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Browsing College of Agriculture and Life Sciences (CALS) by Subject "05 Environmental Sciences"
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- Counterions, smectite, and palygorskite increase microstructural stability of saline-sodic soilsJavaheri, F.; Esfandiarpour-Boroujeni, Isa; Farpoor, Mohammad Hady; Holthusen, D.; Stewart, Ryan D. (Elsevier, 2022-02-01)Saline-sodic soils are susceptible to wind and water erosion when the dispersive effect of sodium overcomes inter-particle bonds. Rheological parameters of viscoelasticity can help to quantify inter-particle attractive forces and account for the effect of salinity in these soils. The main objective of the present study was to investigate the viscoelasticity behavior of saline-sodic soils of the Sirjan playa in south-central Iran. Three representative pedons were excavated and described by horizon. Soil physicochemical properties and rheological properties were determined, namely the micromechanical parameters flow point (γf), loss factor tan δ, and integral z, with samples analyzed at three matric potentials (0, −6, and −15 kPa). Results showed that soil microstructural stiffness was mainly influenced by soil texture, clay minerals, gypsum, calcium carbonate equivalent (CCE), and matric potential. The dispersive effect of sodium, as indicated by low integral z and γf values, decreased with increasing gypsum content in − 6 and − 15 kPa matric potentials (0.6 < r < 0.8) and CCE percentage in the quasi-saturated (0 kPa) condition (r > 0.8). However, greater microstructural stability (i.e., higher integral z and γf) was observed for fine-textured soils with relatively high amounts of smectite and palygorskite and low pH. Furthermore, integral z and γf increased with lower matric potentials due to the stabilizing effect of menisci forces. Therefore, the viscoelastic behavior of the saline-sodic soils was negatively associated with water content and high sodium concentration, while the presence of smectite, palygorskite, gypsum, and CCE improved the soil physical conditions and thus the rigidity of the porous system. These results demonstrate that rheological measurements can identify saline-sodic soils that have strongly degraded microstructural stability and would most benefit from active management and amelioration.
- Effects of Large Wood on Floodplain Connectivity in a Headwater Mid-Atlantic StreamKeys, Tyler A.; Governer, Heather; Jones, C. Nathan; Hession, W. Cully; Hester, Erich T.; Scott, Durelle T. (2018-05-08)Large wood (LW) plays an essential role in aquatic ecosystem health and function. Traditionally, LW has been removed from streams to minimize localized flooding and increase conveyance efficiency. More recently, LW is often added to streams as a component of stream and river restoration activities. While much research has focused on the role of LW in habitat provisioning, geomorphic stability, and hydraulics at low to medium flows, we know little about the role of LW during storm events. To address this question, we investigated the role of LW on floodplain connectivity along a headwater stream in the Mid-Atlantic region of the United States. Specifically, we conducted two artificial floods, one with and one without LW, and then utilized field measurements in conjunction with hydrodynamic modeling to quantify floodplain connectivity during the experimental floods and to characterize potential management variables for optimized restoration activities. Experimental observations show that the addition of LW increased maximum floodplain inundation extent by 34%, increased floodplain inundation depth by 33%, and decreased maximum thalweg velocity by 10%. Model results demonstrated that different placement of LW along the reach has the potential to increase floodplain flow by up to 40%, with highest flooding potential at cross sections with high longitudinal velocity and shallow depth. Additionally, model simulations show that the effects of LW on floodplain discharge decrease as storm recurrence interval increases, with no measurable impact at a recurrence interval of more than 25 years.
