumulator with Si levels reaching 5–10% of its mass; this can result in desilication and Si-deficiency if plant residues are not managed correctly. Rice is also uniquely subject to arsenic (As) and cadmium (Cd) contamination depending on soil conditions. Our goal is to quantify the effects of rice husk (a Si-rich milling byproduct) amendments and different water management strategies on rice uptake of Si, As, and Cd. Methods We employed 4 husk amendment treatments: Control (no husk), Husk (untreated husk), Biochar (husk pyrolyzed at 450 °C), and CharSil (husk combusted at > 1000 °C). Each of these amendments was studied under nonflooded, alternate wetting and drying (AWD), and flooded water management in a pot study. Porewater chemistry and mature plant elemental composition were measured. Results Husk and Biochar treatments, along with flooding, increased porewater and plant Si. Vegetative tissue As decreased with increasing porewater Si, but grain As and plant Cd were primarily controlled by water management. Grain As and Cd were inversely correlated and are simultaneously minimized in a redox potential (Eh) range of 225–275 mV in the studied soil. Ferrihydrite in root iron plaque decreased As translocation from porewater to grain, but amendments were not able to increase plaque ferrihydrite content. Conclusion We conclude moderate husk amendment rates (i.e., 4 years’ worth) with minimal pretreatment strongly increases rice Si content but may not be sufficient to decrease grain As in low Si and As soil.
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    Rice husk and husk biochar soil amendments store soil carbon while water management controls dissolved organic matter chemistry in well-weathered soil
    (Journal of Environmental Management, 2023-04-15) Linam, Franklin; Limmer, Matt A.; Ebling, Alina M.; Seyfferth, Angelia L.
    Rice agriculture feeds over half the world's population, and paddy soils impact the carbon cycle through soil organic carbon (SOC) preservation and production of carbon dioxide (CO2) and methane (CH4), which are greenhouse gases (GHG). Rice husk is a nutrient-rich, underutilized byproduct of rice milling that is sometimes pyrolyzed or combusted. It is unresolved how the incorporation of these residues affects C dynamics in paddy soil. In this study, we sought to determine how untreated (Husk), low-temperature pyrolyzed (Biochar), and combusted (CharSil) husk amendments affect SOC levels, GHG emissions, and dissolved organic matter (DOM) chemistry. We amended Ultisol paddy mesocosms and collected SOC and GHG data for three years of rice grown under alternate wetting and drying (AWD) conditions. We also performed a greenhouse pot study that included water management treatments of nonflooded, AWD, and flooded. Husk, Biochar, and CharSil amendments and flooding generally increased SOC storage and CH4 emissions, while nonflooded conditions increased N2O emissions and nonflooded and CharSil treatments increased CO2 emissions. All amendments stored ∼0.15 kg C m−2 y−1 more SOC than CH4 emissions (as CO2 equivalents), but the combustion of husk to produce CharSil resulted in the net release of CO2 which negates any SOC storage. UV–visible absorption/fluorescence spectroscopy from the pot study suggests that nonflooded treatment decreased DOM aromaticity and molecular size. Our data show that flooding and amendment of Husk and Biochar maximized C storage in the highly weathered rice paddy soil under study despite Husk increasing CH4 emissions. Water management affected dissolved organic matter chemistry more strongly than amendments, but this requires further investigation. Return of rice husk that is untreated or pyrolyzed at low temperature shows promise to close nutrient loops and preserve SOC in rice paddy soils. Graphical abstract available at:
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    Unraveling the Mechanisms of Fe Oxidation and Mn Reduction on Mn Indicators of Reduction in Soil (IRIS) Films
    (Environmental Science and Technology, 2023-04-25) Limmer, Matt A.; Linam, Franklin A.; Evans, Abby E.; Seyfferth, Angelia L.
    Indicators of reduction in soil (IRIS) devices are low-cost soil redox sensors coated with Fe or Mn oxides, which can be reductively dissolved from the device under suitable redox conditions. Removal of the metal oxide coating from the surface, leaving behind the white film, can be quantified and used as an indicator of reducing conditions in soils. Manganese IRIS, coated with birnessite, can also oxidize Fe(II), resulting in a color change from brown to orange that complicates the interpretation of coating removal. Here, we studied field-deployed Mn IRIS films where Fe oxidation was present to unravel the mechanisms of Mn oxidation of Fe(II) and the resulting minerals on the IRIS film surface. We observed reductions in the Mn average oxidation state when Fe precipitation was evident. Fe precipitation was primarily ferrihydrite (30–90%), but lepidocrocite and goethite were also detected, notably when the Mn average oxidation state decreased. The decrease in the average oxidation state of Mn was due to the adsorption of Mn(II) to the oxidized Fe and the precipitation of rhodochrosite (MnCO3) on the film. The results were variable on small spatial scales (<1 mm), highlighting the suitability of IRIS in studying heterogeneous redox reactions in soil. Mn IRIS also provides a tool to bridge lab and field studies of the interactions between Mn oxides and reduced constituents.