- Fecal Indicator Bacteria and Antibiotic Resistance Genes in Storm Runoff from Dairy Manure and Compost-Amended Vegetable PlotsJacobs, Kyle; Wind, Lauren L.; Krometis, Leigh-Anne H.; Hession, W. Cully; Pruden, Amy (American Society for Agronomy, 2019-07-01)Given the presence of antibiotics and resistant bacteria in livestock manures, it is important to identify the key pathways by which land-applied manure-derived soil amendments potentially spread resistance. The goal of this field-scale study was to identify the effects of different types of soil amendments (raw manure from cows treated with cephapirin and pirlimycin, compost from antibiotic-treated or antibiotic-free cows, or chemical fertilizer only) and crop type (lettuce [Lactuca sativa L.] or radish [Raphanus sativus L.]) on the transport of two antibiotic resistance genes (ARGs; sul1 and ermB) via storm runoff from six naturally occurring storms. Concurrent quantification of sediment and fecal indicator bacteria (FIB; Escherichia coli and enterococci) in runoff permitted comparison to traditional agricultural water quality targets that may be driving factors of ARG presence. Storm characteristics (total rainfall volume, storm duration, etc.) significantly influenced FIB concentration (two-way ANOVA, p < 0.05), although both effects from individual storm events (Kruskal-Wallis, p < 0.05) and vegetative cover influenced sediment levels. Composted and raw manure-amended plots both yielded significantly higher sul1 and ermB levels in runoff for early storms, at least 8 wk following initial planting, relative to fertilizer-only or unamended barren plots. There was no significant difference between sul1 or ermB levels in runoff from plots treated with compost derived from antibiotic-treated versus antibiotic-free dairy cattle. Our findings indicate that agricultural fields receiving manure-derived amendments release higher quantities of these two “indicator” ARGs in runoff, particularly during the early stages of the growing season, and that composting did not reduce effects of ARG loading in runoff.
- The invasive tree, Ailanthus altissima, impacts understory nativity, not seedbank nativityBrooks, Rachel K.; Barney, Jacob; Salom, Scott M. (Elsevier, 2021-06-01)Ailanthus altissima, the invasive forest tree commonly known as the tree-of-heaven, has been associated with decreased levels of plant species richness and native species diversity. However, this relationship with resident plants has been inconsistently found and the tree's influence on the seedbank has yet to be studied. To further understand the long-term impact of this tree, ten paired invaded-uninvaded sites were identified in Virginia, USA in a variety of different-aged stands. The herbaceous and woody understories for each plot were inventoried and soil samples were collected and grown out for 34 weeks in a greenhouse. All plants were identified to the most detailed taxonomic level possible. In total, 35 woody understory species, 62 herbaceous understory taxa, and 77 seedbank taxa were identified. The relationship between A. altissima presence and i) the proportion of individual plants that are native, ii) the proportion of species that are native, iii) the native diversity, and iv) the nonnative diversity were analyzed. In addition, models including the invasion age were also considered. We show that A. altissima invasions were associated with a decrease in the proportion of native plants and species in the understory, but not in the seedbank. Nonnative woody diversity also increased with A. altissima presence. Additionally, the impact on the nativity of the woody understory became more extreme over time. We end by discussing the benefits of both managing A. altissima invasions early to limit its overall impact and including the management of other nonnative plants in A. altissima restoration plans.
- Macroinvertebrate sensitivity thresholds for sediment in Virginia streamsGovenor, Heather; Krometis, Leigh-Anne H.; Willis, Lawrence; Angermeier, Paul L.; Hession, W. Cully (2019-01)Sediment is the most commonly identified pollutant associated with macroinvertebrate community impairments in freshwater streams nationwide. Management of this physical stressor is complicated by the multiple measures of sediment available (e.g., suspended, dissolved, bedded) and the variability in natural "healthy" sediment loadings across ecoregions. Here we examine the relative importance of 9 sediment parameters on macroinvertebrate community health as measured by the Virginia Stream Condition Index (VSCI) across 5 ecoregions. In combination, sediment parameters explained 27.4% of variance in the VSCI in a multiregion data set and from 20.2% to 76.4% of variance for individual ecoregions. Bedded sediment parameters had a stronger influence on VSCI than did dissolved or suspended parameters in the multiregion assessment. However, assessments of individual ecoregions revealed conductivity had a key influence on VSCI in the Central Appalachian, Northern Piedmont and Piedmont ecoregions. In no case was a single sediment parameter sufficient to predict VSCI scores or individual biological metrics. Given the identification of embeddedness and conductivity as key parameters for predicting biological condition, we developed family-level sensitivity thresholds for these parameters, based on extirpation. Resulting thresholds for embeddedness were 68% for combined ecoregions, 65% for the Mountain bioregion (composed of Central Appalachian, Ridge and Valley, and Blue Ridge ecoregions), and 88% for the Piedmont bioregion (composed of Northern Piedmont and Piedmont ecoregions). Thresholds for conductivity were 366 μS/cm for combined ecoregions, 391 μS/cm for the Mountain bioregion, and 136 μS/cm for the Piedmont bioregion. These thresholds may help water quality professionals identify impaired and at-risk waters designated to support aquatic life and develop regional strategies to manage sediment-impaired streams. Inclusion of embeddedness as a restoration endpoint may be warranted; this could be facilitated by application of more quantitative, less time-intensive measurement approaches. We encourage refinement of thresholds as additional data and genus-based metrics become available. Integr Environ Assess Manag 2019;15:77-92. Published 2018. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
- Measuring shrinkage of undisturbed soil pedsShockey, Matthew C.; Stewart, Ryan D.; Keim, Richard F. (Wiley, 2021-10-19)Methods to measure shrinkage curves typically either disturb natural aggregate structure or include difficult or slow volume measurement techniques. Additionally, most shrinkage curves are obtained by serial measurement of a few samples. We obtained shrinkage curves by collecting rapid, one-off measurements of volume and moisture content for each of 200 undisturbed peds extracted from a field soil, taking measurements as peds slowly dried in the laboratory. The large sample size increased robustness of the shrinkage curve parameter estimates to noise generated by this rapid measurement technique, but a much smaller sample would have resulted in similar parameter estimates.
- Prediction of condition-specific regulatory genes using machine learningSong, Qi; Lee, Jiyoung; Akter, Shamima; Rogers, Matthew; Grene, Ruth; Li, Song (Oxford University Press, 2020-06-19)Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.
- Rheological evaluation of soil aggregate microstructure and stability across a forested catenaJavaheri, Fatemeh; Esfandiarpour-Boroujeni, Isa; Kourki, Hajir; Farpoor, Mohammad Hady; Stewart, Ryan D. (Elsevier, 2021-12-01)Rheological characteristics of soils, including their deformation and flow behaviors when subjected to external stress, can provide important information on microstructural stability. In this study we used rheological measurements to examine the soil aggregate microstructure and stability of four different soil orders – Alfisol, Mollisol, Inceptisol, and Entisol – along a forested catena in Mazandaran Province, northern Iran. Amplitude sweep tests were used to quantify the initial values of the storage and loss moduli, deformation limit (when the material begins to transition from reversible to irreversible deformation), deformation at flow point (when the material becomes viscous), and integral z (which summarizes the overall visco-elasticity of the material). The deformation limit was significantly higher in subsoil layers than topsoil layers, and was also higher in the Mollisol than the other pedons. The flow point and integral z values, which relate to the structural stiffness of soil matrices, were largest in the Btg horizons of the Alfisol and Mollisol, implying that these soils had more rigid microstructures. In contrast, the Entisol Ckg horizon, which had high sand content and little soil development, had the lowest values for all properties, thus indicating a lack of micro-aggregate stability. Regression analyses revealed that integral z was influenced by soil physicochemical properties, and was higher in soils whose clay fraction was dominated by expansive clay minerals and pedogenic iron and aluminum sesquioxides. Altogether, the rheological parameters indicated that older, more developed soils had greater microstructural stability than their less developed counterparts. As a result, rheological measurements may be useful for identifying the major factors that affect soil aggregation, and can indicate the relative amount of soil development along gradients such as the studied forest catena.