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    Moso bamboo expansion into a broadleaved forest alters the dominant soil organic carbon source
    (European Journal of Soil Science, 2023-05-09) Shao, Shuai; He, Hongbo; Liang, Chenfei; Chen, Junhui; Qin, Hua; Wang, Shanshan; Wang, Zhongqian; Li, Yi; Jia, Weina; Zheng, Xuli; Chen, Yong; Fuhrmann, Jeffry J.; Xu, Qiufang; Zhang, Xudong
    Both microbes and plants contribute to soil organic carbon (SOC) formation and retention, but their roles in controlling SOC dynamics in forest soils under Moso bamboo (Phyllostachys edulis) expansion remain unclear. Here, amino sugars and lignin monomers were measured to represent microbial necromass and plant-derived components, respectively. The observed decline in both amino sugars and lignin monomers during Moso bamboo expansion indicates a reduction in microbial necromass and recalcitrant plant contributions to SOC composition. This could be attributed to a limitation of microbial substrates and proliferation caused by the reduced litter inputs resulting from the expansion. The proportion of microbial necromass contributing to the SOC pool increased, but that of lignin monomers decreased, as SOC content decreased with Moso bamboo expansion. This suggests that the decrease of SOC during bamboo expansion was mainly due to the reduction of lignin, while the increased contribution of microbial-derived carbon to SOC may serve to improve SOC stability. Our study sheds light on the altered SOC source inputs resulting from Moso bamboo expansion and emphasizes the need for sustainable forestry management practices that differentiate between microbial- and plant-derived carbon pools. HIGHLIGHTS 1. Both soil amino sugars and lignin monomers decreased with Moso bamboo expansion. 2. The dominant source of SOC changed during the Moso bamboo expansion. 3. SOC reduction was mainly due to the decline of lignin during Moso bamboo expansion. 4. Microbial necromass plays a key role in SOC retention during Moso bamboo expansion.
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    Surfactin and Spo0A-Dependent Antagonism by Bacillus subtilis Strain UD1022 against Medicago sativa Phytopathogens
    (Plants, 2023-02-23) Rosier, Amanda; Pomerleau, Maude; Beauregard, Pascale B.; Samac, Deborah A.; Bais, Harsh P.
    Plant growth-promoting rhizobacteria (PGPR) such as the root colonizers Bacillus spp. may be ideal alternatives to chemical crop treatments. This work sought to extend the application of the broadly active PGPR UD1022 to Medicago sativa (alfalfa). Alfalfa is susceptible to many phytopathogens resulting in losses of crop yield and nutrient value. UD1022 was cocultured with four alfalfa pathogen strains to test antagonism. We found UD1022 to be directly antagonistic toward Collectotrichum trifolii, Ascochyta medicaginicola (formerly Phoma medicaginis), and Phytophthora medicaginis, and not toward Fusarium oxysporum f. sp. medicaginis. Using mutant UD1022 strains lacking genes in the nonribosomal peptide (NRP) and biofilm pathways, we tested antagonism against A. medicaginicola StC 306-5 and P. medicaginis A2A1. The NRP surfactin may have a role in the antagonism toward the ascomycete StC 306-5. Antagonism toward A2A1 may be influenced by B. subtilis biofilm pathway components. The B. subtilis central regulator of both surfactin and biofilm pathways Spo0A was required for the antagonism of both phytopathogens. The results of this study indicate that the PGPR UD1022 would be a good candidate for further investigations into its antagonistic activities against C. trifolii, A. medicaginicola, and P. medicaginis in plant and field studies.
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    Soil health tradeoffs may be minimal in phosphorus-enriched Coastal Plain soils
    (Agricultural & Environmental Letters, 2023-03-31) Mosesso, Lauren R.; Shober, Amy L.
    Soil health practices can improve soil conditions and provide ecosystem services, but increased risk of phosphorus (P) loss can be an unintended consequence. We investigated conservation tillage and cover crops effects on soil P stratification, P accumulation at depth, and soil aggregation for sandy Coastal Plain soils from the Mid-Atlantic United States soil cores from 10 agricultural fields with 0–15 years of conservation tillage or cover cropping were analyzed for Mehlich-3 P and dry aggregate stability. We found no evidence that conservation tillage or cover cropping caused P stratification or accumulation in study fields that were already enriched with P prior to soil health implementation. Annual particulate, dissolved runoff, and leachate P loads decreased when estimated using the North Carolina Phosphorus Loss Assessment Tool assuming no-till and cover crops (soil health) compared to conventional till and winter fallow (conventional). We suggest that soil health practices are unlikely to exacerbate P losses from high P Coastal Plain soils beyond their initial risk profile. Core Ideas: - Soil health practices may increase the risk of surface and subsurface phosphorus (P) loss in P-enriched soils. - Soil P stratification in 10 fields with and without soil health practices were compared. - There is no evidence that soil health practices increased the risk for dissolved soil P losses. - Soil health practices may reduce P loads in fields with significant sources of dissolved P. Abbreviations: DP dissolved phosphorus NC-PLAT North Carolina Phosphorus Loss Assessment Tool PP particulate phosphorus
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    Isolation of dissolved organic matter from aqueous solution by precipitation with FeCl3: mechanisms and significance in environmental perspectives
    (Scientific Reports, 2023-03-20) Zhang, Jie; Mostofa, Khan M. G.; Yang, Xuemei; Mohinuzzaman, Mohammad; Liu, Cong-Qiang; Senesi, Nicola; Senesi, Giorgio S.; Sparks, Donald L.; Teng, H. Henry; Li, Longlong; Yuan, Jie; Li, Si-Liang
    Ferric ions can bind strongly with dissolved organic matter (DOM), including humic acids (HA), fulvic acids (FA), and protein-like substances, whereas isolation of Fe-DOM precipitates (Fe-DOMP) and their biochemical characteristics remain unclear. In this work FeCl3 was used to isolate DOM components from various sources, including river, lake, soil, cow dung, and standard tryptophan and tyrosine, through precipitation at pH 7.5–8.5. The Fe-DOMP contribute to total DOM by approximately 38.6–93.8% of FA, 76.2% of HA and 25.0–30.4% of tryptophan and tyrosine, whilst fluorescence spectra allowed to monitor/discriminate the various DOM fractions in the samples. The relative intensity of the main infrared peaks such as 3406‒3383 cm−1 (aromatic OH), 1689‒1635 cm−1 (‒COOH), 1523–1504 cm−1 (amide) and 1176–1033 cm−1 (‒S=O) show either to decline or disappear in Fe‒DOMP. These results suggest the occurrence of Fe bonds with various functional groups of DOM, indicating the formation of π–d electron bonding systems of different strengths in Fe‒DOMP. The novel method used for isolation of Fe-DOMP shows promising in opening a new frontier both at laboratory and industrial purposes. Furthermore, results obtained may provide a better understanding of metal–organic complexes involved in the regulation of the long-term stabilization/sequestration of DOM in soils and waters.
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    Evaluation of quantitative synchrotron radiation micro-X-ray fluorescence in rice grain
    (Journal of Synchrotron Radiation, 2023-03-15) Limmer, Matt A.; Webb, Samuel M.; Seyffertha, Angelia L.
    Concentrations of nutrients and contaminants in rice grain affect human health, specifically through the localization and chemical form of elements. Methods to spatially quantify the concentration and speciation of elements are needed to protect human health and characterize elemental homeostasis in plants. Here, an evaluation was carried out using quantitative synchrotron radiation microprobe X-ray fluorescence (SR-µXRF) imaging by comparing average rice grain concentrations of As, Cu, K, Mn, P, S and Zn measured with rice grain concentrations from acid digestion and ICP-MS analysis for 50 grain samples. Better agreement was found between the two methods for high-Z elements. Regression fits between the two methods allowed quantitative concentration maps of the measured elements. These maps revealed that most elements were concentrated in the bran, although S and Zn permeated into the endosperm. Arsenic was highest in the ovular vascular trace (OVT), with concentrations approaching 100 mg kg−1 in the OVT of a grain from a rice plant grown in As-contaminated soil. Quantitative SR-µXRF is a useful approach for comparison across multiple studies but requires careful consideration of sample preparation and beamline characteristics.
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    Plant community dynamics following non-native shrub removal depend on invasion intensity and forest site characteristics
    (Ecosphere, 2023-01-13) Moore, Eric; D'Amico, Vincent; Trammell, Tara L. E.
    Globally, temperate deciduous forests are threatened by invasion of non-native (exotic) plant species. In the eastern United States, Rosa multiflora is a dominant shrub invader in forests, which often forms dense thickets that reduce sunlight availability in the understory, where decreased native plant diversity and abundance are observed. Management and restoration are difficult but desirable, especially when invasion intensity is still low. Few studies have examined the relative success of different management strategies under varying invasion intensities. Our study objectives were to conduct a R. multiflora removal experiment in three forest sites experiencing different invasion intensities and to restore native plant biodiversity while preventing secondary invasion. We utilized three management strategies: invasive plant removal, removal followed by native seed addition, and removal plus native seed and mulched invasive stem addition. We investigated the similarity between seed bank species composition and existing vegetation before and after removal to assess the potential for passive restoration. Two seasons after removal, we found that simply removing roses increased native species richness, native floristic quality assessment (FQAIN), and native shrub abundance in our medium invasion site, and total species richness in our low and medium invasion sites. Compared to removal alone, native seed addition, with and without mulch addition, resulted in larger native and total species richness and FQAIN increases at all sites, larger increases in native shrub abundance and exotic species richness in our medium invasion site, and larger reductions in exotic and total shrub abundance in our low and medium invasion sites. Following removal, species similarity between the seed bank and vegetation improved for all three sites. Our results indicate that removal of R. multiflora alone increased native plant biodiversity in the medium invasion scenario, but the seed bank may not provide a large native species pool. Additional management strategies lead to improved outcomes, especially in our most invaded forest, demonstrating the need to conduct multiple plant removal treatments across forests with varying site conditions and plant invasion intensity to improve management recommendations.
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